Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs
Abstract
Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum ('Candidatus Kryptonia') found exclusively in higherature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.
- Authors:
-
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Univ. of Calgary, AB (Canada)
- Univ. of Nevada, Las Vegas, NV (United States)
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Geological Survey of Canada, Calgary, AB (Canada)
- McMaster Univ., Hamilton, ON (Canada)
- Miami Univ., Oxford, OH (United States)
- Univ. of Alaska, Anchorage, AK (United States)
- Sun Yat-Sen Univ., Guangzhou, (China)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1467799
- Alternate Identifier(s):
- OSTI ID: 1379050
- Report Number(s):
- LLNL-JRNL-737993
Journal ID: ISSN 2041-1723; 891150
- Grant/Contract Number:
- AC52-07NA27344; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 7; Journal Issue: na; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; Biodiversity; Metagenomics
Citation Formats
Eloe-Fadrosh, Emiley A., Paez-Espino, David, Jarett, Jessica, Dunfield, Peter F., Hedlund, Brian P., Dekas, Anne E., Grasby, Stephen E., Brady, Allyson L., Dong, Hailiang, Briggs, Brandon R., Li, Wen-Jun, Goudeau, Danielle, Malmstrom, Rex, Pati, Amrita, Pett-Ridge, Jennifer, Rubin, Edward M., Woyke, Tanja, Kyrpides, Nikos C., and Ivanova, Natalia N. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. United States: N. p., 2016.
Web. doi:10.1038/ncomms10476.
Eloe-Fadrosh, Emiley A., Paez-Espino, David, Jarett, Jessica, Dunfield, Peter F., Hedlund, Brian P., Dekas, Anne E., Grasby, Stephen E., Brady, Allyson L., Dong, Hailiang, Briggs, Brandon R., Li, Wen-Jun, Goudeau, Danielle, Malmstrom, Rex, Pati, Amrita, Pett-Ridge, Jennifer, Rubin, Edward M., Woyke, Tanja, Kyrpides, Nikos C., & Ivanova, Natalia N. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. United States. https://doi.org/10.1038/ncomms10476
Eloe-Fadrosh, Emiley A., Paez-Espino, David, Jarett, Jessica, Dunfield, Peter F., Hedlund, Brian P., Dekas, Anne E., Grasby, Stephen E., Brady, Allyson L., Dong, Hailiang, Briggs, Brandon R., Li, Wen-Jun, Goudeau, Danielle, Malmstrom, Rex, Pati, Amrita, Pett-Ridge, Jennifer, Rubin, Edward M., Woyke, Tanja, Kyrpides, Nikos C., and Ivanova, Natalia N. Wed .
"Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs". United States. https://doi.org/10.1038/ncomms10476. https://www.osti.gov/servlets/purl/1467799.
@article{osti_1467799,
title = {Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs},
author = {Eloe-Fadrosh, Emiley A. and Paez-Espino, David and Jarett, Jessica and Dunfield, Peter F. and Hedlund, Brian P. and Dekas, Anne E. and Grasby, Stephen E. and Brady, Allyson L. and Dong, Hailiang and Briggs, Brandon R. and Li, Wen-Jun and Goudeau, Danielle and Malmstrom, Rex and Pati, Amrita and Pett-Ridge, Jennifer and Rubin, Edward M. and Woyke, Tanja and Kyrpides, Nikos C. and Ivanova, Natalia N.},
abstractNote = {Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum ('Candidatus Kryptonia') found exclusively in higherature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.},
doi = {10.1038/ncomms10476},
journal = {Nature Communications},
number = na,
volume = 7,
place = {United States},
year = {Wed Jan 27 00:00:00 EST 2016},
month = {Wed Jan 27 00:00:00 EST 2016}
}
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Evaluation of prokaryotic diversity of five hot springs in Eritrea
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Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments
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Living on the edge: biofilms developing in oscillating environmental conditions
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Exemplar Abstract for Kryptobacter tengchongensis Eloe-Fadrosh et al. 2016.
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Exemplar Abstract for Thermokryptus mobilis Eloe-Fadrosh et al. 2016.
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Exemplar Abstract for Chrysopegis kryptomonas (sic) Eloe-Fadrosh et al. 2016 and Chryseopegocella kryptomonas corrig. Eloe-Fadrosh et al. 2016.
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Nomenclature Abstract for Incertae sedis 386 Eloe-Fadrosh et al. 2016.
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Nomenclature Abstract for Kryptonium Eloe-Fadrosh et al. 2016.
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Nomenclature Abstract for Kryptobacter Eloe-Fadrosh et al. 2016.
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Nomenclature Abstract for Kryptobacter tengchongensis Eloe-Fadrosh et al. 2016.
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Nomenclature Abstract for Chrysopegis kryptomonas (sic) Eloe-Fadrosh et al. 2016.
dataset, January 2019
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Nomenclature Abstract for Chryseopegocella corrig. Eloe-Fadrosh et al. 2016.
dataset, January 2019
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Nomenclature Abstract for Chryseopegocella kryptomonas corrig. Eloe-Fadrosh et al. 2016.
dataset, January 2019
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Nomenclature Abstract for Kryptonium thompsonii corrig. Eloe-Fadrosh et al. 2016.
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Taxonomic Abstract for the class Incertae sedis 384 Eloe-Fadrosh et al. 2016
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Taxonomic Abstract for the species.
dataset, January 2019
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Taxonomic Abstract for the species.
dataset, January 2019
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Taxonomic Abstract for the species.
dataset, January 2019
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Unraveling the microbial and functional diversity of Coamo thermal spring in Puerto Rico using metagenomic library generation and shotgun sequencing
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Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
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Novel prosthecate bacteria from the candidate phylum Acetothermia
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Analyzing large scale genomic data on the cloud with Sparkhit
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The Evolution of Reverse Gyrase Suggests a Nonhyperthermophilic Last Universal Common Ancestor
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IMG/M: integrated genome and metagenome comparative data analysis system
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Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements
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The MAR databases: development and implementation of databases specific for marine metagenomics
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Novel prosthecate bacteria from the candidate phylum Acetothermia revealed by culture-independent genomics and advanced microscopy
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Bioremediation at a global scale: from the test tube to planet Earth
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Functional and taxonomic classification of a greenhouse water drain metagenome
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Freiburg RNA tools: a central online resource for RNA-focused research and teaching.
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Carbon and Sulfur Cycling below the Chemocline in a Meromictic Lake and the Identification of a Novel Taxonomic Lineage in the FCB Superphylum, Candidatus Aegiribacteria
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Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments
journal, January 2017
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Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures
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Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the Chlorobia and Ignavibacteria Species: Robust Demarcation of Two Family-Level Clades within the Order Chlorobiales and Proposal for the Family Chloroherpetonaceae fam. nov
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