Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities

Abstract

In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior data, suggesting that multiple functional guilds feed on methane, likely through guild-to-guild carbon transfer, and potentially through intraguild and intraspecies interactions. We observed that, under two simulated dioxygen partial pressures—low versus high—community trajectories were different, with considerable variability among the replicates. In all microcosms, four major functional guilds were prominently present, representing Methylococcaceae (the true methanotrophs), Methylophilaceae (the nonmethanotrophic methylotrophs), Burkholderiales, and Bacteroidetes. Additional functional guilds were detected in multiple samples, such as members of Opitutae, as well as the predatory species, suggesting additional complexity for methane-oxidizing communities. Metatranscriptomic analysis suggested simultaneous expression of the two alternative types of methanol dehydrogenases in both Methylococcaceae and Methylophilaceae, while high expression of the oxidative/nitrosative stress response genes suggested competition for dioxygen among the community members. The transcriptomic analysis further suggested that Burkholderiales likely feed on acetate that is produced by Methylococcaceae under hypoxic conditions, while Bacteroidetes likely feed on biopolymers produced by both Methylococcaceae and Methylophilaceae.

Methanol excretion by Methylomonas methanica is induced by the supernatant of a methanotrophic consortium

“…Although the sequencing results identified the presence of bacterial clades frequently enriched along methanotrophs (e.g. Burkholderiales, Rhizobiales, Sphingomonadales, Bacteroidetes), 26‐28 it was unexpected to find that the only methanotroph detected, an Alphaproteobacteria belonging to the genus Methylocystis , represented only 1% of the total community composition. Instead, ≈89% of the consortium was composed of methylotrophs from the family Methylophilaceae.…”

The Proteobacterial Methanotroph Methylosinus trichosporium OB3b Remodels Membrane Lipids in Response to Phosphate Limitation

“…We detected 209 PlcP homologs in this data set ( Fig. 7 ), the majority of which were classified as Methylobacter tundripaludum (75%) which is known to be the dominant methanotroph in the lake sediment ( 27 ). In scaffolds that were assembled from these metatranscriptomics data sets, plcP retrieved from these environmental samples showed conserved gene synteny to that of the genome of Methylobacter tundripaludum and a DAG glucosyltransferase involved in glycolipid production is also found in the environmental scaffold ( 28 ).…”

“…To gain further insights into plcP -mediated lipid remodeling in environmental samples and to determine whether plcP transcripts of methanotrophs can be readily detectable, we analyzed recently published metatranscriptomics data sets from Lake Washington ( 27 ). This data set contains comprehensive metatranscriptomics sequencing of microbial communities from the lake sediments and how they responded to oxygen tension in a 14-week period.…”

“…Many previous studies have focused on the regulation of methanotroph activities in the environment, and it has been firmly established that, among many intrinsically interlinked abiotic factors, substrate availability for methanotrophs, i.e., methane and oxygen, is one of the most influential factors for controlling methanotroph populations in natural ecosystems (see, for example, references 4 and 27 ). A comprehensive metatranscriptomics analysis of the microbial populations involved in methane cycling in Lake Washington provided new insight into how different methanotroph ecotypes ( Methylobacter versus Methylosarcina ) respond to oxygen levels ( 27 , 31 ). However, studies on how methane oxidation is affected by macronutrients, particularly P, are not always consistent.…”

“…Assembled metatranscriptomes of Lake Washington microbial communities (under the study name Freshwater Sediment Methanotrophic Microbial Communities from Lake Washington under Simulated Oxygen Tension) ( 27 ) were analyzed for the presence of PlcP using BLASTP searches carried out at the JGI-IMG site ( https://img.jgi.doe.gov ). BLASTP searches were carried out with the PlcP of strain OB3b as the query sequence with an e value cutoff of 1e–40.…”