Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments

Abstract

Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (Methylococcus and Methylocaldum) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named “Methylotetracoccus oryzae” C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C16:1ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems. IMPORTANCE Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.

Description and Genome Analysis of <em>Methylotetracoccus aquaticus sp. nov</em>. , a Novel Tropical Wetland Methanotroph, with the Amended Description of <em>Methylotetracoccus gen. nov.</em>

“…Meanwhile, in July 2019, a new genus Methylotetracoccus oryzae C50C1 with very similar morphological features was described [8]. Draft genome of C50C1 was available after July 2019 after which we compared it with that of FWC3.…”

“…rRNA gene data is available. Additionally, Methylotetracoccus oryzae C50C1 has not been deposited in international culture collections and therefore not described validly, so far [8]. In the present paper, we compare the properties of FWC3 and C50C1 on the genomic, morphological and biochemical levels.…”

“…Wetlands and rice fields from tropical regions have been largely unexplored for culturable methanotrophic diversity and are predicted to possess novel and unique methanotrophic taxa studies [6] [7]. Culture independent data suggests that many novel Type Ib methanotrophs might be existing in freshwater wetlands, small water bodies and rice fields [8]. Type Ib methanotrophs show a high metabolic diversity, however, many of the clades lack isolates [8].…”

“…Culture independent data suggests that many novel Type Ib methanotrophs might be existing in freshwater wetlands, small water bodies and rice fields [8]. Type Ib methanotrophs show a high metabolic diversity, however, many of the clades lack isolates [8]. Additionally, very few methanotrophs isolated from wetlands, have been described.…”

“…Very recently, a strain C50C1, isolated from a temperate rice field in China represented a novel genus and species within Type Ib methanotrophs and tentatively named as 'Methylotetracoccus oryzae' [8]. In our present study we describe the enrichment and isolation of a methanotroph, strain FWC3, which could represent a putative new species of Methylotetracoccus [8]. FWC3 was probably isolated before C50C1, as the 16S rRNA gene sequence of our strain is available since August 2018 and the genome sequence since February 2019.…”