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Title: Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines

Abstract

Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absencemore » of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermace ae-related draft genome were indicative of a "salt-in" strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [1]
  1. Univ. of Amsterdam (Netherlands). Inst. for Biodiversity and Ecosystem Dynamics
  2. Miguel Hernandez Univ., San Juan de Alicante (Spain); Biology Centre of the Czech Academy of Sciences, Ceske Budejovice (Czech Republic)
  3. Miguel Hernandez Univ., San Juan de Alicante (Spain)
  4. Russian Academy of Sciences (RAS), Moscow (Russian Federation). Research Centre of Biotechnology; Delft Univ. of Technology (Netherlands). Dept. of Biotechnology
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  6. Univ. of Queensland, Brisbane (Australia). Australian Centre for Ecogenomics
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379108
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 7; Journal Issue: FEB; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES

Citation Formats

Vavourakis, Charlotte D., Ghai, Rohit, Rodriguez-Valera, Francisco, Sorokin, Dimitry Y., Tringe, Susannah G., Hugenholtz, Philip, and Muyzer, Gerard. Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. United States: N. p., 2016. Web. doi:10.3389/fmicb.2016.00211.
Vavourakis, Charlotte D., Ghai, Rohit, Rodriguez-Valera, Francisco, Sorokin, Dimitry Y., Tringe, Susannah G., Hugenholtz, Philip, & Muyzer, Gerard. Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. United States. doi:10.3389/fmicb.2016.00211.
Vavourakis, Charlotte D., Ghai, Rohit, Rodriguez-Valera, Francisco, Sorokin, Dimitry Y., Tringe, Susannah G., Hugenholtz, Philip, and Muyzer, Gerard. Thu . "Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines". United States. doi:10.3389/fmicb.2016.00211. https://www.osti.gov/servlets/purl/1379108.
@article{osti_1379108,
title = {Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines},
author = {Vavourakis, Charlotte D. and Ghai, Rohit and Rodriguez-Valera, Francisco and Sorokin, Dimitry Y. and Tringe, Susannah G. and Hugenholtz, Philip and Muyzer, Gerard},
abstractNote = {Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermace ae-related draft genome were indicative of a "salt-in" strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.},
doi = {10.3389/fmicb.2016.00211},
journal = {Frontiers in Microbiology},
number = FEB,
volume = 7,
place = {United States},
year = {Thu Feb 25 00:00:00 EST 2016},
month = {Thu Feb 25 00:00:00 EST 2016}
}

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Works referenced in this record:

KAAS: an automatic genome annotation and pathway reconstruction server
journal, May 2007

  • Moriya, Y.; Itoh, M.; Okuda, S.
  • Nucleic Acids Research, Vol. 35, Issue S2, p. W182-W185
  • DOI: 10.1093/nar/gkm321

The Pfam protein families database
journal, January 2004

  • Bateman, Alex; Coin, Lachlan; Durbin, Richard
  • Nucleic Acids Research, Vol. 32, Issue S1, p. D138-D141
  • DOI: 10.1093/nar/gkh121

Autotrophic CO2 fixation via the reductive tricarboxylic acid cycle in different lineages within the phylum Aquificae: evidence for two ways of citrate cleavage
journal, January 2007


The COG database: an updated version includes eukaryotes
journal, January 2003

  • Tatusov, Roman L.; Fedorova, Natalie D.; Jackson, John D.
  • BMC Bioinformatics, Vol. 4, Article No. 41
  • DOI: 10.1186/1471-2105-4-41