A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments.pdf (2.24 MB)
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A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments.

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journal contribution
posted on 18.09.2019, 08:36 by HJ Jones, E Kröber, J Stephenson, MA Mausz, E Jameson, A Millard, KJ Purdy, Y Chen
BACKGROUND: Coastal environments are dynamic and rapidly changing. Living organisms in coastal environments are known to synthesise large quantities of organic osmolytes, which they use to cope with osmotic stresses. The organic osmolyte glycine betaine (GBT) is ubiquitously found in marine biota from prokaryotic Bacteria and Archaea to coastal plants, marine protozoa, and mammals. In intertidal coastal sediment, GBT represents an important precursor of natural methane emissions and as much as 90% of total methane production in these ecosystems can be originated from methanogenesis from GBT and its intermediate trimethylamine through microbial metabolism. RESULTS: We set out to uncover the microorganisms responsible for methanogenesis from GBT using stable isotope labelling and metagenomics. This led to the recovery of a near-complete genome (2.3 Mbp) of a novel clostridial bacterium involved in anaerobic GBT degradation. Phylogenetic analyses of 16S rRNA gene, functional marker genes, and comparative genomics analyses all support the establishment of a novel family Candidatus 'Betainaceae' fam. nov. in Clostridiales and its role in GBT metabolism. CONCLUSIONS: Our comparative genomes and metagenomics analyses suggest that this bacterium is widely distributed in coastal salt marshes, marine sediments, and deep subsurface sediments, suggesting a key role of anaerobic GBT metabolism by this clostridial bacterium in these ecosystems.

Funding

This work was supported by the Natural Environment Research Council (NERC) through a PhD studentship (to HJJ) and a research grant (NE/I027061/1). We thank New England Biolabs for providing NEBNext Ultra II FS DNA Library Prep Kit before it was commercially available.

History

Citation

Microbiome, 2019, 7, Article number: 120

Author affiliation

/Organisation/COLLEGE OF LIFE SCIENCES/School of Medicine/Department of Infection, Immunity and Inflammation

Version

VoR (Version of Record)

Published in

Microbiome

Publisher

BMC (part of Springer Nature)

eissn

2049-2618

Acceptance date

13/08/2019

Copyright date

2019

Available date

18/09/2019

Publisher version

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0732-4

Notes

Read data have been submitted to the Sequence Read Archive (SRA) under the accession numbers SRR7964927, SRR7968363, SRR8068353, and SUB5592648.

Language

en

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