Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils

Lemos, Leandro Nascimento ; Manoharan, Lokeshwaran LU orcid ; Mendes, Lucas William ; Venturini, Andressa Monteiro ; Pylro, Victor Satler and Tsai, Siu Mui (2020) In Environmental microbiology reports 12(6). p.651-655
Abstract

Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here we analyzed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size 4-fold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also,... (More)

Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here we analyzed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size 4-fold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analyzing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil. This article is protected by copyright. All rights reserved.

(Less)
Please use this url to cite or link to this publication:
author
; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Environmental microbiology reports
volume
12
issue
6
pages
5 pages
publisher
Wiley-Blackwell
external identifiers
  • pmid:32815317
  • scopus:85090218320
ISSN
1758-2229
DOI
10.1111/1758-2229.12880
language
English
LU publication?
yes
additional info
This article is protected by copyright. All rights reserved.
id
458da253-e48b-4da0-946f-4cd85626d495
alternative location
https://sfamjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.12880
date added to LUP
2020-08-25 12:51:44
date last changed
2024-02-16 21:00:45
@article{458da253-e48b-4da0-946f-4cd85626d495,
  abstract     = {{<p>Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here we analyzed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size 4-fold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analyzing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil. This article is protected by copyright. All rights reserved.</p>}},
  author       = {{Lemos, Leandro Nascimento and Manoharan, Lokeshwaran and Mendes, Lucas William and Venturini, Andressa Monteiro and Pylro, Victor Satler and Tsai, Siu Mui}},
  issn         = {{1758-2229}},
  language     = {{eng}},
  number       = {{6}},
  pages        = {{651--655}},
  publisher    = {{Wiley-Blackwell}},
  series       = {{Environmental microbiology reports}},
  title        = {{Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils}},
  url          = {{http://dx.doi.org/10.1111/1758-2229.12880}},
  doi          = {{10.1111/1758-2229.12880}},
  volume       = {{12}},
  year         = {{2020}},
}