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

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.

Methanogens Within a High Salinity Oil Reservoir From the Gulf of Mexico

“…Searching the metagenome for genes in methylotrophic methanogenesis shows that the majority of wells contain nearly the full pathway. The metabolic potential of the Methanohalophilus MAGs did not vary beyond what is known about M. euhalobius, so we do presume that genome completion hampered our ability to retrieve metabolic genes for methylotrophic methanogenesis, but that these are methylotrophic methanogens as this is highly conserved in the Methanohalophilus lineage (Guan et al, 2019).…”

“…Since the Methanohalophilus genus is well known for the production of glycine betaine (GB), used as a compatible solute to allow salt tolerance (Guan et al, 2019), and GB can be fermented by Halanaerobium spp., producing trimethylamine, which in turn can feed Methanohalophilus spp. (Daly et al, 2016), we examined our data for genes that could indicate GB fermentation.…”

Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin

“…In contrast to highly diverse bacterial lineages, relatively few archaeal lineages were recovered (Fig 4). Most hypersaline brine and sediment clone libraries were dominated by two lineages: the Marine Group-I (MG-I) Thaumarchaeota, a clade at present represented by aerobic, chemolithotrophic ammonia oxidizers that are the predominant archaea in the open-ocean water column [61], and by Methanohalophilus spp., a genus of methylotrophic, halotolerant to halophilic methanogens [62]. Within this Orca Basin dataset, MG-I archaea appear to be the only major group that can be potentially linked to nitrification.…”

Metagenomic Investigation of a Low Diversity, High Salinity Offshore Oil Reservoir

“…Methanohalophilus euhalobius (MAG 3) was the only methanogen found within the formation water sample. This organism is commonly detected in highly saline oil reservoirs and is known as an obligate methylotrophic methanogen [54]. Methanohalophilus spp.…”