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Microbial community analysis of pH 4 thermal springs in Yellowstone National Park

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Abstract

The pH of the majority of thermal springs in Yellowstone National Park (YNP) is from 1 to 3 and 6 to 10; relatively few springs (~5%) have a pH range of 4–5. We used 16S rRNA gene pyrosequencing to investigate microbial communities sampled from four pH 4 thermal springs collected from four regions of YNP that differed in their fluid temperature and geochemistry. Our results revealed that the composition of bacterial communities varied among the sites, despite sharing similar pH values. The taxonomic composition and metabolic functional potential of the site with the lowest temperature (55 °C), a thermal spring from the Seven Mile Hole (SMH) area, were further investigated using shotgun metagenome sequencing. The taxonomic classification, based on 372 Mbp of unassembled metagenomic reads, indicated that this community included a high proportion of Chloroflexi, Bacteroidetes, Proteobacteria, and Firmicutes. Functional comparison with other YNP thermal spring metagenomes indicated that the SMH metagenome was enriched in genes related to energy production and conversion, transcription, and carbohydrate transport. Analysis of genes involved in nitrogen metabolism revealed assimilatory and dissimilatory nitrate reduction pathways, whereas the majority of genes involved in sulfur metabolism were related to the reduction of sulfate to adenylylsulfate, sulfite, and H2S. Given that pH 4 thermal springs are relatively less common in YNP and thermal areas worldwide, they may harbor novel microbiota and the communities that inhabit them deserve further investigation.

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Acknowledgements

We are very grateful for the valuable suggestions from three anonymous reviewers. We appreciate helpful discussions with David J. Van Horn and Daniel R. Colman related to data analyses performed in the study, as well as sample collection from Kendra R. Mitchell, and sample processing by George Rosenberg of the Center for Evolutionary and Theoretical Immunology (CETI), University of New Mexico. This work was supported by NSF Biodiversity Surveys and Inventories Grant 02-06773 to CTV and NIH-sponsored CETI 454 Voucher Program funding to XJ. Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number P30GM110907. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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    Xiaoben Jiang & Cristina D. Takacs-Vesbach

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Correspondence to Cristina D. Takacs-Vesbach.

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792_2016_889_MOESM5_ESM.tif

Fig. S1 Two-way hierarchical clustering of normalized COG protein family abundance data averaged across the level of COG categories. The data were standardized (subtract mean and divide by standard deviation) across sites before clustering, so that the color scale units represent standard deviations from the mean across sites. Red colors correspond to values that are higher than the site mean and green colors to values that are lower than the mean. The full names of metagenomes for this analysis are listed in Table S1 (TIFF 3280 kb)

792_2016_889_MOESM6_ESM.tif

Fig. S2 Taxonomic assignment of unassembled SMH metagenomic sequences based on GenBank (NCBI-nr), M5NR, and RefSeq databases at the class level (Only top four most abundant phyla listed) (TIFF 1256 kb)

792_2016_889_MOESM7_ESM.tif

Fig. S3 Partial nitrogen pathways identified by KEGG affiliation of the sequences from the site 04YSHM020. Boxes indicate the KEGG identifiers and numbers in gray circles indicate the number of sequences assigned to the KEGG function (TIFF 835 kb)

792_2016_889_MOESM8_ESM.tif

Fig. S4 Partial sulfur pathways identified by KEGG affiliation of the sequences from the site 04YSHM020. Boxes indicate the KEGG identifiers, and numbers in gray circles indicate the number of sequences assigned to the KEGG function (TIFF 894 kb)

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Jiang, X., Takacs-Vesbach, C.D. Microbial community analysis of pH 4 thermal springs in Yellowstone National Park. Extremophiles 21, 135–152 (2017). https://doi.org/10.1007/s00792-016-0889-8

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