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Title: Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages

Abstract

Background: As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown. Results: Here, we assembled 133 global clone libraries/studies and 19 publicly available genomes to profile these patterns for Woesearchaeota. Phylogenetic analysis shows a high diversity with 26 proposed subgroups for this recently discovered archaeal phylum, which are widely distributed in different biotopes but primarily in inland anoxic environments. Ecological patterns analysis and ancestor state reconstruction for specific subgroups reveal that oxic status of the environments is the key factor driving the distribution and evolutionary diversity of Woesearchaeota. A selective distribution to different biotopes and an adaptive colonization from anoxic to oxic environments can be proposed and supported by evidence of the presence of ferredoxin-dependent pathways in the genomes only from anoxic biotopes but not from oxic biotopes. Metabolic reconstructions support an anaerobic heterotrophic lifestyle with conspicuous metabolic deficiencies, suggesting the requirement for metabolic complementarity with other microbes. Both lineage abundance distribution and co-occurrence network analyses across diverse biotopes confirmed metabolic complementation and revealed a potential syntrophic relationship between Woesearchaeota and methanogens, which is supported by metabolic modeling. If correct, Woesearchaeotamore » may impact methanogenesis in inland ecosystems. Conclusions: The findings provide an ecological and evolutionary framework for Woesearchaeota at a global scale and indicate their potential ecological roles, especially in methanogenesis.« less

Authors:
 [1]; ORCiD logo [2];  [3];  [4];  [1];  [2];  [2];  [3];  [5]
  1. Univ. of Hong Kong (China)
  2. Shenzen Univ. (China)
  3. Univ. of California, Berkeley, CA (United States)
  4. Univ. of California, Berkeley, CA (United States); Univ. of Duisburg, Essen (Germany)
  5. City Univ. of Hong Kong (China); Univ. of Hong Kong (China)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1479416
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Microbiome
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2049-2618
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Liu, Xiaobo, Li, Meng, Castelle, Cindy J., Probst, Alexander J., Zhou, Zhichao, Pan, Jie, Liu, Yang, Banfield, Jillian F., and Gu, Ji-Dong. Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages. United States: N. p., 2018. Web. doi:10.1186/s40168-018-0488-2.
Liu, Xiaobo, Li, Meng, Castelle, Cindy J., Probst, Alexander J., Zhou, Zhichao, Pan, Jie, Liu, Yang, Banfield, Jillian F., & Gu, Ji-Dong. Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages. United States. doi:10.1186/s40168-018-0488-2.
Liu, Xiaobo, Li, Meng, Castelle, Cindy J., Probst, Alexander J., Zhou, Zhichao, Pan, Jie, Liu, Yang, Banfield, Jillian F., and Gu, Ji-Dong. Fri . "Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages". United States. doi:10.1186/s40168-018-0488-2. https://www.osti.gov/servlets/purl/1479416.
@article{osti_1479416,
title = {Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages},
author = {Liu, Xiaobo and Li, Meng and Castelle, Cindy J. and Probst, Alexander J. and Zhou, Zhichao and Pan, Jie and Liu, Yang and Banfield, Jillian F. and Gu, Ji-Dong},
abstractNote = {Background: As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown. Results: Here, we assembled 133 global clone libraries/studies and 19 publicly available genomes to profile these patterns for Woesearchaeota. Phylogenetic analysis shows a high diversity with 26 proposed subgroups for this recently discovered archaeal phylum, which are widely distributed in different biotopes but primarily in inland anoxic environments. Ecological patterns analysis and ancestor state reconstruction for specific subgroups reveal that oxic status of the environments is the key factor driving the distribution and evolutionary diversity of Woesearchaeota. A selective distribution to different biotopes and an adaptive colonization from anoxic to oxic environments can be proposed and supported by evidence of the presence of ferredoxin-dependent pathways in the genomes only from anoxic biotopes but not from oxic biotopes. Metabolic reconstructions support an anaerobic heterotrophic lifestyle with conspicuous metabolic deficiencies, suggesting the requirement for metabolic complementarity with other microbes. Both lineage abundance distribution and co-occurrence network analyses across diverse biotopes confirmed metabolic complementation and revealed a potential syntrophic relationship between Woesearchaeota and methanogens, which is supported by metabolic modeling. If correct, Woesearchaeota may impact methanogenesis in inland ecosystems. Conclusions: The findings provide an ecological and evolutionary framework for Woesearchaeota at a global scale and indicate their potential ecological roles, especially in methanogenesis.},
doi = {10.1186/s40168-018-0488-2},
journal = {Microbiome},
number = 1,
volume = 6,
place = {United States},
year = {2018},
month = {6}
}

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Works referenced in this record:

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
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