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

Liu, Xiaobo; Li, Meng; Castelle, Cindy J.; Probst, Alexander J.; Zhou, Zhichao; Pan, Jie; Liu, Yang; Banfield, Jillian F.; Gu, Ji-Dong

doi:10.1186/s40168-018-0488-2

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

Journal Article · Fri Jun 08 00:00:00 EDT 2018 · Microbiome

DOI:https://doi.org/10.1186/s40168-018-0488-2· OSTI ID:1479416

Liu, Xiaobo ^[1];

^[2]; Castelle, Cindy J. ^[3]; Probst, Alexander J. ^[4]; Zhou, Zhichao ^[1]; Pan, Jie ^[2]; Liu, Yang ^[2]; Banfield, Jillian F. ^[3]; Gu, Ji-Dong ^[5]

Univ. of Hong Kong (China)
Shenzen Univ. (China)
Univ. of California, Berkeley, CA (United States)
Univ. of California, Berkeley, CA (United States); Univ. of Duisburg, Essen (Germany)
City Univ. of Hong Kong (China); Univ. of Hong Kong (China)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1479416

Journal Information:: Microbiome, Vol. 6, Issue 1; ISSN 2049-2618

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 131 works

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Additional file 2: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465692.v1 The current record is supplemented by this dataset	dataset	June 2018
Additional file 3: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/M9.FIGSHARE.6465707 The current record is supplemented by this dataset	dataset	June 2018
Additional file 3: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465707.v1 The current record is supplemented by this dataset	dataset	June 2018
Additional file 4: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/M9.FIGSHARE.6465719 The current record is supplemented by this dataset	dataset	June 2018
Additional file 4: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465719.v1 The current record is supplemented by this dataset	dataset	June 2018
Additional file 5: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465734.v1 The current record is supplemented by this dataset	dataset	June 2018
Additional file 6: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465752 The current record is supplemented by this preprint	preprint	June 2018
Additional file 6: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465752.v1 The current record is supplemented by this preprint	preprint	June 2018
Additional file 7: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/M9.FIGSHARE.6465770 The current record is supplemented by this dataset	dataset	June 2018
Additional file 7: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465770.v1 The current record is supplemented by this dataset	dataset	June 2018
Additional file 8: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465791 The current record is supplemented by this dataset	dataset	June 2018
Additional file 8: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465791.v1 The current record is supplemented by this dataset	dataset	June 2018
Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages [Supplemental Data] Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/M9.FIGSHARE.C.4128482 The current record is supplemented by this collection	collection	June 2018
Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages [Supplemental Data] Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.c.4128482.v1 The current record is supplemented by this collection	collection	June 2018
Additional file 1: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465674.v1 The current record is supplemented by this figure	figure	June 2018
Additional file 2: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465692 The current record is supplemented by this dataset	dataset	June 2018
Additional file 5: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465734 The current record is supplemented by this dataset	dataset	June 2018
Additional file 1: of Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages Li, Meng; Castelle, Cindy; Probst, Alexander https://doi.org/10.6084/m9.figshare.6465674 The current record is supplemented by this figure	figure	June 2018