Metagenome Assembled Genome of a Novel Verrucomicrobial Methanotroph From Pantelleria Island.

Nunzia Picone,Theo Van Alen,Arjan Pol,Paola Quatrini,Jeroen Frank,Antonina L Gagliano,Huub J M Op Den Camp,Carmen Hogendoorn,Pieter Blom,Walter D’Alessandro,Mike S M Jetten

doi:10.3389/fmicb.2021.666929

Abstract

Verrucomicrobial methanotrophs are a group of aerobic bacteria isolated from volcanic environments. They are acidophiles, characterized by the presence of a particulate methane monooxygenase (pMMO) and a XoxF-type methanol dehydrogenase (MDH). Metagenomic analysis of DNA extracted from the soil of Favara Grande, a geothermal area on Pantelleria Island, Italy, revealed the presence of two verrucomicrobial Metagenome Assembled Genomes (MAGs). One of these MAGs did not phylogenetically classify within any existing genus. After extensive analysis of the MAG, we propose the name of “Candidatus Methylacidithermus pantelleriae” PQ17 gen. nov. sp. nov. The MAG consisted of 2,466,655 bp, 71 contigs and 3,127 predicted coding sequences. Completeness was found at 98.6% and contamination at 1.3%. Genes encoding the pMMO and XoxF-MDH were identified. Inorganic carbon fixation might use the Calvin-Benson-Bassham cycle since all genes were identified. The serine and ribulose monophosphate pathways were incomplete. The detoxification of formaldehyde could follow the tetrahydrofolate pathway. Furthermore, “Ca. Methylacidithermus pantelleriae” might be capable of nitric oxide reduction but genes for dissimilatory nitrate reduction and nitrogen fixation were not identified. Unlike other verrucomicrobial methanotrophs, genes encoding for enzymes involved in hydrogen oxidation could not be found. In conclusion, the discovery of this new MAG expands the diversity and metabolism of verrucomicrobial methanotrophs.

Highlights

Novel Genus of Verrucomicrobial Methanotrophs methanol dehydrogenase (MDH) to transform methanol to formate. The peculiarity of their XoxF-MDH is the strict dependence on rare earth elements (REEs), which are present in the active site together with the pyrroloquinoline quinone (PQQ) cofactors (Pol et al, 2014)
Methanotrophs belonging to the Gammaproteobacteria and Verrucomicrobia phyla could be identified through pmoA sequencing (Gagliano et al, 2014). 16S rRNA gene amplicon sequencing analysis, instead, did not detect Verrucomicrobia in the soil of Favara Grande, but potential methanotrophy was mainly attributed to Gammaproteobacteria (Gagliano et al, 2016)
Considering the AAI thresholds proposed by Konstantinidis et al (2017) for uncultivated microorganisms (45–65% for the same family, 65–95% for the same genus and 95–100% for the same species), these results classified MAG9 as representing a new species of a new genus, for which we propose the name “Candidatus Methylacidithermus pantelleriae” sp

Summary

Introduction

Verrucomicrobial methanotrophs are a group of aerobic bacteria usually found in the acidic soil of geothermal active regions (Dunfield et al, 2007; Pol et al, 2007; Islam et al, 2008; Sharp et al, 2014; van Teeseling et al, 2014). Their genomes all encode one or up to three particulate methane monooxygenase enzymes (pMMO) for the conversion of methane to methanol and a XoxF-type. The current classification divides verrucomicrobial methanotrophs into two genera: Methylacidimicrobium, generally mesophilic and extremely acidophilic and the thermophilic but less acidophilic Methylacidiphilum (Dunfield et al, 2007; Pol et al, 2007; Islam et al, 2008; Sharp et al, 2014; van Teeseling et al, 2014; Picone et al, 2021)

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