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Molecular phylogeny of nitrogen-fixing unicellular cyanobacteria
Abstract
Molecular phylogenetic study was conducted using maximum likelihood tree inference methods with small subunit ribosomal RNA sequence data to ascertain the evolutionary relationships among sheathless, single-cell cyanobacteria capable of nitrogen fixation. Cyanobacterial strains of the genus Cyanothece (circumscribed by Waterbury and Rippka, 1989) fall into ar least three independent lines of descent within a larger assemblage previously designated the SPM sequence group. No strong correlation between aerobic versus anaerobic nitrogen-fixing activity and phylogenetic relationships was observed. The results support a hypothesis of multiple gains and/or losses of nitrogen-fixation abilities among the sheathless, unicellular cyanobacteria.
... Two explanations for this have been provided. One is that the last common ancestor of the Cyanobacteria did not have the ability to fix nitrogen, and some lineages independently obtained this ability by horizontal gene transfer from other phyla [7][8][9][10]. Alternatively, the last common ancestor may have been capable of nitrogen fixation, but this ability was subsequently lost in some lineages [11,12]. ...
... Alternatively, the last common ancestor may have been capable of nitrogen fixation, but this ability was subsequently lost in some lineages [11,12]. The former hypothesis is supported by evidence from a small number of species; however, diazotrophic species that diverged from the common ancestor of Cyanobacteria were not included in these analyses [7][8][9][10]. For example, Synechococcus sp. ...
... In this analysis, we used 179 cyanobacterial species including 85 diazotrophs. As the number of species and lineages used was increased from the previous studies [7][8][9][10][11][12]14], it is presumed that reliable results were obtained. However, as a sufficient number of nif genes could not be detected, certain diazotrophic cyanobacteria were excluded from the analysis and therefore, could not be considered in this study. ...
Nitrogen fixation plays a crucial role in the nitrogen cycle by helping to convert nitrogen into a form usable by other organisms. Bacteria capable of fixing nitrogen are found in six phyla including Cyanobacteria. Molybdenum dependent nitrogenase (nif) genes are thought to share a single origin as they have homologs in various phyla. However, diazotrophic bacteria have a mosaic distribution within the cyanobacterial lineage. Therefore, the aim of this study was to determine the cause of this mosaic distribution. We identified nif gene operon structures in the genomes of 85 of the 179 cyanobacterial strains for which whole genome sequences were available. Four nif operons were conserved in each diazotroph Cyanobacterium, although there were some gene translocations and insertions. Phylogenetic inference of these genes did not reveal horizontal gene transfer from outside the phylum Cyanobacteria. These results support the hypothesis that the mosaic distribution of diazotrophic bacteria in the cyanobacterial lineage is the result of the independent loss of nif genes inherited from common cyanobacterial ancestors in each lineage.
... Analysis of the 1240-bp nucleotide sequence of the 16S rRNA gene of strain Z-M001 and a GenBank search among both cultured and uncultured organisms (from clone libraries) revealed that the strain was most closely related to representatives of the not yet legitimate but widely studied genus of unicellular coccoid halophilic cyanobacteria Euhalothece [9][10][11][12][13][14][15][16] (97-98% homology levels) (Fig. 1). Depending on the group of microorganisms, this similarity level can be regarded as an intra-or interspecies one. ...
... All known Euhalothece strains were isolated earlier from hypersaline reservoirs around the world [9-16 and a number of unpublished works (http://srs.ebi.ac.uk)]: Solar Lake and the Dead Sea (Israel) [14], Shark Bay (Australia) [13], hypersaline evaporative ponds in Guerrero Negro (Mexico) [9,11,16], Eilat (Israel) [9,11,12,16], Salinas del Cabo de Gata (Spain) [9], and salt works in Italy, Greece, and Somalia [14]. Of these clones and strains, only four were isolated from the Wadi Al-Natrun alkaline hypersaline lakes (Egypt) with pH 8.5-9.8 [10]; in these lakes, however, NaCl is still the predominant salt (up to 30% wt/vol). ...
... All known Euhalothece strains were isolated earlier from hypersaline reservoirs around the world [9-16 and a number of unpublished works (http://srs.ebi.ac.uk)]: Solar Lake and the Dead Sea (Israel) [14], Shark Bay (Australia) [13], hypersaline evaporative ponds in Guerrero Negro (Mexico) [9,11,16], Eilat (Israel) [9,11,12,16], Salinas del Cabo de Gata (Spain) [9], and salt works in Italy, Greece, and Somalia [14]. Of these clones and strains, only four were isolated from the Wadi Al-Natrun alkaline hypersaline lakes (Egypt) with pH 8.5-9.8 [10]; in these lakes, however, NaCl is still the predominant salt (up to 30% wt/vol). ...
Strain Z-M001 of a unicellular cyanobacterium, assigned by analysis of the 16S rRNA gene sequence to the phylogenetic group
of the generic level Euhalothece, was isolated from soda Lake Magadi. It was shown that strain Z-M001, unlike all other known cultured and uncultured organisms
of the Euhalothece group, is extremely natronophilic, and it was named accordingly “Euhalothece natronophila”. In its ecophysiological characteristics, it is comparable to extremely alkaliphilic organotrophic natronobacteria, which
is essential for soda ecosystems, because cyanobacteria belong to primary producers. E. natronophila exhibits considerable morphological variability depending on the concentration of carbonates in the medium. The polymorphism
of “ E. natronophila” is primarily connected to limitation by utilizable forms of carbon.
... The various strategies to overcome the inherent conflict between oxygenic photosynthesis and nitrogen fixation reflect the wide-ranging flexibility and niches occupied by cyanobacteria: from anaerobic sediments to pelagic waters saturated with oxygen. Molecular phylogenies, of N 2 fixers using the nifH gene and small subunit ribosomal RNA sequences, showed no correlation between the phylogenetic relationships and the type of N 2 fixation (Raymond et al., 2004;Turner et al., 2001). This lack of correlation suggests multiple gains and/or losses of N 2 fixation among the different cyanobacteria (Raymond et al., 2004;Turner et al., 2001). ...
... Molecular phylogenies, of N 2 fixers using the nifH gene and small subunit ribosomal RNA sequences, showed no correlation between the phylogenetic relationships and the type of N 2 fixation (Raymond et al., 2004;Turner et al., 2001). This lack of correlation suggests multiple gains and/or losses of N 2 fixation among the different cyanobacteria (Raymond et al., 2004;Turner et al., 2001). The loss of cyanobacterial nif genes implies that different strategies arose early in the evolution of the clade, where some organisms were able to adapt to an oxic world, while others were not (e.g. ...
Analysis suggests that feedbacks between carbon (C), nitrogen (N), and oxygen (O) cycles helped prevent the oxidation of Earth in the Paleoproterozic. This stabilizing feedback, which was ultimately overridden, led to the contemporary nitrogen cycle where nitrate, rather than ammonium, was the stable form of fixed inorganic nitrogen in the oceans. Barring some minor changes in the trace element composition in nitrogenases, the core proteins remained essentially unchanged following the transition to an oxidized atmosphere. In the contemporary ocean, approximately 20%-30% of nitrogenase activity is inhibited at any moment in time by O2. This inhibition results in a negative feedback which constrains the upper level of O2 on Earth. Three central aspects of cyanobacterial nitrogen fixation remain curious. First, although some trace elements have been altered in the evolution of nitrogenases, the core proteins have remained virtually unchanged. Second, while there is abundant evidence of lateral transfer of nitrogenase genes between prokaryotes, in the endosymbiotic appropriation of cyanobacteria into heterotrophic hosts to photosynthetic eukaryotes, nitrogenases were lost. Third, although free-living heterocystous cyanobacteria are abundant in lakes and brackish water ecosystems, they appear to be rare in the open ocean.
... strains can fix nitrogen only when incubated under anoxic conditions (Steunou et al., 2006). Members of the genus Cyanothece have been reported to engage in both aerobic and anaerobic nitrogen fixation, with nitrogenase activity peaking during the night (Reddy et al., 1993;Bergman et al., 1997;Turner et al., 2001). This suggests that, in addition to the regulations imposed by the diurnal cycle, strain-specific intracellular cues govern the process of nitrogen fixation in unicellular cyanobacteria, which may vary according to the genotype or the ecotype of the strains. ...
... Earlier studies have indicated that the members of the genus Cyanothece can engage in either aerobic or anaerobic nitrogen fixation (Waterbury and Rippka, 1989;Turner et al., 2001;Bandyopadhyay et al., 2011). Two of the five Cyanothece spp. ...
In order to accommodate the physiologically incompatible processes of photosynthesis and nitrogen fixation within the same cell, unicellular nitrogen fixing cyanobacteria have to maintain a dynamic metabolic profile in the light as well as the dark phase of a diel cycle. The transition from the photosynthetic to the nitrogen-fixing phase is marked by the onset of various biochemical and regulatory responses, which prime the intracellular environment for nitrogenase activity. Cellular respiration plays an important role during this transition, quenching the oxygen generated by photosynthesis and by providing energy necessary for the process. Although the underlying principles of nitrogen fixation predict unicellular nitrogen fixing cyanobacteria to function in a certain way, significant variations are observed in the diazotrophic behavior of these microbes. In an effort to elucidate the underlying differences and similarities that govern the nitrogen fixing ability of unicellular diazotrophic cyanobacteria, we analyzed six members of the genus Cyanothece. Cyanothece 51142, a member of this genus, has been shown to perform efficient aerobic nitrogen fixation and hydrogen production. Our study revealed significant differences in the patterns of respiration and nitrogen fixation among the Cyanothece strains that were grown under identical culture conditions, suggesting that these processes are not solely controlled by cues from the diurnal cycle but that strain specific intracellular metabolic signals play a major role. Despite these inherent differences, the ability to perform high rates of aerobic nitrogen fixation and hydrogen production appears to be a characteristic of this genus.
... They described the geneta Cyanobacterium and Cyanobinr and used the name "Cyanothece" for the third type. The fiISt two genera were later supported by cytological (KoMAREK et al. 1999) as well as by molecular (RuDr et al. 1997, CASTENHoLZ 2001 methods, but rhe geneic name " Cr-qnothece " (sensu RrppKA) appeared in designations of numerous other strains, which were classified in different places of a phylogenetic tree (GRoMov et al. 1986, REDDv et al. 1993, CEPAK 1996, DE PHrl-rpprs et al. 1997, GARCTA-P|CHEL et al. 1998, MARGHERT et al. 1999, PoRrA et al. 2000, CASTENHOLZ 2001, TURNER et al. 2001. ...
... What are the cyanobacterial genera Cyanothece and Cyanobacterium? 13 4. "Euhaloahece" (Figs 5,ll,12) Literature: WATERBURY & RrppKA 1989, GARCTA-PrcHEL et al. 1998, MARGHERI et al. 1999, CAsTENHoLz 2001, TURNER et al. 2001. The evaluation of CASTENHoLZ (2001) should be the staning point for the taxonomic position of this cluster ("Euhalothece", cells 3-l0 pm A, al strains were isolated from halophilic habitats). ...
Isolated strains of the cyanobacterial genus Cyanothece Kom. 1976 (related to another genus Cyanobacterium Rippka et Cohen-Bazire 1983) were repeatedly included in molecular evaluations of unicellular cyanobacteria. However, this group was found heterogeneous, inconsequences appeared in results and in strain designations, and sometimes the taxonomic positions following from molecular studies of strains and from phenotype analyses of natural populations were not in agreement. In this article, the criterion of ultrastructural characters (nucleoids, thylakoid pattern) is introduced to the synthesis and preliminary review of all material concerning the diversity of both genera. The genera Cyanothece (in original sense vs. in later sense of Rippka) and Cyanobacterium were found as independent taxa, which contain several subclusters (characterised by complex of molecular, cytomorphological and ecological features), and which should be classified as units on the "specific level". The taxonomic position of further related, up to now taxonomically not defined and not validly described clusters "Euhalothece" and "Halothece", is discussed. The authors stress the demand of the complex (molecular + biochemical + cytomorphological + ecological) evaluation of diversity for any taxonomic classification.
... The fi lamentous Nostocales (with false branching) and Stigonematales (with true branching) feature specialized heterocytes capable of fi xing atmospheric nitrogen. Both orders have been confi rmed as monophyletic in molecular studies ( Ishida et al., 1997 ; Honda et al., 1999 ; Turner et al., 2001 ; Henson et al., 2004 ). Lichenized cyanobacteria were mostly assigned to either Chroococcales (unicellular morphotypes) or Nostocales (fi lamentous morphotypes) ( Ahmadjian, 1967 ; Parmasto, 1978 ; Arvidsson, 1982 ; Tschermak-Woess, 1988 ); the photobiont of the well-known tropical montane lichen Dictyonema glabratum was originally identifi ed as Chroococcus and that of the closely related Dictyonema sericeum as Scytonema , although it was later suspected that both belong to the same genus ( Parmasto, 1978 ; Tschermak-Woess, 1988 ; Chaves et al., 2004 ). ...
... In this paper, we report on the surprising fi nding that the lichenized photobionts supposed to represent Scytonema actually do not belong to that genus and instead form a novel, previously unrecognized lineage within the fi lamentous cyanobacteria with heterocytes.Table 1 ). We added GenBank sequences from 23 specimens representing freeliving and lichenized members of Nostoc and Scytonema (Nostocales), including unidentifi ed cyanobacteria reported from cephalodia of the genus Stereocaulon , 14 sequences representing nonlichenized members of the Nostocales , and 10 sequences representing basal cyanobacterial lineages according to various sources ( Ishida et al., 1997 ; Honda et al., 1999 ; Schultz et al., 2001 ; Turner et al., 2001 ; Rikkinen et al., 2002 ; Schultz and B ü del, 2002 ; Rikkinen, 2003 ; Henson et al., 2004 ). ...
Phylogenetic diversity of lichen photobionts is low compared to that of fungal counterparts. Most lichen fungi are thought to be associated with just four photobiont genera, among them the cyanobacteria Nostoc and Scytonema, two of the most important nitrogen fixers in humid ecosystems. Although many Nostoc photobionts have been identified using isolated cultures and sequences, the identity of Scytonema photobionts has never been confirmed by culturing or sequencing. We investigated the phylogenetic placement of presumed Scytonema photobionts and unicellular morphotypes previously assigned to Chroococcus, from tropical Dictyonema, Acantholichen, Coccocarpia, and Stereocaulon lichens. While we confirm that filamentous and unicellular photobiont morphotypes belong to a single clade, this clade does not cluster with Scytonema but represents a novel, previously unrecognized, highly diverse, exclusively lichenized lineage, for which the name Rhizonema is available. The phylogenetic structure observed in this novel lineage suggests absence of coevolution with associated mycobionts at the species or clade level. Instead, highly efficient photobiont strains appear to have evolved through photobiont sharing between unrelated, but ecologically similar, coexisting lineages of lichenized fungi ("lichen guilds"), via the selection of particular photobiont strains through and subsequent horizontal transfer among unrelated mycobionts, a phenomenon not unlike crop domestication.
... In the genus Cyanothece, for example, the seven described strains could fix nitrogen either aerobically or anaerobically [75]. Recent molecular phylogenies, for 33 strains of unicellular N 2 fixers using small subunit ribosomal RNA sequences, showed no correlation between the phylogenetic relationships and the type of N 2 fixation [74]. Moreover, the authors hypothesize that the results of the phylogeny are indicative of multiple gains and/or losses of N 2 fixation abilities among the unicellular cyanobacteria [74]. ...
... Recent molecular phylogenies, for 33 strains of unicellular N 2 fixers using small subunit ribosomal RNA sequences, showed no correlation between the phylogenetic relationships and the type of N 2 fixation [74]. Moreover, the authors hypothesize that the results of the phylogeny are indicative of multiple gains and/or losses of N 2 fixation abilities among the unicellular cyanobacteria [74]. Thus, the loss of cyanobacterial nif genes could suggest that different strategies existed early, where some organisms were able to adapt to an oxic world, while others were not (e.g., Oscillatoria). ...
The biological reduction of N(2) is catalyzed by nitrogenase, which is irreversibly inhibited by molecular oxygen. Cyanobacteria are the only diazotrophs (nitrogen-fixing organisms) that produce oxygen as a by-product of the photosynthetic process, and which must negotiate the inevitable presence of molecular oxygen with an essentially anaerobic enzyme. In this review, we present an analysis of the geochemical conditions under which nitrogenase evolved and examine how the evolutionary history of the enzyme complex corresponds to the physiological, morphological, and developmental strategies for reducing damage by molecular oxygen. Our review highlights biogeochemical constraints on diazotrophic cyanobacteria in the contemporary world.
... strains WH 8902, WH 8904, and PCC8801 (also known as Synechococcus sp. strain RF-1 [25]) and Crocosphaera sp. strain WH 8501 lie (Fig. 1) by using the probe design and probe match tools from the ARB program. ...
... strains ATCC 51142 and PCC8801 (ϭ Synechococcus sp. strain RF-1 [25]) show the greatest diversity (93.2% identity). Alignment of the 16S rDNA sequences of all members of this unicellular cyanobacterial diazotroph lineage (designated the UCYN 2 -fix lineage) and comparison with all other cyanobacterial and environmental DNA sequences in the databases allowed the design of an oligonucleotide primer, NITRO821R (Table 1), that showed complete identity to sequences of all members of this UCYN 2 -fix lineage. ...
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.
... Представители рода используют оксигенный и аноксигенный фотосинтез (источником электронов является H 2 S). Было высказано предположение, что представители рода Synechocystis изначально обладали способностью фиксировать газообразный азот, но затем в ходе эволюции утратили гены, определяющие азотфиксацию [Turner et al. 2001]. ...
Книга посвящена цианобактериям, древнейшим обитателям нашей планеты. Отличаясь особой жизнестойкостью, они существуют во всех регионах Земли при самых разных климатических условиях. Цианобактерии играют значительную роль в экологии биосферы, морей, океанов, иных водоемов, в сельскохозяйственной экологии, в геоэкологии и др. В книге обобщены материалы о строении
и метаболизме цианобактерий, их систематике и методах идентификации. Дана характеристика цианотоксинов и процессов их образования, их распространения в природных экосистемах, их роли в патологии человека и животных. Рассмотрены клинические данные острых и хронических заболеваний, вызванных токсичными метаболитами цианобактерий. Особое внимание уделено образованию
цианобактериями метаболитов, которые могут быть использованы в народном хозяйстве, для фармацевтических целей, как продукты питания человека и животных, в целях биоремедиации. Рассмотрены условия, которые способствуют развитию цианобактерий в водной среде и почвах, особенности воздействия их интенсивного размножения на окружающую среду. Приведены методы регуляции их развития, способы очистки воды как от самих цианобактерий, так и от их метаболитов. В книге подчеркивается ограниченность существующих пред-
ставлений о цианобактериях и их метаболитах. Формулируются те направления исследований, результаты которых способствовали бы положительному влиянию
цианобактерий на окружающую среду, применению их метаболитов в различных областях, в том числе для целей здравоохранения. Книга рассчитана на экологов и специалистов иных дисциплин, интересующихся цианобактериями.
... Berrendero et al. (2011) found that morphological features of Calothrix changed in the culture condition, making them to look like Tolypothrix. To avoid these issues arising from morphological plasticity, phylogenetic relationships among cyanobacteria at all catagories have been inferred using the 16S rRNA gene (Giovannoni et al. 1988, Turner et al. 2001, Suda et al. 2002, Komárek and Kaštovský 2003 since it is highly conserved among all characteristics resembling Nostoc in successive stages of their life cycle. However, they did not fall within the main Nostoc cluster based on a phylogenetic analysis. ...
... Cyanobacterial taxonomy, at present, uses criteria that include mostly molecular sequencing and genetic approaches. Several molecular biological methods have been applied for cyanobacterial taxonomy [12][13][14][15][16]. However, molecular sequencing methods are also not an absolute method, as, in many instances, they are not in good agreement with the morphology-based classification system. ...
Twenty-five marine cyanobacteria isolated from Irish coasts were characterized based on their morphological characters and 16S rRNA gene sequence analysis. In addition, superoxide dismutase (SOD) and malate dehydrogenase (MDH) isoenzyme banding patterns were used to differentiate two morphologically ambiguous isolates. In this study, six new cyanobacteria-specific primers were designed, and a 16S rRNA gene of twenty-five morphologically diverse cyanobacteria was successfully PCR amplified (1198–1396 bps). Assembled 16S rRNA sequences were used both for a basic local alignment search tool (BLAST) analysis for genus-level identification and to generate a phylogenetic tree, which yielded two major clusters: One with morphologically homogenous cyanobacteria and the other with morphologically very diverse cyanobacteria. Kamptonema okenii and Tychonema decoloratum were isolated from a single field sample of Ballybunion and were originally identified as the same ‘Oscillatoria sp.’ based on preliminary morphological observations. However, an alignment of 16S rRNA gene sequences and SOD and MDH isoenzyme banding pattern analyses helped in differentiating the morphologically-indistinguishable ‘Oscillatoria sp.’. Finally, after a re-evaluation of their morphological characters using modern taxonomic publications, the originally identified ‘Oscillatoria sp.’ were re-identified as Kamptonema okenii and Tychonema decoloratum, thus supporting the polyphasic approach of cyanobacteria characterization.
... The cyanobacterial strain Cyanothece 8801 was originally isolated from a rice field in Taiwan [26][27][28][29]. This strain is a unicellular diazotrophic cyanobacterium and the cells lack a sheath and divide in one plane [26,27]. ...
Analysis of fatty acids from the cyanobacterium Cyanothece sp. PCC 8801 revealed that this species contained high levels of myristic acid (14:0) and linoleic acid in its glycerolipids, with minor contributions from palmitic acid (16:0), stearic acid, and oleic acid. The level of 14:0 relative to total fatty acids reached nearly 50%. This 14:0 fatty acid was esterified primarily to the sn-2 position of the glycerol moiety of glycerolipids. This characteristic is unique because, in most of the cyanobacterial strains, the sn-2 position is esterified exclusively with C16 fatty acids, generally 16:0. Transformation of Synechocystis sp. PCC 6803 with the PCC8801_1274 gene for lysophosphatidic acid acyltransferase (1-acyl-sn-glycerol-3-phosphate acyltransferase) from Cyanothece sp. PCC 8801 increased the level of 14:0 from 2% to 17% in total lipids and the increase in the 14:0 content was observed in all lipid classes. These findings suggest that the high content of 14:0 in Cyanothece sp. PCC 8801 might be a result of the high specificity of this acyltransferase toward the 14:0-acyl-carrier protein.
... The genus Cyanothece was suggested by Komarek (1976) to accommodate the cyanobacteria that was inaccurately placed in genus Synechococcus. The major features to distinguishthese two genus were Cyanothece are present in single cells or pairs, and able to fix nitrogen whereas Synechococcus can be found in chains and unable to fix nitrogen (Komárek and Cepák, 1998;Reddy et al., 1993;Turner et al., 2001). Subsequently, Waterbury and Rippka (1979), proposed that the coccoid to rod-shaped cyanobacteria with cells larger than 3 μm in diameter dividing by binary fission and lacking a sheath to be provisionally place in the Cyanothece group. ...
A novel halotolerant species of cyanobacterium of the order Chroococcales was isolated from hypersaline estuary in Kwa-Zulu Natal, South Africa. A comprehensive polyphasic approach viz., cell morphology, pigment composition and complete genome sequence analysis was conducted to elucidate the taxonomic position of the isolated strain. The blue-green oval to rod-shaped cells were 14–18 μm in size, and contained a high amount of phycocyanin pigments. The strain was moderate thermotolerant/alkalitolerant halophile with the optimum conditions for growth at 35 °C, pH 8.5 and 120 g/l of NaCl. Based on 16S rRNA gene sequence phylogeny, the strain was related to members of the ‘Euhalothece’ subcluster (99%). The whole genome sequence was determined, and the annotated genes showed a 90% sequence similarity to the gas-vacuolate, spindle-shaped Dactylococcopsis salina PCC 8305. The size of the genome was determined to be 5,113,178 bp and contained 4332 protein-coding genes and 69 RNA genes with a G + C content of 46.7%. Genes encoding osmoregulation, oxidative stress, heat shock, persister cells, and UV-absorbing secondary metabolites, among others, were identified. Based on the phylogenetic analysis of the 16S rRNA gene sequences, physiological data, pigment compositions and genomic data, the strain is considered to represent a novel species of Euhalothece
... cyanobacteria (Geiss et al. 2001a,b). Some nonheterocystous anaerobic nitrogen fixers [except Cyanothece 7424, which has been reported as both an anaerobic (Turner et al. 2001) and aerobic (Bandyopadhyay et al. 2011)] grouped together (highlighted in brown) and appear to have evolved from a common ancestor. The pcbcontaining Prochlorothrix and marine Synechococcus KORDI-100 grouped together with the Prochlorococcus strains (which also contain pcb genes) which were used as an outlier in this study (highlighted in green). ...
IsiA is a membrane-bound Chl a-antenna protein synthesized in cyanobacteria under iron deficiency. Since iron deficiency is a common nutrient stress in significant fractions of cyanobacterial habitats, IsiA is likely to be essential for some cyanobacteria. However, the role it plays in cyanobacteria is not fully understood. In this review paper, we summarize the research efforts directed towards characterizing IsiA over the past three decades and attempt to bring all the pieces of the puzzle together to get a more comprehensive understanding of the function of this protein. Moreover, we analyzed the genomes of over 390 cyanobacterial strains available in the JGI/IMG database to assess the distribution of IsiA across the cyanobacterial kingdom. Our study revealed that only 125 such strains have an IsiA homolog, suggesting that the presence of this protein is a niche specific requirement, and cyanobacterial strains that lack IsiA might have developed other mechanisms to survive iron deficiency.
... Primary production by cyanobacteria might, in principle, have been limited by competition from anoxygenic phototrophs in anoxic oceans, although the strong limitation of electron donors on anoxygenic photosynthesis would seem to favor organisms capable of splitting water. Alternatively, primary production could have been limited in early cyanobacteria that lacked the molecular capacity to fix nitrogen (Grula, 2005); the pattern of phylogenetic spread of nitrogen fixation through the cyanobacteria remains uncertain (Turner et al., 2001;Tomitani et al., 2006), but currently recognized basal lineages do not exhibit this trait (Sánchez-Baracaldo et al., 2005). Regardless of Archean uncertainties, cyanobacteria made possible the initial oxygenation of the atmosphere and surface oceans, and blue-greens came to dominate primary production and nitrogen fixation in the oceans (see Chapter 15). ...
... The modern re-evaluation and revision of cyanobacterial taxonomy should be based on the molecular data, for which the 16S rRNA gene has been most widely used (Turner 2001;Suda et al. 2002;Koma´rek & Kaštovský 2003). Based on the 16S rRNA phylogeny, simple filamentous cyanobacteria from diverse categories (at specific, generic, familial, and ordinal levels) have proven polyphyletic in origin (Wilmotte & Golubić 1991;Honda et al. 1999;Turner et al. 1999;Ishida et al. 2001;Wilmotte & Herdman 2001;Hoffmann et al. 2005;Koma´rek et al. 2014). ...
Five strains that were morphologically identified as Planktolyngbya circumcreta were isolated from three geographical regions in China. The strains were phylogenetically and taxonomically characterised based on a polyphasic approach that merged morphological and genetic characteristics, as well as ultrastructure. The ultrastructure of these strains showed a similar arrangement of thylakoids, with four to eight parallel layers that were parietally distributed, suggesting that they belonged to the order Synechococcales, family Leptolyngbyaceae. As inferred from 16S rRNA gene sequence analysis, these pure cultures share ≥ 98.5% similarity and were grouped into a unique and robust cluster with high bootstrap values. This unique cluster was separated from a clade composed of two strains of Planktolyngbya limnetica, which belonged to the type species of the genus Planktolyngbya. Thus, we transferred these five P. circumcreta strains to the new genus Limnolyngbya. The species Limnolyngbya circumcreta nov. comb. was designated as the type of the genus.
... The Synechocystis/Pleurocapsa/Microcystis sequence group identifi ed by Turner et al. (1999) does not derive much support from the work of Tomitani et al. (2006), although Prochloron and Pleurocapsalean cyanobacteria formed a cluster. Turner et al. (2001) compared phylogeny, based on 16S rRNA gene sequencing by using ML method, of strains of nitrogen-fi xing unicellular cyanobacteria. Three independent lines of descent have been identifi ed without any correlation between aerobic versus anaerobic nitrogen-fi xing activity. ...
... Nitrogen fixation by blue green algae vis a vis its release in the soil water system may be more useful for crop production during the vegetative growth stage of rice plants than at later stages (Ghosh and Saha, 1993;Roger et al., 1993). Turner et al. (2001) conducted molecular phylogenetic study using maximum likelihood tree inference methods with small subunit ribosomal RNA sequence data to ascertain the evolutionary relationships among sheathless, single-cell cyanobacteria capable of nitrogen fixation. They showed that cyanobacterial strains of the genus Cyanothece fall into at least three independent lines of descent within a larger assemblage previously designated the SPM sequence group. ...
... It is interesting that the basic pattern of the internal structure of cells (the thylakoidal system) is in good agreement with phylogenetic clades (komárek & kaštovSký 2003b). Heterocytous cyanobacteria represent a monophyletic cluster (Giovannoni et al. 1988;Turner 1997Turner , 2001CaStenholz 2001;litvaitiS 2002;gugger & hoffmann 2004), but coccoid or simple filamentous types (in which the morphological criteria are particularly unclear) are heterogeneous, etc. ...
... Since cyanobacteria are strongly influenced by environmental stimuli morphologically, it has been difficult to classify cyanobacteria in appropriate taxonomic groups. For example, many species of the genera Oscillatoria, Lyngbya, Phormidium, Schizothrix, Plectonema were included in Schizothrix calcicola (Turner et al., 2001), which was originally classified on the basis of sheath characterization and the presence or absence of false branching. Accordingly, this strain was identified by 16S rRNA gene partial sequencing. ...
Rad, A. (2011). Physiological variability in cyanobacterium Phormidium sp. Kützing ISC31 (Oscillatoriales) as response to varied microwave intensities Journal of Agricultural Technology 7(3): 665-677. The influence of microwave radiation on physiological behaviors of Phormidium sp. Kützing ISC31 (Oscillatoriales) was investigated. The organism grown in BG-11 medium was microwave-treated at a frequency of 2450 MHz using a microwave oven. Fifteen (15) microwave pretreatments were established, combining five intensities (180, 360, 540, 720 and 900 W/cm 2) and three periods of pretreatment [10, 20 and 30 second(s)]. Results revealed that samples exposed to microwave various intensities showed significantly higher growth rates and biomass than that of non-irradiated controls. The content of chlorophyll a, which exists in the thylakoid membrane, decreased with increase in field strength and duration of exposure. Synthesis of the phycobiliproteins (PBP), phycocyanin (PC), phycoerythrin (PE) and allophycocyanin (APC), except in 720 & 900 W/cm 2 (30s), increased in all exposures as compared to that of control Photosynthetic activity rate compared to nitrogenase activity increased in all microwave exposures except in 180W (10s) and 720W (10s). Identification was carried out by molecular method. The result of PCR blasted with sequenced cyanobacteria in NCBI showed 97% homology to the 16S rRNA of Phormidium sp. This study revealed that various microwave intensities induce different physiological effects, depending on field strength and duration of exposure.
... Primary production by cyanobacteria might, in principle, have been limited by competition from anoxygenic phototrophs in anoxic oceans, although the strong limitation of electron donors on anoxygenic photosynthesis would seem to favor organisms capable of splitting water. Alternatively, primary production could have been limited in early cyanobacteria that lacked the molecular capacity to fix nitrogen (Grula, 2005); the pattern of phylogenetic spread of nitrogen fixation through the cyanobacteria remains uncertain (Turner et al., 2001; Tomitani et al., 2006), but currently recognized basal lineages do not exhibit this trait (Baracaldo et al., 2005). Regardless of Archean uncertainties, cyanobacteria made possible the initial oxygenation of the atmosphere and surface oceans, and blue-greens came to dominate primary production and nitrogen fixation in the oceans (see Chapter 15). ...
... This conclusion, which was inherent in the first genetic evaluations (Wilmotte and Golubić 1991) (Fig. 2), was confirmed by later investigations. The first phylogenetic trees separated already clearly heterocytous types from coccoid and simple trichal genera (Wilmotte and Golubić 1991;Turner 2001, Castenholz 2001, and identified several groups characterized by prominent morphological characters (Oscillatoria/Lyngbya complex with thick trichomes and short cells, group of genera producing baeocytes, etc.) (Figs 3, 4). Numerous discrepancies (mixture of simple coccoid and trichal types) occurred, especially among coccoid and simple filamentous genera with thin trichomes (cf. ...
The application of modern ecological, ultrastructural and molecular methods, aided by the cultivation of numerous cyanobacterial morphotypes, has substantially changed our knowledge of these organisms. It has led to major advances in cyanobacterial taxonomy and criteria for their phylogenetic classification. Molecular data provide basic criteria for cyanobacterial taxonomy; however, a correct phylogenetic system cannot be constructed without combining genetic data with knowledge from the previous 150 years research of cyanobacterial diversity. Thus, studies of morphological variation in nature, and modern morphological, ultrastructural, ecophysiological and biochemical characters need to be combined in a “polyphasic” approach. Taxonomic concepts for generic and infrageneric ranks are re-evaluated in light of combined phenotypic and molecular criteria. Despite their usefulness in experimental studies, the limitations of using strains from culture collections for systematic and nomenclatural purposes is highlighted. The need for a continual revision of strain identification and proper nomenclatural practice associated with either the bacteriological or botanical codes is emphasized. Recent advances in taxonomy are highlighted in the context of prospects for understanding cyanobacterial diversity from natural habitats, and the evolutionary and adaptational processes that cyanobacteria undergo.
... Most phylogenetic analyses have been performed on single genes, for instance SSU (small subunit) rDNA (Ishida et al ., 1997;Neilan et al ., 1997;Honda et al ., 1999;Turner et al ., 1999Turner et al ., , 2001Ishida et al ., 2001;Iteman et al ., 2002;Litvaitis, 2002;Gugger & Hoffmann, 2004); psbA (Morden & Golden, 1989;Zeidner et al ., 2003); the phycocyanin operon (Robertson et al ., 2001;Crosbie et al ., 2003); nif D (Henson et al ., 2004); rbcL (Watson & Tabita, 1997); rDNA-ITS (Boyer et al ., 2002;Rocap et al ., 2002); tufA (Delwiche et al ., 1995); rnpB (Honda et al ., 1999); and rpoD1 , gyrB , and rpoC1 (Seo & Yokota, 2003). A few studies have been performed on several genes (Honda et al ., 1999;Seo & Yokota, 2003), however, none have reported on combined multiple-gene analyses. ...
ABSTRACTA phylogenomic approach was used to study the evolution of traits in the Cyanobacteria. A cyanobacterial backbone tree was constructed using multiple concatenated sequences from whole genome sequences. Additional taxa were added using a separate alignment that contained morphological characters, SSU (small subunit) and LSU (large subunit) rDNA, rpoC, rpoD, tufA, and gyrB genes. A compartmentalization approach was then used to construct a robust phylogeny with resolved deep branches. Additional morphological characters (e.g. unicellular or filamentous growth, presence or absence of heterocysts) were coded, mapped onto the backbone cyanobacterial tree, and the ancestral character states inferred. Our analyses show that the earliest cyanobacterial lineages were likely unicellular coccoid/ellipsoidal/short rods that lived in terrestrial/freshwater environments. Later cyanobacterial lineages independently gained the ability to colonize brackish, marine, and hypersaline environments while acquiring a large number of more complex traits: sheath, filamentous growth, nitrogen fixation, thermophily, motility, and use of sulphide as an electron donor. Many of these adaptations would have been important in the appearance of dense microbial mats early in Earth's history. Complex traits such as hormogonia, heterocysts, and akinetes had a single ancestor. Within the Nostocales, hormogonia and heterocysts arose before akinetes.
... On the basis of phylogeny and morphological data, we propose that these three significantly different clusters should be assigned to three genera. Turner 2001, Willame et al. 2006. Such phylogenetic studies of cyanobacteria have demonstrated that genetic relationships sometimes conflict with the classification based on morphological data (Lyra et al. 2001, Iteman et al. 2002, Gugger and Hoffmann 2004, Willame et al. 2006. ...
To date, phylogenies have been based on known gene sequences accessible at GenBank, and the absence of many cyanobacterial lineages from collections and sequence databases has hampered their classification. Investigating new biotopes to isolate more genera and species is one way to enrich strain collections and subsequently enhance gene sequence databases. A polyphasic approach is another way of improving our understanding of the details of cyanobacterial classification. In this work, we have studied phylogenetic relationships in strains isolated from freshwater bodies in Senegal and Burkina Faso to complement existing morphological and genetic databases. By comparing 16S rDNA sequences of African strains to those of other cyanobacteria lineages, we placed them in the cyanobacterial phylogeny and confirmed their genus membership. We then focused on the Nostocaceae family by concatenated analysis of four genes (16S rDNA, hetR, nifH, and rpoC1 genes) to characterize relationships among Anabaena morphospecies, in particular, Anabaena sphaerica var. tenuis G. S. West. Using a polyphasic approach to the Nostocaceae family, we demonstrate that A. sphaerica var. tenuis is more closely related to Cylindrospermospsis/Raphidiopsis than to other planktonic Anabaena/Aphanizomenon. On the basis of phylogeny and morphological data, we propose that these three significantly different clusters should be assigned to three genera.
... These cells must be able to protect their nitrogenase from damage by O 2 , but the mechanisms for this are largely unknown. The subject on unicellular N 2 -Wxing cyanobacteria has extensively been reviewed (Fay 1992;Turner et al. 2001;Berman-Frank et al. 2003;Stal and Zehr 2008) and shall not be repeated here. As discussed in the following, some N 2 -Wxing unicellular cyanobacteria have recently been discovered to have an inactive photosynthetic reaction II, the O 2 -evolving part of the photosynthetic apparatus in cyanobacteria, eukaryotic algae, and plants. ...
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.
... To the above listed early Archean findings, reports of ascertained younger Archean fossils can be added [4,14,17,19]. Colonial coccoid cyanobacteria have not yet been discovered in rocks older than about 2.6 Ga, although their very early origin is suggested by molecular phylogenetic analyses [34]. Recognition of Neoarchean and Proterozoic fossils raises comparably minor problems because fossils are more abundant and often much better preserved. ...
The oldest fossils found thus far on Earth are c. 3.49- and 3.46-billion-year-old filamentous and coccoidal microbial remains in rocks of the Pilbara craton, Western Australia, and c. 3.4-billion-year-old rocks from the Barberton region, South Africa. Their biogenicity was recently questioned and they were reinterpreted as contaminants, mineral artefacts or inorganic carbon aggregates. Morphological, geochemical and isotopic data imply, however, that life was relatively widespread and advanced in the Archean, between 3.5 and 2.5 billion years ago, with metabolic pathways analogous to those of recent prokaryotic organisms, including cyanobacteria, and probably even eukaryotes at the terminal Archean.
... strain MBIC10216 (94%) (unpublished data) and Cyanothece sp. strain PCC 8801 (97%) (66). The remaining two phylotypes, represented by clones LC3-54 and SC3-15, were most similar (both 97%) to chloroplast DNA sequences from the diatoms Haslea salstonica and Bacillaria paxillifer, respectively (unpublished data). ...
Though a large fraction of primary production and organic matter cycling in the oceans occurs on continental shelves dominated by sandy deposits, the microbial communities associated with permeable shelf sediments remain poorly characterized. Therefore, in this study, we provide the first detailed characterization of microbial diversity in marine sands of the South Atlantic Bight through parallel analyses of small-subunit (SSU) rRNA gene (Bacteria), nosZ (denitrifying bacteria), and amoA (ammonia-oxidizing bacteria) sequences. Communities were analyzed by parallel DNA extractions and clone library construction from both sediment core material and manipulated sediment within column experiments designed for geochemical rate determinations. Rapid organic-matter degradation and coupled nitrification-denitrification were observed in column experiments at flow rates resembling in situ conditions over a range of oxygen concentrations. Numerous SSU rRNA phylotypes were affiliated with the phyla Proteobacteria (classes Alpha-, Delta-, and Gammaproteobacteria), Planctomycetes, Cyanobacteria, Chloroflexi, and Bacteroidetes. Detectable sequence diversity of nosZ and SSU rRNA genes increased in stratified redox-stabilized columns compared to in situ sediments, with the Alphaproteobacteria comprising the most frequently detected group. Alternatively, nitrifier communities showed a relatively low and stable diversity that did not covary with the other gene targets. Our results elucidate predominant phylotypes that are likely to catalyze carbon and nitrogen cycling in marine sands. Although overall diversity increased in response to redox stabilization and stratification in column experiments, the major phylotypes remained the same in all of our libraries, indicating that the columns sufficiently mimic in situ conditions.
... Thermophilic cyanobacteria are the primary producers in microbial communities in geothermal springs worldwide at temperatures up to 75 8C (Castenholz 2000), which is the maximum temperature limit for performing oxygenic photosynthesis (Ferris and Ward 1997). Previous studies have revealed great phenotypic plasticity in some cyanobacteria ( Nadeau et al. 2001; de la Torre et al. 2003) and phylogenetic classification based on gene sequences would to some extent give a more accurate classification and evolutionary placement (Wilmotte 1994), despite discrepancies between morphological and molecular (16S rRNA gene) taxonomy ( Rippka et al. 1979;Rippka and Herdman 1992;Turner et al. 2001;Litvaitis 2002). ...
Two thermophilic cyanobacterial strains, Ts and Bs, collected from Asian geothermal springs were identified morphologically and phylogenetically as Synechococcus in the order Chroococcales and were isolated into axenic cultures. In addition to the high similarities between their full 16S rRNA gene sequences, both strains also shared similar pigment profiles and fatty acid compositions but with varied ratios. Strain Ts had elevated levels of photoprotective pigments such as carotenoid and scytonemin even after prolonged culture under identical laboratory conditions, whereas strain Bs produced more chlorophyll a per unit cell volume, perhaps resulting from UV adaptation in the natural habitats. In addition, strain Ts had more content than strain Bs in terms of the total fatty acids and the proportion of unsaturated fatty acids. Neither isolate was able to fix nitrogen, and they had zero susceptibility to ampicillin and streptomycin.
The precise identification of the cyanobacteria that comprise an endolithic biofilm is hindered by difficulties in culturing the organisms found in these biofilms and a lack of previous molecular and ultrastructural data. This study characterizes, both at the ultrastructural and molecular level, two different cyanobacterial biofilms found in fissures of granite from continental Antarctica. Electron microscopy revealed structural differences between the two biofilms. One was only loosely adhered to the substrate, while the other biofilm showed a closer association between cells and rock minerals and was tightly attached to the substrate. Cells from both biofilms where ultrastructurally distinct, displaying, for instance, clear differences in their sheaths. The amounts of EPS and their organization associated with the cyanobacteria may determine the differences in adhesion and effects on the lithic substrate observed in the biofilms. By sequencing part of the 16S rRNA gene, the two cyanobacteria were also genetically characterized. The gene sequence of the cells comprising the biofilm that was tightly attached to the lithic substrate showed most homology with that of an endolithic cyanobacterium from Switzerland (AY153458), and the cyanobacterial type loosely adhered to the rock, clustered with Acaryochloris marina, the only organism unequivocally known to contain chlorophyll d. This study reveals the presence of at least two different types of endolithic biofilm, dominated each by a single type of cyanobacterium, able to withstand the harsh conditions of the Antarctic climate.
We investigated the influence of microwave radiation on physiological behaviors of Phormidium sp. Kützing ISC31 (Oscillatoriales). The organism grown in BG-11 medium was microwave-treated at a frequency of 2450 MHz using a microwave oven. Fifteen (15) microwave pretreatments were established, combining five intensities (180, 360, 540, 720 and 900 W/cm2) and three periods of pretreatment [10, 20 and 30 second(s)]. Our results revealed that samples exposed to microwave various intensities showed significantly higher growth rates and biomass than that of non-irradiated controls. The content of chlorophyll a, which exists in the thylakoid membrane, decreased with increase in field strength and duration of exposure. Synthesis of the phycobiliproteins (PBP), phycocyanin (PC), phycoerythrin (PE) and allophycocyanin (APC), except in 720 and 900 W/cm2 (30 s), increased in all exposures as compared to that of control. Photosynthetic activity rate compared to nitrogenase activity increased in all microwave exposures except in 180 W (10 s) and 720 W (10 s). Identification was carried out by molecular method. The result of PCR blasted with sequenced cyanobacteria in NCBI showed 97% homology to the 16S rRNA of Phormidium sp. This study revealed that various microwave intensities induce different physiological effects, depending on field strength and duration of exposure.
Cytomorphological characters of six strains of unicellular cyanophytes, all belonging to "Euhalothece/Halothece" group in the sense of Garcia-Pichel et al. (1998), but of different hypersaline origin, have been studied using DAPI fluorescent staining and light and transmission electron microscopy. They can be divided into two clades, which are well separated according to phenotypic taxonomy (morphology, cytology and ultrastructure). The first group (four strains) could be included in the subcluster "Euhalothece" (on the generic level, but not yet validly described). Broad oval cells of ca 4-6 μm breadth with indistinct chromatoplasm, net like nucleoids and parallel lengthwise-arranged thylakoids often in fascicles are characteristic for this group. The second subcluster should be classified into another genus because of oblong or rod-shaped cells of smaller size (cca 2-4 μm wide), peripheral "chromatoplasm" (position of mostly lengthwise parietal thylakoids) and more or less compact nucleoid. These strains belong into the vicinity of the genus Cyanobium.
Among various microscopic organisms producing photobiological hydrogen, cyanobacteria have long been recognized as the promising biological agents for hydrogen economy in 21 century. For photobiological production of hydrogen energy, marine unicellular -fixing cyanobacteria have been evaluated as an ideal subgroup of Cyanophyceae. To develope the hydrogen production technology using unicellular -fixing cyanobacteria, 3 important factors are pre-requisite: 1) isolation of the best strain from marine natural environment, 2) exploration on the strain-specific optimal conditions for the photobiological hydrogen production, and finally 3) application of the molecular genetic tools to improve the natural ability of the strain to produce hydrogen. Here we reviewed the recent research & development to commercialize photobiological hydrogen production technology, and suggest that intensive R&D during next 10-15 years should be imperative for the future Korean initiatives in the field of the photobiological hydrogen production technology using photosynthetic marine unicellular cyanobacterial strains.
Photobiological H2 from marine cyanobacterial strains is widely accepted to be an ideal clean and renewable energy source. Using the two Korean N2-fixing unicellular cyanobacterial strains (Cyanothece sp. KNU CB MAL-031 and Cyanothece sp. KNU CB MAL-058) and the Synechococcus sp. Miami strain BG043511 we performed flask-scale experiments to measure the effect of CO and HCN addition on photobiological H2 production. For the test, 1, 5, 10 and 30% v/v of CO in the N2 atmosphere was applied. Enhancement of H2 production was remarkable at 1–5% concentration range of CO addition. At CO concentrations over 5% no further cost-effective enhancement of H2 production was detectable, which suggests to us that 1–5% CO addition should be adopted for practical photobiological H2 production by the cyanobacterial strains. Maximum enhancement of the photobiological H2 production by CO additions was 2–6 times over the control flasks without CO. When 3 ppm of HCN was injected into the cell suspension of BG043511, the enhancement of hydrogen production was 50–60% of that under 5% CO. Present result implies the possible recycling of waste CO and HCN for the enhancement of the photobiological H2 production using marine cyanobacterial strains.
Due to the irreversible inhibition of nitrogenase by O2, N2 fixation is incompatible with the oxygenic photosynthesis of cyanobacteria. These organisms have therefore evolved various strategies for growing diazotrophically. One group of N2-fixing cyanobacteria has specialized cells, heterocysts, which contain the nitrogenase, lack the oxygenic photosystem II, and are virtually anoxic inside as the result of respiratory activity and a thick glycolipid cell wall. The hetR gene encodes a serine protease which is thought to be involved in the regulation of heterocyst development and in DNA binding. Although hetR is also present in many non-heterocystous N2-fixing cyanobacteria, its function in these organisms is unknown. In this study, hetR sequences of the N2-fixing, non-heterocystous cyanobacterium Trichodesmium spp. and related genera were examined for signatures of selection. In parsimony- or distance-based hetR phylogenies, the filamentous non-heterocystous cyanobacteria Symploca sp. and Leptolyngbya sp. were closest to Trichodesmium sp. However, accommodating molecular attributes of hetR such as nucleotide frequencies and rate heterogeneity in phylogenetic analyses suggested that many other genera could not be excluded as sister taxa of Trichodesmium. Maximum likelihood analysis of the dN/dS ratio (ω) showed that—irrespective of the use of Symploca, Leptolyngbya, or more distant taxa as an outgroup—the lineage between an outgroup and Trichodesmium (ω1=0.02–0.05) and a lineage leading to Trichodesmium erythraeum (ω1=0.02) were under much stronger purifying selection than the other lineages in Trichodesmium (ω0=0.13–0.32). Although the results from the maximum likelihood analyses are most trustworthy because of codon usage bias in Trichodesmium, the results from a simpler tree-based McDonald–Kreitman test were in general agreement. Due to their quite different assumptions, the combination of these two methods of analysis circumvents multiple testing which, in general, is problematic when using branch models. Although the causal selective forces underlying the substitution patterns in hetR have not yet been identified, these findings parallel the variety of physiological, molecular, and behavioral differences in cyanobacteria related to N2 fixation. The heterogeneity of selection pressures in Trichodesmium is more surprising, because multiple adaptation mechanisms have not been described in this genus.
The unambiguous evidence for the presence of life in the Archean is only limited by the preservation potential of sedimentary
rocks. Throughout Earth’ preserved sedimentary deposits, prokaryotic bodily fossils and geochemical fossils, for example,
products of the Calvin-cycle dependent carbon isotopic fractionation, can be found. Nevertheless, irreproducible analyses
in organic geochemistry, misinterpretations of artifacts from sample preparation and of organic contaminants, and uncertainties
on the age and nature of the Archean rock formations are copious in evaluation of the earliest traces of life.
The understanding of geological processes strongly influence discussions of the ancient, supposed biological relicts from
c. 3.8 billion years old (3.8 Ga) metasedimentary rocks. The evidence for prokaryotic bodily preserved microfossils of the
Neoarchean, at 2.7 to 2.5 Ga is by orders of magnitude stronger, as rocks of this age are abundant and better preserved.
This chapter will largely focus on the N-metabolism, N-stress response and niche adaptation of major phytoplankton groups, as they impact significantly on the N-cycle in marine water bodies. Much emphasis is on the molecular ecology and phylogeny of these groups, which have seen a rapid development over the last decade. An increased understanding of the flow of matter via the microbial food web has resulted in an appreciation of high N-regeneration rates within the photic layer. Nevertheless, large oceanic regions, mostly in the (sub)tropics are characterized by N-deplete surface waters, from the surface down to below the 1% isolume. Such waters are more often than not populated with cyanobacteria as the major phytoplankton group. These cyanobacteria may be either the microscopically small Synechococcus, Prochlorococcus, Cyanothece , and Chrocosphaera unicells or the large colonies o f N2-fixing Trichodesmium filaments. Cyanobacteria are key components of marine microbial communities contributing up to two-thirds of carbon dioxide fixed in oceanic systems. Although it is with C cycling that cyanobacteria are most notably associated, their contribution to the transformation of nitrogenous compounds is equally important, and indeed with roles in both regenerated and new N production and utilization, they are also inextricably linked to the global N-cycle. In nutrient-depleted surface layers of the ocean cyanobacteria often experience sudden pulses of N either by physical mechanisms such as upwellings that provide nitrate to the euphotic zone or by biological mechanisms such as animal excretion that add regenerated N forms such as ammonia and urea.
In 1998, Garcia-Pichel and coworkers studied 13 strains of extremely halotolerant, unicellular cyanobacteria. One strain, which was isolated from a coastal salty habitat in Baja California, Mexico, was found to represent a genetically distinct subcluster, different from another related coherent group of 12 morphologically similar types. This subcluster was designated as 'true Halothece', in comparison with 'Euhalothece' strains. The genetic characters clearly indicated their separation of Halothece at the generic level (less than 91% of genetic similarity), but the formal description, corresponding with bacteriological or botanical nomenclatoric rules, was never published. The present article comprises the valid description of the genus Halothece based on the type strain MPI 96P605, Supported by new original Studies of the morphological, ecophysiological and ultrastructural variability of the type strain.
Cytomorphological characters of six strains of unicellular cyanophytes, all belonging to "Euhalothece/ Halothece" group in the sense of GarCia–piChel et al. (1998), but of different hypersaline origin, have been studied using DAPI fluorescent staining and light and transmission electron microscopy. They can be divided into two clades, which are well separated according to phenotypic taxonomy (morphology, cytology and ultrastructure). The first group (four strains) could be included in the subcluster "Euhalothece" (on the generic level, but not yet validly described). Broad oval cells of ca 4–6 µm breadth with indistinct chromatoplasm, net like nucleoids and parallel lengthwise–arranged thylakoids often in fascicles are characteristic for this group. The second subcluster should be classified into another genus because of oblong or rod–shaped cells of smaller size (cca 2–4 μm wide), peripheral "chromatoplasm" (position of mostly lengthwise parietal thylakoids) and more or less compact nucleoid. These strains belong into the vicinity of the genus Cyanobium.
Cyanobacteria are the microscopic photosynthetic ‘cell factories’ that are known to produce a wide variety of bioactive compounds and have a very significant role in environment and ecology of water bodies and other ecosystems. However, the systematics and classification of this group of organism is presently in a state of disarray. These were traditionally identified on the basis of morphology, and were classified as blue-green algae (Cyanophyta) under the Botanical codes whereas; the Bergey’s Manual of Systematic Bacteriology uses Bacteriological approach for this purpose. Their greater morphological, physiological, biochemical and molecular variability; incorrect use of old or revised names; misidentification of the strains; horizontal gene transfer; and lack of appropriate genetic information complicates the process. Further, this group of microorganisms has wide adaptation qualities, show spatial and temporal variation in their genetic community structure, and respond differently to factors such as nutrient deprivation, light intensity and predation. Therefore, the application of various molecular tools, functional genomics, proteomics, metabolomics, and analysis of important bioactive compounds along with the morphological, physiological and biochemical attributes will magnify the diversity present among the members of this group and will be highly useful in correct deciphering of their phylogenetic relationships.
Nitrogen fixation, the reduction of atmospheric dinitrogen (N2) to biologically available ammonium, has been important in the balance of biologically available nitrogen since early in
the evolution of life on Earth. The nitrogen fixation reaction requires ATP and reductant and also reduces H+ to H2. Nitrogenase is composed of two multi-subunit metalloproteins. There are at least three evolutionarily related nitrogenase
gene families that require different metals (Mo, V or Fe) in the cofactor for the protein component (Component I) that contains
the active site for N2 reduction. The requirements for metals probably played an important role in the evolution of nitrogenases, as the oceans
progressed from anoxic waters containing relatively high concentrations of reduced Fe, to low-Fe oxic waters.
Cyanothece RF-1 (Synechococcus RF-1) is a unicellular N2-fixing cyano-bacterium isolated from a rice field in Taiwan. The activity of nitrogen fixation in RF-1 revealed circadian
rhythms when the cultures were placed in continuous light after diurnal regimen. RF-1 is the first prokaryotic organism shown
to exhibit cir-cadian rhythms regulated by a “biological clock.” In addition to nitrogen fixation, the uptake rate of several
amino acids and the activity of photosynthesis in RF-1 also exhibit circadian rhythmic patterns in free-running conditions.
Finally, several rhythms of various proteins are described in this chapter.
The taxonomy of cyanobacteria has been substantially modified in the last few decades, particularly after application of modern
ultrastructural and molecular methods. The group of heterocytous cyanobacteria (Nostocales) was found to be monophyletic,
but the concept and content of different genera must be continually corrected and revised. The widespread introduction of
the molecular approach (especially 16S rRNA gene sequencing) has confirmed almost all traditional genera based on distinct
and morphologically recognizable type species, but indicated also broader diversity resulting in separation of more genetic
and generic entities in several genera. The combination of molecular and phenotype analyses enables also a better and more
objective definition of criteria for describing newly researched generic units, discovered from various habitats in the biosphere.
Here, the nostocacean generic taxa are reviewed after recent necessary taxonomic corrections. Nostocacean cyanobacteria are
filamentous, heterocytous, not branched and not polarized morphotypes, classified traditionally into one family (Nostocaceae).
The main part of the review focuses on the genera containing planktic species.
A maximum likelihood method for inferring evolutionary trees from DNA sequence data was developed by Felsenstein (1981). In evaluating the extent to which the maximum likelihood tree is a significantly better representation of the true tree, it is important to estimate the variance of the difference between log likelihood of different tree topologies. Bootstrap resampling can be used for this purpose (Hasegawa et al. 1988; Hasegawa and Kishino 1989), but it imposes a great computation burden. To overcome this difficulty, we developed a new method for estimating the variance by expressing it explicitly.The method was applied to DNA sequence data from primates in order to evaluate the maximum likelihood branching order among Hominoidea. It was shown that, although the orangutan is convincingly placed as an outgroup of a human and African apes clade, the branching order among human, chimpanzee, and gorilla cannot be determined confidently from the DNA sequence data presently available when the evolutionary rate constancy is not assumed.
To determine the evolutionary positions of the conifer genera Amentotaxus, Phyllocladus, and Nageia, we obtained 18S rRNA sequences from 11 new taxa representing the major living orders and families of gymnosperms. With the published Chlamydomonas as an outgroup, phylogenetic analyses of our new data and available sequences indicate that (1) the Gnetales form a monophyletic group, which is an outgroup to the conifers, (2) the conifers are monophyletic, (3) Taxaceae, Cephalotaxaceae, Cupressaceae, and Taxodiaceae form a monophyletic group, (4) Amentotaxus is closer to Torreya than to Cephalotaxus, suggesting that Amentotaxus is better to be classified as a member of Taxaceae, (5) Phyllocladus, Dacrycarpus, Podocarpus, and Nageia form a monophyletic group, and (6) Pinaceae is an out-group to the other families of conifers. Our finding that Phyllocladus is a sister group of the Podocarpaceae disagrees with the suggestion that the phylloclade of the genus is an ancient structure and that the genus is a terminal taxon within the Podocarpaceae. The genus Nageia is more closely related to Podocarpus than to Dacrycarpus and was derived from within the Podocarpaceae. In conclusion, our data indicate that in conifers, the uniovulate cone occurred independently in Taxacaeae and Cephalotaxaceae, and in Podocarpaceae after the three families separated from Pinaceae, and support the hypothesis that the uniovulate cone is derived from reduction of a multiovulate cone.
Although molecular phylogenetic studies of cyanobacteria on the basis of the 16S rRNA gene sequence have been reported, the topologies were unstable, especially in the inner branchings. Our analysis of 16S rRNA gene phylogeny by the maximum-likelihood and neighbor-joining methods combined with rate homogeneous and heterogeneous models revealed seven major evolutionary lineages of the cyanobacteria, including prochlorophycean organisms. These seven lineages are always stable on any combination of these methods and models, fundamentally corresponding to phylogenetic relationships based on other genes, e.g., psbA, rbcL, rnpB, rpoC, and tufA. Moreover, although known genotypic and phenotypic characters sometimes appear paralleled in independent lineages, many characters are not contradictory within each group. Therefore we propose seven evolutionary groups as a working hypothesis for successive taxonomic reconstruction. New 16S rRNA sequences of five unicellular cyanobacterial strains, PCC 7001, PCC 7003, PCC 73109, PCC 7117, and PCC 7335 of Synechococcus sp., were determined in this study. Although all these strains have been assigned to "marine clusters B and C," they were separated into three lineages. This suggests that the organisms classified in the genus Synechococcus evolved diversely and should be reclassified in several independent taxonomic units. Moreover, Synechococcus strains and filamentous cyanobacteria make a monophyletic group supported by a comparatively high statistical confidence value (80 to 100%) in each of the two independent lineages; therefore, these monophylies probably reflect the convergent evolution of a multicellular organization.
A new N2-fixing unicellular cyanobacterium identified as a Synechococcus sp. was isolated and purified as an axenic culture. It fixed N2 aerobically either under continuous illumination or in alternating light-dark cycle. The N2-fixing properties of the new isolate and Gloeocapsa are discussed.
A new N2-fixing unicellular cyanobacterium identified as a Synechococcus sp. was isolated and purified as an axenic culture. It fixed N2 aerobically either under continuous illumination or in alternating light-dark cycle. The N2-fixing properties of the new isolate and Gloeocapsa are discussed.
Among nitrogen-fixing microorganisms, nitrogen-fixing cyanobacteria are unique in their ability to carry out oxygen-evolving photosynthesis and oxygen-labile nitrogen fixation within the same organisms1–3. These seemingly incompatible reactions take place in heterocystous cyanobacteria by the spatial separation of the site of nitrogen fixation (heterocysts) from the site of photosynthesis (vegetative cells)4,5. Several hypotheses have been proposed to explain these mechanisms in non-heterocystous cyanobacteria3,6–11. Using batch cultures of Gloeothece (Gloeocapsa) spp., Gallon and collaborators demonstrated the mechanism of temporal separation of photosynthesis and nitrogen fixation into the light and dark periods of growth, respectively9. However, the mechanisms by which these two incompatible reactions can occur under continuous light conditions still remained ambiguous. Using novel strains of aerobic nitrogen-fixing, unicellular marine cyanobacteria, Synechococcus spp., grown under synchronized conditions, we report here that nitrogen fixation and photosynthesis occur at different phases in the cell division cycle. Our data, obtained under both diurnal light/dark cycle and continuous illumination, indicate that the temporal separation of the two phases during the cell division cycle is the mechanism by which these unicells can grow photoautotrophically under nitrogen-fixing conditions.
Small subunit rRNA sequence data were generated for 27 strains of cyanobacteria and incorporated into a phylogenetic analysis of 1,377 aligned sequence positions from a diverse sampling of 53 cyanobacteria and 10 photosynthetic plastids. Tree inference was carried out using a maximum likelihood method with correction for site-to-site variation in evolutionary rate. Confidence in the inferred phylogenetic relationships was determined by construction of a majority-rule consensus tree based on alternative topologies not considered to be statistically significantly different from the optimal tree. The results are in agreement with earlier studies in the assignment of individual taxa to specific sequence groups. Several relationships not previously noted among sequence groups are indicated, whereas other relationships previously supported are contradicted. All plastids cluster as a strongly supported monophyletic group arising near the root of the cyanobacterial line of descent.
Frequent growth of unicellular blue-green alga Aphanothece sp. was observed in medium free of combined nitrogen. Its generation time was 12 h and more than 2 mg of nitrogen was fixed in 25 days. Its growth and nitrogen fixation were comparable to other heterocystous algae.
The aerobic synchronous growth of marine unicellular cyanobacteriaSynechococcus spp., with molecular nitrogen as the sole nitrogen growth nutrient source, was experimentally demonstrated. Cell division synchrony was induced by withholding aeration and illumination for 20 h. Three distinct cell division cycles of approximately 20 h each were observed. During the first cell division cycle, high degrees of synchrony of 78%–86% were observed in the series of cultures studied. The aerobic nitrogenase activity appeared shortly while the cell division was completed and the cell size was still small, and it disappeared after the cells were enlarging photosynthetically. Thus, three distinct cycles in aerobic nitrogenase activity were also observed having approximately the same 20-h interval as the cell division cycle. The peak aerobic nitrogenase activity was determined to be as high as 840–1220 nmol C2H2 reduced per milligram dry weight per hour.
The fine structure of the type species of the genusCyanothece
Komrek 1976,C. aeruginosa, is described and compared with the main cytological characteristics of morphologically related members of the generaCyanobium, Cyanobacterium andSynechococcus. Several morphological features, such as cell walls with thick outer layers containing a special type of vesicles, position of thylakoids, keritomy (net-like appearance of protoplast caused by arrangement of thylakoids, net-like nucleoids and/or by tendency to form intrathylakoidal spaces) and a special structure of mucilaginous envelopes were found to be characteristic of this genus, supporting its separate position among coccal cyanoprokaryotes (cyanobacteria, cyanophytes). The taxonomic significance of ultrastructural features in all mentioned genera is discussed.
A rapid procedure for the isolation of intact total cellular RNA from cultured cells is described. This method combines the simultaneous disruption of cells and extraction of nucleic acids in a single step with the use of phenol and a buffer containing 100 mM LiCl. Total cellular RNA can be isolated in approximately 2 hours. The yield and quality of the RNA is comparable to the more widely employed methods requiring extensive preparatory steps such as extraction using guanidinium thiocyanate and subsequent CsCl gradient centrifugation. The RNA isolated using our procedure contains transcripts up to 10 kb in length and is suitable for Northern analysis. This procedure also yields high-molecular-weight DNA, which is a suitable substrate for restriction endonucleases.
We examined the morphology, physiology, and 16S rRNA gene sequences of three culture collection strains and of ten novel isolates of unicellular cyanobacteria from hypersaline environments. The strains were morphologically diverse, with average cell widths ranging from 2.8 to 10.3 micron. There were single-celled, colonial, and baeocyte-forming strains. However, morphological traits were markedly variable with culture conditions. In contrast, all strains displayed extreme halotolerance (growing close to optimally at above 12% salinity); all were obligately marine, euryhaline, and moderately thermophilic; and all shared a suite of chemotaxonomic markers including phycobilins, carotenoids, and mycosporine-like amino acids. 16S rRNA gene sequence analysis indicated that the strains were related to each other. Sequence similarity analysis placed the strains in a monophyletic cluster (which we named the Halothece cluster) apart from all cultured or uncultured, not extremely halotolerant cyanobacteria whose 16S rRNA gene sequences are available in public nucleotide sequence databases. This represents the first case in which a phylogenetically coherent group of cyanobacteria can be defined on the basis of physiology. The Halothece cluster contained two subclusters that may be divergent at the generic level, one encompassing 12 strains (spanning 5% 16S rRNA gene sequence divergence and named the Euhalothece subcluster), and a single deep-branching isolate. Phenotypic characterization of the isolates, including morphological, physiological, and chemotaxonomic traits, did not distinguish these subclusters and only weakly suggested the existence of two separate clades, one encompassing strains of small cell size (cell width < 5 m) and another one encompassing strains of larger cell size.
This chapter discusses the cloning of hormone genes from a mixture of complementary deoxyribonucleic acid (cDNA) molecules. The molecular cloning of cDNA synthesized from a purified messenger ribonucleic acid (mRNA) is a well-established method for obtaining purified DNA for sequence analysis and use as a hybridization probe. Only a limited number of purified mRNAs are currently available that include those from specialized cells producing predominantly a single protein, such as globin, immunoglubin, or ovalbumin. The chapter describes the procedures used to isolate and clone specific hormone cDNAs from an impure mRNA population. The method employs the restriction endonuclease cleavage of double-stranded cDNA transcribed from a complex mixture of mRNA. The method does not require any extensive purification of RNA but instead makes use of the transcription of RNA into cDNA, the sequence-specific fragmentation of this cDNA, with one or two restriction endonucleases, and the fractionation of the cDNA restriction fragments on the basis of their lengths. The use of restriction endonucleases eliminates size heterogeneity and produces homogeneous-length DNA fragments from any cDNA species that contains at least two restriction sites. From the initially heterogeneous population of cDNA transcripts, uniform-sized fragments of desired sequence are produced. The chapter discusses a complete scheme for cDNA cloning.
As a logical consequence of the definition of a bacterium (Stanier and van Niel, 1962), R. Y. Stanier created the name "cyanobacteria" as a replacement for "blue-green algae". As such, cyanobacteria entered the 8th issue of Bergey's Manual of Determinative Bacteriology 1974 as members of the Procaryotae Murray 1968, this kingdom being composed of two divisions, Cyanobacteria and Bacteria. An even tighter integration of cyanobacteria with other bacteria was proposed by Gibbons and Murray (1978) for the next edition of Bergey's Manual. These authors suggested that the cyanobacteria be integrated as an order Cyanobacteriales in the class Photobacteria. However, this proposal was doomed to failure by constraints imposed under present rules of the Bacteriological Code (Lapage et al., 1976), one of which is that the type of an order is the genus upon whose name the higher taxon is based. A genus Cyanobacterium did not exist when Gibbons and Murray made their proposal, and a subsequent special request by the same authors for an exemption from this rule was not granted (Judicial Commission of the International Committee on Systematic Bacteriology, Holt, 1978). We present here a revised classification for unicellular cyanobacteria dividing in one plane wherein we propose, among other changes, the creation of two new genera. Cyanobium and Cyanobacterium. With the creation of the latter genus, the requirement for recognition of cyanobacteria as a legal order Cyanobacteriales under the Bacteriological Code should be fulfilled. We suggest that the type species of this genus by Cyanobacterium stanieri, in honor of the late Roger Y. Stanier.
The prokaryotic Synechococcus sp. RF-1 exhibited a nitrogen fixation circadian rhythm with characteristics remarkably similar to the circadian rhythm of eukaryotes. The rhythm had a free-running period of about 24 hours when the length of the preen-trained cycle did not differ too much from 24 hours, and it was insensitive to changes in temperature from 22 degrees C to 33 degrees C. Because the endogenous rhythm of nitrogen fixation was not affected by a phase-shift of its previous cycles, the circadian rhythm in Synechococcus sp. RF-1 was not considered to be controlled simply by a feedback mechanism.
The continuous growth in a medium free of combined nitrogen and the experimental production of ethylene via acetylene reduction indicate that nitrogen fixation by blue-green algae is not solely confined to filamentous genera with heterocysts. Axenic cultures of Gloeocapsa sp., adapted to nitrate-free medium, form ethylene at rates comparable to those of species known to fix nitrogen.