Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil
Abstract
Summary Members of the bacterial candidate phylum WPS‐2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron–sulfur spring, we found that WPS‐2 comprised up to 24% of the bacterial community and up to 10 8 cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus‐level cluster ( Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome‐assembled genomes (MAGs). Surprisingly, given the abundance of WPS‐2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi , Actinobacteria , and candidate phylum AD3 (or Dormibacterota) co‐occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS‐2 includes bacteria with diverse metabolic capabilities.
- Authors:
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[1];
[1];
[2];
[2];
[1];
[2];
[2];
[2];
[3];
[2];
[1]
- Univ. of Calgary, AB (Canada)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Geological Survey of Canada, Calgary, AB (Canada)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); Natural Sciences and Engineering Research Council of Canada (NERSC)
- OSTI Identifier:
- 1725806
- Alternate Identifier(s):
- OSTI ID: 1635291
- Grant/Contract Number:
- AC02-05CH11231; 2019-06265
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Environmental Microbiology
- Additional Journal Information:
- Journal Volume: 22; Journal Issue: 8; Journal ID: ISSN 1462-2912
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Sheremet, Andriy, Jones, Gareth M., Jarett, Jessica, Bowers, Robert M., Bedard, Isaac, Culham, Cassandra, Eloe‐Fadrosh, Emiley A., Ivanova, Natalia, Malmstrom, Rex R., Grasby, Stephen E., Woyke, Tanja, and Dunfield, Peter F. Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil. United States: N. p., 2020.
Web. doi:10.1111/1462-2920.15054.
Sheremet, Andriy, Jones, Gareth M., Jarett, Jessica, Bowers, Robert M., Bedard, Isaac, Culham, Cassandra, Eloe‐Fadrosh, Emiley A., Ivanova, Natalia, Malmstrom, Rex R., Grasby, Stephen E., Woyke, Tanja, & Dunfield, Peter F. Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil. United States. https://doi.org/10.1111/1462-2920.15054
Sheremet, Andriy, Jones, Gareth M., Jarett, Jessica, Bowers, Robert M., Bedard, Isaac, Culham, Cassandra, Eloe‐Fadrosh, Emiley A., Ivanova, Natalia, Malmstrom, Rex R., Grasby, Stephen E., Woyke, Tanja, and Dunfield, Peter F. Sun .
"Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil". United States. https://doi.org/10.1111/1462-2920.15054. https://www.osti.gov/servlets/purl/1725806.
@article{osti_1725806,
title = {Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil},
author = {Sheremet, Andriy and Jones, Gareth M. and Jarett, Jessica and Bowers, Robert M. and Bedard, Isaac and Culham, Cassandra and Eloe‐Fadrosh, Emiley A. and Ivanova, Natalia and Malmstrom, Rex R. and Grasby, Stephen E. and Woyke, Tanja and Dunfield, Peter F.},
abstractNote = {Summary Members of the bacterial candidate phylum WPS‐2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron–sulfur spring, we found that WPS‐2 comprised up to 24% of the bacterial community and up to 10 8 cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus‐level cluster ( Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome‐assembled genomes (MAGs). Surprisingly, given the abundance of WPS‐2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi , Actinobacteria , and candidate phylum AD3 (or Dormibacterota) co‐occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS‐2 includes bacteria with diverse metabolic capabilities.},
doi = {10.1111/1462-2920.15054},
journal = {Environmental Microbiology},
number = 8,
volume = 22,
place = {United States},
year = {Sun Jun 28 00:00:00 EDT 2020},
month = {Sun Jun 28 00:00:00 EDT 2020}
}
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