Ammonia‐oxidising archaea living at low pH: Insights from comparative genomics
Abstract
Summary Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus ( Ca . N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca . Nitrosotalea strains, extracted an almost complete Ca . Nitrosotalea metagenome‐assembled genome from an acidic fen, and performed comparative genomics of the four Ca . Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca . Nitrosotalea strains represent separate species within the genus. The four Ca . Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia‐oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca . Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive successmore »
- Authors:
-
[1];
[2];
[1];
[1];
[1];
[7]
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science Research Network Chemistry meets Microbiology, University of Vienna Vienna Austria
- School of Biological Sciences University of East Anglia, Norwich Research Park Norwich NR4 7TJ UK, School of Biological Sciences University of Aberdeen, Cruickshank Building, St Machar Drive Aberdeen AB24 3UU UK
- Department of Microbiology Chungbuk National University, 1 Chungdae‐ro, Seowon‐Gu Cheongju 362‐763 South Korea
- Department of Molecular Systems Biology Helmholtz‐Centre for Environmental Research‐UFZ Leipzig 04318 Germany
- Department of Microorganisms Leibniz Institute DSMZ ‐ German Collection of Microorganisms and Cell Cultures Inhoffenstr. 7B Braunschweig 38124 Germany
- Department of Botany and Plant Pathology Oregon State University, 2082 Cordley Hall Corvallis OR 97331‐2902 USA
- School of Biological Sciences University of Aberdeen, Cruickshank Building, St Machar Drive Aberdeen AB24 3UU UK
- Laboratoire Ampère, École Centrale de Lyon, L'Université de Lyon, 36 avenue Guy de Collongue 69134 Ecully CEDEX France
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1411259
- Alternate Identifier(s):
- OSTI ID: 1411477; OSTI ID: 1625851
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Environmental Microbiology
- Additional Journal Information:
- Journal Name: Environmental Microbiology Journal Volume: 19 Journal Issue: 12; Journal ID: ISSN 1462-2912
- Publisher:
- Wiley-Blackwell
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- Microbiology
Citation Formats
Herbold, Craig W., Lehtovirta‐Morley, Laura E., Jung, Man‐Young, Jehmlich, Nico, Hausmann, Bela, Han, Ping, Loy, Alexander, Pester, Michael, Sayavedra‐Soto, Luis A., Rhee, Sung‐Keun, Prosser, James I., Nicol, Graeme W., Wagner, Michael, and Gubry‐Rangin, Cécile. Ammonia‐oxidising archaea living at low pH: Insights from comparative genomics. United Kingdom: N. p., 2017.
Web. doi:10.1111/1462-2920.13971.
Herbold, Craig W., Lehtovirta‐Morley, Laura E., Jung, Man‐Young, Jehmlich, Nico, Hausmann, Bela, Han, Ping, Loy, Alexander, Pester, Michael, Sayavedra‐Soto, Luis A., Rhee, Sung‐Keun, Prosser, James I., Nicol, Graeme W., Wagner, Michael, & Gubry‐Rangin, Cécile. Ammonia‐oxidising archaea living at low pH: Insights from comparative genomics. United Kingdom. https://doi.org/10.1111/1462-2920.13971
Herbold, Craig W., Lehtovirta‐Morley, Laura E., Jung, Man‐Young, Jehmlich, Nico, Hausmann, Bela, Han, Ping, Loy, Alexander, Pester, Michael, Sayavedra‐Soto, Luis A., Rhee, Sung‐Keun, Prosser, James I., Nicol, Graeme W., Wagner, Michael, and Gubry‐Rangin, Cécile. Mon .
"Ammonia‐oxidising archaea living at low pH: Insights from comparative genomics". United Kingdom. https://doi.org/10.1111/1462-2920.13971.
@article{osti_1411259,
title = {Ammonia‐oxidising archaea living at low pH: Insights from comparative genomics},
author = {Herbold, Craig W. and Lehtovirta‐Morley, Laura E. and Jung, Man‐Young and Jehmlich, Nico and Hausmann, Bela and Han, Ping and Loy, Alexander and Pester, Michael and Sayavedra‐Soto, Luis A. and Rhee, Sung‐Keun and Prosser, James I. and Nicol, Graeme W. and Wagner, Michael and Gubry‐Rangin, Cécile},
abstractNote = {Summary Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus ( Ca . N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca . Nitrosotalea strains, extracted an almost complete Ca . Nitrosotalea metagenome‐assembled genome from an acidic fen, and performed comparative genomics of the four Ca . Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca . Nitrosotalea strains represent separate species within the genus. The four Ca . Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia‐oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca . Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca . Nitrosotalea lineage in acidic environments.},
doi = {10.1111/1462-2920.13971},
journal = {Environmental Microbiology},
number = 12,
volume = 19,
place = {United Kingdom},
year = {Mon Dec 04 00:00:00 EST 2017},
month = {Mon Dec 04 00:00:00 EST 2017}
}
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https://doi.org/10.1111/1462-2920.13971
https://doi.org/10.1111/1462-2920.13971
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Cited by: 63 works
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Figures / Tables:
Fig. 1: Heat maps showing pairwise ANI and AAI values inferred from the four Ca. Nitrosotalea genomes (bold) and other available Thaumarchaeota genomes. Dendrograms were calculated by hierarchical clustering (hclust, method = complete linkage) in R with distances calculated as (100% – % identity, that is, 100% ANI = 0more »
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