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Title: Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

Abstract

Summary Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large‐scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 ( n  = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low‐ and high‐affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Among many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic nitrogen sources (such as via extracellular peptidases), was detected – both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H 2 , now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large‐scale acidobacteria genome analysis reveal traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment.

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [1]; ORCiD logo [3]; ORCiD logo [1]
+ Show Author Affiliations
  1. Division of Microbial Ecology, Department of Microbiology and Ecosystem Science Research Network “Chemistry Meets Biology”, University of Vienna Vienna Austria
  2. Department of Energy Joint Genome Institute Walnut Creek CA USA
  3. Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science Research Network “Chemistry Meets Biology”, University of Vienna Vienna Austria
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE
OSTI Identifier:
1425534
Alternate Identifier(s):
OSTI ID: 1425535; OSTI ID: 1529108
Grant/Contract Number:  
DE‐AC02–05CH11231; AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Name: Environmental Microbiology Journal Volume: 20 Journal Issue: 3; Journal ID: ISSN 1462-2912
Publisher:
Wiley-Blackwell
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Eichorst, Stephanie A., Trojan, Daniela, Roux, Simon, Herbold, Craig, Rattei, Thomas, and Woebken, Dagmar. Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. United Kingdom: N. p., 2018. Web. doi:10.1111/1462-2920.14043.
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Eichorst, Stephanie A., Trojan, Daniela, Roux, Simon, Herbold, Craig, Rattei, Thomas, & Woebken, Dagmar. Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. United Kingdom. https://doi.org/10.1111/1462-2920.14043
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Eichorst, Stephanie A., Trojan, Daniela, Roux, Simon, Herbold, Craig, Rattei, Thomas, and Woebken, Dagmar. Mon . "Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments". United Kingdom. https://doi.org/10.1111/1462-2920.14043.
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@article{osti_1425534,
title = {Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments},
author = {Eichorst, Stephanie A. and Trojan, Daniela and Roux, Simon and Herbold, Craig and Rattei, Thomas and Woebken, Dagmar},
abstractNote = {Summary Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large‐scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 ( n  = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low‐ and high‐affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Among many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic nitrogen sources (such as via extracellular peptidases), was detected – both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H 2 , now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large‐scale acidobacteria genome analysis reveal traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment.},
doi = {10.1111/1462-2920.14043},
journal = {Environmental Microbiology},
number = 3,
volume = 20,
place = {United Kingdom},
year = {Mon Mar 12 00:00:00 EDT 2018},
month = {Mon Mar 12 00:00:00 EDT 2018}
}
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https://doi.org/10.1111/1462-2920.14043
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Proteolytic activity in soil: A review
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Nitrate reductases: Structure, functions, and effect of stress factors
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Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools
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Genetic and life-history traits associated with the distribution of prophages in bacteria
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Cytochrome bd oxidase and bacterial tolerance to oxidative and nitrosative stress
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Isolation and Characterization of Soil Bacteria That Define Terriglobus gen. nov., in the Phylum Acidobacteria
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Prokaryotic Nitrate Reduction: Molecular Properties and Functional Distinction among Bacterial Nitrate Reductases
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Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds
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Seasonal Changes in an Alpine Soil Bacterial Community in the Colorado Rocky Mountains
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Identification of Cellulose-Responsive Bacterial and Fungal Communities in Geographically and Edaphically Different Soils by Using Stable Isotope Probing
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Viral dark matter and virus–host interactions resolved from publicly available microbial genomes
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Genomic insights that advance the species definition for prokaryotes
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Comparative genomic and physiological analysis provides insights into the role of Acidobacteria in organic carbon utilization in Arctic tundra soils
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Mechanisms for Accessing Insoluble Fe(III) Oxide during Dissimilatory Fe(III) Reduction by Geothrix fermentans
journal, May 2002

Cryptic prophages help bacteria cope with adverse environments
journal, December 2010

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