However, the key microbes and the metabolic pathways responsible for methanogenesis from choline are yet to be established.

Published online 2018 Sep 11.

PMCID: PMC6331629 PMID: 30206424 Deltaproteobacteria ( Pelobacter ) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment Eleanor Jameson, 1 Jason Stephenson, 1 Helen Jones, 1 Andrew Millard, 2 Anne-Kristin Kaster, 3 Kevin J.

Purdy 1 School of Life Sciences, University of Warwick, Warwick, CV4 7AL UK Find articles by Kevin J.

Purdy Ruth Airs 4 Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH UK Find articles by Ruth Airs J.

Colin Murrell 5 University of East Anglia, Norwich Research Park, Norfolk, Norwich, NR4 7TJ UK Find articles by J.

Received 2018 Jan 22; Revised 2018 Jun 11; Accepted 2018 Jul 26.

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In this study, we combine DNA stable isotope probing with high throughput sequencing of 16S rRNA genes and 13 C 2 -choline enriched metagenomes, followed by metagenome data assembly, to identify the key microbes responsible for methanogenesis from choline.

Microcosm incubation with 13 C 2 -choline leads to the formation of trimethylamine and subsequent methane production, suggesting that choline-dependent methanogenesis is a two-step process involving trimethylamine as the key intermediate.

Amplicon sequencing analysis identifies Deltaproteobacteria of the genera Pelobacter as the major choline utilizers.

Methanogenic Archaea of the genera Methanococcoides become enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine.

The binning of metagenomic DNA results in the identification of bins classified as Pelobacter and Methanococcoides.

Analyses of these bins reveal that Pelobacter have the genetic potential to degrade choline to trimethylamine using the choline-trimethylamine lyase pathway, whereas Methanococcoides are capable of methanogenesis using the pyrrolysine-containing trimethylamine methyltransferase pathway.

Together, our data provide a new insight on the diversity of choline utilizing organisms in coastal sediments and support a syntrophic relationship between Bacteria and Archaea as the dominant route for methanogenesis from choline in this environment.

Subject terms: Microbial ecology, Metagenomics Introduction Coastal saltmarsh sediments represent a highly productive environment, which are predominantly anaerobic and characterized by a high rate of carbon cycling 1.

These sediments represent a significant source of natural methane emissions, resulting from the degradation of organic matter, facilitated by the microorganisms inhabiting these sediments.

It has been estimated that between 35 and 90 of the methane production in intertidal mudflats and saltmarshes originates from trimethylamine (TMA) 2, 3.

Quaternary amines are precursors of TMA and are ubiquitous in marine microbes, where they act as osmolytes and essential cellular components.

Along with the common marine osmolyte glycine betaine (GBT), choline has been identified as an important precursor of TMA 2, 4.

Choline is a widely distributed component of membrane lipids and is essential for the formation of polar membrane lipids (such as phosphatidylcholine) in all eukaryotes and some bacteria 5.

Standing concentrations of choline have not been assessed in saltmarsh sediments due to the lack of a suitable method, however the concentrations of TMA range from low nanomolar (nM) in oceanic samples to low micromolar (mM) in marine and coastal sediments 6 8.

In marine and coastal systems, cycling of quaternary amines, such as choline, leads to atmospheric fluxes of methylated amines and methane, both of which are important climate-active trace gases 2, 7, 8.

In anaerobic marine and coastal sediments, methanogenesis is a key final step in organic matter degradation.

Saltmarsh Dmg 2