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Unicellular Cyanobacterium Symbiotic with a Single-Celled Eukaryotic Alga
Abstract
Symbioses between nitrogen (N)2–fixing prokaryotes and photosynthetic eukaryotes are important for nitrogen acquisition in N-limited environments. Recently,
a widely distributed planktonic uncultured nitrogen-fixing cyanobacterium (UCYN-A) was found to have unprecedented genome
reduction, including the lack of oxygen-evolving photosystem II and the tricarboxylic acid cycle, which suggested partnership
in a symbiosis. We showed that UCYN-A has a symbiotic association with a unicellular prymnesiophyte, closely related to calcifying
taxa present in the fossil record. The partnership is mutualistic, because the prymnesiophyte receives fixed N in exchange
for transferring fixed carbon to UCYN-A. This unusual partnership between a cyanobacterium and a unicellular alga is a model
for symbiosis and is analogous to plastid and organismal evolution, and if calcifying, may have important implications for
past and present oceanic N2 fixation.
Supplementary resource (1)
... UCYN-A lives symbiotically with haptophyte algae where it exchanges fixed nitrogen for fixed carbon produced by its algal host (8,(11)(12)(13). Unlike other cyanobacteria, and because of genomic streamlining, UCYN-A has lost genes for photosystem II and therefore cannot evolve oxygen via photosynthesis (8,14,15). ...
... (ASVe5c7 in Fig. 5 and fig. S12)-are in general agreement with current views that a small prymnesiophyte is the host of UCYN-A1 (12,35,40). Not only does our network analysis provide evidence of the symbiotic UCYN-A/host consortium within the Bedford Basin, but presumably other nonsymbiotic microbial interactions involving UCYN-A are embedded within our nifH versus 16S rRNA datasets. ...
... Previous Ka/Ks ratios calculated for >200 genes between A2 versus A1 and A2 versus A3 have also shown purifying selection between published genomes for aforesaid ecotypes (17,18). The finding that major ASVs had no nonsynonymous mutations indicates that the nifH region examined is in theory under selective pressure to produce an identical nifH amino acid sequence across the major UCYN-A ASVs for each ecotype-a pattern that likely reflects the fact that diazotrophy, and hence the nifH gene and protein region in question, is integral to the overall function of this organism as a nitrogen fixing symbiont (12). The lack of annually reoccurring rare ASVs ultimately implies that seasonal cycling restructured the UCYN-A community composition especially for rare ASVs (Fig. 2). ...
UCYN-A is a globally important nitrogen-fixing symbiotic microbe often found in colder regions and coastal areas where nitrogen fixation has been overlooked. We present a 3-year coastal Northwest Atlantic time series of UCYN-A by integrating oceanographic data with weekly nifH and16 S rRNA gene sequencing and quantitative PCR assays for UCYN-A ecotypes. High UCYN-A relative abundances dominated by A1 to A4 ecotypes reoccurred annually in the coastal Northwest Atlantic. Although UCYN-A was detected every summer/fall, the ability to observe separate ecotypes may be highly dependent on sampling time given intense interannual and weekly variability of ecotype-specific occurrences. Additionally, much of UCYN-A’s rarer diversity was populated by short-lived neutral mutational variants, therefore providing insight into UCYN-A’s microevolutionary patterns. For instance, rare ASVs exhibited community composition restructuring annually, while also sharing a common connection to a dominant ASV within each ecotype. Our study provides additional perspectives for interpreting UCYN-A intraspecific diversity and underscores the need for high-resolution datasets when deciphering spatiotemporal ecologies within UCYN-A.
... The first study that applied this technique to marine organisms observed a cluster of nifH sequences belonging to a clade termed "UCYN-A", for "unicellular cyanobacterial group A" [7]. This clade of organisms has been tentatively named Candidatus Atelocyanobacterium thalassa [8], and is now recognized as a major contributor to biological nitrogen fixation (e.g., [9,10]). ...
... UCYN-A is an aberrant cyanobacterium, lacking Photosystem II and key components of cellular pathways, such as the Krebs cycle [11]. Its metabolism is streamlined because it lives in symbiosis with a photosynthetic haptophyte host, exchanging fixed nitrogen for carbon compounds [8,12]. Four clades of UCYN-A are currently recognized based on their nifH sequences, although more may exist [13]. ...
... Four clades of UCYN-A are currently recognized based on their nifH sequences, although more may exist [13]. UCYN-A1, the most extensively studied type of UCYN-A, associates with a coccolith-forming member of the genus Braarudosphaera [8], and is found primarily in open-ocean regions [14,15]. UCYN-A1 is <1 μm in diameter while host cells have a diameter of 1-3 μm and can house 1-2 symbionts each [13,16]. ...
Biological nitrogen fixation, the conversion of N 2 gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A’s presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by “universal primers” from monthly samples and resolved into Amplicon Sequence Variants, allowing us to observe multiple UCYN-A symbioses. UCYN-A1 relative abundances increased following the 2015-2016 El Niño event. This “open ocean ecotype” was present when coastal upwelling declined, and Ekman transport brought tropical waters into the region. Network analyses reveal all strains of UCYN-A co-occur with dinoflagellates including Lepidodinium , a potential predator, and parasitic Syndiniales . UCYN-A2 appeared to pair with multiple hosts and was not tightly coupled to its predominant host, while UCYN-A1 maintained a strong host-symbiont relationship. These biological relationships are particularly important to study in the context of climate change, which will alter UCYN-A distribution at regional and global scales.
... In the ocean, some of these diazotrophs are symbiotic with phytoplankton species, which is the case for the group of unicellular N 2 -fixing symbiotic cyanobacteria known as Candidatus Atelocyanobacterium thalassa (hereafter UCYN-A). UCYN-A live in symbiosis with the unicellular haptophyte alga Braarudosphaera bigelowii and close relative species (Thompson et al., 2012;Hagino et al., 2013), being both symbiotic partners relevant contributors to marine N 2 and carbon fixation, respectively, (Montoya et al., 2004;Martínez-Pérez et al., 2016;Zehr et al., 2016). ...
... The diversity of the UCYN-A/haptophyte symbiosis has been explored using both phylogenetic and functional gene markers, which results have yielded differences in the number of phylotypes. For instance, while the 16S rDNA phylogenetic marker has resolved up to 3 distinct UCYN-A sublineages (UCYN-A1, −A2, and −A3) (Thompson et al., 2012;Hagino et al., 2013;Cornejo-Castillo et al., 2019), the diversity of the nifH gene, typically used for exploring the diversity of N 2 -fixers, has served to define up to 6-7 distinct UCYN-A sublineages with different biogeographical distributions Turk-Kubo et al., 2017). However, regarding the diversity of the haptophyte species symbiotic with UCYN-A, only 2 different species have been identified based on the sequence diversity of the 18S rRNA phylogenetic marker (Thompson et al., 2012;Hagino et al., 2013;Cornejo-Castillo et al., 2019). ...
... For instance, while the 16S rDNA phylogenetic marker has resolved up to 3 distinct UCYN-A sublineages (UCYN-A1, −A2, and −A3) (Thompson et al., 2012;Hagino et al., 2013;Cornejo-Castillo et al., 2019), the diversity of the nifH gene, typically used for exploring the diversity of N 2 -fixers, has served to define up to 6-7 distinct UCYN-A sublineages with different biogeographical distributions Turk-Kubo et al., 2017). However, regarding the diversity of the haptophyte species symbiotic with UCYN-A, only 2 different species have been identified based on the sequence diversity of the 18S rRNA phylogenetic marker (Thompson et al., 2012;Hagino et al., 2013;Cornejo-Castillo et al., 2019). Therefore, we currently lack a functional gene marker that could provide a finer phylogenetic resolution for these symbiotic haptophytes similar to the nifH gene marker in UCYN-A. ...
The multiple symbiotic partnerships between closely related species of the haptophyte algae Braarudosphaera bigelowii and the nitrogen-fixing cyanobacteria Candidatus Atelocyanobacterium thalassa (UCYN-A) contribute importantly to the nitrogen and carbon cycles in vast areas of the ocean. The diversity of the eukaryotic 18S rDNA phylogenetic gene marker has helped to identify some of these symbiotic haptophyte species, yet we still lack a genetic marker to assess its diversity at a finer scale. One of such genes is the ammonium transporter (amt) gene, which encodes the protein that might be involved in the uptake of ammonium from UCYN-A in these symbiotic haptophytes. Here, we designed three specific PCR primer sets targeting the amt gene of the haptophyte species (A1-Host) symbiotic with the open ocean UCYN-A1 sublineage, and tested them in samples collected from open ocean and near-shore environments. Regardless of the primer pair used at Station ALOHA, which is where UCYN-A1 is the pre-dominant UCYN-A sublineage, the most abundant amt amplicon sequence variant (ASV) was taxonomically classified as A1-Host. In addition, two out of the three PCR primer sets revealed the existence of closely-related divergent haptophyte amt ASVs (>95% nucleotide identity). These divergent amt ASVs had higher relative abundances than the haptophyte typically associated with UCYN-A1 in the Bering Sea, or co-occurred with the previously identified A1-Host in the Coral Sea, suggesting the presence of new diversity of closely-related A1-Hosts in polar and temperate waters. Therefore, our study reveals an overlooked diversity of haptophytes species with distinct biogeographic distributions partnering with UCYN-A, and provides new primers that will help to gain new knowledge of the UCYN-A/haptophyte symbiosis.
... These include the uncultivated unicellular cyanobacteria Candidatus Atelocyanobacterium thalassa (UCYN-A) because of their high N 2 fixation and growth rates [3][4][5] and potential for N transfer into the food web through grazers [3,6,7]. DNA sequencing showed that UCYN-A has a massively streamlined genome [8,9] that lacks the machinery required for carbon fixation, including photosystem II (PSII) and RuBisCO, as well as other key metabolic pathways, e.g. the entire tricarboxylic acid cycle (TCA) [8,10,11]. Later it was discovered that UCYN-A lives in symbiosis with a photosynthetic haptophyte, related to Braarudosphaera bigelowii, with which it exchanges fixed N for fixed carbon [10,11]. Subsequent work showed that disrupting photosynthesis by the host arrested UCYN-A cell division and changed its daily transcription pattern of the key enzyme in N 2 fixation, the nitrogenase gene (nifH) [12]. ...
... DNA sequencing showed that UCYN-A has a massively streamlined genome [8,9] that lacks the machinery required for carbon fixation, including photosystem II (PSII) and RuBisCO, as well as other key metabolic pathways, e.g. the entire tricarboxylic acid cycle (TCA) [8,10,11]. Later it was discovered that UCYN-A lives in symbiosis with a photosynthetic haptophyte, related to Braarudosphaera bigelowii, with which it exchanges fixed N for fixed carbon [10,11]. Subsequent work showed that disrupting photosynthesis by the host arrested UCYN-A cell division and changed its daily transcription pattern of the key enzyme in N 2 fixation, the nitrogenase gene (nifH) [12]. ...
... For Stn. ALOHA, CTD data from all casts (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20) were used to calculate the mixed-layer depths based on a potential density (σ θ ) offset of 0.03 kg/m 3 relative to 10 dbar [51]. The mean and standard deviation were used for analysis (S2 Table and S5 Fig). ...
Decades of research on marine N2 fixation focused on Trichodesmium, which are generally free-living cyanobacteria, but in recent years the endosymbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) has received increasing attention. However, few studies have shed light on the influence of the host versus the habitat on UCYN-A N2 fixation and overall metabolism. Here we compared transcriptomes from natural populations of UCYN-A from oligotrophic open-ocean versus nutrient-rich coastal waters, using a microarray that targets the full genomes of UCYN-A1 and UCYN-A2 and known genes for UCYN-A3. We found that UCYN-A2, usually regarded as adapted to coastal environments, was transcriptionally very active in the open ocean and appeared to be less impacted by habitat change than UCYN-A1. Moreover, for genes with 24 h periodic expression we observed strong but inverse correlations among UCYN-A1, A2, and A3 to oxygen and chlorophyll, which suggests distinct host-symbiont relationships. Across habitats and sublineages, genes for N2 fixation and energy production had high transcript levels, and, intriguingly, were among the minority of genes that kept the same schedule of diel expression. This might indicate different regulatory mechanisms for genes that are critical to the symbiosis for the exchange of nitrogen for carbon from the host. Our results underscore the importance of N2 fixation in UCYN-A symbioses across habitats, with consequences for community interactions and global biogeochemical cycles.
... Diverse diazotrophic Bacteria and Archaea have been shown to have the potential to fix N 2 as identified through amplification of their nifH genes 8 , which encodes a component of the nitrogenase enzyme that catalyzes N 2 fixation 9 . Photoautotrophic cyanobacteria, such as Trichodesmium, heterocyst-forming symbionts of diatoms, and unicellular cyanobacteria (Crocosphaera and the symbiont UCYN-A), all have been shown to be important N 2 -fixers in warm, low-nutrient, surface ocean waters through culture-based studies [10][11][12][13] and single cell analyses [14][15][16][17] . However, amplification of nifH genes from ocean waters shows that there are abundant and diverse non-cyanobacterial diazotroph (NCD) nifH sequences 8,18,19 that often exceed the relative abundance of amplified cyanobacterial nifH genes 18,20,21 . ...
... Nanoscale secondary ion mass spectrometry (nanoSIMS) analysis has been used extensively to identify single cell activity, including N 2 fixation by uncultured diazotrophs 38,39 . Diazotrophs for which there are 16S rRNA gene sequences can be identified by catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) or related methods 14,38,40 and shown to fix N 2 by nano-SIMS analysis measuring cellular 15 N incorporation. However, most NCDs are only known by their nifH gene sequence, so visualization and identification using 16S rRNA gene-based CARD-FISH is not possible. ...
... Rate values above LOD as well as values that fell below the LOD but above the MQR are reported. Community N 2 fixation incubation protocols and data reporting follow recommendations from White et al., (2020) 78 : all samples were run in triplicate except as described above (T o station 14) and 15 N incubation filters contained >10 µg N per filter. Our experimental design differed from recommendations by White et al., (2020) 78 in that incubations were not initiated before dawn, our 24-h incubations started at various times throughout the day. ...
Biological nitrogen fixation is a major important source of nitrogen for low-nutrient surface oceanic waters. Nitrogen-fixing (diazotrophic) cyanobacteria are believed to be the primary contributors to this process, but the contribution of non-cyanobacterial diazotrophic organisms in oxygenated surface water, while hypothesized to be important, has yet to be demonstrated. In this study, we used simultaneous ¹⁵N-dinitrogen and ¹³C-bicarbonate incubations combined with nanoscale secondary ion mass spectrometry analysis to screen tens of thousands of mostly particle-associated, cell-like regions of interest collected from the North Pacific Subtropical Gyre. These dual isotope incubations allow us to distinguish between non-cyanobacterial and cyanobacterial nitrogen-fixing microorganisms and to measure putative cell-specific nitrogen fixation rates. With this approach, we detect nitrogen fixation by putative non-cyanobacterial diazotrophs in the oxygenated surface ocean, which are associated with organic-rich particles (<210 µm size fraction) at two out of seven locations sampled. When present, up to 4.1% of the analyzed particles contain at least one active putative non-cyanobacterial diazotroph. The putative non-cyanobacterial diazotroph nitrogen fixation rates (0.76 ± 1.60 fmol N cell⁻¹ d⁻¹) suggest that these organisms are capable of fixing dinitrogen in oxygenated surface water, at least when attached to particles, and may contribute to oceanic nitrogen fixation.
... The composition and abundance of these microbes are related to environmental factors, such as temperature [13], dissolved oxygen (DO) [14], and salinity [15], especially the processes of the nitrogen cycle in water, which are mostly carried out by microbes [16]. For example, cyanobacteria can fix nitrogen by immobilizing N 2 from the air to ammonia nitrogen for bioenergy use [17]. Mycobacterium tuberculosis is involved in assimilatory nitrate reduction and in ultimately converting nitrate into bacterial proteins [18]. ...
... Cyanobiaceae are bacterial markers of WD's early stage, whose abundance was 9.02% in WD3. Cyanobacteria are often considered potential nitrogen-fixing agents in the ocean, converting free nitrogen in the air into a form that can be directly used by organisms [17,50]. Furthermore, the results of functional prediction analysis showed that WD had strong photosynthetic capacity in the early stage. ...
Industrial farming is one of the main farming systems used for L. vannamei, and it is also the main direction of development in the future. To investigate the role of the bacterial community in nitrogen transformation in industrial L. vannamei farming systems, we studied the concentration of nitrogen compounds, the bacterial community using 16S rRNA sequencing, and nitrogen cycling genes' abundance using absolute quantitative PCR in aquaculture water (using seawater (WD) and groundwater mixed with seawater (CY)) and analyzed the correlations between them using a person analysis. The results showed that the bacterial α-diversity index (ACE, Shannon, and Sobs) significantly changed during culture in WD but not in CY. Bacterial community species composition analysis and linear discriminant analysis effect size (LEfSe analysis) revealed that Cyanobiaceae and Microbacteriaceae were the dominant bacteria and biomarkers in WD. Vibrionaceae, Ateromonadaceae, Microbacteriaceae, Saprospiraceae, and Cryomorphaceae were the dominant bacteria and biomarkers in CY. A functional annotation of procaryotic taxa (FAPROTAX) analysis revealed that the bacterial community in WD exhibited a greater phototrophic activity at early culture stages, while at the same stage, CY exhibited strong nitrate reduction. A correlation analysis of nitrogen cycling genes and environmental factors revealed that napA, narG, ureC, amoA, and nirK were significantly correlated with the concentrations of total ammonia nitrogen (TAN), nitrite (NO 2 −-N), nitrate (NO 3 −-N), and total nitrogen (TN) in WD. In CY, amoA was positively correlated and napA and nirK were negatively correlated with TAN and TN concentrations. A correlation analysis between bacterial abundance and environmental factors revealed that Flavobacteriaceae, Saprospiraceae, Cryomorphaceae, Cyanobiaceae, Halieaceae, and Cyclobacteriaceae were significantly correlated with the concentrations of TAN and NO 2 −-N. The above results indicated that the bacterial community in industrial shrimp farming systems changed under different conditions, with consequent changes in the abundance of genes being involved in the nitrogen cycle and in this biogeochemical process in the water. Our study facilitates further understanding of microbes and their functions in nitrogen cycling in industrial shrimp farming systems.
... A closer look at the whole lineage ( Figure 2b) reveals that widespread non-photosynthetic diazotrophic unicellular endosymbionts of eukaryotic algae have formed sister clades to Crocosphaera. One of them, UCYN-A or Candidatus Atelocyanobacterium thalassae, contained endosymbionts of marine Prymnesiophytes (Hagino et al., 2013;Thompson et al., 2012); another more distantly related lineage contained the endosymbionts (also called "spheroid bodies") of rhopalodiacean diatoms (Nakayama & Inagaki, 2017). In both cases, the symbionts had abandoned oxygenic photosynthesis; they function almost as organelles, providing fixed N 2 to their hosts in exchange for fixed carbon (Prechtl et al., 2004;Thompson et al., 2012). ...
... One of them, UCYN-A or Candidatus Atelocyanobacterium thalassae, contained endosymbionts of marine Prymnesiophytes (Hagino et al., 2013;Thompson et al., 2012); another more distantly related lineage contained the endosymbionts (also called "spheroid bodies") of rhopalodiacean diatoms (Nakayama & Inagaki, 2017). In both cases, the symbionts had abandoned oxygenic photosynthesis; they function almost as organelles, providing fixed N 2 to their hosts in exchange for fixed carbon (Prechtl et al., 2004;Thompson et al., 2012). Intriguingly, the marine diatom Climacodium frauenfeldianum has been shown to be capable of hosting Crocosphaera as a photosynthetic diazotrophic endosymbiont (Caputo et al., 2019;Carpenter & Janson, 2000). ...
Crocosphaera watsonii is a unicellular N 2 ‐fixing (diazotrophic) cyanobacterium observed in tropical and subtropical oligotrophic oceans. As a diazotroph, it can be a source of bioavailable nitrogen (N) to the microbial community in N‐limited environments, and this may fuel primary production in the regions where it occurs. Crocosphaera watsonii has been the subject of intense study, both in culture and in field populations. Here, we summarize the current understanding of the phylogenetic and physiological diversity of C. watsonii , its distribution, and its ecological niche. Analysis of the relationships among the individual Crocosphaera species and related free‐living and symbiotic lineages of diazotrophs based on the nif H gene have shown that the C. watsonii group holds a basal position and that its sequence is more similar to Rippkaea and Zehria than to other Crocosphaera species. This finding warrants further scrutiny to determine if the placement is related to a horizontal gene transfer event. Here, the nif H UCYN‐B gene copy number from a recent synthesis effort was used as a proxy for relative C. watsonii abundance to examine patterns of C. watsonii distribution as a function of environmental factors, like iron and phosphorus concentration, and complimented with a synthesis of C. watsonii physiology. Furthermore, we have summarized the current knowledge of C. watsonii with regards to N 2 fixation, photosynthesis, and quantitative modeling of physiology. Because N availability can limit primary production, C. watsonii is widely recognized for its importance to carbon and N cycling in ocean ecosystems, and we conclude this review by highlighting important topics for further research on this important species.
... This ASV was assigned to the family Cyanobacteriaceae ( Figure 5; Table S12). Although some cyanobacteria are unicellular and free-living organisms from the photic zone, many members of this family are known to form symbioses with other marine organisms [51] and inhabit dark environments [52]. A well-described example of this type of symbiosis is the sponge-Cyanobacteria association, in which the marine sponge host provides nutrients and shelter, and the symbiont fixed carbon, nitrogen, and secondary metabolites [53]. ...
... This ASV was assigned to the family Cyanobacteriaceae ( Figure 5; Table S12). Although some cyanobacteria are unicellular and free-living organisms from the photic zone, many members of this family are known to form symbioses with other marine organisms [51] and inhabit dark environments [52]. A well-described example of this type of symbiosis is the sponge-Cyanobacteria association, in which the marine sponge Our results also revealed that several ASVs detected in the gastropod and assigned to the Saprospiraceae family (Chitinophagales order) either only occurred or were more abundant in treatments without oil contamination ( Figure 6; Table S13). ...
Ecosystem functioning depends on complex interactions between microorganisms, hosts, and the environment. Changes in environmental conditions (e.g., ocean acidification) in combination with anthropogenic pollution have been shown to affect the composition and function of free-living microbial communities, but little is known about the effects these stressors on host-associated communities. This study aims to characterize the response of host-associated bacterial communities of the bottom-dwelling polychaete Hediste diversicolor and the epibenthic gastropod Peringia ulvae to oil contamination and reduced seawater pH. The independent and interactive effects of both stressors were simulated under controlled conditions. The response of host-associated bacterial communities was assessed using the high-throughput sequencing of the 16S rRNA gene and several biochemical markers related to host metabolic pathways, e.g., neurotransmission, anaerobic metabolism, biotransformation, oxidative stress, and energy consumption. In H. diversicolor, reduced seawater pH was associated with a high relative abundance of Cyanobacteria, while in P. ulvae oil contamination was associated with a reduction in the relative abundance of Chitinophagales. In P. ulvae, enrichment with oil hydrocarbon-degrading bacteria suggests a possible role of these organisms in the dispersion of oil hydrocarbon degraders. Furthermore, oil supplementation shifted some specific biochemical markers of gastropods related to oxidative stress and energy consumption, which suggests host stress. In general, the bacterial communities and biochemical markers of the gastropod were more affected by stressors than those of the polychaete. Overall, this study contributes to a better understanding of the response of host-associated bacterial communities of benthic macrofauna to anthropogenic contamination and environmental change.
... UCYN-A lives symbiotically with a single-celled haptophyte alga related to Braarudosphaera bigelowii (Hagino et al., 2013;Thompson et al., 2012). The basis of this symbiosis is the transfer of fixed carbon from the host in exchange for fixed N (Thompson et al., 2012) since UCYN-A lacks oxygenic photosynthesis, carbon fixation and many other essential metabolic pathways (Tripp et al., 2010;Zehr et al., 2008). ...
... UCYN-A lives symbiotically with a single-celled haptophyte alga related to Braarudosphaera bigelowii (Hagino et al., 2013;Thompson et al., 2012). The basis of this symbiosis is the transfer of fixed carbon from the host in exchange for fixed N (Thompson et al., 2012) since UCYN-A lacks oxygenic photosynthesis, carbon fixation and many other essential metabolic pathways (Tripp et al., 2010;Zehr et al., 2008). Eight UCYN-A sublineages (UCYN-A1 to -A8) have been defined based on the phylogenetic diversity of nifH gene sequences (Farnelid et al., 2016;Henke et al., 2018;Thompson et al., 2014;Turk-Kubo et al., 2017), of which UCYN-A1 to -A4 are known to occupy different ecological niches (Farnelid et al., 2016;Turk-Kubo et al., 2017). ...
The unicellular cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN‐A) is a key diazotroph in the global ocean owing to its high N2 fixation rates and wide distribution in marine environments. Nevertheless, little is known about UCYN‐A in oxygen‐deficient zones (ODZs), which may be optimal environments for marine diazotrophy. Therefore, the distribution and diversity of UCYN‐A were studied in two consecutive years under contrasting phases (La Niña vs. El Niño) of El Niño Southern Oscillation (ENSO) along a transect in the ODZ of the Mexican Pacific upwelling system. Of the three UCYN‐A sublineages found, UCYN‐A1 and UCYN‐A3 were barely detected, whereas UCYN‐A2 was dominant in all the stations and showed a wide distribution in both ENSO phases. The presence of UCYN‐A was associated with well‐oxygenated waters, but it was also found for the first time under suboxic conditions (<20 μM) at the bottom of a shallow coastal station, within the oxygen‐poor and nutrient‐rich Subsurface Subtropical water mass. This study contributes to the understanding of UCYN‐A distribution under different oceanographic conditions associated with ENSO phases in upwelling systems, especially because of the current climate change and increasing deoxygenation in many areas of the world's oceans.
... In contrast, in the bacterial fraction (0.2-3 µm), most arctic diazotroph MAGs were rarely found. This size-dependent difference in the abundance could be due to the cell size of these bacteria or their symbiotic/particle-attached lifestyle [4,[54][55][56][57]. For example, UCYN-A is a symbiotic diazotroph with haptophytes, and its size including its host is >3 µm [4,54]. ...
... This size-dependent difference in the abundance could be due to the cell size of these bacteria or their symbiotic/particle-attached lifestyle [4,[54][55][56][57]. For example, UCYN-A is a symbiotic diazotroph with haptophytes, and its size including its host is >3 µm [4,54]. Therefore, UCYN-A was detected in the total fraction but was rarely detected in the bacterial fraction. ...
Dinitrogen (N2) fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that N2 fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed diazotroph genomes, including that of cyanobacterium UCYN-A (Candidatus 'Atelocyanobacterium thalassa'), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Further, we show that diazotrophs within genera Arcobacter, Psychromonas, and Oceanobacter are prevalent in the <0.2 µm fraction in the Arctic Ocean, indicating that current methods cannot capture their N2 fixation. Diazotrophs in the Arctic Ocean were either Arctic-endemic or cosmopolitan species from their global distribution patterns. Arctic-endemic diazotrophs, including Arctic UCYN-A, were similar to low-latitude-endemic and cosmopolitan diazotrophs in genome-wide function, however, they had unique gene sets (e.g., diverse aromatics degradation genes), suggesting adaptations to Arctic-specific conditions. Cosmopolitan diazotrophs were generally non-cyanobacteria and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters of global ocean and polar surface waters. This study shows global distribution pattern of diazotrophs with their genomes and provides clues to answering the question of how diazotrophs can inhabit polar waters.
... respectively (Church et al., 2005b;Webb et al., 2009;Foster et al., 2007;Taniuchi et al., 2012). When UCYN-A, recently named Candidatus Atelocyanobacterium thalassa (Thompson et al., 2012), is of picoplanktonic size (0.5-1.8 µm) and still uncultured. Significant concentrations of UCYN-A have been measured in the western basin of the Mediterranean Sea (99.9% of < 3 µm of UCYN concentration, ) with the help of the Nitro-821 molecular probe, specific to UCYN 16S rRNA, which light up UCYN cells with fluorescent dye using TSA-FISH technique and allow microscopic counts (Biegala et al., 2002;Biegala and Raimbault, 2008). ...
... These cells were free living, similarly as the one observed in this study (Fig. 3H-I), while it has been claimed that they were obligate symbionts due to their partial genome, which lacks the ability to fix CO 2 and to synthesize several amino-acids and purines (Tripp et al., 2010). However, other studies have shown that symbiose was fragile and partial (Thompson et al., 2012;Krupke et al., 2013). The concentration of UCYN was slightly higher than mean concentrations observed across the Mediterranean Sea (Le Moal and Biegala, 2009;Le Moal et al., 2011), and an order of magnitude lower than the concentrations recorded off Marseille. ...
Gabès Gulf is limited by ultra-oligotrophic waters which are regularly fertilized with both phosphate and iron-enriched atmospheric dust. Despite the lack of a river-run nitrogen source, an essential nutrient for ecosystem productivity. Diazotrophic cyanobacteria are an important source of new nitrogen in oligotrophic oceans and seas. So far only the filamentous diazotrophic cyanobacteria Trichodesmium spp. has been investigated in Gabès gulf, while it is known that other diazotrophic cyanobacteria, such as the heterocysts Richelia intracellularis and unicellular cyanobacteria (UCYN), are a major source of new nitrogen in oligotrophic ecosystems. In this study, we investigated the diversity and abundance of marine diazotrophic cyanobacteria within two size fractions (> 10 µm and 0.2-3 µm) during July in the central coastal area of the Gulf of Gabès. Richelia intracellularis were present under free-living and hosted in the diatoms Hemiaulus hauckii. Unicellular diazotrophic cyanobacteria were classified under two size classes (small cells: 0.8-1.5 µm and large cells: 1.6-3.2 µm) with a predominance of the small cells (98 %). Richelia intracellularis reached concentrations that can be considered a blooming phenomenon (up to 227.5 cells mL −1), while the concentration of UCYN (from 8.8 to 23.9 cells mL −1) was slightly higher than the mean concentrations observed across the Mediterranean Sea. High temperature and dissolved nitrogen and orthophosphate concentrations in the central coastal area of the Gulf of Gabès seem to be the main factors leading to such abundances. The contribution of each diazotrophic cyanobacteria to the N/P balance in the central coastal area of the Gulf was also discussed.
... Nature has inspired us with natural strategies for delivering probiotics, as evidenced by the symbiotic relationship between bacteria and algae that has been observed since the early stages of biological evolution [16,17]. This symbiosis serves as a structural pillar of ecosystems and has practical applications in various fields, including industrial and municipal wastewater treatment [18,19], carbon dioxide emission reduction, bioreactors, and energy production [20][21][22]. ...
The gut microbiota is one of the essential contributors of the pathogenesis and progress of inflammatory bowel disease (IBD). Compared with first-line drug therapy, probiotic supplementation has emerged as a viable and secure therapeutic approach for managing IBD through the regulation of both the immune system and gut microbiota. Nevertheless, the efficacy of oral probiotic supplements is hindered by their susceptibility to the gastrointestinal barrier, leading to diminished bioavailability and restricted intestinal colonization. Here, we developed a bacteria-microalgae symbiosis system (EcN-SP) for targeted intestinal delivery of probiotics and highly effective treatment of colitis. The utilization of mircroalge Spirulina platensis (SP) as a natural carrier for the probiotic Escherichia coli Nissle 1917 (EcN) demonstrated potential benefits in promoting EcN proliferation, facilitating effective intestinal delivery and colonization. The alterations in the binding affinity of EcN-SP within the gastrointestinal environment, coupled with the distinctive structural properties of the SP carrier, served to overcome gastrointestinal barriers, minimizing transgastric EcN loss and enabling sustained intestinal retention and colonization. The oral administration of EcN-SP could effectively treat IBD by reducing the expression of intestinal inflammatory factors, maintaining the intestinal barrier and regulating the balance of gut microbiota. This probiotic delivery approach is inspired by symbiotic interactions found in nature and offers advantages in terms of feasibility, safety, and efficacy, thus holding significant promise for the management of gastrointestinal disorders.
... Phylogenetically distinct clades of UCYN have been detected. The Candidatus Atelocyanobacterium thalassa in group A (UCYN-A) appears to be an obligate endosymbiont of the single-celled prymnesiophyte algae (Thompson et al., 2012;Coale et al., 2024), whereas UCYN-B is mostly free-living, and a culturable representative, Crocosphaera watsonii, has been successfully isolated. Compared with other major N 2 fixers like Trichodesmium and C. watsonii, the UCYN-A can be detected in colder and deeper open-ocean waters (Moisander et al., 2010), as well as coastal waters (Hagino et al., 2013), further demonstrating their importance in global N 2 fixation. ...
Kuroshio intrusion (KI) is a key process that transports water from the western Pacific Ocean to the northern South China Sea (nSCS), where KI-induced surface water mixing often causes variations in microbial assemblages. Yet, how interannual KIs affect the biogeography of diazotrophs and associated environmental factors remains poorly characterized. Here, by quantifying the degree of KIs in 2 consecutive years, coupled with monitoring the diversity and distribution of nitrogenase-encoding nifH phylotypes with quantitative PCR and high-throughput sequencing, we show that changes in the diazotrophic community structure in the nSCS are highly correlated with KI-induced variations in a range of physicochemical parameters. Specifically, the filamentous cyanobacteria in the genus Trichodesmium were more abundant at stations strongly affected by KI and thereby with a deeper mixed layer and higher surface salinity and temperature; the unicellular N2-fixing cyanobacteria in group B (UCYN-B) were more abundant at stations least affected by KI and correlated with nutrient availability, whereas UCYN-C and the γ-proteobacteria were prevalent at stations moderately affected by KI. The neutral community model further demonstrated that dominant diazotrophic subcommunities were significantly affected by environmental factors in 2017 when KI was stronger compared to 2018 when KI retreated. Our analyses provide insightful evidence for the role of KI in shaping the diazotrophic community structure primarily as a stochastic process, implying a potential region-scale redistribution of diazotrophs and nitrogen budget, given that KIs are projected to intensify in a future warming ocean.
... It has been shown from frequent observations that microalgae require bacteria for morphology development and growth (Bolch et al. 2011;Windler et al. 2014). Bacteria are able to fix nitrogen (Foster et al. 2011;Thompson et al. 2012) and synthesize an array of molecules, including vitamins (Grant et al. 2014;Xie et al. 2013), the growth-promoting hormone indole acetic acid (IAA) (Amin et al. 2015;Dao et al. 2018) and the siderophore vibrioferrin (Amin et al. 2007;Lupette et al. 2016) for microalgae to exchange for dissolved organic matter. Like macroalgae-associated archaea, archaea co-occurring with microalgae have often been overlooked. ...
Algae and archaea co-exist in diverse aquatic ecosystems and play a significant role in ecological functions and biogeochemical cycles. Compared to well-studied algal–bacterial interactions, there is a lack of information on algal–archaeal interactions and how their interactions affect their physiological fitness and nutrient cycles in either artificial cultivation systems or natural environments. The vast archaeal biodiversity, as indicated by genomic sequencing and computational approaches, has stimulated great interest in exploring uncultivated archaea to expand our knowledge of algae-archaea symbiosis. In this review, we summarize the latest studies on the diversity of algae-associated archaea and their (putative) symbiotic interactions, highlight the effects of algal–archaeal interactions on biogeochemical cycles and extend such knowledge to facilitate novel archaeal isolation and a broad range of algae-based biotechnological applications.
... Trichodesmium is highly active in N-depleted waters where phosphorus and iron, a key constituent of the nitrogenase enzyme which mediates N 2 fixation, are available. Subsequent development and broad application of both molecular and microscopic approaches led to the identification of numerous other diazotrophs which differ in their biogeography (Zehr & Capone, 2020), including several symbiotic diazotrophic clades residing within diatom (Carpenter et al., 1999;Schvarcz et al., 2022) and haptophyte (Thompson et al., 2012) hosts. These groups are thought to be less sensitive to ambient dissolved inorganic N (Zehr & Capone, 2020) and, in some cases, appear to thrive in coastal upwelling systems (e.g., Mills et al., 2020;Selden et al., 2022;Voss et al., 2006), potentially extending the life of phytoplankton blooms where ambient N is drawn down in advance of other nutrients. ...
Continental shelves contribute a large fraction of the ocean's new nitrogen (N) via N2 fixation; yet, we know little about how physical processes at the ocean's margins shape diazotroph biogeography and activity. Here, we test the hypothesis that frontal mixing favors N2 fixation at the Mid‐Atlantic Bight shelfbreak. Using the ¹⁵N2 bubble release method, we measured N2 fixation rates on repeat cross‐frontal transects in July 2019. N2 fixation rates in shelf waters (median = 5.42 nmol N L⁻¹ d⁻¹) were higher than offshore (2.48 nmol N L⁻¹ d⁻¹) but did not significantly differ front frontal waters (8.42 nmol N L⁻¹ d⁻¹). However, specific N2 uptake rates, indicative of the relative contribution of diazotroph‐derived N to particulate N turnover, were significantly higher in frontal waters, suggesting that diazotroph‐derived N is of greater importance in supporting productivity there. This study furthered captured an ephemeral shelf‐water streamer, which resulted from the impingement of a warm core ring on the shelf. The streamer transported shelf‐water diazotrophs (including UCYN‐A and Richelia spp., as assessed by qPCR) offshore with sustained high N2 fixation rates. This feature injected >50 metric tons d⁻¹ of newly fixed N to the Slope Sea—a rate equivalent to ∼4% of the total N flux estimated for the entire Mid‐Atlantic Bight. As intrusions of Gulf Stream meanders and eddies onto the shelf are increasing in frequency due to climate change, episodic lateral fluxes of new N into the Slope Sea may become increasingly important to regional budgets and ecosystem productivity.
... The low identities and phylogenetic distribution obtained showed that there are no described lineages closely related to the genus Pannus and emphasized that generating new sequences for type species and recently isolated species of Cyanobacteria will significantly advance the field of taxonomy within this clade. Furthermore, it illustrated the need for efforts to isolate and characterize traditionally uncultivated Cyanobacteria strains by sampling underexplored habitats and locations [110][111][112]. ...
The freshwater Pannus genus comprises cyanobacterial unicellular species with a particular morphology, forming free-floating rounded colonies with thin, homogenous, and colorless colonial mucilage. There is little literature on the taxonomy of the Pannus and none on its metabolism. This study presents the first genomic characterization of a Pannus strain isolated from Pantanal Biome, Brazil. The genome was assembled into 117 contigs with a total size of 5.1 Mb and 99.12% completeness. It contained 4988 protein-encoding genes, including some involved in secondary metabolite biosynthesis, such as cyanobactin and terpenes. Interestingly, P. brasiliensis CCIBt3594 has a complete set of nitrogen fixation genes and is a non-heterocytou unicellular cyanobacterium. Finally, the phylogenomic analyses revealed the lack of information on closely related strains and anchored the genus Pannus within the order Chroococcales, Microcystaceae family, closest to Microcystis spp. representatives. This work presents novel evidence concerning a sparsely characterized genus of the Cyanobacteria phylum and contributes to elucidating taxonomic and systematic issues within the group of unicellular cyanobacteria.
... While the diversity of marine cyanobacte-ria has been extensively studied in the context of marine microbial ecology, previous analyses have mainly focused on free-living cyanobacteria, leaving our understanding of species in symbiosis with other organisms limited. In recent years, previously unrecognized lineages of marine cyanobacteria have been discovered within symbiotic relationships with eukaryotes (Nakayama et al., 2019;Schvarcz et al., 2022;Thompson et al., 2012). Such findings suggest the need for further investigation of cyanobacteria that engage in symbiosis to fully understand the diversity of marine cyanobacteria. ...
The diversity of marine cyanobacteria has been extensively studied due to their vital roles in ocean primary production. However, little is understood about the diversity of cyanobacterial species involved in symbiotic relationships. In this study, we successfully sequenced the complete genome of a cyanobacterium in symbiosis with Citharistes regius, a dinoflagellate species thriving in the open ocean. A phylogenomic analysis revealed that the cyanobacterium (CregCyn) belongs to the marine picocyanobacterial lineage, akin to another cyanobacterial symbiont (OmCyn) of a different di-noflagellate closely related to Citharistes. Nevertheless , these two symbionts are distinct lineages, suggesting independent origins of their symbiotic lifestyles. Despite the distinct origins, the genome analyses of CregCyn revealed shared characteristics with OmCyn, including an obligate symbiotic relationship with the host dinoflagellates and a degree of genome reduction. In contrast, a detailed analysis of genome subregions unveiled that the CregCyn genome carries genomic islands that are not found in the OmCyn genome. The presence of the genomic islands implies that exogenous genes have been integrated into the CregCyn genome at some point in its evolution. This study contributes to our understanding of the complex history of the symbiosis between dinoflagellates and cyanobacte-ria, as well as the genomic diversity of marine pico-cyanobacteria. cyanobacteria | genome reduction | symbiosis Correspondence: ntakuro@ccs.tsukuba.ac.jp
... Although the base excision repair and nucleotide repair pathway were found in SH4, the exonuclease Exo VII complex in the mismatch repair pathway, the exonuclease V complex (RecBCD) in the homologous recombination pathway, and ATP-dependent DNA ligase were not detected (Table 1; see Table S3 in the supplemental material). There are also reports of a reduction of DNA repair genes in the symbiotic cyanobacterium UCYN-A (44) and in the cyanobacteriumoriginating inclusions termed chromatophores (28). The absence of DNA repair genes in "Ca. ...
“Candidatus Synechococcus spongiarum” is a cyanobacterial symbiont widely distributed in sponges, but its functions at the genome level remain unknown. Here, we obtained the draft genome (1.66 Mbp, 90% estimated genome recovery) of “Ca. Synechococcus spongiarum” strain SH4 inhabiting the Red Sea sponge Carteriospongia foliascens. Phylogenomic analysis revealed a high dissimilarity between SH4 and free-living cyanobacterial strains. Essential functions, such as photosynthesis, the citric acid cycle, and DNA replication, were detected in SH4. Eukaryoticlike domains that play important roles in sponge-symbiont interactions were identified exclusively in the symbiont. However, SH4 could not biosynthesize methionine and polyamines and had lost partial genes encoding low-molecular-weight peptides of the photosynthesis complex, antioxidant enzymes, DNA repair enzymes, and proteins involved in …
... The conversion factor for UCYN-A was updated because it has been found to live symbiotically with haptophyte Braarudosphaera bigelowii and relatives (Thompson et al., 2012;Hagino et al., 2013). Because the host and UCYN-A should function together, the host biomass is allocated to UCYN-A. ...
Marine diazotrophs convert dinitrogen (N2) gas into bioavailable nitrogen (N), supporting life in the global ocean. In 2012, the first version of the global oceanic diazotroph database (version 1) was published. Here, we present an updated version of the database (version 2), significantly increasing the number of in situ diazotrophic measurements from 13 565 to 55 286. Data points for N2 fixation rates, diazotrophic cell abundance, and nifH gene copy abundance have increased by 184 %, 86 %, and 809 %, respectively. Version 2 includes two new data sheets for the nifH gene copy abundance of non-cyanobacterial diazotrophs and cell-specific N2 fixation rates. The measurements of N2 fixation rates approximately follow a log-normal distribution in both version 1 and version 2. However, version 2 considerably extends both the left and right tails of the distribution. Consequently, when estimating global oceanic N2 fixation rates using the geometric means of different ocean basins, version 1 and version 2 yield similar rates (43–57 versus 45–63 Tg N yr−1; ranges based on one geometric standard error). In contrast, when using arithmetic means, version 2 suggests a significantly higher rate of 223±30 Tg N yr−1 (mean ± standard error; same hereafter) compared to version 1 (74±7 Tg N yr−1). Specifically, substantial rate increases are estimated for the South Pacific Ocean (88±23 versus 20±2 Tg N yr−1), primarily driven by measurements in the southwestern subtropics, and for the North Atlantic Ocean (40±9 versus 10±2 Tg N yr−1). Moreover, version 2 estimates the N2 fixation rate in the Indian Ocean to be 35±14 Tg N yr−1, which could not be estimated using version 1 due to limited data availability. Furthermore, a comparison of N2 fixation rates obtained through different measurement methods at the same months, locations, and depths reveals that the conventional 15N2 bubble method yields lower rates in 69 % cases compared to the new 15N2 dissolution method. This updated version of the database can facilitate future studies in marine ecology and biogeochemistry.
... Despite many of these interactions being endosymbiotic, N 2 fixation has never been associated with any extant organelle. A genomically reduced cyanobacterium called UCYN-A is a N 2 -fixing endosymbiont (spheroid body) of a marine unicellular haptophyte, Braarudosphaera bigelowii, and supplies fixed nitrogen to the host in return for fixed carbon [2]. This symbiosis is particularly intriguing because it appears to be an obligate endosymbiosis similar to the hypothetical "nitroplast", evidenced by extreme genome and metabolic reduction in the UCYN-A cyanobacterium. ...
... The partnership is mutualistic because Emiliania. huxleyi receive fixed N from UCYN-A, and in exchange, transfer fixed carbon to UCYN-A [110]. It has been characterized that UCYN-A also establishes an endosymbiotic relationship with the microalga Braarudosphaera bigelowii [106]. ...
Microalgae are used in various biotechnological processes, such as biofuel production due to their high biomass yields, agriculture as biofertilizers, production of high-value-added products, decontamination of wastewater, or as biological models for carbon sequestration. The number of these biotechnological applications is increasing, and as such, any advances that contribute to reducing costs and increasing economic profitability can have a significant impact. Nitrogen fixing organisms, often called diazotroph, also have great biotechnological potential, mainly in agriculture as an alternative to chemical fertilizers. Microbial consortia typically perform more complex tasks than monocultures and can execute functions that are challenging or even impossible for individual strains or species. Interestingly, microalgae and diazotrophic organisms are capable to embrace different types of symbiotic associations. Certain corals and lichens exhibit this symbiotic relationship in nature, which enhances their fitness. However, this relationship can also be artificially created in laboratory conditions with the objective of enhancing some of the biotechnological processes that each organism carries out independently. As a result, the utilization of microalgae and diazotrophic organisms in consortia is garnering significant interest as a potential alternative for reducing production costs and increasing yields of microalgae biomass, as well as for producing derived products and serving biotechnological purposes. This review makes an effort to examine the associations of microalgae and diazotrophic organisms, with the aim of highlighting the potential of these associations in improving various biotechnological processes.
... New nitrogen cycle pathways have been discovered in recent years such as anaerobic ammonium oxidation (anammox) [12], complete ammonia oxidation (comammox) [13], ANRA [14], DNRA [15], and aerobic denitrification [16]. These nitrogen transformation pathways are mainly driven by Bacteria, but novel microorganisms were identified as part of these processes, including symbiotic heterotrophic nitrogen-fixing Cyanobacteria [17], ammonia-oxidizing Archaea [18], Streptomyces [19], and Eukaryota [20][21][22]. ...
Nitrogen is one of the most important elements involved in ecosystem biogeochemical cycling. However, little is known about the characteristics of nitrogen cycling during the ice-covered period in seasonally frozen lakes. In this study, shotgun metagenomic sequencing of subglacial water and sediment from Lake Ulansuhai was performed to identify and compare nitrogen metabolism pathways and microbes involved in these pathways. In total, ammonia assimilation was the most prominent nitrogen transformation pathway, and Bacteria and Proteobacteria (at the domain and phylum levels, respectively) were the most abundant portion of microorganisms involved in nitrogen metabolism. Gene sequences devoted to nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction to ammonium, and ammonia assimilation were significantly higher in sediment than in surface and subsurface water. In addition, 15 biomarkers of nitrogen-converting microorganisms, such as Ciliophora and Synergistetes, showed significant variation between sampling levels. The findings of the present study improve our understanding of the nitrogen cycle in seasonally frozen lakes.
... In turn, associated partners in the phycosphere may provide CO2, nitrogen, phosphorous, sulphur and trace elements to the Cyanobacteria (Havens, 2008). Reports have shown that Cyanobacteria form relationships within the phycosphere; one common obligate mutualism exists between heterocyst-forming Cyanobacteria and diatoms whereby the Cyanobacteria provide fixed nitrogen to the diatom in exchange for amino acids and organic carbon (Foster et al., 2011;Hilton et al., 2013;Thompson et al., 2012). with Microcystis spp. ...
The presence of taste and odour compounds (T&O) in drinking water lead to numerous complaints to water companies worldwide. Geosmin and 2-MIB are common T&O compounds, with Cyanobacteria being the primary biological source in drinking water reservoirs. Both compounds have low odour thresholds in humans and require expensive additional treatment. This thesis used molecular and statistical analysis of water from Welsh Water reservoirs, to provide a framework for predicting and monitoring T&O events and understanding their causes.
Elevated T&O concentrations were confined to warmer months, except for a one geosmin event in winter 2019. There was no correlation between cyanobacterial abundance and T&O concentrations, but qPCR analysis based on eDNA sampling demonstrated that geosmin synthase (geoA) was a suitable proxy for predicting geosmin concentrations. Abundances of geoA and 2-MIB cyclase (mic) were significantly non-linearly associated with high ammonium-to-nitrate ratios, identifying thresholds for heightened T&O risk. The ratio of total inorganic nitrogen to total phosphorous was significantly non-linearly associated with increases in geoA. Increased geoA was also significantly negatively associated with temperature and dissolved reactive silicate in all reservoirs. Next-generation sequencing of bacterial and algal communities showed that community compositions clustered according to T&O concentrations. Bacterial and algal co-occurrence networks uncovered significant positive and negative associations, highlighting cyanospheres in all reservoirs. Random Forest models were developed for geosmin (Alaw) and 2-MIB (Pentwyn) using significantly co-occurring taxa exposing indicative T&O taxa and the probable Cyanobacteria causing the T&O. Cyanobacteria had more negative than positive associations in their cyanospheres.
This thesis illustrates the importance of nutrient ratios in triggering potential geosmin and 2-MIB events. It also indicates that Cyanobacteria subjected to environmental stress (negative biotic interactions and low temperatures) increase their T&O-production. These findings provide a useful framework for water monitoring to enable the prediction and possible prevention of T&O events.
... These complex consortia often contain many interactions between members whereby one species impacts the abundances of another. Interactions in these communities can determine the outcome of invasions [1], metabolic processes such as carbon and nitrogen remineralization [2], or the phenotype of the host [3]. Crucially, however, interactions between members of a microbial consortium depend on the environmental context. ...
Photosynthetic microbes associated with non-photosynthetic, heterotrophic, bacteria play a key role in the global primary production. Understanding these phototroph-heterotroph associations is therefore important, but remains challenging because they reside in chemically complex aquatic and terrestrial environments. We do not understand how the myriad of environmental parameters from nutrient availability to pH impact interactions between phototrophs and their heterotrophic partners. Here, we leverage a massively parallel droplet microfluidic platform that enables us to interrogate algae-bacteria interactions in > 100,000 communities across ∼525 environmental conditions with varying pH, carbon availability and phosphorous availability. By developing a statistical framework to dissect interactions in this complex dataset, we reveal that dependance of algae-bacteria interactions on nutrient availability is strongly modulated by pH and buffering capacity. Furthermore, we show that the chemical identity of the available organic carbon source controls how pH, buffering capacity, and nutrient availability modulate algae-bacteria interactions. By leveraging a high-throughput platform, our study reveals the previously underappreciated role of pH in modulating phototroph-heterotroph interactions.
... Besides the lattice-bound N, the recalcitrant organic matter of muddy rocks is considered the main depository of organic nitrogen that can be microbially transferred to the terrestrial ecosystem more readily than the clay minerals-fixed nitrogen (Morford et al. 2016;Bingham et al. 2021). The transformation of N from seawater into shale deposits can be summarized through three main steps (Peterson 1981;de Leeuw and Largeau 1993;Mayer 1994a, b;Macko et al. 1994;Holloway and Dahlgren 2002;Knicker 2004; Thompson et al. 2012;Delmint et al. 2018;Pajares and Ramos 2019) as follows: (a) N-fixation and nitrification from the surface seawater by diazotrophs (e.g., diverse group of bacteria, algae, and diatoms) which convert N 2 into bioavailable NH 4 + and NO 3 − stored in the living tissues as peptides and amino acids; (b) as diazotrophs become dead, the nitrogen-bearing organic compounds accumulate downward with the settling clay particles; (c) during sediment diagenesis, some of the deposited N-organic compounds are microbially degraded under anoxic conditions into NH 4 + that encapsulated into the silicate structure of clay minerals, while the other fraction is stabilized into the recalcitrant organic matter. In addition to the foregoing literature, other studies (e.g., Mingram et al. 2003;Schneider-Mor et al 2012;Ristic et al. 2016;Li et al. 2019;Zhu et al. 2021) utilized nitrogen isotope composition to reconstruct the paleoenvironmental conditions of carbonaceous shales and to investigate the behavior of nitrogen-organic compounds during diagenesis and shale gas generation. ...
Besides nitrate deposits located in the Atacama Desert of Chile and the Mojave Desert of California, the present work documents, for the first time, the occurrence of potassium nitrate as oval-suboval-shaped aggregations associated with the Late Maastrichtian-Early Paleocene Dakhla Shale and the Paleocene-Early Eocene Esna Shale encountered in the northeastern part of the Kharga Oasis, particularly at G. Um El-Ghanayem and G. Ghaneima. Consequently, integrated petrographic, mineralogical, and geochemical investigations were carried out for shale deposits and nitrate salts to reconstruct the paleoenvironmental conditions of shale, reveal the extent to which nitrate salts are genetically related to the paleoenvironment of shale deposits, and build up a complete scenario about the source and the formation mechanism of nitrate salts. The overall results showed that the studied shale deposits were sourced from mafic igneous and quartzose sedimentary provenances where humid climatic conditions were dominant; the transported detrital particles were then settled down under oxidizing bottom water and shallow depositional conditions. Moreover, the nitrate salts are of an epigenetic origin and sourced from the microbial nitrification of organic matter and the wet atmospheric deposition that is believed to be triggered by the active volcanic eruptions during the Late Eocene/Early Oligocene transition where warm climatic conditions prevailed.
... The conversion factor for UCYN-A is also updated because it has been found to live symbiotically with prymnesiophyte or coccolitophore species (Thompson et al., 2012). Similar to DDAs, the host biomass is allocated to UCYN-A. ...
Marine diazotrophs convert dinitrogen (N2) in seawater into bioavailable nitrogen (N), contributing approximately half of the external input of bioavailable N to the global ocean. A global oceanic diazotroph database was previously published in 2012. Here, we compiled version 2 of the database by adding 23,095 in situ measurements of marine diazotrophic abundance and N2 fixation rates published in the past decade, increasing the number of N2 fixation rates and microscopic and qPCR-based diazotrophic abundance data by 140 %, 26 % and 443 %, respectively. Although the updated database expanded spatial coverage considerably, particularly in the Indian Ocean, the data distribution was still not uniform and most data were sampled in the surface Pacific and Atlantic Oceans. By summing the arithmetic means of the N2 fixation rates in each ocean basin, the updated database substantially increased the estimate of global oceanic N2 fixation from 137 ± 9 Tg N yr-1 using the old database to 260 ± 20 Tg N yr-1 (mean ± standard error). However, using geometric means instead, the updated database gave an estimate of global oceanic N2 fixation (60 Tg N yr-1) similar to that estimated from the old database (62 Tg N yr-1), while the new estimate had a larger uncertainty (confidence intervals based on one standard error: 47 – 107 Tg N yr-1 versus 52 – 73 Tg N yr-1), mostly attributable to elevated uncertainties in the Pacific Ocean. An analysis comparing N2 fixation rates measured at the same months and location (1° × 1° grids) showed that the new 15N2 dissolution method obtained N2 fixation rates higher than the conventional 15N2 bubble method in 65 % of cases, with this percentage increasing when the N2 fixation rates were high (> approximately 3 μmol N m-3 d-1 using the 15N2 dissolution method). With greatly increased data points, this version 2 of the global oceanic diazotrophic database can support future studies in marine ecology and biogeochemistry. The database is stored at the Figshare repository (https://doi.org/10.6084/m9.figshare.21677687) (Shao et al., 2022).
... Lichens Microalgae-fungi [33] Microalgal mats or biofilms: microalgae such as diatoms, cyanobacteria, and anoxygenic phototrophic bacteria and sulfatereducing bacteria Microalgae-bacteria [34] Algal blooms Microalgae and microalgaebacteria [17,35] Diatom Epithemia turgida and the coccoid cyanobacteria Rhopalodia gibba Microalgae-cyanobacteria [36] Diatom Hemiaulus, Rhizosolenia, Chaetoceros, and N2 fixing cyanobacteria R. intracellularis and C. rhizosoleniae Microalgae-cyanobacteria [11,37,38] Microalgae (Microcystis aeruginosa., etc.) and bacteria (E. coli, Pseudomonas sp., and Bacillus sp., etc.): phosphorus transfer Microalage-bacteria [39] Microalgae (Stichococcus sp., Chlorella sp., and S. quadricauda), cyanobacteria (Phormidium sp., and Nostoc sp.,), and alcanotrophic bacteria Microalgae/Cyanobacteriabacteria [40] Nitrogen-fixing cyanobacterium can transform atmospheric nitrogen into fixed nitrogen, such as ammonia, that other microorganisms could directly absorb without nitrogen-fixing ability. ...
Microalgae have been considered a promising and sustainable candidate for wastewater treatment and valuable bioproducts, such as feedstocks for food, nutrients, and energy. However, many challenging bottlenecks, such as low biomass productivity, expensive biomass harvesting techniques, and inefficient extraction of biofuels restrict its large-scale commercial production. Symbiotic relationships between microalgae and bacteria, also known as microalgal consortia, have proven to be effective solutions for mitigating technical and economic limitations. The natural and artificial symbiotic microalgal consortia combine microorganisms with various metabolic activities, which leads to valuable biomass production and the removal of nutrients, pharmaceuticals, and personal care products (PPCP) from wastewater. Many microalgal consortia have been applied for various wastewater treatments with reduced energy costs and higher efficiency in recovering valuable resources. In this study we review the present research status and prospects of microalgal consortia, emphasizing the associated mechanism of microalgae consortia cooperative symbiosis and its studies on diverse environmental and biotechnological applications.
... Interestingly, many strains within Chroococcales thrive in an environment with higher mineral content, such as thermal mineral springs, brackish or saline waters, and many of them were found to be euryhaline. Members of the Crocosphaera lineage (in Microcystaceae) are important free-living and endosymbiotic marine diazotrophs of the so-called UCYN lineages such as Candidatus Atelocyanobacterium thalassae (Thompson et al. 2012). Many genera also prosper in (semi)terrestrial environments such as rocks (Gloeothece, Chroococcus) or in freshwater phytoplankton blooms (Microcystis, Woronichinia, Snowella, etc.). ...
Cyanobacterial taxonomy is facing a period of rapid changes thanks to the ease of 16S rRNA gene sequencing and established workflows for description of new taxa. Since the last comprehensive review of the cyanobacterial system in 2014 until 2021, at least 273 species in 140 genera were newly described. These taxa were mainly placed into previously defined orders and families although several new families were proposed. However, the classification of most taxa still relied on hierarchical relationships inherited from the classical morphological taxonomy. Similarly, the obviously polyphyletic orders such as Synechococcales and Oscillatoriales were left unchanged. In the current study, the rising number of genomic sequences of cyanobacteria and well described reference strains allowed us to reconstruct a robust phylogenomic tree for taxonomic purposes. A less robust but better sampled 16S rRNA gene phylogeny was mapped to the phylogenomic backbone. Based on both these phylogenies, a polyphasic classification throughout the whole phylum of Cyanobacteria was created, with ten new orders and fifteen new families. The proposed system of cyanobacterial orders and families relied on a phylogenomic tree but still employed phenotypic apomorphies where possible to make it useful for professionals in the field. It was, however, confirmed that morphological convergence of phylogenetically distant taxa was a frequent phenomenon in cyanobacteria. Moreover, the limited phylogenetic informativeness of the 16S rRNA gene, resulting in ambiguous phylogenies above the genus level, emphasized the integration of genomic data as a prerequisite for the conclusive taxonomic placement of a vast number of cyanobacterial genera in the future.
... particle-or aggregate-associated), or if NCDs can fix N 2 aerobically (like some terrestrial counterparts) and if so, how they mitigate O 2 inactivation of nitrogenase. Another interesting question to resolve is whether some NCD taxa have formed obligate symbioses with other planktonic species, an evolutionary strategy that has led to many symbioses between cyanobacterial diazotrophs and algae (Villareal, 1992, Thompson et al., 2012, Schvarcz et al., 2022. ...
Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.
... A complex food web and syntrophic interactions sustain the various steps needed for nitrogen cycle regulation. In addition to the symbiotic relationships between microalgae and bacteria [91], essential cooperation between nitrogen-cycle bacteria for nitrogen transformation processes is prevalent. The steps in the nitrogen cycle are linked: the products of one step are the substrates for the next step in the cycle. ...
Rice paddies are unique waterlogged wetlands artificially constructed for agricultural production. Periphytic biofilms (PBs) at the soil-water interface play an important role in rice paddies characterized by high nutrient input but low utilization efficiency. PBs are composed of microbial aggregates, including a wide variety of microorganisms (algae, bacteria, fungi, protozoa, and metazoa), extracellular polymeric substances and minerals (iron, aluminum, and calcium), which form an integrated food web and energy flux within a relatively stable micro-ecosystem. PBs are crucial to regulate and streamline the nitrogen cycle by neutralizing nitrogen losses and improving rice production since PBs can serve as both a sink by capturing surplus nitrogen and a source by slowly re-releasing this nitrogen for reutilization. Here the ecological advantages of PBs in regulating the nitrogen cycle in rice paddies are illustrated. We summarize the key functional importance of PBs, including the intricate and delicate community structure, microbial interactions among individual phylotypes, a wide diversity of self-produced organics, the active adaptation of PBs to constantly changing environments, and the intricate mechanisms by which PBs regulate the nitrogen cycle. We also identify the future challenges of microbial interspecific cooperation in PBs and their quantitative contributions to agricultural sustainability, optimizing nitrogen utilization and crop yields in rice paddies.
... Some UCYN-A ecotypes (e.g. UCYN-A2) live in obligate symbiosis with a calcified coccolithophore [51], hence their export is likely enhanced by this ballast mineral increasing the density of sinking particles to which they are associated. In future studies, better constrains on UCYN-A sedimentation rates and aggregation processes would be of primary importance to assess their role in particle flux and cycling. ...
Diazotrophs are widespread microorganisms that alleviate nitrogen limitation in 60% of our oceans, thereby regulating marine productivity. Yet, the group-specific contribution of diazotrophs to organic matter export has not been quantified, which so far has impeded an accurate assessment of their impact on the biological carbon pump. Here, we examine the fate of five groups of globally-distributed diazotrophs by using an original combination of mesopelagic particle sampling devices across the subtropical South Pacific Ocean. We demonstrate that cyanobacterial and non-cyanobacterial diazotrophs are exported down to 1000 m depth. Surprisingly, group-specific export turnover rates point to a more efficient export of small unicellular cyanobacterial diazotrophs (UCYN) relative to the larger and filamentous Trichodesmium. Phycoerythrin-containing UCYN-B and UCYN-C-like cells were recurrently found embedded in large (>50 µm) organic aggregates or organized into clusters of tens to hundreds of cells linked by an extracellular matrix, presumably facilitating their export. Beyond the South Pacific, our data are supported by analysis of the Tara Oceans metagenomes collected in other ocean basins, extending the scope of our results globally. We show that, when diazotrophs are found in the euphotic zone, they are also systematically present in mesopelagic waters, suggesting their transport to the deep ocean. We thus conclude that diazotrophs are a significant part of the carbon sequestered in the deep ocean and, therefore, they need to be accounted in regional and global estimates of export.
The diversity of marine cyanobacteria has been extensively studied due to their vital roles in ocean primary production. However, little is understood about the diversity of cyanobacterial species involved in symbiotic relationships. In this study, we successfully sequenced the complete genome of a cyanobacterium in symbiosis with Citharistes regius, a dinoflagellate species thriving in the open ocean. A phylogenomic analysis revealed that the cyanobacterium (CregCyn) belongs to the marine picocyanobacterial lineage, akin to another cyanobacterial symbiont (OmCyn) of a different dinoflagellate closely related to Citharistes. Nevertheless, these two symbionts are representing distinct lineages, suggesting independent origins of their symbiotic lifestyles. Despite the distinct origins, the genome analyses of CregCyn revealed shared characteristics with OmCyn, including an obligate symbiotic relationship with the host dinoflagellates and a degree of genome reduction. In contrast, a detailed analysis of genome subregions unveiled that the CregCyn genome carries genomic islands that are not found in the OmCyn genome. The presence of the genomic islands implies that exogenous genes have been integrated into the CregCyn genome at some point in its evolution. This study contributes to our understanding of the complex history of the symbiosis between dinoflagellates and cyanobacteria, as well as the genomic diversity of marine picocyanobacteria.
Nitrogen (N2) fixation in oligotrophic surface waters is the main source of new nitrogen to the ocean¹ and has a key role in fuelling the biological carbon pump². Oceanic N2 fixation has been attributed almost exclusively to cyanobacteria, even though genes encoding nitrogenase, the enzyme that fixes N2 into ammonia, are widespread among marine bacteria and archaea3–5. Little is known about these non-cyanobacterial N2 fixers, and direct proof that they can fix nitrogen in the ocean has so far been lacking. Here we report the discovery of a non-cyanobacterial N2-fixing symbiont, ‘Candidatus Tectiglobus diatomicola’, which provides its diatom host with fixed nitrogen in return for photosynthetic carbon. The N2-fixing symbiont belongs to the order Rhizobiales and its association with a unicellular diatom expands the known hosts for this order beyond the well-known N2-fixing rhizobia–legume symbioses on land⁶. Our results show that the rhizobia–diatom symbioses can contribute as much fixed nitrogen as can cyanobacterial N2 fixers in the tropical North Atlantic, and that they might be responsible for N2 fixation in the vast regions of the ocean in which cyanobacteria are too rare to account for the measured rates.
A bacterial endosymbiont of marine algae evolved to an organelle
Symbiotic interactions were key to the evolution of chloroplast and mitochondria organelles, which mediate carbon and energy metabolism in eukaryotes. Biological nitrogen fixation, the reduction of abundant atmospheric nitrogen gas (N 2 ) to biologically available ammonia, is a key metabolic process performed exclusively by prokaryotes. Candidatus Atelocyanobacterium thalassa, or UCYN-A, is a metabolically streamlined N 2 -fixing cyanobacterium previously reported to be an endosymbiont of a marine unicellular alga. Here we show that UCYN-A has been tightly integrated into algal cell architecture and organellar division and that it imports proteins encoded by the algal genome. These are characteristics of organelles and show that UCYN-A has evolved beyond endosymbiosis and functions as an early evolutionary stage N 2 -fixing organelle, or “nitroplast.”
Light plays a crucial role in ecological dynamics, both as a consumable resource and as an environmental factor. Prokaryotic and eukaryotic photoautotrophs use light as an energy source for photosynthesis, which forms the basis of food chains and determines the flow of energy and matter in ecosystems. Light availability and quality can influence resource complementarity and species coexistence, as well as the stoichiometry of primary producers and the transfer efficiency of food webs. In addition, light serves as an important source of information for organisms, influencing their activities and interactions with the environment. Light shapes biotic interactions, including competition, predator-prey relationships, and mutualistic and antagonistic relationships between photoautotrophs and heterotrophs. Anthropogenic activities affect these photoecological processes, with largely unknown consequences. Hence, understanding the ecological role and control of light is essential for understanding the functioning of ecosystems and biogeochemical cycles.
Associations and interactions between bacteria and phytoplankton are prevalent in aquatic systems. However, the coexistence of bacteria with the smallest phytoplankton groups is mostly unknown. Here, the associated bacteria (AB) of photosynthetic picoeukaryotes (PPEs) in the Yangtze-connected Lake Dongting were studied using flow cytometry sorting combined with high-throughput sequencing of the 16S rRNA gene throughout the seasonal cycle. Bacteria in the corresponding whole water (WWB) were also investigated for comparison. Our results revealed a distinct bacterial community of AB compared to WWB. The taxonomic and phylogenetic diversity indices, as well as the richness, of AB were significantly lower than those of WWB; however, AB showed higher Pielou’s evenness. Proteobacteria (53.8%) was the most abundant phylum in AB, whereas Actinobacteria was predominant in WWB (36.0%). Several abundant clades, including Flavobacterium, Pseudomonas, Rheinheimera, Novosphingobium, and Sphingomonas , were significantly enriched in AB. Functional prediction analysis identified 116 KEGG pathways differing significantly between AB and WWB. Particularly, functional properties involved in cellular processes (mainly bacterial chemotaxis), environmental information processing, organismal systems and xenobiotics biodegradation and metabolism were greatly enriched in AB. Total nitrogen, temperature and chlorophyll a correlated significantly with the community dissimilarity between AB and WWB. Our results shed new light on the bacterial diversity and function associated with the smallest phytoplankton.
Our understanding of the interactions between bacteria and phytoplankton in the freshwater phycosphere, including the development of algal blooms, is very limited. To identify the taxa and compositional variation within microbial communities, we performed 16S rRNA amplicon sequencing research on samples collected weekly through summer from mesocosms that differed in temperature and mixing regimes. We investigated, for the first time, the abundance diversity of microalgae, including Chlorophyta, Cryptophyta, and Cyanobacteria species, using visualization-based FlowCAM analysis and classification of microbial communities to species level by nanopore next-generation sequencing. We found that nanopore metagenomics, in parallel with complementary imaging flow cytometry, can depict the fine temporal dynamics of microbiomes associated with visually identified Microcystis morphospecies, Chlorophyta, and Cryptophyta during algal bloom development. Our results showed that the temporal characteristics of microbiomes combined with a visual approach may be a key tool to predict the metacommunity structure and dynamics of algal blooms in response to anthropogenic effects and climate change.
Biological nitrogen (N2) fixation is critical in global biogeochemical cycles and in sustaining the productivity of the oceans. There remain many unanswered questions, unresolved hypotheses, and unchallenged paradigms. The fundamental balance of N input and losses has not been fully resolved. One of the major N2-fixers, Trichodesmium, remains an enigma with intriguing biological and ecological secrets. Cyanobacterial N2 fixation, once thought to be primarily due to free-living cyanobacteria, now also appears to be dependent on microbial interactions, from microbiomes to unicellular symbioses, which remain poorly characterized. Nitrogenase genes associated with diverse non-cyanobacterial diazotrophs (NCDs) are prevalent, but their significance remains a huge knowledge gap. Answering questions, new and old, such as those discussed here, is needed to understand the ocean's N and C cycles and their responses to environmental change.
Diazotrophic organisms are vulnerable to physical dynamic processes. However, the interactions and mechanisms of multiple dynamic processes on nitrogen fixation remain unclear. This study aimed to investigate one of these interactions; we conducted field investigations and bioassay experiments in the northeastern South China Sea, which faces the Kuroshio current and coastal upwelling. Using 15N tracer and molecular biology methods, we found that the eastern Guangdong upwelling, having high phosphorus and a lower N:P ratio, had higher nitrogen fixation rates as well as a higher abundance of diazotrophic cyanobacteria Trichodesmium spp. and UCYN-A compared with nonupwelling area. Additionally, a higher abundance of diazotrophic cyanobacteria occurred near the bottom of the euphotic zone along the shelf break that was affected by the Kuroshio current. Field incubation experiments confirmed that phosphorus, increased the nitrogen fixation rates and stimulated the growth of cyanobacteria in the area affected by upwelling. Taken together, our results indicated that warmer surface water with a high N:P ratio likely mixed with upwelled phosphorus-rich water containing diazotrophic cyanobacteria, which were transported by the intensified Kuroshio current under the influence of the 2015/16 El Niño. This mixing then triggered a high abundance of diazotrophic cyanobacteria. These findings provide new insights into how the interaction of multiple dynamic processes can regulate nitrogen fixation.
Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics.
Expected final online publication date for the Annual Review of Marine Science, Volume 16 is January 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Viruses, bacteria, and eukaryotic symbionts interact with algae in a variety of ways to cause disease complexes, often shaping marine and freshwater ecosystems. The advent of phyconomy (a.k.a. seaweed agronomy) represents a need for a greater understanding of algal disease interactions, where underestimated cryptic diversity and lack of phycopathological basis are prospective constraints for algal domestication. Here, we highlight the limited yet increasing knowledge of algal pathogen biodiversity and the ecological interaction with their algal hosts. Finally, we discuss how ecology and cultivation experience contribute to and reinforce aquaculture practice, with the potential to reshape biosecurity policies of seaweed cultivation worldwide.
Expected final online publication date for the Annual Review of Phytopathology, Volume 61 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
The coral reef crisis has influenced research for over two decades, during which time the capacity of corals to withstand and respond to environmental stress has been documented from the cellular to ecosystem level. Over the past decade, research is increasingly working towards uncovering the extent of coral–bacterial interactions, finding that diverse and stable microbial interactions can be indicative of the health of the coral host. However, we have yet to determine at which level of organismal organisation these interactions occur, in particular those with the coral’s photosynthetic dinoflagellate symbionts. This information is critical if we are to understand the impact of stress on meta-organism functioning. Using 16S gene amplicon sequencing, we investigated the bacterial microbiome of endosymbiotic Symbiodiniaceae from thermally stressed Acropora aspera, under 3 ecologically relevant temperature trajectories (defined as protective, repetitive and single) that are expected under a changing climate. We show that endosymbiotic Symbiodiniaceae host a distinct and diverse bacterial assemblage when compared with the A. aspera host. Alphaproteobacteria (mainly Rhodobacteraceae and Bradyrhizobiaceae), from the Rhizobiales order dominated the Symbiodiniaceae microbiome, while Gammaproteobacteria (mainly Endozoicomonadaceae) dominated the coral microbiome. The Symbiodiniaceae core microbiome also reflected the distinct microbiomes of the two partners, specifically, Rhizobiales were not present in the A. aspera core, while Endozoicomonadaceae were not present in the Symbiodiniaceae core. We show the Symbiodiniaceae-associated microbiome was highly responsive to increases in temperature, and the microbial consortium was significantly altered in the Symbiodiniaceae retained in the host exposed to different temperature. Most notably, Myxococcolaes were up to 25-fold higher relative abundance in dinoflagellate partner microbiomes under the single temperature trajectory, compared with the repetitive and control treatments. The distinct composition of bacteria associated with Symbiodiniaceae suggests a previously unrecognised, yet important functional role of these associations to overall coral health, which is increasingly important as reefs decline worldwide. Our study provides the first characterisation of Symbiodiniaceae-associated microbes from a coral host under a range of temperature trajectories occurring on the Great Barrier Reef.
Although bacterial amendments can enhance algal productivity and stability, the development of algal-bacteria consortia for commercial-scale utilization is limited. Here, we used an established high-throughput approach to generate algal-bacteria consortia, and tested consortia performance at spatial scales from microplates to 320 L raceway ponds. Our initial screening for beneficial bacteria resulted in the identification of over 20 unique taxa. We used both lab and field-reared strains of Nannochloropsis oceanica to build consortia. In some experiments, we imposed environmental perturbations to test the ability of bacteria to enhance algal culture stability. In repeated assays at the scale of well plates, flasks, and bioreactors, strong effects of bacterial amendments on N. oceanica were observed. These effects were most dramatic when cultures experienced stressors such as temperature perturbations or removal of CO2 augmentation. Isolates that were advanced for field testing included species in the genera Algoriphagus, Oceanicaulis, and Marinobacter. When consortia were generated in the field, positive effects of bacterial amendments were not observed. The amended bacteria were outcompeted, and bacterial community composition across treatments converged after the first grow out. These results highlight the complexity of using consortia in open systems, where interactions between the existing bacterial community, inoculated bacteria, and changing environmental conditions are layered upon other differences in scale and cultivation regimes. Moreover, functionally redundant bacteria are likely present in the field. Following this work, we hypothesize that tight interactions (e.g., obligate relationships between partners, physically attached bacteria, and algae) will scale more predictably to outdoor systems. As such, we suggest relying on true synthetic ecological approaches in which the relationships between bacteria and algae partners are well understood, or synthetic ecological approaches coupled with high throughput approaches to design and test consortia. We also recommend future work to examine the effect of algae-bacteria inoculation ratios on productivity and stability, track dynamics of partners through time, and manage ponds to retain beneficial symbioses.
Understanding the complex interaction between urbanization and the eco-environment is necessary for rapid and quality urbanization, eco-environmental protection, and the harmonious coexistence of humans and nature within a region. Based on panel data from Hebei Province between 1985 and 2019, we suggested a symbiosis hypothesis of urbanization and the eco-environment (SHUE) and used the distance coordination coupling model, the Tapio decoupling model, and the symbiosis model to quantitatively determine the interaction relationship between urbanization and the eco-environment. We found that (1) the improved ‘Northam curve’ of urbanization in Hebei Province met the logistic equation. (2) During the study period, the coordinated coupling degree (CCD) of urbanization and eco-environment exhibited an overall upward trend, while the coupling type gradually changed from the endangered imbalance recession type to the coordinated development type. (3) The decoupling types showed strong and weak decoupling fluctuations, with a high frequency of strong decoupling; the growth rate of the urbanization index was higher than that of the eco-environment index; and there was a positive effect between urbanization and eco-environment indicating positive urbanization. (4) The research results verified SHUE. The symbiosis mode of urbanization and eco-environment was mainly asymmetric mutualism, with the two demonstrating mutual promotion and mutualism. However, in 2016–2019, the symbiosis mode became parasitic, urbanization development enforced upon the eco-environment. The study constructed a set of quantitative method to systematically discuss the interaction relationship from two dimensions: coupling and decoupling. The results provide reference for the coordinated development of urbanization and eco-environment in Hebei Province and consequentially enrich this research field.
Nucleotide sequences of the nuclear-encoded small subunit (18S rDNA) and partial large subunit (28S rDNA) ribosomal DNA were determined in 30 different species of the haptophyte genera Prymnesium, Chrysocampanula, Chrysochromulina, Imantonia and Platychrysis, all belonging to the order Prymnesiales. Phylogenies based on these and other available haptophyte 18S, 28S and plastid 16S rDNA sequences were reconstructed, and compared with available morphological and ultrastructural data. The rDNA phylogenies indicate that the genus Chrysochromulina is paraphyletic and is divided into two major clades. This is supported by ultrastructural and morphological data. There is a major split between Chrysochromulina species with a saddle-shaped cell form (clade B2) and the remaining species in the genus (clade B1). Clade B2 includes the type species C. parva and taxa belonging to this clade thus retain the name Chrysochromulina. The non-saddle-shaped Chrysochromulina species analysed are closely related to Hyalolithus, Prymnesium and Platychrysis species. Imantonia species are sister taxa to these species within clade B1. An amendment to the classification of the order Prymnesiales and the genera Prymnesium, Platychrysis and Chrysochromulina is proposed with one new and one emended family (Chrysochromulinaceae and Prymnesiaceae, respectively), two new genera (Haptolina and Pseudohaptolina), and one new species (Pseudohaptolina arctica). We suggest a revision of the taxonomy of the Prymnesiales that is in accordance with available molecular evidence and supported by morphological data.
Many diatoms that inhabit low-nutrient waters of the open ocean live in close association with cyanobacteria. Some of these associations are believed to be mutualistic, where N2-fixing cyanobacterial symbionts provide N for the diatoms. Rates of N2 fixation by symbiotic cyanobacteria and the N transfer to their diatom partners were measured using a high-resolution nanometer scale secondary ion mass spectrometry approach in natural populations. Cell-specific rates of N2 fixation (1.15–71.5 fmol N per cell h−1) were similar amongst the symbioses and rapid transfer (within 30 min) of fixed N was also measured. Similar growth rates for the diatoms and their symbionts were determined and the symbiotic growth rates were higher than those estimated for free-living cells. The N2 fixation rates estimated for Richelia and Calothrix symbionts were 171–420 times higher when the cells were symbiotic compared with the rates estimated for the cells living freely. When combined, the latter two results suggest that the diatom partners influence the growth and metabolism of their cyanobacterial symbionts. We estimated that Richelia fix 81–744% more N than needed for their own growth and up to 97.3% of the fixed N is transferred to the diatom partners. This study provides new information on the mechanisms controlling N input into the open ocean by symbiotic microorganisms, which are widespread and important for oceanic primary production. Further, this is the first demonstration of N transfer from an N2 fixer to a unicellular partner. These symbioses are important models for molecular regulation and nutrient exchange in symbiotic systems.Keywords: nanoSIMS; symbioses; cyanobiont; diatoms; N2 fixation
Metagenomic data sets were generated from samples collected along a coastal to open ocean transect between Southern California Bight and California Current waters during a seasonal upwelling event, providing an opportunity to examine the impact of episodic pulses of cold nutrient-rich water into surface ocean microbial communities. The data set consists of ~5.8 million predicted proteins across seven sites, from three different size classes: 0.1–0.8, 0.8–3.0 and 3.0–200.0 μm. Taxonomic and metabolic analyses suggest that sequences from the 0.1–0.8 μm size class correlated with their position along the upwelling mosaic. However, taxonomic profiles of bacteria from the larger size classes (0.8–200 μm) were less constrained by habitat and characterized by an increase in Cyanobacteria, Bacteroidetes, Flavobacteria and double-stranded DNA viral sequences. Functional annotation of transmembrane proteins indicate that sites comprised of organisms with small genomes have an enrichment of transporters with substrate specificities for amino acids, iron and cadmium, whereas organisms with larger genomes have a higher percentage of transporters for ammonium and potassium. Eukaryotic-type glutamine synthetase (GS) II proteins were identified and taxonomically classified as viral, most closely related to the GSII in Mimivirus, suggesting that marine Mimivirus-like particles may have played a role in the transfer of GSII gene functions. Additionally, a Planctomycete bloom was sampled from one upwelling site providing a rare opportunity to assess the genomic composition of a marine Planctomycete population. The significant correlations observed between genomic properties, community structure and nutrient availability provide insights into habitat-driven dynamics among oligotrophic versus upwelled marine waters adjoining each other spatially.Keywords: marine; metagenomics; upwelling; California Current
Among small photosynthetic eukaryotes that play a key role in oceanic food webs, picoplanktonic Mamiellophyceae such as Bathycoccus, Micromonas, and Ostreococcus are particularly important in coastal regions. By using a combination of cell sorting by flow cytometry, whole genome amplification (WGA), and 454 pyrosequencing, we obtained metagenomic data for two natural picophytoplankton populations from the coastal upwelling waters off central Chile. About 60% of the reads of each sample could be mapped to the genome of Bathycoccus strain from the Mediterranean Sea (RCC1105), representing a total of 9 Mbp (sample T142) and 13 Mbp (sample T149) of non-redundant Bathycoccus genome sequences. WGA did not amplify all regions uniformly, resulting in unequal coverage along a given chromosome and between chromosomes. The identity at the DNA level between the metagenomes and the cultured genome was very high (96.3% identical bases for the three larger chromosomes over a 360 kbp alignment). At least two to three different genotypes seemed to be present in each natural sample based on read mapping to Bathycoccus RCC1105 genome.
1. INTRODUCTIONSymbioses between cyanobacteria and marine organisms are abundant and widespreadamong marine plants and animals. Generally, they are most likely to be found inoligotrophic areas in which either fixation or dissolved organic carbon (DOC) releasebenefit the host organism, although a few occur in nutrient rich areas such as mudflats.Research on these symbioses is in its infancy, and generally there is very little knownabout the nature of many of these symbioses. Furthermore, from microscopicobservations, it appears that there are many more symbiotic relationships yet to bediscovered.In the marine environment, symbioses are known to occur between cyanobacteriaand sponges, Ascidians (sea squirts), and Echuroid worms in the benthos, and diatoms,dinoflagellates and a protozoan among the plankton. These symbioses can often besignificant in terms of the biogeochemistry of coastal and open ocean areas. Forexample, the heterocystous cyanobacterium,
The atmospheric and deep sea reservoirs of carbon dioxide are linked via physical, chemical, and biological processes. The last of these include photosynthesis, particle settling, and organic matter remineralization, and are collectively termed the "biological carbon pump." Herein, we present results from a 13-y (1992-2004) sediment trap experiment conducted in the permanently oligotrophic North Pacific Subtropical Gyre that document a large, rapid, and predictable summertime (July 15-August 15) pulse in particulate matter export to the deep sea (4,000 m). Peak daily fluxes of particulate matter during the summer export pulse (SEP) average 408, 283, 24.1, 1.1, and 67.5 μmol·m(-2)·d(-1) for total carbon, organic carbon, nitrogen, phosphorus (PP), and biogenic silica, respectively. The SEP is approximately threefold greater than mean wintertime particle fluxes and fuels more efficient carbon sequestration because of low remineralization during downward transit that leads to elevated total carbon/PP and organic carbon/PP particle stoichiometry (371:1 and 250:1, respectively). Our long-term observations suggest that seasonal changes in the microbial assemblage, namely, summertime increases in the biomass and productivity of symbiotic nitrogen-fixing cyanobacteria in association with diatoms, are the main cause of the prominent SEP. The recurrent SEP is enigmatic because it is focused in time despite the absence of any obvious predictable stimulus or habitat condition. We hypothesize that changes in day length (photoperiodism) may be an important environmental cue to initiate aggregation and subsequent export of organic matter to the deep sea.
Myelodysplastic syndromes (MDS) are hematopoietic stem cell disorders that often progress to chemotherapy-resistant secondary acute myeloid leukemia (sAML). We used whole-genome sequencing to perform an unbiased comprehensive screen to discover the somatic mutations in a sample from an individual with sAML and genotyped the loci containing these mutations in the matched MDS sample. Here we show that a missense mutation affecting the serine at codon 34 (Ser34) in U2AF1 was recurrently present in 13 out of 150 (8.7%) subjects with de novo MDS, and we found suggestive evidence of an increased risk of progression to sAML associated with this mutation. U2AF1 is a U2 auxiliary factor protein that recognizes the AG splice acceptor dinucleotide at the 3' end of introns, and the alterations in U2AF1 are located in highly conserved zinc fingers of this protein. Mutant U2AF1 promotes enhanced splicing and exon skipping in reporter assays in vitro. This previously unidentified, recurrent mutation in U2AF1 implicates altered pre-mRNA splicing as a potential mechanism for MDS pathogenesis.
Common acquired melanocytic nevi are benign neoplasms that are composed of small, uniform melanocytes and are typically present as flat or slightly elevated pigmented lesions on the skin. We describe two families with a new autosomal dominant syndrome characterized by multiple, skin-colored, elevated melanocytic tumors. In contrast to common acquired nevi, the melanocytic neoplasms in affected family members ranged histopathologically from epithelioid nevi to atypical melanocytic proliferations that showed overlapping features with melanoma. Some affected individuals developed uveal or cutaneous melanomas. Segregating with this phenotype, we found inactivating germline mutations of BAP1, which encodes a ubiquitin carboxy-terminal hydrolase. The majority of melanocytic neoplasms lost the remaining wild-type allele of BAP1 by various somatic alterations. In addition, we found BAP1 mutations in a subset of sporadic melanocytic neoplasms showing histological similarities to the familial tumors. These findings suggest that loss of BAP1 is associated with a clinically and morphologically distinct type of melanocytic neoplasm.
Because only a small fraction of asbestos-exposed individuals develop malignant mesothelioma, and because mesothelioma clustering is observed in some families, we searched for genetic predisposing factors. We discovered germline mutations in the gene encoding BRCA1 associated protein-1 (BAP1) in two families with a high incidence of mesothelioma, and we observed somatic alterations affecting BAP1 in familial mesotheliomas, indicating biallelic inactivation. In addition to mesothelioma, some BAP1 mutation carriers developed uveal melanoma. We also found germline BAP1 mutations in 2 of 26 sporadic mesotheliomas; both individuals with mutant BAP1 were previously diagnosed with uveal melanoma. We also observed somatic truncating BAP1 mutations and aberrant BAP1 expression in sporadic mesotheliomas without germline mutations. These results identify a BAP1-related cancer syndrome that is characterized by mesothelioma and uveal melanoma. We hypothesize that other cancers may also be involved and that mesothelioma predominates upon asbestos exposure. These findings will help to identify individuals at high risk of mesothelioma who could be targeted for early intervention.
We have identified a novel protein, BAP1, which binds to the RING finger domain of the Breast/Ovarian Cancer Susceptibility Gene product, BRCA1. BAP1 is a nuclear-localized, ubiquitin carboxy-terminal hydrolase, suggesting that deubiquitinating enzymes may play a role in BRCA1 function. BAP1 binds to the wild-type BRCA1-RING finger, but not to germline mutants of the BRCA1-RING finger found in breast cancer kindreds. BAP1 and BRCA1 are temporally and spatially co-expressed during murine breast development and remodeling, and show overlapping patterns of subnuclear distribution. BAP1 resides on human chromosome 3p21.3; intragenic homozygous rearrangements and deletions of BAP1 have been found in lung carcinoma cell lines. BAP1 enhances BRCA1-mediated inhibition of breast cancer cell growth and is the first nuclear-localized ubiquitin carboxy-terminal hydrolase to be identified. BAP1 may be a new tumor suppressor gene which functions in the BRCA1 growth control pathway.
Notch signalling is a central regulator of differentiation in a variety of organisms and tissue types. Its activity is controlled by the multi-subunit γ-secretase (γSE) complex. Although Notch signalling can play both oncogenic and tumour-suppressor roles in solid tumours, in the haematopoietic system it is exclusively oncogenic, notably in T-cell acute lymphoblastic leukaemia, a disease characterized by Notch1-activating mutations. Here we identify novel somatic-inactivating Notch pathway mutations in a fraction of patients with chronic myelomonocytic leukaemia (CMML). Inactivation of Notch signalling in mouse haematopoietic stem cells (HSCs) results in an aberrant accumulation of granulocyte/monocyte progenitors (GMPs), extramedullary haematopoieisis and the induction of CMML-like disease. Transcriptome analysis revealed that Notch signalling regulates an extensive myelomonocytic-specific gene signature, through the direct suppression of gene transcription by the Notch target Hes1. Our studies identify a novel role for Notch signalling during early haematopoietic stem cell differentiation and suggest that the Notch pathway can play both tumour-promoting and -suppressive roles within the same tissue.
Leukemia is one of the leading journals in hematology and oncology. It is published monthly and covers all aspects of the research and treatment of leukemia and allied diseases. Studies of normal hemopoiesis are covered because of their comparative relevance.
Rising atmospheric carbon dioxide (CO2), primarily from human fossil fuel combustion, reduces ocean pH and causes wholesale shifts in seawater carbonate chemistry. The process of ocean acidification is well documented in field data, and the rate will accelerate over this century unless future CO2 emissions are curbed dramatically. Acidification alters seawater chemical speciation and biogeochemical cycles of many elements and compounds. One well-known effect is the lowering of calcium carbonate saturation states, which impacts shell-forming marine organisms from plankton to benthic molluscs, echinoderms, and corals. Many calcifying species exhibit reduced calcification and growth rates in laboratory experiments under high-CO2 conditions. Ocean acidification also causes an increase in carbon fixation rates in some photosynthetic organisms (both calcifying and noncalcifying). The potential for marine organisms to adapt to increasing CO2 and broader implications for ocean ecosystems are not well known; both are high priorities for future research. Although ocean pH has varied in the geological past, paleo-events may be only imperfect analogs to current conditions.
Some unicellular N(2)-fixing cyanobacteria have recently been found to lack a functional photosystem II of photosynthesis. Such organisms, provisionally termed UCYN-A, of the oceanic picoplanktion are major contributors to the global marine N-input by N(2)-fixation. Since their photosystem II is inactive, they can perform N(2)-fixation during the day. UCYN-A organisms cannot be cultivated as yet. Their genomic analysis indicates that they lack genes coding for enzymes of the Calvin cycle, the tricarboxylic acid cycle and for the biosynthesis of several amino acids. The carbon source in the ocean that allows them to thrive in such high abundance has not been identified. Their genomic analysis implies that they metabolize organic carbon by a new mode of life. These unicellular N(2)-fixing cyanobacteria of the oceanic picoplankton are evolutionarily related to spheroid bodies present in diatoms of the family Epithemiaceae, such as Rhopalodia gibba. More recently, spheroid bodies were ultimately proven to be related to cyanobacteria and to express nitrogenase. They have been reported to be completely inactive in all photosynthetic reactions despite the presence of thylakoids. Sequence data show that R. gibba and its spheroid bodies are an evolutionarily young symbiosis that might serve as a model system to unravel early events in the evolution of chloroplasts. The cell metabolism of UCYN-A and the spheroid bodies may be related to that of the acetate photoassimilating green alga Chlamydobotrys.
Among eukaryotes, four major phytoplankton lineages are responsible for marine photosynthesis; prymnesiophytes, alveolates, stramenopiles, and prasinophytes. Contributions by individual taxa, however, are not well known, and genomes have been analyzed from only the latter two lineages. Tiny "picoplanktonic" members of the prymnesiophyte lineage have long been inferred to be ecologically important but remain poorly characterized. Here, we examine pico-prymnesiophyte evolutionary history and ecology using cultivation-independent methods. 18S rRNA gene analysis showed pico-prymnesiophytes belonged to broadly distributed uncultivated taxa. Therefore, we used targeted metagenomics to analyze uncultured pico-prymnesiophytes sorted by flow cytometry from subtropical North Atlantic waters. The data reveal a composite nuclear-encoded gene repertoire with strong green-lineage affiliations, which contrasts with the evolutionary history indicated by the plastid genome. Measured pico-prymnesiophyte growth rates were rapid in this region, resulting in primary production contributions similar to the cyanobacterium Prochlorococcus. On average, pico-prymnesiophytes formed 25% of global picophytoplankton biomass, with differing contributions in five biogeographical provinces spanning tropical to subpolar systems. Elements likely contributing to success include high gene density and genes potentially involved in defense and nutrient uptake. Our findings have implications reaching beyond pico-prymnesiophytes, to the prasinophytes and stramenopiles. For example, prevalence of putative Ni-containing superoxide dismutases (SODs), instead of Fe-containing SODs, seems to be a common adaptation among eukaryotic phytoplankton for reducing Fe quotas in low-Fe modern oceans. Moreover, highly mosaic gene repertoires, although compositionally distinct for each major eukaryotic lineage, now seem to be an underlying facet of successful marine phytoplankton.
Polycomb group (PcG) proteins are transcriptional repressors that control processes ranging from the maintenance of cell fate decisions and stem cell pluripotency in animals to the control of flowering time in plants. In Drosophila, genetic studies identified more than 15 different PcG proteins that are required to repress homeotic (HOX) and other developmental regulator genes in cells where they must stay inactive. Biochemical analyses established that these PcG proteins exist in distinct multiprotein complexes that bind to and modify chromatin of target genes. Among those, Polycomb repressive complex 1 (PRC1) and the related dRing-associated factors (dRAF) complex contain an E3 ligase activity for monoubiquitination of histone H2A (refs 1-4). Here we show that the uncharacterized Drosophila PcG gene calypso encodes the ubiquitin carboxy-terminal hydrolase BAP1. Biochemically purified Calypso exists in a complex with the PcG protein ASX, and this complex, named Polycomb repressive deubiquitinase (PR-DUB), is bound at PcG target genes in Drosophila. Reconstituted recombinant Drosophila and human PR-DUB complexes remove monoubiquitin from H2A but not from H2B in nucleosomes. Drosophila mutants lacking PR-DUB show a strong increase in the levels of monoubiquitinated H2A. A mutation that disrupts the catalytic activity of Calypso, or absence of the ASX subunit abolishes H2A deubiquitination in vitro and HOX gene repression in vivo. Polycomb gene silencing may thus entail a dynamic balance between H2A ubiquitination by PRC1 and dRAF, and H2A deubiquitination by PR-DUB.
Nitrogen (N2)–fixing microorganisms (diazotrophs) are an important source of biologically available fixed N in terrestrial and aquatic
ecosystems and control the productivity of oligotrophic ocean ecosystems. We found that two major groups of unicellular N2-fixing cyanobacteria (UCYN) have distinct spatial distributions that differ from those of Trichodesmium, the N2-fixing cyanobacterium previously considered to be the most important contributor to open-ocean N2 fixation. The distributions and activity of the two UCYN groups were separated as a function of depth, temperature, and water
column density structure along an 8000-kilometer transect in the South Pacific Ocean. UCYN group A can be found at high abundances
at substantially higher latitudes and deeper in subsurface ocean waters than Trichodesmium. These findings have implications for the geographic extent and magnitude of basin-scale oceanic N2 fixation rates.
Nitrogen (N(2))-fixing marine cyanobacteria are an important source of fixed inorganic nitrogen that supports oceanic primary productivity and carbon dioxide removal from the atmosphere. A globally distributed, periodically abundant N(2)-fixing marine cyanobacterium, UCYN-A, was recently found to lack the oxygen-producing photosystem II complex of the photosynthetic apparatus, indicating a novel metabolism, but remains uncultivated. Here we show, from metabolic reconstructions inferred from the assembly of the complete UCYN-A genome using massively parallel pyrosequencing of paired-end reads, that UCYN-A has a photofermentative metabolism and is dependent on other organisms for essential compounds. We found that UCYN-A lacks a number of major metabolic pathways including the tricarboxylic acid cycle, but retains sufficient electron transport capacity to generate energy and reducing power from light. Unexpectedly, UCYN-A has a reduced genome (1.44 megabases) that is structurally similar to many chloroplasts and some bacteria, in that it contains inverted repeats of ribosomal RNA operons. The lack of biosynthetic pathways for several amino acids and purines suggests that this organism depends on other organisms, either in close association or in symbiosis, for critical nutrients. However, size fractionation experiments using natural populations have so far not provided evidence of a symbiotic association with another microorganism. The UCYN-A cyanobacterium is a paradox in evolution and adaptation to the marine environment, and is an example of the tight metabolic coupling between microorganisms in oligotrophic oceanic microbial communities.
Photosynthetic picoeukaryotes (PPE) with a cell size less than 3 microm play a critical role in oceanic primary production. In recent years, the composition of marine picoeukaryote communities has been intensively investigated by molecular approaches, but their photosynthetic fraction remains poorly characterized. This is largely because the classical approach that relies on constructing 18S rRNA gene clone libraries from filtered seawater samples using universal eukaryotic primers is heavily biased toward heterotrophs, especially alveolates and stramenopiles, despite the fact that autotrophic cells in general outnumber heterotrophic ones in the euphotic zone.
In order to better assess the composition of the eukaryotic picophytoplankton in the South East Pacific Ocean, encompassing the most oligotrophic oceanic regions on earth, we used a novel approach based on flow cytometry sorting followed by construction of 18S rRNA gene clone libraries. This strategy dramatically increased the recovery of sequences from putative autotrophic groups. The composition of the PPE community appeared highly variable both vertically down the water column and horizontally across the South East Pacific Ocean. In the central gyre, uncultivated lineages dominated: a recently discovered clade of Prasinophyceae (IX), clades of marine Chrysophyceae and Haptophyta, the latter division containing a potentially new class besides Prymnesiophyceae and Pavlophyceae. In contrast, on the edge of the gyre and in the coastal Chilean upwelling, groups with cultivated representatives (Prasinophyceae clade VII and Mamiellales) dominated.
Our data demonstrate that a very large fraction of the eukaryotic picophytoplankton still escapes cultivation. The use of flow cytometry sorting should prove very useful to better characterize specific plankton populations by molecular approaches such as gene cloning or metagenomics, and also to obtain into culture strains representative of these novel groups.
Planktic microfossils arguably provide the most complete (stratigraphic and taxonomic) record of biodiversity of any group of organisms. The phytoplankton record is of particular significance as it most likely tracks global changes in the climate-ocean system and, in turn, influenced biodiversity and productivity of higher trophic levels of the biosphere. Coccolithophores and associated calcareous nannoplankton first appear in the fossil record in Upper Triassic sediments (~225 Ma) and, despite significant extinctions at the Triassic/Jurassic boundary, the Mesozoic diversity record is one of relatively uniform increase punctuated by short periods of turnover and decline. Rates of speciation that are significantly above background were restricted to the Late Triassic, Early Jurassic and Tithonian-Berriasian intervals. Enhanced rates of extinction occurred at the Triassic/Jurassic, Jurassic/Cretaceous and Cretaceous/Tertiary boundaries.
The deubiquitinating enzyme BRCA1-associated protein 1 (BAP1) possesses growth inhibitory activity and functions as a tumor
suppressor. In this study we report that BAP1 also plays positive roles in cell proliferation. BAP1 depletion by RNAi inhibits
cell proliferation as does overexpression of a dominant negative mutant of BAP1. Mass spectrometry analyses of copurified
proteins revealed that BAP1 is associated with factors involved in chromatin modulation and transcriptional regulation. We
show that the interaction with host cell factor-1 (HCF-1), a cell-cycle regulator composed of HCF-1N and HCF-1C, is critical
for the BAP1-mediated growth regulation. We found that HCF-1N is modified with Lys-48-linked polyubiquitin chains on its Kelch
domain. The HCF-1 binding motif of BAP1 is required for interaction with HCF-1N and mediates deubiquitination of HCF-1N by
BAP1. The importance of the BAP1-HCF-1 interaction is underscored by the fact that growth suppression by the dominant negative
BAP1 mutant is entirely dependent on the HCF-1 binding motif. These results suggest that BAP1 regulates cell proliferation
by deubiquitinating HCF-1.
Recently the World Health Organization (WHO), in collaboration with the European Association for Haematopathology and the Society for Hematopathology, published a revised and updated edition of the WHO Classification of Tumors of the Hematopoietic and Lymphoid Tissues. The 4th edition of the WHO classification incorporates new information that has emerged from scientific and clinical studies in the interval since the publication of the 3rd edition in 2001, and includes new criteria for the recognition of some previously described neoplasms as well as clarification and refinement of the defining criteria for others. It also adds entities-some defined principally by genetic features-that have only recently been characterized. In this paper, the classification of myeloid neoplasms and acute leukemia is highlighted with the aim of familiarizing hematologists, clinical scientists, and hematopathologists not only with the major changes in the classification but also with the rationale for those changes.
Protein ubiquitination provides an efficient and reversible mechanism to regulate cell cycle progression and checkpoint control.
Numerous regulatory proteins direct the addition of ubiquitin to lysine residues on target proteins, and these are countered
by an army of deubiquitinating enzymes (DUBs). BRCA1-associated protein-1 (Bap1) is a ubiquitin carboxy-terminal hydrolase
and is frequently mutated in lung and sporadic breast tumors. Bap1 can suppress growth of lung cancer cells in athymic nude
mice and this requires its DUB activity. We show here that Bap1 interacts with host cell factor 1 (HCF-1), a transcriptional
cofactor found in a number of important regulatory complexes. Bap1 binds to the HCF-1 β-propeller using a variant of the HCF-binding
motif found in herpes simplex virus VP16 and other HCF-interacting proteins. HCF-1 is K48 and K63 ubiquitinated, with a major
site of linkage at lysines 1807 and 1808 in the HCF-1C subunit. Expression of a catalytically inactive version of Bap1 results in the selective accumulation of K48 ubiquitinated
polypeptides. Depletion of Bap1 using small interfering RNA results in a modest accumulation of HCF-1C, suggesting that Bap1 helps to control cell proliferation by regulating HCF-1 protein levels and by associating with genes
involved in the G1-S transition.
Biological nitrogen (N2) fixation is important in controlling biological productivity and carbon flux in the oceans. Unicellular N2-fixing cyanobacteria have only recently been discovered and are widely distributed in tropical and subtropical seas. Metagenomic
analysis of flow cytometry–sorted cells shows that unicellular N2-fixing cyanobacteria in “group A” (UCYN-A) lack genes for the oxygen-evolving photosystem II and for carbon fixation, which
has implications for oceanic carbon and nitrogen cycling and raises questions regarding the evolution of photosynthesis and
N2 fixation on Earth.
Quantitative information on the ecophysiology of individual microorganisms is generally limited because it is difficult to assign specific metabolic activities to identified single cells. Here, we develop and apply a method, Halogen In Situ Hybridization-Secondary Ion Mass Spectroscopy (HISH-SIMS), and show that it allows simultaneous phylogenetic identification and quantitation of metabolic activities of single microbial cells in the environment. Using HISH-SIMS, individual cells of the anaerobic, phototropic bacteria Chromatium okenii, Lamprocystis purpurea, and Chlorobium clathratiforme inhabiting the oligotrophic, meromictic Lake Cadagno were analyzed with respect to H¹³CO3⁻ and ¹⁵NH4⁺ assimilation. Metabolic rates were found to vary greatly between individual cells of the same species, showing that microbial populations in the environment are heterogeneous, being comprised of physiologically distinct individuals. Furthermore, C. okenii, the least abundant species representing ≈0.3% of the total cell number, contributed more than 40% of the total uptake of ammonium and 70% of the total uptake of carbon in the system, thereby emphasizing that numerically inconspicuous microbes can play a significant role in the nitrogen and carbon cycles in the environment. By introducing this quantification method for the ecophysiological roles of individual cells, our study opens a variety of possibilities of research in environmental microbiology, especially by increasing the ability to examine the ecophysiological roles of individual cells, including those of less abundant and less active microbes, and by the capacity to track not only nitrogen and carbon but also phosphorus, sulfur, and other biological element flows within microbial communities.
• anaerobic phototrophs
• nanoSIMS
Polymerase chain reaction conditions were established for the in vitro amplification of eukaryotic small subunit ribosomal (16S-like) rRNA genes. Coding regions from algae, fungi, and protozoa were amplified from nanogram quantities of genomic DNA or recombinant plasmids containing rDNA genes. Oligodeoxynucleotides that are complementary to conserved regions at the 5' and 3' termini of eukaryotic 16S-like rRNAs were used to prime DNA synthesis in repetitive cycles of denaturation, reannealing, and DNA synthesis. The fidelity of synthesis for the amplification products was evaluated by comparisons with sequences of previously reported rRNA genes or with primer extension analyses of rRNAs. Fewer than one error per 2000 positions were observed in the amplified rRNA coding region sequences. The primary structure of the 16S-like rRNA from the marine diatom, Skeletonema costatum, was inferred from the sequence of its in vitro amplified coding region.
An oligonucleotide primer, NITRO821R, targeting the 16S rRNA gene of unicellular cyanobacterial N2 fixers was developed based on newly derived sequences from Crocosphaera sp. strain WH 8501 and Cyanothece sp. strains WH 8902 and WH 8904 as well as several previously described sequences of Cyanothece sp. and sequences of intracellular cyanobacterial symbionts of the marine diatom Climacodium frauenfeldianum. This oligonucleotide is specific for the targeted organisms, which represent a well-defined phylogenetic lineage, and can
detect as few as 50 cells in a standard PCR when it is used as a reverse primer together with the cyanobacterium- and plastid-specific
forward primer CYA359F (U. Nübel, F. Garcia-Pichel, and G. Muyzer, Appl. Environ. Microbiol. 63:3327-3332, 1997). Use of this primer pair in the PCR allowed analysis of the distribution of marine unicellular cyanobacterial
diazotrophs along a transect following the 67°E meridian from Victoria, Seychelles, to Muscat, Oman (0.5°S to 26°N) in the
Arabian Sea. These organisms were found to be preferentially located in warm (>29°C) oligotrophic subsurface waters between
0 and 7°N, but they were also found at a station north of Oman at 26°N, 56°35′E, where similar water column conditions prevailed.
Slightly cooler oligotrophic waters (<29°C) did not contain these organisms or the numbers were considerably reduced, suggesting
that temperature is a key factor in dictating the abundance of this unicellular cyanobacterial diazotroph lineage in marine
environments.
Dinitrogen (N2)-fixing microorganisms (diazotrophs) play important roles in ocean biogeochemistry and plankton productivity. In this study,
we examined the presence and expression of specific planktonic nitrogenase genes (nifH) in the upper ocean (0 to 175 m) at Station ALOHA in the oligotrophic North Pacific Ocean. Clone libraries constructed from
reverse-transcribed PCR-amplified mRNA revealed six unique phylotypes. Five of the nifH phylotypes grouped with sequences from unicellular and filamentous cyanobacteria, and one of the phylotypes clustered with
γ-proteobacteria. The cyanobacterial nifH phylotypes retrieved included two sequence types that phylogenetically grouped with unicellular cyanobacteria (termed groups
A and B), several sequences closely related (97 to 99%) to Trichodesmium spp. and Katagnymene spiralis, and two previously unreported phylotypes clustering with heterocyst-forming nifH cyanobacteria. Temporal patterns of nifH expression were evaluated using reverse-transcribed quantitative PCR amplification of nifH gene transcripts. The filamentous and presumed unicellular group A cyanobacterial phylotypes exhibited elevated nifH transcription during the day, while members of the group B (closely related to Crocosphaera watsonii) unicellular phylotype displayed greater nifH transcription at night. In situ nifH expression by all of the cyanobacterial phylotypes exhibited pronounced diel periodicity. The γ-proteobacterial phylotype
had low transcript abundance and did not exhibit a clear diurnal periodicity in nifH expression. The temporal separation of nifH expression by the various phylotypes suggests that open ocean diazotrophic cyanobacteria have unique in situ physiological
responses to daily fluctuations of light in the upper ocean.
The seasonal variation in the grazing effect of mixotrophic flagellates on bacterioplankton was assessed during an annual cycle in an oligotrophic coastal station in the northwest Mediterranean Sea. Ingestion rates of fluorescently labeled bacteria were estimated for different size categories of phytoflagellates (PF) and heterotrophic flagellates (HF) in short-term experiments and compared with long-term grazing estimates and published empirical models. The mixotrophic flagellates included haptophyte-like cells, cryptophytes, and dinoflagellates. The group-specific grazing rates (SGR) averaged 1.1 (3-5 μm PF), 1.3 (5-20 μm PF), 4.0 (<5 μm HF), and 15.4 bacteria individual-1 h-1 (5-20 μm HF). Lower SGR but higher abundances of PF resulted in an average mixotroph contribution of 50% to the total flagellate grazing. Remarkably, the effect was relatively high all through the year (35-65%). Regardless of the presence of chloroplasts, flagellates <5 μm in size accounted, on average, for about 80% of total flagellate bacterivory and ingested a large percentage of their cell carbon per day from bacteria. Soluble reactive phosphorus concentration was negatively correlated with the ingestion rate of both groups of PF, suggesting that mixotrophic flagellates would be using their phagotrophic capability to obtain phosphorus when this nutrient is limiting. HF grazing activity showed a marked seasonality, with grazing being higher during the warmer seasons, and clearance rates were positively correlated with water temperature. Total bacterivory accounted for most of the bacterial production. Short-term and long-term bacterivory measurements were highly correlated, confirming that the smallest flagellates were the main causative agent of bacterial loss. The bacterivory values were also well correlated to a published empirical model that considers HF as the only bacterivorous. However, this model underestimated (up to 50%) total flagellate grazing during periods of high effect of mixotrophic flagellates. © 2007, by the American Society of Limnology and Oceanography, Inc.
In large areas of the world's oceans, biological dinitrogen (N2) fixation supports a significant fraction of ecosystem productivity; to date, however, there is little information on the abundances of specific diazotrophs in the ocean. In this study, the vertical distributions of several different groups of N2-fixing bacteria were examined using quantitative polymerase chain reaction (QPCR) amplification of group-specific dinitrogenase reductase (nifH) genes from Stn ALOHA in the subtropical North Pacific Ocean. Depth distributions (<200 m) of 3 cyanobacterial nifH phylotypes and 1 previously uncharacterized Cluster III nifH phylotype were evaluated. The nifH-containing cyanobacteria included sequence-types similar to Trichodesmium spp. and 2 nifH sequences closely related to unicellular cyanobacteria (termed Groups A and B). The Group A cyanobacteria (most closely related to Cyanothece sp.) were the most abundant of all phylotypes examined, comprising 2 × 105 nifH gene copies l-1 in the high-irradiance (>700 μmol quanta m-2 s-1), nitrate-depleted (<10 nmol l-1) upper-ocean waters. Group B cyanobacterial phylotypes (most closely related to Crocosphaera watsonii) demonstrated a depth distribution similar to Group A, but Group B nifH abundance was considerably lower, averaging 2 × 103 nifH gene copies l-1 in the upper photic zone. The abundance of Trichodesmium spp. ranged from 1 × 103 to 7 × 103 nifH gene copies l-1 in the upper ocean, declining to <100 nifH gene copies l-1 below the mixed layer (∼82 m). The Cluster III nifH phylotype was the most abundant nifH phylotype in the dimly lit (<12 μmol quanta m-2 s-1) lower photic zone (>100 m). These results revealed differences in the depth distributions of N2-fixing plankton at Stn ALOHA, and suggest that unicellular diazotrophs comprise a significant component of plankton biomass in this oligotrophic marine ecosystem.
Measurements of Mo : C and Fe : C ratios in cultured cells of two N2-fixing cyanobacteria,Crocosphaera watsonii strain WH8501 and Trichodesmium erythraeumstrain IMS101, agree with estimated metal : carbon ratios based on growth rate and the metal use efficiency of the nitrogenase enzyme. Crocosphaera, a single-celled nocturnal N2 fixer, showed two- to eightfold increases in Mo and Fe cellular concentrations in response to nitrogen fixation activity. Mo required for N2 assimilation can account for almost the entire Mo pool measured in the cells, implying that Crocosphaerasynthesizes its entire nitrogenase pool de novo each night. In contrast, cultures of Trichodesmium, a filamentous, diurnal N 2-fixing cyanobacterium, did not show diel variations in Mo or Fe carbon ratios or in cellular metal concentrations. Trichodesmium appears to maintain an internal pool of Mo. In Trichodesmium cultures, Mo concentrations were up to 30% higher than needed to support measured N2 fixation. Trichodesmium colonies col- lected from the field had Mo : C ratios 10-fold larger than those measured in culture, far in excess of what is needed to fix N 2 at rates normally measured in the field, despite equivalent Fe : C ratios (66 6 39 (field samples) and 87 6 64 (cultures) mmol mol 21 ). The average Fe : C ratio measured in N2-fixingCrocosphaera (16 6 11 mmol mol 21 ) was equivalent to theoretical estimates of Fe demand based on nitrogenase requirements (13 6 5 mmol mol 21 ). These results demonstrate the extremely efficient use of Fe by these organisms and provide support for the use of theoretical estimates of Fe : C ratios to calculate biological Fe demand for N 2 fixation.
The seasonal variation in the grazing effect of mixotrophic flagellates on bacterioplankton was assessed during an annual cycle in an oligotrophic coastal station in the northwest Mediterranean Sea. Ingestion rates of fluorescently labeled bacteria were estimated for different size categories of phytoflagellates (PF) and heterotrophic flagellates (HF) in short-term experiments and compared with long-term grazing estimates and published empirical models. The mixotrophic flagellates included haptophyte-like cells, cryptophytes, and dinoflagellates. The group-specific grazing rates (SGR) averaged 1.1 (3-5 μm PF), 1.3 (5-20 μm PF), 4.0 (<5 μm HF), and 15.4 bacteria individual ⁻¹ h⁻¹ (5-20 μm HF). Lower SGR but higher abundances of PF resulted in an average mixotroph contribution of 50% to the total flagellate grazing. Remarkably, the effect was relatively high all through the year (35-65%). Regardless of the presence of chloroplasts, flagellates <5 μm in size accounted, on average, for about 80% of total flagellate bacterivory and ingested a large percentage of their cell carbon per day from bacteria. Soluble reactive phosphorus concentration was negatively correlated with the ingestion rate of both groups of PF, suggesting that mixotrophic flagellates would be using their phagotrophic capability to obtain phosphorus when this nutrient is limiting. HF grazing activity showed a marked seasonality, with grazing being higher during the warmer seasons, and clearance rates were positively correlated with water temperature. Total bacterivory accounted for most of the bacterial production. Short-term and long-term bacterivory measurements were highly correlated, confirming that the smallest flagellates were the main causative agent of bacterial loss. The bacterivory values were also well correlated to a published empirical model that considers HF as the only bacterivorous. However, this model underestimated (up to 50%) total flagellate grazing during periods of high effect of mixotrophic flagellates.
The phylogenetic position of an enigmatic calcareous nannoplankton Braarudosphaera bigelowii, whose taxonomic position has long been questioned, was investigated using molecular genetic methods. The SSU rDNA sequences of B. bigelowii were obtained using a single cell PCR technique independently from two single cells isolated from field samples. A BLAST search revealed that the SSU rDNA of B. bigelowii was most similar to those of the division Haptophyta. Subsequent phylogenetic analyses showed that B. bigelowii was included in a clade comprising members of the orders Isochrysidales and Coccolithales, the genus Chrysoculter and two unidentified haptophytes. Morphometric measurements of extant B. bigelowii populations were made to obtain precise information on their intraspecific size variation. The results showed that these populations could be subdivided into a small form (
Emiliania huxleyi is numerically the most important coccolithophorid in the modem ocean and has been intensely studied in the contexts of biogeochemistry (especially relating to the global carbon cycle), plankton ecology, biomineralization, and cellular carbon transport. This paper reviews older as well as more recently acquired information on reproduction, morphology, ecophysiology, and cell physiology of E. huxleyi, emphasizing aspects that are relevant to coccolith formation and calcification-photosynthesis interactions. The existence of a number of ecotypes, which probably accounts for the wide distribution of this species in nature, complicates comparisons between laboratory studies in which different clones have been used. Coccolith formation is a strongly regulated process; use of mutants may be helpful in elucidating the control mechanisms involved. Conceptual models illustrating the role of calcification in photosynthetic carbon supply are supported by extensive experimental evidence, but the exact mechanisms of calcium and bicarbonate ion transport and of CO2 entry into the cell remain to be established.
In the gulf of Maine life conditions of the phytoplankton were found to be in agreement with those described from the coastal waters of Northern Europe. The surface layers are during summer more or less stratified, indicating a fairly low degree of turbulence. Where the stratification is broken up, by vertical mixing, the waters are so transparent that the total effect of the turbulence on the productivity is favourable, the supply of nutrient salts resulting in an increase of the population, exceeding the loss by vertical transport.
The genus Chrysochromulina Lackey (1939) comprises a number of golden-brown flagellates now included in the class Haptophyceae {sensu Christensen, 1962, 1966). So far 21 species have been described and their scale morphology and fine structure are well documented.
Cyanobacterial symbionts (cyanobionts) have been identified forming associations with various open ocean eukaryotic host genera, including two dinophysoid genera, Histioneis sp. and Ornithocercus sp., two radiolarians, Spongastaurus and Dictyocoryne truncatum, sp., and a tintinnid, Codonella sp. The TEM analysis revealed that single individual hosts were closely associated with one to two different cyanobacterial morphotypes (cyanobionts) and two hosts had in addition to cyanobionts, one to two bacterial cell types. Eleven significantly (P<0.01) different cell types were identified as cyanobionts, with cell diameters ranging 0.5±0.38–3.7±0.66 μm. Using immunogold-labeling techniques coupled to the TEM, four of the five cell types contained phycoerythrin (PE) at high levels (>71±28 gold particles·μm−2). Immunolabeling-TEM using nitrogenase antisera demonstrated a significant (P<0.01) nitrogenase content in cell type four cyanobionts of Histioneis sp. host 1 (39±34 gold particles·μm−2). The cyanobionts of the radiolarians were of a cell diameter (0.5–0.8 μm) and showed ultrastructural characters (peripheral thylakoids) reminiscent of Prochlorococcus sp. Also, an open ocean tintinnid, Codonella sp., was shown to contain cyanobacteria as symbionts for the first time. In all cyanobionts, glycogen storage was obvious, no cellular degradation was visible, cells were observed in the process of cellular division, and antisera localization was apparent. These observations suggest that the relationship between host eukaryote and cyanobacteria is an active one, and likely symbiotic.
A molecular clock has been constructed for the haptophyte algae using the 18S rDNA gene and calibrated using the fossil record of the coccolithophorid algae, which have the best fossil record of any microalgal group. There is high consistency between the molecular genetic estimates of relative timing of divergence and palaeontological estimates of divergence times, so ages can be inferred for undated nodes in the tree with a reasonable degree of confidence. The placement of the K/T boundary across the tree strongly supports the palaeontological model that extant coccolithophorid algae diversified after this event and are the survivors of a few lineages that survived this major extinction. In contrast, the non-calcifying haptophytes are diverse before and after the extinction, with no evidence of bottlenecking associated with the event. This result is surprising, because it has been assumed that ability to produce resting stages was a key determinant of phytoplankton survival across the K/T boundary, but in this regard the coccolithophores and non-calcifying haptophytes are similar. The adaptation of non-calcifying haptophytes to eutrophic coastal environments and their ability to switch modes of nutrition from autotrophy to mixotrophy are discussed as possible explanations for their survival during this abrupt global change event.
Partial SSU rDNA sequences were obtained from 13 naturally collected cells of Braarudosphaera bigelowii obtained from various parts of seas surrounding Japan. Together with the two previously reported sequences, 15 specimens were classified into five SSU rDNA Genotypes I–V. Based on the side length of the pentaliths forming the coccosphere, these specimens were also classified into three size-morphotypes; Intermediate form-A, Intermediate form-B, and Large form. Genotypes of B. bigelowii were well correlated with size-morphotypes but not with sampling area. This result indicates that size differences in B. bigelowii are the results of speciation and not of intra-population variety. Therefore, Genotypes I and II (Intermediate form-A) and Genotypes IV and V (Large form) are regarded as pseudo-cryptic sibling species of typical B. bigelowii (Genotype III, Intermediate form-B), which corresponds to the original description of the species. From the SSU rDNA sequences, it is evident that Genotype V arose from Genotype IV, and Genotype IV originated from Genotype III. The specimens of Genotypes III–V showed size increase of pentaliths in accordance with their branching order. The consistency in the relationship between genotypes and size-morphotypes of living B. bigelowii-complex observed in this study suggests that inconsistency of size range of ‘B. bigelowii’ pentaliths among different geological ages reported by palaeontological studies stems from additional pseudo-cryptic speciation in the lineage of ‘B. bigelowii’ in the geological past.
Long-term ocean observations are needed to gain a comprehensive understanding of natural habitat variability as well as global environmental change that might arise from human activities. In 1988, a multidisciplinary deep-water oceanographic station was established at a site north of Oahu, Hawaii, with the intent of establishing a long-term ( > 20 years) data base on oceanic variability. The primary objective of the Hawaii Ocean Time-series (HOT) program is to obtain high-quality time-series measurements of selected oceanographic properties, including: water mass structure, dynamic height, currents, dissolved and particulate chemical constituents, biological processes and particulate matter fluxes. These data will be used, in part, to help achieve the goals of the World Ocean Circulation Experiment (WOCE) and the Joint Global Ocean Flux Study (JGOFS) research programs. More importantly, these data sets will be used to improve our description and understanding of ocean circulation and ocean climatology, to elucidate further the processes that govern the fluxes of carbon into and from the oceans, and to generate novel hypotheses. These are necessary prerequisites for developing a predictive capability for global environmental change.
We describe an open-source freeware programme for high throughput analysis of nanoSIMS (nanometre-scale secondary ion mass spectrometry) data. The programme implements basic data processing and analytical functions, including display and drift-corrected accumulation of scanned planes, interactive and semi-automated definition of regions of interest (ROIs), and export of the ROIs' elemental and isotopic composition in graphical and text-based formats. Additionally, the programme offers new functions that were custom-designed to address the needs of environmental microbiologists. Specifically, it allows manual and automated classification of ROIs based on the information that is derived either from the nanoSIMS dataset itself (e.g. from labelling achieved by halogen in situ hybridization) or is provided externally (e.g. as a fluorescence in situ hybridization image). Moreover, by implementing post-processing routines coupled to built-in statistical tools, the programme allows rapid synthesis and comparative analysis of results from many different datasets. After validation of the programme, we illustrate how these new processing and analytical functions increase flexibility, efficiency and depth of the nanoSIMS data analysis. Through its custom-made and open-source design, the programme provides an efficient, reliable and easily expandable tool that can help a growing community of environmental microbiologists and researchers from other disciplines process and analyse their nanoSIMS data.
Unialgal cultures were used to investigate relationships between cell volume and the carbon and nitrogen content of nondiatomaceous marine nanophytoplankton. Cell dimensions were deter- mined by image-analyzed epifluorescence microscopy and particulate C and N by high-temperature dry combustion. Volumes were calculated by direct integration with published algorithms (biovol- ume), but could be estimated equally well from linear dimensions as prolate spheres. Preservation with 0.5% glutaraldehyde reduced cell volumes 29% on average. Correlations were highly significant between biovolume of preserved cells and C and N contents. Nonlinear regression models appeared most appropriate because smaller cells contained more C and N per unit volume than did larger cells. Suggested general C densities for estimating cell C from preserved volume were 0.36 pg pm-3 for 10' pm3 cells, 0.24 pg pm-3 for lo2 pm3 cells, and 0.16 pg C pm-3 for lo3 pm3 cells. Previous regression models substantially underestimated the C densities of nanophytoplankton of lo*-lo3 l.cm3. The explanation for these differences includes the method of determining mean population volumes, the use of preservatives, and the occurrence of significant vacuolar volume in larger phytoplankton.
Global estimates indicate the oceans are responsible for approximately half of the carbon dioxide fixed on Earth. Organisms < or =5 microm in size dominate open ocean phytoplankton communities in terms of abundance and CO(2) fixation, with the cyanobacterial genera Prochlorococcus and Synechococcus numerically the most abundant and more extensively studied compared with small eukaryotes. However, the contribution of specific taxonomic groups to marine CO(2) fixation is still poorly known. In this study, we show that among the phytoplankton, small eukaryotes contribute significantly to CO(2) fixation (44%) because of their larger cell volume and thereby higher cell-specific CO(2) fixation rates. Within the eukaryotes, two groups, herein called Euk-A and Euk-B, were distinguished based on their flow cytometric signature. Euk-A, the most abundant group, contained cells 1.8+/-0.1 microm in size while Euk-B was the least abundant but cells were larger (2.8+/-0.2 microm). The Euk-B group comprising prymnesiophytes (73+/-13%) belonging largely to lineages with no close cultured counterparts accounted for up to 38% of the total primary production in the subtropical and tropical northeast Atlantic Ocean, suggesting a key role of this group in oceanic CO(2) fixation.
Photosynthetic picoeukaryotes (PPEs), comprising organisms < 3 mum in size, are important primary producers in marine food webs and include representatives from all known algal lineages. Little is known, however, regarding the composition and distribution of PPE communities, particularly at large spatial scales, or in relation to the underlying biotic and abiotic factors that influence this structure. Here, we analysed PPE community structure along a transect in the South East Pacific Ocean (BIOSOPE cruise) that encompassed a large trophic gradient, including hyper-oligotrophic waters in the South Pacific Gyre (SPG), considered to be some of the 'clearest' natural waters on Earth. Using dot blot hybridizations with 16S rRNA oligonucleotide probes, we established that the PPE community was dominated by members of the classes Prymnesiophyceae and Chrysophyceae throughout the transect. Moreover, clone library construction followed by phylogenetic analysis of sequenced clones revealed several novel 16S rRNA gene lineages, including new clades of prymnesiophytes (designated Prym 16S-III) and prasinophytes (Pras 16S-VIII). Pras 16S-VIII was found at all five stations at which clone libraries were constructed, representing a range of trophic conditions, including the South Pacific Gyre, suggesting members of this clade have a broad distribution in this part of the South East Pacific at least. In contrast, Prym 16S-III sequences were largely restricted to oligotrophic stations of the SPG. Subsequent multivariate statistical analyses showed that, within the measured factors, chemical and biological factors seem to influence PPE community structure more than physical parameters. However, more than 50% of the variation in distribution of PPE classes remained unexplained.
Planktonic algae <5 m in size are major fixers of inorganic carbon in the ocean. They dominate phytoplankton biomass in post-bloom, stratified oceanic temperate waters. Traditionally, large and small algae are viewed as having a critical growth dependence on inorganic nutrients, which the latter can better acquire at lower ambient concentrations owing to their higher surface area to volume ratios. Nonetheless, recent phosphate tracer experiments in the oligotrophic ocean have suggested that small algae obtain inorganic phosphate indirectly, possibly through feeding on bacterioplankton. There have been numerous microscopy-based studies of algae feeding mixotrophically in the laboratory and field as well as mathematical modelling of the ecological importance of mixotrophy. However, because of methodological limitations there has not been a direct comparison of obligate heterotrophic and mixotrophic bacterivory. Here we present direct evidence that small algae carry out 40-95% of the bacterivory in the euphotic layer of the temperate North Atlantic Ocean in summer. A similar range of 37-70% was determined in the surface waters of the tropical North-East Atlantic Ocean, suggesting the global significance of mixotrophy. This finding reveals that even the smallest algae have less dependence on dissolved inorganic nutrients than previously thought, obtaining a quarter of their biomass from bacterivory. This has important implications for how we perceive nutrient acquisition and limitation of carbon-fixing protists as well as control of bacterioplankton in the ocean.
A combination of fluorescent rRNA-targeted oligonucleotide probes ("phylogenetic stains") and flow cytometry was used for a high resolution automated analysis of mixed microbial populations. Fixed cells of bacteria and yeasts were hybridized in suspension with fluorescein- or tetramethylrhodamine-labeled oligonucleotide probes complementary to group-specific regions of the 16S ribosomal RNA (rRNA) molecules. Quantifying probe-conferred cell fluorescence by flow cytometry, we could discriminate between target and nontarget cell populations. We critically examined changes of the hybridization conditions, kinetics of the hybridization, and posthybridization treatments. Intermediate probe concentrations, addition of detergent to the hybridization buffer, and a posthybridization washing step were found to increase the signal to noise ratio. We could demonstrate a linear correlation between growth rate and probe-conferred fluorescence of Escherichia coli and Pseudomonas cepacia cells. Oligonucleotides labeled with multiple fluorochromes showed elevated levels of nonspecific binding and therefore could not be used to lower the detection limits, which still restrict studies with fluorescing rRNA-targeted oligonucleotide probes to well-growing microbial cells. Two probes of different specificities--one labeled with fluorescein, the other with tetramethylrhodamine--could be applied simultaneously for dual color analysis.
Picoplankton--cells with a diameter of less than 3 microm--are the dominant contributors to both primary production and biomass in open oceanic regions. However, compared with the prokaryotes, the eukaryotic component of picoplankton is still poorly known. Recent discoveries of new eukaryotic algal taxa based on picoplankton cultures suggest the existence of many undiscovered taxa. Conventional approaches based on phenotypic criteria have limitations in depicting picoplankton composition due to their tiny size and lack of distinctive taxonomic characters. Here we analyse, using an approach that has been very successful for prokaryotes but has so far seldom been applied to eukaryotes, 35 full sequences of the small-subunit (18S) ribosomal RNA gene derived from a picoplanktonic assemblage collected at a depth of 75 m in the equatorial Pacific Ocean, and show that there is a high diversity of picoeukaryotes. Most of the sequences were previously unknown but could still be assigned to important marine phyla including prasinophytes, haptophytes, dinoflagellates, stramenopiles, choanoflagellates and acantharians. We also found a novel lineage, closely related to dinoflagellates and not previously described.
The diversity and mode of life of microbial eukaryotes in hydrothermal systems is very poorly known. We carried out a molecular survey based on 18S ribosomal RNA genes of eukaryotes present in different hydrothermal niches at the Mid-Atlantic Ridge. These included metal-rich and rare-earth-element-rich hydrothermal sediments of the Rainbow site, fluid-seawater mixing regions, and colonization devices (microcolonizers) containing organic, iron-rich, and porous mineral substrates that were exposed for 15 days to a fluid source. We identified considerable phylogenetic diversity, both at kingdom level and within kinetoplastids and alveolates. None of our sequences affiliates to photosynthesizing lineages, suggesting that we are targeting only autochthonous deep-sea communities. Although sediment harbored most phylogenetic diversity, microcolonizers predominantly contained bodonids and ciliates, indicating that these protists pioneer the colonization process. Given the large variety of divergent lineages detected within the alveolates in deep-sea plankton, hydrothermal sediments, and vents, alveolates seem to dominate the deep ocean in terms of diversity. Compared with data from the Pacific Guaymas basin, some protist lineages seem ubiquitous in hydrothermal areas, whereas others, notably kinetoplastid lineages, very abundant and diverse in our samples, so far have been detected only in Atlantic systems. Unexpectedly, although alvinellid polychaetes are considered endemic of Pacific vents, we detected alvinellid-related sequences at the fluid-seawater interface and in microcolonizers. This finding can boost further studies on deep-sea vent animal biology and biogeography.
PHYML Online is a web interface to PHYML, a software that implements a fast and accurate heuristic for estimating maximum
likelihood phylogenies from DNA and protein sequences. This tool provides the user with a number of options, e.g. nonparametric
bootstrap and estimation of various evolutionary parameters, in order to perform comprehensive phylogenetic analyses on large
datasets in reasonable computing time. The server and its documentation are available at http://atgc.lirmm.fr/phyml.