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Title: Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs

Abstract

Recent progress based on single-cell genomics and metagenomic investigations of archaea in a variety of extreme environments has led to significant advances in our understanding of the diversity, evolution, and metabolic potential of archaea, yet the vast majority of archaeal diversity remains undersampled. In this work, we coordinated single-cell genomics with metagenomics in order to construct a near-complete genome from a deeply branching uncultivated archaeal lineage sampled from Great Boiling Spring (GBS) in the U.S. Great Basin, Nevada. This taxon is distantly related (distinct families) to an archaeal genome, designated “Novel Archaeal Group 1” (NAG1), which was extracted from a metagenome recovered from an acidic iron spring in Yellowstone National Park (YNP). We compared the metabolic predictions of the NAG1 lineage to better understand how these archaea could inhabit such chemically distinct environments. Similar to the NAG1 population previously studied in YNP, the NAG1 population from GBS is predicted to utilize proteins as a primary carbon source, ferment simple carbon sources, and use oxygen as a terminal electron acceptor under oxic conditions. However, GBS NAG1 populations contained distinct genes involved in central carbon metabolism and electron transfer, including nitrite reductase, which could confer the ability to reduce nitrite under anaerobicmore » conditions. Despite inhabiting chemically distinct environments with large variations in pH, GBS NAG1 populations shared many core genomic and metabolic features with the archaeon identified from YNP, yet were able to carve out a distinct niche at GBS.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [4];  [5]
  1. Northern Illinois Univ., DeKalb, IL (United States); Bigelow Lab. for Ocean Sciences, East Boothbay, ME (United States)
  2. California State Univ. (CalState), San Bernardino, CA (United States); Univ. of Nevada, Las Vegas, NV (United States)
  3. Univ. of Nevada, Las Vegas, NV (United States); Université Paris-Saclay, Jouy-en-Josas (France). Institut National de la Recherche Agronomique (INRA)
  4. Univ. of Nevada, Las Vegas, NV (United States)
  5. Northern Illinois Univ., DeKalb, IL (United States)
  6. Bigelow Lab. for Ocean Sciences, East Boothbay, ME (United States)
Publication Date:
Research Org.:
Nevada System of Higher Education (NSHE), Las Vegas, NV (United States); Univ. of California, Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE); USDOE Office of Science (SC)
OSTI Identifier:
1510510
Grant/Contract Number:  
EE0000716; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 8; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; extreme microbiology; microbial ecology; uncultivated archaea; NAG1 lineage; Great Boiling Spring

Citation Formats

Becraft, Eric D., Dodsworth, Jeremy A., Murugapiran, Senthil K., Thomas, Scott C., Ohlsson, J. Ingemar, Stepanauskas, Ramunas, Hedlund, Brian P., and Swingley, Wesley D. Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs. United States: N. p., 2017. Web. doi:10.3389/fmicb.2017.02082.
Becraft, Eric D., Dodsworth, Jeremy A., Murugapiran, Senthil K., Thomas, Scott C., Ohlsson, J. Ingemar, Stepanauskas, Ramunas, Hedlund, Brian P., & Swingley, Wesley D. Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs. United States. doi:10.3389/fmicb.2017.02082.
Becraft, Eric D., Dodsworth, Jeremy A., Murugapiran, Senthil K., Thomas, Scott C., Ohlsson, J. Ingemar, Stepanauskas, Ramunas, Hedlund, Brian P., and Swingley, Wesley D. Tue . "Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs". United States. doi:10.3389/fmicb.2017.02082. https://www.osti.gov/servlets/purl/1510510.
@article{osti_1510510,
title = {Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs},
author = {Becraft, Eric D. and Dodsworth, Jeremy A. and Murugapiran, Senthil K. and Thomas, Scott C. and Ohlsson, J. Ingemar and Stepanauskas, Ramunas and Hedlund, Brian P. and Swingley, Wesley D.},
abstractNote = {Recent progress based on single-cell genomics and metagenomic investigations of archaea in a variety of extreme environments has led to significant advances in our understanding of the diversity, evolution, and metabolic potential of archaea, yet the vast majority of archaeal diversity remains undersampled. In this work, we coordinated single-cell genomics with metagenomics in order to construct a near-complete genome from a deeply branching uncultivated archaeal lineage sampled from Great Boiling Spring (GBS) in the U.S. Great Basin, Nevada. This taxon is distantly related (distinct families) to an archaeal genome, designated “Novel Archaeal Group 1” (NAG1), which was extracted from a metagenome recovered from an acidic iron spring in Yellowstone National Park (YNP). We compared the metabolic predictions of the NAG1 lineage to better understand how these archaea could inhabit such chemically distinct environments. Similar to the NAG1 population previously studied in YNP, the NAG1 population from GBS is predicted to utilize proteins as a primary carbon source, ferment simple carbon sources, and use oxygen as a terminal electron acceptor under oxic conditions. However, GBS NAG1 populations contained distinct genes involved in central carbon metabolism and electron transfer, including nitrite reductase, which could confer the ability to reduce nitrite under anaerobic conditions. Despite inhabiting chemically distinct environments with large variations in pH, GBS NAG1 populations shared many core genomic and metabolic features with the archaeon identified from YNP, yet were able to carve out a distinct niche at GBS.},
doi = {10.3389/fmicb.2017.02082},
journal = {Frontiers in Microbiology},
number = ,
volume = 8,
place = {United States},
year = {2017},
month = {10}
}

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Figures / Tables:

Table 1 Table 1: NAG1 statistics for the Great Boiling Spring (GBS) single assembled genome (SAG) co-assembly, the GBS MLP metagenome assembly, and the Yellowstone National Park (YNP) metagenome assembly (Kozubal et al., 2013).

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