The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing

Abstract

Microbial-mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin at Yellowstone National Park have been studied for nearly 50 years. The emphasis has mostly focused on the chlorophototrophic bacterial organisms of the phyla Cyanobacteria and Chloroflexi. In contrast, the diversity and metabolic functions of the heterotrophic community in the microoxic/anoxic region of the mat are not well understood. In this study we analyzed the orange-colored undermat of the microbial community of Mushroom Spring using metagenomic and rRNA-amplicon (iTag) analyses. Our analyses disclosed a highly diverse community exhibiting a high degree of unevenness, strongly dominated by a single taxon, the filamentous anoxygenic phototroph, Roseiflexus spp. The second most abundant organisms belonged to the Thermotogae, which have been hypothesized to be a major source of H 2 from fermentation that could enable photomixotrophic metabolism by Chloroflexus and Roseiflexus spp. Other abundant organisms include two members of the Armatimonadetes (OP10); Thermocrinis sp.; and phototrophic and heterotrophic members of the Chloroflexi. Further, an Atribacteria (OP9/JS1) member; a sulfate-reducing Thermodesulfovibrio sp.; a Planctomycetes member; a member of the EM3 group tentatively affiliated with the Thermotogae, as well as a putative member of the Arminicenantes (OP8) represented ≥1% of the reads. Archaea were not abundant in the iTag analysis, and no metagenomic bin representing an archaeon was identified. A high microdiversity of 16S rRNA gene sequences was identified for the dominant taxon, Roseiflexus spp. Previous studies demonstrated that highly similar Synechococcus variants in the upper layer of the mats represent ecological species populations with specific ecological adaptations. This study suggests that similar putative ecotypes specifically adapted to different niches occur within the undermat community, particularly for Roseiflexus spp.

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses

“…As noted above, the composition and diversity of the undermat was described in a previous report (Thiel et al, 2016). In this report, we focus on a description of the metabolic potentials and hypothesized interactions among mat community members.…”

Microbial diversity and iron oxidation at Okuoku‐hachikurou Onsen, a Japanese hot spring analog of Precambrian iron formations

“…The Anaerolineae have generally been isolated as obligately anaerobic heterotrophs (e.g., Sekiguchi et al, 2003;Yamada et al, 2006), but genome sequencing has revealed the capacity for aerobic respiration in diverse members of this clade (e.g., Pace, Hemp, Ward, & Fischer, 2015;. Furthermore, a genome for an organism closely related to the Anaerolineae with genes for photosynthesis has been assembled from a Yellowstone National Park metagenome (Klatt et al, 2011;Tank, Thiel, Ward, & Bryant, 2017;Thiel et al, 2016 (Podosokorskaya, Bonch-Osmolovskaya et al, 2013;Yamada et al, 2007).…”

Microbial diversity of thermophiles with biomass deconstruction potential in a foliage‐rich hot spring

“…To analyze microbial diversity, 16S rRNA amplicon‐based sequencing has been widely used in various engineered or environmental samples (Hess et al., ; Singh et al., ; Chan et al., ; Mhuantong, Charoensawan, Kanokratana, Tangphatsornruang, & Champreda, ; Vishnivetskaya et al., ). Culture independent studies at hot springs in YNP have a long research history where the clonal library was initially used (Brock, ; Thiel et al., ). Microbial diversity in Octopus and Mushroom Springs at YNP were revisited using high‐throughput NGS (Thiel et al., ).…”

“…Culture independent studies at hot springs in YNP have a long research history where the clonal library was initially used (Brock, ; Thiel et al., ). Microbial diversity in Octopus and Mushroom Springs at YNP were revisited using high‐throughput NGS (Thiel et al., ). Most of the studied hot springs lack lignocellulosic plant materials.…”

“…Microbial diversity in Octopus and Mushroom Springs at YNP were revisited using high-throughput NGS (Thiel et al, 2016). Most of the studied hot springs lack lignocellulosic plant materials.…”