Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes
Abstract
Thermal spring ecosystems are a valuable resource for the discovery of novel hyperthermophilic Bacteria and Archaea, and harbor deeply-branching lineages that provide insight regarding the nature of early microbial life. We characterized bacterial populations in two circumneutral (pH ~8) Yellowstone National Park thermal (T ~80°C) spring filamentous “streamer” communities using random metagenomic DNA sequence to investigate the metabolic potential of these novel populations. Four de novo assemblies representing three abundant, deeply-branching bacterial phylotypes were recovered. Analysis of conserved phylogenetic marker genes indicated that two of the phylotypes represent separate groups of an uncharacterized phylum (for which we propose the candidate phylum name “Pyropristinus”). The third new phylotype falls within the proposed Calescamantes phylum. Metabolic reconstructions of the “Pyropristinus” and Calescamantes populations showed that these organisms appear to be chemoorganoheterotrophs and have the genomic potential for aerobic respiration and oxidative phosphorylation via archaeal-like V-type, and bacterial F-type ATPases, respectively. A survey of similar phylotypes (>97% nt identity) within 16S rRNA gene datasets suggest that the newly described organisms are restricted to terrestrial thermal springs ranging from 70 to 90°C and pH values of ~7–9. The characterization of these lineages is important for understanding the diversity of deeply-branching bacterial phyla, and theirmore »
- Authors:
-
- Univ. of New Mexico, Albuquerque, NM (United States). Dept. of Biology
- Montana State Univ., Bozeman, MT (United States). Thermal Biology Inst. Dept. of Land Resources and Environmental Sciences
- Indiana Univ., Bloomington, IN (United States). Center for Genomics and Bioinformatics
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1628144
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 7; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Microbiology; Aquificales; hot springs; Thermotogae; Calescamantes; Pyropristinus; hyperthermophiles; Yellowstone National Park
Citation Formats
Colman, Daniel R., Jay, Zackary J., Inskeep, William P., Jennings, Ryan deM., Maas, Kendra R., Rusch, Douglas B., and Takacs-Vesbach, Cristina D. Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes. United States: N. p., 2016.
Web. doi:10.3389/fmicb.2016.00304.
Colman, Daniel R., Jay, Zackary J., Inskeep, William P., Jennings, Ryan deM., Maas, Kendra R., Rusch, Douglas B., & Takacs-Vesbach, Cristina D. Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes. United States. https://doi.org/10.3389/fmicb.2016.00304
Colman, Daniel R., Jay, Zackary J., Inskeep, William P., Jennings, Ryan deM., Maas, Kendra R., Rusch, Douglas B., and Takacs-Vesbach, Cristina D. Tue .
"Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes". United States. https://doi.org/10.3389/fmicb.2016.00304. https://www.osti.gov/servlets/purl/1628144.
@article{osti_1628144,
title = {Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes},
author = {Colman, Daniel R. and Jay, Zackary J. and Inskeep, William P. and Jennings, Ryan deM. and Maas, Kendra R. and Rusch, Douglas B. and Takacs-Vesbach, Cristina D.},
abstractNote = {Thermal spring ecosystems are a valuable resource for the discovery of novel hyperthermophilic Bacteria and Archaea, and harbor deeply-branching lineages that provide insight regarding the nature of early microbial life. We characterized bacterial populations in two circumneutral (pH ~8) Yellowstone National Park thermal (T ~80°C) spring filamentous “streamer” communities using random metagenomic DNA sequence to investigate the metabolic potential of these novel populations. Four de novo assemblies representing three abundant, deeply-branching bacterial phylotypes were recovered. Analysis of conserved phylogenetic marker genes indicated that two of the phylotypes represent separate groups of an uncharacterized phylum (for which we propose the candidate phylum name “Pyropristinus”). The third new phylotype falls within the proposed Calescamantes phylum. Metabolic reconstructions of the “Pyropristinus” and Calescamantes populations showed that these organisms appear to be chemoorganoheterotrophs and have the genomic potential for aerobic respiration and oxidative phosphorylation via archaeal-like V-type, and bacterial F-type ATPases, respectively. A survey of similar phylotypes (>97% nt identity) within 16S rRNA gene datasets suggest that the newly described organisms are restricted to terrestrial thermal springs ranging from 70 to 90°C and pH values of ~7–9. The characterization of these lineages is important for understanding the diversity of deeply-branching bacterial phyla, and their functional role in high-temperature circumneutral “streamer” communities.},
doi = {10.3389/fmicb.2016.00304},
journal = {Frontiers in Microbiology},
number = ,
volume = 7,
place = {United States},
year = {Tue Mar 15 00:00:00 EDT 2016},
month = {Tue Mar 15 00:00:00 EDT 2016}
}
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Accounting For Alignment Uncertainty in Phylogenomics
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A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem
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Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups
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The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem
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Metagenome Sequence Analysis of Filamentous Microbial Communities Obtained from Geochemically Distinct Geothermal Channels Reveals Specialization of Three Aquificales Lineages
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Works referencing / citing this record:
Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments
journal, January 2017
- Saxena, Rituja; Dhakan, Darshan B.; Mittal, Parul
- Frontiers in Microbiology, Vol. 7
The Evolution of Reverse Gyrase Suggests a Nonhyperthermophilic Last Universal Common Ancestor
journal, September 2019
- Catchpole, Ryan J.; Forterre, Patrick
- Molecular Biology and Evolution, Vol. 36, Issue 12
Exemplar Abstract for Thermoproauctor sp. Colman et al. 2016.
dataset, January 2020
- Parker, Charles Thomas; Garrity, George M.
- NamesforLife
Taxonomic Abstract for the species Thermoproauctor sp. Colman et al. 2016.
dataset, January 2020
- Parker, Charles Thomas; Garrity, George M.
- NamesforLife
Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes
journal, September 2016
- DeCastro, María-Eugenia; Rodríguez-Belmonte, Esther; González-Siso, María-Isabel
- Frontiers in Microbiology, Vol. 7
Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities
journal, February 2017
- Jennings, Ryan de Montmollin; Moran, James J.; Jay, Zackary J.
- Frontiers in Microbiology, Vol. 8