A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments

Abstract

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. Electronic supplementary material The online version of this article (10.1186/s40168-019-0732-4) contains supplementary material, which is available to authorized users.

Phosphorus stress induces the synthesis of novel glycolipids in Pseudomonas aeruginosa that confer protection against a last-resort antibiotic

“…The metatranscriptomics datasets of sputum samples obtained from a CF patient 7-days (SRX5145606) and 8days (SRX5145605) before death [26], CF patient G (SRR6833349) from Denmark [27] and a patient (SRR6833340) with chronic wound infection [27] were retrieved from the short reads archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra). The reads were downloaded using fastq-dump and mapped using the BBMap aligner as described previously [28]. Briefly, the SRA reads were mapped to the genome sequence of P. aeruginosa PAO1 using a stringent cut-off of minid = 0.97.…”

“…PA3219 has 47% protein sequence identity to PlcP from Phaeobacter sp. MED193 and 46% identity to PlcP from Sinorhizobium meliloti [26][27][28]. In these bacteria, PlcP is essential in the lipid remodelling pathway for the formation of the diacylglycerol (DAG) backbone, representing the essential intermediate for the production of glycolipids [32,33].…”

Structure and Function of the Arctic and Antarctic Marine Microbiota as Revealed by Metagenomics

“…Recent advances in molecular ecological techniques, such as metagenomics, have enabled a more efficient pathway to address the taxonomic and functional composition of marine microbiota, including the free-living bacterioplankton [1,2,3], the sediment-dwelling microbes [4,5,6], the surface-attached biofilms [7,8,9], and the animal-associated symbionts [10,11,12]. Pursuing the goal characterisng the global seawater microbiota, the Tara Oceans expedition collected seawater samples from 68 locations, representing all main oceanic regions, and performed metagenomics to study the structure and function of the global ocean microbiota [1].…”

Betaine Modulates Rumen Archaeal Community and Functioning during Heat and Osmotic Stress Conditions In Vitro

“…In the liquid phase, Methanobrevibacter had positive correlation with [2H] utilized to form CH 4 , which is a more reliable estimator of archaea activity compared to CH 4 formation itself, as CH 4 is also a product of betaine degradation [ 46 ]. The stoichiometric production of CH 4 is 1 mole per mole of betaine degradation [ 47 ]. Nevertheless, Methanobrevibacter also possessed a strong positive correlation with CH 4 formation contrary to Methanosphaera , which was negatively correlated with CH 4 formation in the liquid phase.…”