Draft genome of a novel methanotrophic Methylobacter sp. from the volcanic soils of Pantelleria Island

Carmen Hogendoorn,Paola Quatrini,Walter D’Alessandro,Huub J M Op Den Camp,Antonia L Gagliano,Sophie Vijverberg,Femke Van Hout,Jeroen Frank,Mike S M Jetten,Lianna Poghosyan,Nunzia Picone,Theo A Van Alen,Arjan Pol

doi:10.1007/s10482-021-01525-7

Abstract

The genus Methylobacter is considered an important and often dominant group of aerobic methane-oxidizing bacteria in many oxic ecosystems, where members of this genus contribute to the reduction of CH4 emissions. Metagenomic studies of the upper oxic layers of geothermal soils of the Favara Grande, Pantelleria, Italy, revealed the presence of various methane-oxidizing bacteria, and resulted in a near complete metagenome assembled genome (MAG) of an aerobic methanotroph, which was classified as a Methylobacter species. In this study, the Methylobacter sp. B2 MAG was used to investigate its metabolic potential and phylogenetic affiliation. The MAG has a size of 4,086,539 bp, consists of 134 contigs and 3955 genes were found, of which 3902 were protein coding genes. All genes for CH4 oxidation to CO2 were detected, including pmoCAB encoding particulate methane monooxygenase (pMMO) and xoxF encoding a methanol dehydrogenase. No gene encoding a formaldehyde dehydrogenase was present and the formaldehyde to formate conversion follows the tetrahydromethanopterin (H4MPT) pathway. “Ca. Methylobacter favarea” B2 uses the Ribulose-Mono-Phosphate (RuMP) pathway for carbon fixation. Analysis of the MAG indicates that Na+/H+ antiporters and the urease system might be important in the maintenance of pH homeostasis of this strain to cope with acidic conditions. So far, thermoacidophilic Methylobacter species have not been isolated, however this study indicates that members of the genus Methylobacter can be found in distinct ecosystems and their presence is not restricted to freshwater or marine sediments.

Highlights

Volcanic and geothermal areas are hostile environments characterized by low pH, high temperature, geothermal gas emissions, and low O2 concentrations
Thermoacidophilic Methylobacter species have not been isolated, this study indicates that members of the genus Methylobacter can be found in distinct ecosystems and their presence is not restricted to freshwater or marine sediments
Aerobic methanotrophs belong to the phyla Alphaproteobacteria, Gammaproteobacteria or Verrucomicrobia (Op den Camp et al 2009)

Summary

Introduction

Volcanic and geothermal areas are hostile environments characterized by low pH, high temperature, geothermal gas emissions, and low O2 concentrations. Aerobic methanotrophs belong to the phyla Alphaproteobacteria, Gammaproteobacteria or Verrucomicrobia (Op den Camp et al 2009). These methanotrophs are microorganisms that conserve energy by oxidizing CH4 to CO2, while using O2 as terminal electron acceptor (Hanson and Hanson 1996). A recent metagenomic analysis of the volcanic soils of the Favara Grande, the main geothermal active area of Pantelleria Island, Italy, indicated the presence of a unique methanotrophic community, composed of Verrucomicrobia and Gammaproteobacteria (Picone et al 2020). Different metagenome assembled genomes (MAGs) were retrieved One of these MAGs was nearly complete and phylogenetic analysis showed that it represents the genome of a novel Methylobacter species. We determined the phylogenetic position of this Methylobacter, and analysed the encoded metabolic potential

Materials and methods

Results and discussion

Compliance with ethical standards