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The phylogenetic diversity of picocyanobacteria in seven alkaline lakes on the Tibetan Plateau was analyzed using the molecular marker 16S-23S rRNA internal transcribed spacer sequence. A total of 1077 environmental sequences retrieved from the seven lakes were grouped into seven picocyanobacterial clusters, with two clusters newly described here....
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... also as- sessed the correlation between community compositions and en- vironmental and biological factors using a Mantel test. Although all five factors individually or together were not significantly cor- related with the community compositions, TDS still emerged as the most "related" one among them (i.e., it had the highest r value, 0.227, and the lowest P value, 0.125) (Table 4). Microdiversity within dominant picocyanobacterial lin- eages. ...
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... NMDS diagram also showed a random pattern of ice season and non-ice season samples, and the ANOSIM analysis did not support respective groupings of ice season and non-ice season samples (r 0.07; P 0.66) (Fig. 5C). More- over, in the Mantel tests, none of the factors (pH, TDS, and pro- karyotic abundance) showed significant correlation with the sea- sonal community variations (Table 4). The vertical pattern of picocyanobacterial population compositions is more apparent, with Tibetan cluster III-V dominating the upper layers and cluster I occupying the deep waters (Fig. 5B). ...
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... cluster analysis based on relative abundances of OTUs (determined at a 0.01 sequence dissimilarity cutoff) indicated partitioning of the vertical samples, forming two clusters (4 to 44 m and 72 to 92 m) that correspond to depth (Fig. 5D). Mantel tests also predicted sampling depth to be the only factor that significantly correlated with the vertical community compositions (r 0.674; P 0.05) (Table 4). ...
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... it is very possible that some other un- known factor(s) could also contribute to the explanation. The Mantel tests showed little correlation between the picocyanobac- terial community composition and the geographic distances of lake pairs (r 0.072; P 0.326) ( Table 4), suggesting that the picocyanobacterial taxa may not be randomly dispersed on the plateau. However, the Mantel tests failed to identify any environ- mental or biological factor that may constrain the distribution of picocyanobacteria on the plateau. ...
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... Ti- betan cluster I and cluster III-V picocyanobacteria likely favor different salinity ranges, comparison of their relative abundances appeared to result in a random temporal pattern in Lake NMC. On the other hand, we indeed observed a depth-related pattern in a vertical profile of the lake (Fig. 5B and D and Table 4). It seems that Tibetan clusters III-V and I took over the communities in upper and deep waters, respectively, in this single case. ...
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... To date, investigations into the microbial diversity of Xizang's lakes have predominantly employed culture-independent methods (e.g. DNA sequencing) (Huang et al. 2014;Yang et al. 2016;Liu et al. 2021;Zhu et al. 2023) and focused on topics such as seasonal changes in microbial species composition (Liu et al. 2013), the metabolic potential of communities in the carbon and nitrogen cycle (Wei et al. 2023), and mechanisms for coping with extremes (Li et al. 2020). However, few studies have been performed on the species composition and diversity of culturable fungi in Tibetan Plateau lakes. ...
... Picocyanobacteria play a key role in aquatic ecosystems, contributing a significant proportion of total primary production in both marine and fresh waters [1][2][3]. These unicellular cyanobacteria, sized between 0.5 and 2 μm, are distributed globally, from temperate and tropical open oceans to alpine lakes and eutrophic reservoirs [4][5][6]. Freshwater picocyanobacteria are predominantly Synechococcus strains which can dominate the picophytoplankton component (1 -99% [7]) and total biomass (10 -70% [8]) depending on trophic status and depth [9,10]. Other taxonomic names associated with freshwater picocyanobacterial strains are Cyanobium spp. ...
Picocyanobacteria are essential primary producers in freshwaters yet little is known about their genomic diversity and ecological niches. We report here five draft genomes of freshwater picocyanobacteria: Synechococcus sp. CCAP1479/9, Synechococcus sp. CCAP1479/10, and Synechococcus sp. CCAP1479/13 isolated from Lake Windermere in the Lake District, UK; and Synechococcus sp. CCY0621 and Synechococcus sp. CCY9618 isolated from lakes in The Netherlands. Phylogenetic analysis reveals all five strains belonging to sub-cluster 5.2 of the Synechococcus and Prochlorococcus clade of Cyanobacteria. These five strains are divergent from Synechococcus elongatus, an often-used model for freshwater Synechococcus. Functional annotation revealed significant differences in the number of genes involved in the transport and metabolism of several macro-molecules between freshwater picocyanobacteria from sub-cluster 5.2 and Synechococcus elongatus, including amino acids, lipids, and carbohydrates. Comparative genomic analysis identified further differences in the presence of photosynthesis-associated proteins while gene neighbourhood comparisons revealed alternative structures of the nitrate assimilation operon nirA.
... In freshwater, brackish, and coastal environments, Synechococcus and Cyanobium occupy the major niches among picocyanobacteria, and these are phylogenetically related to SC 5.2 (Robertson et al., 2001;Callieri, 2008;Everroad & Wood, 2012). To date, these Synechococcus-related organisms including Synechococcus and Cyanobium have been divided into at least 10 groups (clades) based on 16S rRNA gene phylogeny (Robertson et al., 2001;Crosbie et al., 2003;Ernst et al., 2003;Wu et al., 2010;Jasser et al., 2011;Huang et al., 2014). However, the genetic diversity of these Synechococcus-related organisms is less known than that of major marine lineages, i.e., SC 5.1-5.3. ...
... were clustered in Synechococcus SC 5.1 (discussed below based on petB phylogeny) (Fig. 2). Except for SCs 5.1-5.3, the phylogenetic analysis showed ten groups of Synechococcus-related organisms, which have been reported in previous studies (Robertson et al., 2001;Crosbie et al., 2003;Ernst et al., 2003;Wu et al., 2010;Jasser et al., 2011;Huang et al., 2014). Of these, the NIES strains were included in the Lake Biwa cluster, group A (Cyanobium gracile cluster), group B (subalpine cluster I), and group E with moderate bootstrap support (BP>56) (Fig. 2). ...
... We collected 1,699 ITS sequences (within the Syn/Pro clade) from picocyanobacteria strains and environmental samples on the NCBI website (34,(51)(52)(53)(54)(55)(56)(57)(58)(59)(60)(61)(62)(63). Because a few cyanobacteria not belonging to the Syn/Pro clade could be amplified using the primer set we designed (Table 1), we also collected 669 ITS sequences from cyanobacteria not belonging to the Syn/Pro clade. ...
Picocyanobacteria are the most abundant primary producers in the ocean and play a fundamental role in marine carbon cycling. Quantification of picocyanobacteria on sinking particles and in sediments is essential to understanding their contribution to the biological carbon pump. We designed a primer set targeting the 16S-23S rRNA internal transcribed spacer (ITS) sequence of cyanobacteria and established a quantitative PCR (qPCR) method for quantifying the ITS sequence abundance. High-throughput sequencing confirmed that this primer set can cover broad diversities of marine picocyanobacteria and avoid amplification of other marine cyanobacteria such as Trichodesmium and Crocosphaera. Amplification efficiencies were slightly different when seven marine Synechococcus and Prochlorococcus strains were assayed. The qPCR results were comparable with flow cytometry for water samples. Using this method, we found that, in the dark ocean, picocyanobacterial ITS sequence abundances were 10 to 100 copies/mL in the size fraction of 0.2 to 3 μm, which were 1 to 3 orders of magnitude more abundant than on the >3-μm particles. We also found that picocyanobacterial ITS abundance in sediment ranged from 105 to 107 copies/g along two nearshore-to-offshore transects in the northern South China Sea. These results further explain the important role of picocyanobacteria in carbon export. Collectively, we provide a qPCR method quantifying the total abundance of marine picocyanobacteria on water column particles and in sediments. Moreover, this newly designed primer set can be also applied to investigate the community of picocyanobacteria via high-throughput sequencing. IMPORTANCE Picocyanobacteria are the most abundant primary producers in the ocean. However, quantification of picocyanobacteria on the sinking particles and in sediments remains challenging using flow cytometry or epifluorescence microscopy. Here, we developed a real-time PCR method to quantify picocyanobacteria using a newly designed primer set specifically targeting the 16S-23S rRNA ITS sequence of cyanobacteria. We showed that in the dark ocean, picocyanobacteria are 1 to 3 orders of magnitude more abundant in small particles (0.2 to 3 μm) than in larger particles (>3 μm). This result supports the important role of direct sinking free-living picocyanobacteria cells in the carbon export to deep ocean. We also found that the picocyanobacterial ITS sequence abundance were 105 to 107 copies per gram in sediments, suggesting significant accumulation of sinking picocyanobacteria in the benthic ecosystem. This qPCR method can be used to quantify the contribution of picocyanobacteria to the biological carbon pump.
... Choricystis is the dominant genus among the Chlorophyta, while Synechococcus and Cyanobium are both dominant among the Cyanobacteria. The detection of cyanobacteria (Synechococcus and Cyanobium) in the sediments of Lake Moon is consistent with the findings of molecular studies of contemporary water and ancient sediment samples from remote alpine lakes (Xing et al., 2009;Hou et al., 2014;Huang et al., 2014;Li et al., 2016). ...
Cyanobacterial blooms in water bodies have occurred on a worldwide basis in the last few decades, and knowledge of their occurrence under natural conditions, and of the mechanisms responsible, is important for understanding their origin. However, little is known about the long-term trends in cyanobacterial abundance in the pre-industrial era, and its causes. Traditional microscope analysis of microfossil plankton is widely applied in paleoecology, yet the majority of phytoplankton (e.g., cyanobacteria) are not preserved as microfossils in sediments, although they can leave a fingerprint in the form of sedimentary ancient DNA (sedaDNA). Here, sedaDNA is used for the first time to reconstruct the history of phytoplankton communities in a crater lake in northern China over the past two millennia. Our data show that changes in phytoplankton community structure and diversity were linked to temperature and precipitation variations during ∼0–1400 Common Era (CE). However, after ∼1400 CE the cyanobacterial abundance increased to an unprecedented degree, and cyanobacteria (mainly composed of Synechococcus) became disproportionately dominant relative to other phytoplankton. This rise was concomitant with increased aeolian dust input by winds driven by an intensified Siberian High, which resulted in increased dust transport across the entire mid-latitude region of the Northern Hemisphere. This suggests that dust input can exceed natural climatic variability as the dominant control on lake ecosystems in regions subject to dust deposition. We suggest that future lake ecological management strategies in areas of dust deposition should consider not only the influence of climatic warming but also the impact of nutrient inputs delivered by dust storms.
... OTU02 and OTU03, both of which were detected in summer 2015, were closely related to the Lake Biwa cluster (Ernst et al. 2003) and Cyanobium Suigetsu-CG4 (group IV in Ohki et al. 2012), respectively. OTU04 and OTU05 were detected in winter 2015, with the former being highly affiliated with the Tibetan cluster (Xing et al. 2009;Huang et al. 2014). OTU05 was closely related to uncultured bacteria detected in Feicui Reservoir and Green Lake. ...
... Notably, OTU04 dominated the picocyanobacterial Fig. 1 Seasonal dynamics of picocyanobacterial abundance (line with black dots) and water temperature (gray area) in the epilimnion (5 m) of Lake Biwa from July 2015 to June 2017. The data were modified from Cai et al. (2020) community in winter (66.6%, Fig. S1) and was highly affiliated with the Tibetan cluster (III-V in Wu et al. 2010 andHuang et al. 2014; Fig. 2), which was ubiquitous and abundant in a variety of cold, oligotrophic lakes on the Tibetan Plateau (Table 1). Most of these lakes had low concentrations of total dissolved solids (TDS), except for Lake Nam Co, which was oligosaline (Huang et al. 2014). ...
... The data were modified from Cai et al. (2020) community in winter (66.6%, Fig. S1) and was highly affiliated with the Tibetan cluster (III-V in Wu et al. 2010 andHuang et al. 2014; Fig. 2), which was ubiquitous and abundant in a variety of cold, oligotrophic lakes on the Tibetan Plateau (Table 1). Most of these lakes had low concentrations of total dissolved solids (TDS), except for Lake Nam Co, which was oligosaline (Huang et al. 2014). The phylogenetic analysis based on the V3-V4 region (Fig. 0.3) showed that OTU04 was also affiliated with the Lake Superior cluster containing LSI and LSII, which have been reported as a distinct group endemic to Lake Superior, an extremely oligotrophic lake with low water temperature and TDS content (Table 1; Ivanikova et al. 2007;Callieri et al. 2013). ...
In Lake Biwa, picocyanobacteria blooms usually occur during the summer–autumn thermal stratification period. Intriguingly, a novel bloom was detected in winter 2015–2016, in which picocyanobacterial cell density increased by one order of magnitude despite lower water temperature, suggesting the possibility that “cold-water-preference” species dominate in the picocyanobacterial community. In the present study, we investigated the phylogenetic diversity of picocyanobacteria in Lake Biwa by analyzing the 16S rRNA gene. We found that the picocyanobacterial community were highly diverse in Lake Biwa, with eight Synechococcus-related operational taxonomic units (OTUs) detected in different seasons. These OTUs fell into distinct phylogenetic groups, and the majority were closely related to clusters reported previously. Notably, OTU04, detected during the winter bloom, was highly affiliated with sequences found in a variety of lakes, such as Tibetan lakes and Lake Superior, where the water bodies generally have a low trophic state and temperature, and different concentrations of total dissolved solids. Thus, we inferred that the group containing OTU04 may be a psychrotolerant lineage that is widely distributed in oligotrophic water systems with low–intermediate salinity.
... Genus Cyanobium-PCC6307 (Phylum: Cyanobacteria, Class: Oxyphotobacteria) was dominant in mesohaline lakes (Taigan: TAI, Telmen: TEL, Tsegeen: TSE, and Khag: KHG) and in upper water layers (0-7 m) of Lake Oigon (OIG), a polyhaline lake. A total of 79 zOTUs were identified belonging to this genus, members of which are capable of performing photosynthesis and have been identified in both higher-altitude freshwater and saline lakes of Tibet as well as in lakes from other parts of the world [49,50]. Three genera, Ca. ...
In recent years, climate change coupled with anthropogenic activities has led to monumental changes in saline lakes which are rapidly drying up across the globe and particularly in Central Asia. The landlocked country of Mongolia is rich in lakes which have remained primarily undisturbed by human impact, and many of these lakes have varying salinity regimes and are located across various geographical landscapes. In this study, we sampled 18 lakes with varying salinity regimes (hyperhaline, mesohaline, oligohaline, and polyhaline) covering 7000 km of western Mongolia and its various geographical landscapes (Gobi Desert, forests, and steppe). We identified that the bacterial communities that dominate these lakes are significantly influenced by salinity (p < 0.001) and geographical landscape (p < 0.001). Further, only five zOTUs were shared in all the lakes across the salinity regimes, providing evidence that both local and regional factors govern the community assembly and composition. Furthermore, the bacterial communities of hyperhaline lakes were significantly positively correlated with salinity (ANOVA, p < 0.001) and arsenic concentrations (ANOVA, p < 0.001), whereas bacterial communities of mesohaline and polyhaline lakes situated in forest and steppe landscapes were positively correlated with temperature (ANOVA, p < 0.001) and altitude (ANOVA, p < 0.001), respectively. Functional predictions based on the 16S rRNA gene indicated enrichment of KEGG Ontology terms related to transporters for osmoprotection and-regulation. Overall, our study provides a comprehensive view of the bacterial diversity and community composition present in these lakes, which might be lost in the future.
... Trained expertise required skills and experience to distinguish subtle differences among similar cyanobacterial morphospecies. Molecular method could overcome these limitations, and further recognize pico-cyanobacteria and cryptogenera and cryptospecies (Joyner et al., 2008;Huang et al., 2014;, which were always ignored by morphological inspection. These cryptogenera and cryptospecies exhibited almost identical morphotypes but formed phylogenetically distinct clusters inferred from the molecular analysis (Komárek et al., 2014). ...
In processing metabarcoding data from the 16S rRNA amplicon sequencing, OTUs were commonly binned at 97% similarity, the criteria was once proposed as the limit for species delimitation for prokaryotes. This numeric guide is rather a tunable parameter and has recently been revised and increased up to 99% threshold facilitated with more 16S rRNA sequences available. In the study, we updated 97% identity to 99% in combination with monophyletic species concept rather than OTUs to evaluate cyanobacterial diversity from 11 freshwaters using metabarcoding technique. The cyanobacterial OTUs were first determined by aligning to the SILVA database, and further reassigned through the evolutionary placement algorithm (EPA). Inferred from the EPA, metabarcoding found diverse cyanobacterial community with at least 70 monophyletic species (113 OTUs) from 18 coccoid, 14 simple filamentous, 10 heterocytous genera, and Prochlorothrix by clustering OTUs at 97% similarity. When updating to 99% similarity, 5 cryptic genera were detected with 3 of them should be revised as new genera for they achieved monophyly in the phylogeny. In addition, updating to 99% similarity also detected 48 cryptic monophyletic species from 9 genera. In conclusion, updating 97% identity to 99% in combination with monophyletic species found cryptic genera and species, and provided a much clearer separation of cyanobacterial community between lakes and reservoirs and also between seasons. The combined methods improved the use of metabarcoding technique to elucidate field cyanobacterial community.
... Various PC-and PE-rich picocyanobacterial strains have previously been isolated from Lake Balaton, which belong to Group A (Cyanobium gracile cluster) and Group B (subalpine cluster I), respectively, of the non-marine lineages of the picophytoplankton clade sensu Urbach et al. (1998) (Fig. 6; Felföldi et al. 2011a, b). These two groups are among the most common genotypes of freshwater picocyanobacteria distributed worldwide in diverse types of lakes and ponds (e.g., Crosbie et al. 2003;Callieri et al. 2013;Huang et al. 2014;Vasileva et al. 2017). ...
Occurrence of the smallest phototrophic microorganisms (photoautotrophic picoplankton, APP) in Lake Balaton was discovered in the early 1980s. This triggered a series of systematic studies on APP and resulted in the setting of a unique long-term picoplankton dataset. In this review, we intend to summarize the obtained results and to give a new insight on APP ecology and diversity in Lake Balaton. According to the results, APP dynamics depends on trophic state, temperature, nutrient, and light availability, as well as grazing pressure. APP abundance in Lake Balaton decreased to a low level (1–2 × 105 cells mL−1) as a consequence of decreasing nutrient supply (oligotrophication) during the past more than two decades, and followed a characteristic seasonal dynamics with higher abundance values from spring to autumn than in winter. Concomitantly, however, the APP contribution to both phytoplankton biomass and primary production increased (up to 70% and 40–50%, respectively) during oligotrophication. Regarding annual pattern, picocyanobacteria are dominant from spring to autumn, while in winter, picoeukaryotes are the most abundant, most likely due to the different light and temperature optima of these groups. Within picocyanobacteria, single cells and microcolonies were both observed with mid-summer dominance of the latter which correlated well with the density of cladocerans. Community-level chromatic adaptation (i.e., dominance of phycoerythrin- or phycocyanin-rich forms) of planktonic picocyanobacteria was also found as a function of underwater light quality. Sequence analysis studies of APP in Lake Balaton revealed that both picocyanobacteria and picoeukaryotes represent a diverse and dynamic community consisting several freshwater genotypes (picocyanobacteria: Synechococcus, Cyanobium; picoeukaryotes: Choricystis, Stichococcus, Mychonastes, Nannochloris, and Nannochloropsis).
... The recorded species richness of fish exceeds the count of 150, with most common and abundant 15 group being endemic schizothoracine ( Zheng and Zhao, 2017). As the structure of soil microbial (including fungal) communities are affected by vegetation, climatic and soil parameters, the unique habitats of the TP potentially harbor many unique microbial lineages that are adapted to high altitude and cold environments ( Huang et al., 2014). Mountain building has been directly associated with the development of biodiversity ( Hoorn et al., 2013;Antonelli et al., 2018), and the biodiversity hotspots are located especially in the south and south-east of the TP. ...
The Tibetan Plateau (TP) is the largest alpine plateau on Earth and plays an important role in global climate dynamics. On the TP, climate change is happening particularly fast, with an increase in air temperature twice the global average. The particular sensitivity of this high mountainous environment allows the observation and tracking of abiotic and biotic feedback mechanisms. Closed lake systems, such as the Nam Co on the central TP represent important natural laboratories for tracking past and recent climatic oscillations, as well as geobiological processes and interactions within their respective catchments. This review gives an interdisciplinary overview of modern and paleoenvironmental changes, focusing on Nam Co as model system. In the catchment area, the steep rise in air temperature forced glaciers to melt, leading to a rise in lake levels and changes in water chemistry. Some studies base their conclusions on inconsistent glacier inventories but an ever-increasing deglaciation and thus higher water availability have persisted over the last decades. The enhanced water availability causes translocation of sediments, nutrients and dissolved organic matter to the lake, as well as higher carbon emissions to the atmosphere. The intensity of grazing has a significant effect on CO2 fluxes, with moderate grazing enhancing belowground allocation of carbon while adversely affecting the C-sink potential through reduction of above- and subsurface biomass at higher grazing intensities. Furthermore, increasing pressure from human activities and livestock grazing are enhancing grassland degradation processes, thus shaping biodiversity patterns in the lake and catchment. The environmental signal provided by taxon-specific analysis (e.g. diatoms and ostracods) in Nam Co have revealed profound climatic fluctuations between warmer/cooler and wetter/drier periods since the late Pleistocene and an increasing input of freshwater and nutrients from the catchment in recent years. Based on the reviewed literature, we outline perspectives to further understand the effects of global warming on geo- and biodiversity and their interplay in the Lake Nam Co, which acts as a case study for potentially TP-wide processes that are currently shaping the earth’s future.
