Comparative and Functional Genomics of Anoxygenic Green Bacteria from the Taxa Chlorobi, Chloroflexi, and Acidobacteria

Bryant, Donald A.; Liu, Zhenfeng; Li, Tao; Zhao, Fangqing; Costas, Amaya M. Garcia; Klatt, Christian G.; Ward, David M.; Frigaard, Niels‐Ulrik; Overmann, Jörg

doi:10.1007/978-94-007-1533-2_3

Cited by 125 publications

(207 citation statements)

References 275 publications

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“…Studies of an enrichment culture of Ca. C. thermophilum and its genome (Bryant et al, 2011) confirmed the inferences made from genetic data.…”

Section: Introductionsupporting

confidence: 67%

“…Homologs of genes involved in both BChl-c and BChl-a biosynthesis were present in Cluster-3, indicating that the native Chloroflexus spp. are physiologically similar to known isolates with respect to light-harvesting strategies Frigaard and Bryant, 2006;Bryant et al, 2011) (Table 3). Sequences encoding two key enzymes in the 3-hydroxypropionate pathway, and most closely related to homologs in the Chloroflexus sp.…”

Section: Major Populations and Their Functional Potentialmentioning

confidence: 52%

“…in the mats may be capable of carbon fixation by the 3-hydroxypropionate pathway. Cluster-3 contained a homolog of sulfide-quinone oxidoreductases (sqr) in Chloroflexus spp., which suggested that these organisms might oxidize sulfide to polysulfides (Bryant et al, 2011). Functional genes identified using BLAST and annotated using hidden Markov models, genomic context and/or phylogenetic analysis (see Supplementary Information Section 3).…”

Section: Major Populations and Their Functional Potentialmentioning

confidence: 99%

“…Functional genes found on the scaffolds of this cluster clarified the potential physiological properties of this population. In particular, one scaffold contained a gene encoding a homolog of the Fenna-Matthews-Olson protein, which is a BChl-a-binding antenna protein involved in anoxygenic photosynthesis and only known to occur in the members of the Chlorobiales and chlorophototrophic Acidobacteria (Bryant et al, , 2011. High-performance liquid chromatographic analysis of pigments extracted from the Mushroom Spring mat will be published elsewhere (M Pagel and DA Bryant, unpublished data), but preliminary results indicated the presence of BChl-d, which replaces BChl-c as the aggregated pigments within the chlorosomes of 'green' chlorophototrophic Chlorobiales.…”

Section: Major Populations and Their Functional Potentialmentioning

confidence: 99%

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Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

et al. 2011

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Phototrophic microbial mat communities from 60 1C and 65 1C regions in the effluent channels of Mushroom and Octopus Springs (Yellowstone National Park, WY, USA) were investigated by shotgun metagenomic sequencing. Analyses of assembled metagenomic sequences resolved six dominant chlorophototrophic populations and permitted the discovery and characterization of undescribed but predominant community members and their physiological potential. Linkage of phylogenetic marker genes and functional genes showed novel chlorophototrophic bacteria belonging to uncharacterized lineages within the order Chlorobiales and within the Kingdom Chloroflexi. The latter is the first chlorophototrophic member of Kingdom Chloroflexi that lies outside the monophyletic group of chlorophototrophs of the Order Chloroflexales. Direct comparison of unassembled metagenomic sequences to genomes of representative isolates showed extensive genetic diversity, genomic rearrangements and novel physiological potential in native populations as compared with genomic references. Synechococcus spp. metagenomic sequences showed a high degree of synteny with the reference genomes of Synechococcus spp. strains A and B 0 , but synteny declined with decreasing sequence relatedness to these references. There was evidence of horizontal gene transfer among native populations, but the frequency of these events was inversely proportional to phylogenetic relatedness.

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“…Studies of an enrichment culture of Ca. C. thermophilum and its genome (Bryant et al, 2011) confirmed the inferences made from genetic data.…”

Section: Introductionsupporting

confidence: 67%

Section: Major Populations and Their Functional Potentialmentioning

confidence: 52%

Section: Major Populations and Their Functional Potentialmentioning

confidence: 99%

Section: Major Populations and Their Functional Potentialmentioning

confidence: 99%

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Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

et al. 2011

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“…Furthermore, sequences affiliated to Chlorobi phylum were recovered from both nucleic acid pools of either oxic or anoxic waters and sampling campaigns. Their recovery from oxic waters is an interesting feature and deserves further investigations, but recent evidences pointed toward new Chlorobi representatives able to develop under aerobic conditions performing photoheterotrophic metabolisms [66,67]. Furthermore, higher abundance of AOA was shown in the bulk community in comparison to the potentially active community.…”

Section: Discussionmentioning

confidence: 99%

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

et al. 2015

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The microbial community composition in meromictic Lake Kivu, with one of the largest CH 4 reservoirs, was studied using 16S rDNA and ribosomal RNA (rRNA) pyrosequencing during the dry and rainy seasons. Highly abundant taxa were shared in a high percentage between bulk (DNA-based) and active (RNA-based) bacterial communities, whereas a high proportion of rare species was detected only in either an active or bulk community, indicating the existence of a potentially active rare biosphere and the possible underestimation of diversity detected when using only one nucleic acid pool. Most taxa identified as generalists were abundant, and those identified as specialists were more likely to be rare in the bulk community. The overall number of environmental parameters that could explain the variation was higher for abundant taxa in comparison to rare taxa. Clustering analysis based on operational taxonomic units (OTUs at 0.03 cutoff) level revealed significant and systematic microbial community composition shifts with depth. In the oxic zone, Actinobacteria were found highly dominant in the bulk community but not in the metabolically active community. In the oxic-anoxic transition zone, highly abundant potentially active Nitrospira and Methylococcales were observed. The cooccurrence of potentially active sulfur-oxidizing and sulfatereducing bacteria in the anoxic zone may suggest the presence of an active yet cryptic sulfur cycle.

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Biology of Green Sulfur Bacteria

Imhoff

2014

Encyclopedia of Life Sciences

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Green sulfur bacteria have gained much attention because of a number of highly interesting features including unique structures of the photosynthetic apparatus and the presence of chlorosomes as very powerful light antenna that can capture minute amounts of light. This has important ecological consequences, because the efficient light‐harvesting determines the ecological niche of these bacteria at the lowermost part of stratified environments where the least of light is available. Furthermore, the strict dependency on photosynthesis to provide energy for growth and the obligate phototrophy of green sulfur bacteria together with their characteristic sulfur metabolism have provoked much interest in their physiology, ecology and genomics. The oxidation of sulfide as their outmost important photosynthetic electron donor involves the deposition of elemental sulfur globules outside the cells and separates the process of sulfide oxidation to sulfate into two parts. This is the basis for stable syntrophic associations between green sulfur bacteria and sulfur‐ and sulfate‐reducing bacteria in which the sulfur compounds are recycled. The green sulfur bacteria are distantly related to other bacteria and represent the phylum Chlorobi, though the known representatives are taxonomically treated as Chlorobiaceae with the genera Chlorobium , Chlorobaculum , Prosthecochloris and Chloroherpeton . Key Concepts: Green sulfur bacteria depend on light for life due to their obligate phototrophic metabolism. Green sulfur bacteria perform a highly efficient photosynthesis due to the presence of light harvesting organelles, the chlorosomes, which are filled with special bacteriochlorophyll molecules. Green sulfur bacteria inhabit the lowermost part of the photic environments due to their efficient light capture. Green sulfur bacteria inhabit the lowermost part of the chemocline in the stratified environment due to their sensitivity to oxygen, their high sulfide tolerance and their dependence in light. Green sulfur bacteria are important drivers of oxidation of reduced sulfur compounds in the stratified, sulfide‐containing environment receiving low irradiation.

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Comparative and Functional Genomics of Anoxygenic Green Bacteria from the Taxa Chlorobi, Chloroflexi, and Acidobacteria

Cited by 125 publications

References 275 publications

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

Biology of Green Sulfur Bacteria

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