Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen‐limited methane‐ and iron‐fed bioreactor inoculated with Bothnian Sea sediments

Abstract

Microbial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate, or oxygen can be used. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane‐ and iron‐rich sediments from the Bothnian Sea to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we investigated shifts in microbial community composition after approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were identified and used to infer putative microbial metabolism. Metagenome‐assembled genomes representing novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria were recovered and revealed a potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new hypotheses on the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that microorganisms potentially composing the methane biofilter in these sediments may be more diverse than previously appreciated.

Variations in Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities

“…However, the key methane monooxygenase gene ( pmo ) was not detected. This genetic repertoire is identical to a recently described MAG from the same family ( Pedosphaeraceae ), recovered from a bioreactor community 49 . The authors of that study suggested a potentially novel methane monooxygenase gene that was originally annotated as hypothetical.…”

Microbial community structures and important taxa across oxygen gradients in the Andaman Sea and eastern Bay of Bengal epipelagic waters

“…Arctic97B-4 (affiliated with Verrucomicrobia) was identified as a bioindicator taxa in this study and have also been detected in other oxygen-deficient waters, including the OMZs of the Arabian Sea and Cariaco Basin ( Lüke et al, 2016 ; Suter et al, 2018 ). The ecological roles of Arctic97B-4 remain unclear, but Verrucomicrobia taxa might be capable of surviving under oxygen-depleted conditions and potentially oxidizing methanol or methane ( Dalcin Martins et al, 2021 ). A strong association between Arctic97B-4 and SAR202 was also detected and both were simultaneously present in modules 1 and 2 ( Supplementary Figure 7 ).…”

Krumholzibacteriota and Deltaproteobacteria contain rare genetic potential to liberate carbon from monoaromatic compounds in subsurface coal seams

“…Importantly, each of these genes occurred within two or more genomes from Delphinibacteriota and Krumholzibacteriota; the two phyla with which bin 3.1 had the highest percent identities in the BLASTx results for the elongation factor G gene. The results of the MLSA indicate that bin 3.1 is likely a novel member of the Krumholzibacteriota phylum, of which the closest known relative appears to be a marine sediment enrichment culture MAG from the Bothnian Sea, in the Scandinavian region ( 52 ). Four other closely related Krumholzibacteriota MAGs were also identified, coming from a stratified freshwater reservoir of the Cañas River in Puerto Rico and from Lake Lovojärvi in Finland ( Fig.…”