Comparative Genomics of the Genus Methanohalophilus, Including a Newly Isolated Strain From Kebrit Deep in the Red Sea.

Yue Guan,David K Ngugi,Ulrich Stingl,Manikandan Vinu,James G Ferry,Jochen Blom,Intikhab Alam,Sylvain Guillot

doi:10.3389/fmicb.2019.00839

Abstract

Halophilic methanogens play an important role in the carbon cycle in hypersaline environments, but are under-represented in culture collections. In this study, we describe a novel Methanohalophilus strain that was isolated from the sulfide-rich brine-seawater interface of Kebrit Deep in the Red Sea. Based on physiological and phylogenomic features, strain RSK, which is the first methanogenic archaeon to be isolated from a deep hypersaline anoxic brine lake of the Red Sea, represents a novel species of this genus. In order to compare the genetic traits underpinning the adaptations of this genus in diverse hypersaline environments, we sequenced the genome of strain RSK and compared it with genomes of previously isolated and well characterized species in this genus (Methanohalophilus mahii, Methanohalophilus halophilus, Methanohalophilus portucalensis, and Methanohalophilus euhalobius). These analyses revealed a highly conserved genomic core of greater than 93% of annotated genes (1490 genes) containing pathways for methylotrophic methanogenesis, osmoprotection through salt-out strategy, and oxidative stress response, among others. Despite the high degree of genomic conservation, species-specific differences in sulfur and glycogen metabolisms, viral resistance, amino acid, and peptide uptake machineries were also evident. Thus, while Methanohalophilus species are found in diverse extreme environments, each genotype also possesses adaptive traits that are likely relevant in their respective hypersaline habitats.

Highlights

Hydrogenotrophic, methylotrophic and acetoclastic pathways are the major pathways for methanogenesis – the production of methane by microbial cells (Ferry and Kastead, 2007)
Halophilic methylotrophic methanogens belonging to the order Methanosarcinales use the classical methylotrophic pathway where methylated compounds are dismutated to methane and CO2, whereas “Methanonatronarchaeia” use a heterotrophic methylotrophic pathway in which methylated compounds are used as electron acceptors and formate or hydrogen are being used as electron donors (Sorokin et al, 2017)
The draft genome sequences of strain RSK, M. portucalensis, M. halophilus, and M. euhalobius are deposited in Genbank under BioProject identifier PRJNA500754

Summary

INTRODUCTION

Hydrogenotrophic, methylotrophic and acetoclastic pathways are the major pathways for methanogenesis – the production of methane by microbial cells (Ferry and Kastead, 2007). The salinity and additional factors such as redox potential, permanency of anaerobic conditions, and the concentrations of other terminal electron acceptors determine the distribution and energy-efficiency of the prevailing methanogenic pathways. In these habitats, methylotrophic methanogens are more successful compared to hydrogenotrophic and acetoclastic methanogens due to their higher energy yield and the use of non-competitive substrates, such as methylamines and methanol (McGenity, 2010; Lazar et al, 2011; Oren, 2011; Kelley et al, 2012). We describe comparative genome analyses with multiple, closely related Methanohalophilus species, providing insights into their life styles and adaptive strategies to different harsh environments

MATERIALS AND METHODS

RESULTS AND DISCUSSION

CONCLUSION