Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments

Glass, Jennifer B.; Ranjan, Piyush; Kretz, Cécilia B.; Nunn, Brook L.; Johnson, Abigail M.; Xu, Manlin; McManus, James; Stewart, Frank J.

doi:10.1101/536078

Cited by 12 publications

(26 citation statements)

References 126 publications

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“…In addition, many members of the Firmicutes are able to form spores. Candidatus Atribacteria, which dominated in the core C3, were recently described to harbour functions for survival under extreme conditions like high salinities and cold temperatures (Glass et al, 2019). They are further one of the cosmopolitan groups in the sub-seafloor and dominate the bacterial community in deep anoxic sediments with low organic carbon contents (Orsi, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…About 88 % of this carbon occurs in permafrost soils and deposits (Tarnocai et al, 2009). Permafrost harbours numerous ancient but viable cells (Bischoff et al, 2013;Gilichinsky et al, 2008;Graham et al, 2012;Koch et al, 2009;Mackelprang et al, 2011;Wagner et al, 2007) that can remain active at extremely low temperatures (Hultman et al, 2015;Rivkina et al, 2000). With increasing permafrost age, microbial communities show adaptations to the permafrost biophysical environment and specialize towards long-term survival strategies such as increased dormancy, DNA repair, or stress response (Johnson et al, 2007;Mackelprang et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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Microbial community composition and abundance after millennia of submarine permafrost warming

et al. 2019

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Abstract. Warming of the Arctic led to an increase in permafrost temperatures by about 0.3 ∘C during the last decade. Permafrost warming is associated with increasing sediment water content, permeability, and diffusivity and could in the long term alter microbial community composition and abundance even before permafrost thaws. We studied the long-term effect (up to 2500 years) of submarine permafrost warming on microbial communities along an onshore–offshore transect on the Siberian Arctic Shelf displaying a natural temperature gradient of more than 10 ∘C. We analysed the in situ development of bacterial abundance and community composition through total cell counts (TCCs), quantitative PCR of bacterial gene abundance, and amplicon sequencing and correlated the microbial community data with temperature, pore water chemistry, and sediment physicochemical parameters. On timescales of centuries, permafrost warming coincided with an overall decreasing microbial abundance, whereas millennia after warming microbial abundance was similar to cold onshore permafrost. In addition, the dissolved organic carbon content of all cores was lowest in submarine permafrost after millennial-scale warming. Based on correlation analysis, TCC, unlike bacterial gene abundance, showed a significant rank-based negative correlation with increasing temperature, while bacterial gene copy numbers showed a strong negative correlation with salinity. Bacterial community composition correlated only weakly with temperature but strongly with the pore water stable isotopes δ18O and δD, as well as with depth. The bacterial community showed substantial spatial variation and an overall dominance of Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, and Proteobacteria, which are amongst the microbial taxa that were also found to be active in other frozen permafrost environments. We suggest that, millennia after permafrost warming by over 10 ∘C, microbial community composition and abundance show some indications for proliferation but mainly reflect the sedimentation history and paleoenvironment and not a direct effect through warming.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Microbial community composition and abundance after millennia of submarine permafrost warming

et al. 2019

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“…In addition, many members of the Firmicutes are able to form spores. Atribacteria, which dominated in the core C3, were recently described to harbor functions for survival under extreme conditions like high salinities and cold temperatures (Glass et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Microbial community composition and abundance after millennia of submarine permafrost warming

Mitzscherling¹,

Horn²,

Winterfeld³

et al. 2019

Preprint

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Abstract. Warming of the Arctic led to an increase of permafrost temperatures by about 0.3&#8201;&#176;C during the last decade. Permafrost warming is associated with increasing sediment water content, permeability and diffusivity and could on the long-term alter microbial community composition and abundance even before permafrost thaws. We studied the long-term effect (up to 2500 years) of submarine permafrost warming on microbial communities along an onshore-offshore transect on the Siberian Arctic Shelf displaying a natural temperature gradient of more than 10&#8201;&#176;C. We analysed the in-situ development of bacterial abundance and community composition through total cell counts (TCC), quantitative PCR of bacterial gene abundance and amplicon sequencing, and correlated the microbial community data with temperature, pore water chemistry and sediment physicochemical parameters. On time-scales of centuries, permafrost warming coincided with an overall decreasing microbial abundance while millennia after warming microbial abundance was similar to cold onshore permafrost and DOC content was least. Based on correlation analysis TCC unlike bacterial gene abundance showed a significant rank-based negative correlation with increasing temperature while both TCC and bacterial gene copy numbers showed a negative correlation with salinity. Bacterial community composition correlated only weakly with temperature but strongly with pore-water stable isotope signatures and depth, while it showed no correlation with salinity. Microbial community composition showed substantial spatial variation and an overall dominance of Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes and Proteobacteria which are amongst the microbial taxa that were found to be active in other frozen permafrost environments as well. We suggest that, millennia after permafrost warming by over 10&#8201;&#176;C, microbial community composition and abundance show some indications for proliferation but mainly reflect the sedimentation history and paleo-environment and not a direct effect through warming.

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“…To benchmark and test the performance of METABOLIC in different environments, eight datasets of metagenomes and metagenomic reads from marine, terrestrial, and human environments were used. These included marine subsurface sediments [45] (Deep biosphere beneath Hydrate Ridge offshore Oregon), freshwater lake [46] (Lake Tanganyika, eastern Africa), colorectal cancer (CRC) patient gut [47], healthy human gut [47], deep-sea hydrothermal vent (Guaymas Basin, Gulf of California) [43], terrestrial subsurface sediments and water (Ri e, CO, USA) [2], meadow soils [48] (Angelo Coastal Range Reserve, CA, USA), and advanced water treatment facility [49] (Groundwater Replenishment System, Orange County, CA, USA). Default settings were used for running METABOLIC-C.…”

Section: Test Of Software Performance For Different Environmentsmentioning

confidence: 99%

METABOLIC: High-throughput Profiling of Microbial Genomes for Functional Traits, Biogeochemistry, and Community-scale Metabolic Networks

Zhou

Tran

Breister

et al. 2020

Preprint

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Background: Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent, however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and contributions to biogeochemical cycling. Results: We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, identification of metabolism markers, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the community, potential microbial metabolic handoffs and metabolite exchange, and calculation of microbial community contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or from single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, and community-scale metabolic networks using a newly defined metric ‘MN-score’ (metabolic network score). METABOLIC takes ~3 hours with 40 CPU threads to process ~100 genomes and metagenomic reads within which the most compute-demanding part of hmmsearch takes ~45 mins, while it takes ~5 hours to complete hmmsearch for ~3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut.Conclusion: METABOLIC enables consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available at https://github.com/AnantharamanLab/METABOLIC under GPLv3.

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Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments

Cited by 12 publications

References 126 publications

Microbial community composition and abundance after millennia of submarine permafrost warming

Microbial community composition and abundance after millennia of submarine permafrost warming

Microbial community composition and abundance after millennia of submarine permafrost warming

METABOLIC: High-throughput Profiling of Microbial Genomes for Functional Traits, Biogeochemistry, and Community-scale Metabolic Networks

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