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

Abstract

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.

Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat

“…No sequences obtained from the upper mat layer could definitively be assigned to members of the domain Archaea. In agreement with Klatt et al (2011), the next most abundant sequences were assigned to the kingdoms Firmicutes and Bacteriodetes, which represented less than 2% of the rRNA sequences. Overall, the best matches to these remaining sequences were distributed across hundreds of different bacterial sequence entries.…”

“…396-1 were the closest sequenced representatives from these two genera, respectively. Sequences derived from close relatives of the aerobic chemo-organotroph, Thermomicrobium roseum, which was reported to be present in similar mat systems in Yellowstone Klatt et al, 2011), were also detected, although at a very low level (0.3%). As shown in Figure 2a, about 10% of the remaining sequences were assigned to three different families, mainly Anaerolineaceae.…”

“…The chlorophototrophic microbial mats of alkaline siliceous hot springs in Yellowstone National Park have served for decades as model systems for understanding the composition, structure and function of microbial communities (Brock, 1978;Ward et al, 1998Ward et al, , 2002Ward et al, , 2006Ward et al, , 2011Ward and Castenholz, 2000;Klatt et al, 2011). Members of the kingdoms Cyanobacteria (mostly Synechococcus spp.)…”

“…In a complementary study to that of Klatt et al (2011), two different approaches to transcription profiling of the chlorophototrophic microbial mat community of Mushroom Spring were compared. In the first approach, pyrosequencing (Roche GS FLX, 454 Life Sciences, Branford, CT, USA) of cDNAs produced from RNA extracted from mat samples collected at 60 1C for four different time points in a diel cycle was carried out.…”

Biogeography of bacterial communities in hot springs: a focus on the actinobacteria

“…Microbial biography studies in hot springs, a great number carried out in Yellowstone National Park, have shown these environments containing highly distinct community structures, where archaea, cyanobacteria, chloroflexi and acidobacteria are among the microorganisms most commonly found [35,40,[50][51]23,56]. Such studies have typically focused on the broader microbial community and very little is known on the biogeography of actinobacteria in hot springs.…”