Genome-Resolved Metagenomics Informs the Functional Ecology of Uncultured Acidobacteria in Redox Oscillated Sphagnum Peat
- PMID: 36036503
- PMCID: PMC9599518
- DOI: 10.1128/msystems.00055-22
Genome-Resolved Metagenomics Informs the Functional Ecology of Uncultured Acidobacteria in Redox Oscillated Sphagnum Peat
Abstract
Understanding microbial niche differentiation along ecological and geochemical gradients is critical for assessing the mechanisms of ecosystem response to hydrologic variation and other aspects of global change. The lineage-specific biogeochemical roles of the widespread phylum Acidobacteria in hydrologically sensitive ecosystems, such as peatlands, are poorly understood. Here, we demonstrate that Acidobacteria sublineages in Sphagnum peat respond differentially to redox fluctuations due to variable oxygen (O2) availability, a typical feature of hydrologic variation. Our genome-centric approach disentangles the mechanisms of niche differentiation between the Acidobacteria genera Holophaga and Terracidiphilus in response to the transient O2 exposure of peat in laboratory incubations. Interlineage functional diversification explains the enrichment of the otherwise rare Holophaga in anoxic peat after transient O2 exposure in comparison to Terracidiphilus dominance in continuously anoxic peat. The observed niche differentiation of the two lineages is linked to differences in their carbon degradation potential. Holophaga appear to be primarily reliant on carbohydrate oligomers and amino acids, produced during the prior period of O2 exposure via the O2-stimulated breakdown of peat carbon, rich in complex aromatics and carbohydrate polymers. In contrast, Terracidiphilus genomes are enriched in diverse respiratory hydrogenases and carbohydrate active enzymes, enabling the degradation of complex plant polysaccharides into monomers and oligomers for fermentation. We also present the first evidence for the potential contribution of Acidobacteria in peat nitrogen fixation. In addition to canonical molybdenum-based diazotrophy, the Acidobacteria genomes harbor vanadium and iron-only alternative nitrogenases. Together, the results better inform the different functional roles of Acidobacteria in peat biogeochemistry under global change. IMPORTANCE Acidobacteria are among the most widespread and abundant members of the soil bacterial community, yet their ecophysiology remains largely underexplored. In acidic peat systems, Acidobacteria are thought to perform key biogeochemical functions, yet the mechanistic links between the phylogenetic and metabolic diversity within this phylum and peat carbon transformations remain unclear. Here, we employ genomic comparisons of Acidobacteria subgroups enriched in laboratory incubations of peat under variable O2 availability to disentangle the lineage-specific functional roles of these microorganisms in peat carbon transformations. Our genome-centric approach reveals that the diversification of Acidobacteria subpopulations across transient O2 exposure is linked to differences in their carbon substrate preferences. We also identify a previously unknown functional potential for biological nitrogen fixation in these organisms. This has important implications for carbon, nitrogen, and trace metal cycling in peat systems.
Keywords: Acidobacteria; metagenomics; peatland biogeochemical cycling; peatland microbiome; soil redox dynamics.
Conflict of interest statement
The authors declare no conflict of interest.
Figures
![FIG 1](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/9599518/bin/msystems.00055-22-f001.gif)
![FIG 2](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/9599518/bin/msystems.00055-22-f002.gif)
![FIG 3](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/9599518/bin/msystems.00055-22-f003.gif)
![FIG 4](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/9599518/bin/msystems.00055-22-f004.gif)
Similar articles
-
The role of oxygen in stimulating methane production in wetlands.Glob Chang Biol. 2021 Nov;27(22):5831-5847. doi: 10.1111/gcb.15831. Epub 2021 Aug 18. Glob Chang Biol. 2021. PMID: 34409684 Free PMC article.
-
Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria) Expands the Metabolic Capacities of the Phylum and Highlights Adaptations to Terrestrial Habitats.Appl Environ Microbiol. 2021 Aug 11;87(17):e0094721. doi: 10.1128/AEM.00947-21. Epub 2021 Aug 11. Appl Environ Microbiol. 2021. PMID: 34160232 Free PMC article.
-
Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in Sphagnum-Dominated Northern Wetlands.Appl Environ Microbiol. 2015 Sep;81(18):6333-44. doi: 10.1128/AEM.00324-15. Epub 2015 Jul 6. Appl Environ Microbiol. 2015. PMID: 26150465 Free PMC article.
-
Planctomycetes in boreal and subarctic wetlands: diversity patterns and potential ecological functions.FEMS Microbiol Ecol. 2019 Feb 1;95(2). doi: 10.1093/femsec/fiy227. FEMS Microbiol Ecol. 2019. PMID: 30476049 Review.
-
The Sphagnum microbiome: new insights from an ancient plant lineage.New Phytol. 2016 Jul;211(1):57-64. doi: 10.1111/nph.13993. Epub 2016 May 13. New Phytol. 2016. PMID: 27173909 Review.
Cited by
-
Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities.mSystems. 2023 Jun 29;8(3):e0123822. doi: 10.1128/msystems.01238-22. Epub 2023 Jun 5. mSystems. 2023. PMID: 37272710 Free PMC article.
References
-
- Ludwig W, Bauer SH, Bauer M, Held I, Kirchhof G, Schulze R, Huber I, Spring S, Hartmann A, Schleifer KH. 1997. Detection and in situ identification of representatives of a widely distributed new bacterial phylum. FEMS Microbiol Lett 153:181–190. doi:10.1111/j.1574-6968.1997.tb10480.x. - DOI - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources