Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern

Abstract

Anaerobic archaeal methanogens are key players in the global carbon cycle due to their role in the final stages of organic matter decomposition in anaerobic environments such as wetland sediments. Here we present the first draft metagenome-assembled genome (MAG) sequence of an unclassified Methanosarcinaceae methanogen phylogenetically placed adjacent to the Methanolobus and Methanomethylovorans genera that appears to be a distinct genus and species. The genome is derived from sediments of a hypersaline (97–148 ppt chloride) unrestored industrial saltern that has been observed to be a significant methane source. The source sediment is more saline than previous sources of Methanolobus and Methanomethylovorans. We propose a new genus name, Methanosalis, to house this genome, which we designate with the strain name SBSPR1A. The MAG was binned with CONCOCT and then improved via scaffold extension and reassembly. The genome contains pathways for methylotrophic methanogenesis from trimethylamine and dimethylamine, as well as genes for the synthesis and transport of compatible solutes. Some genes involved in acetoclastic and hydrogenotrophic methanogenesis are present, but those pathways appear incomplete in the genome. The MAG was more abundant in two former industrial salterns than in a nearby reference wetland and a restored wetland, both of which have much lower salinity levels, as well as significantly lower methane emissions than the salterns.

Methylphosphonate Degradation and Salt-Tolerance Genes of Two Novel Halophilic Marivita Metagenome-Assembled Genomes from Unrestored Solar Salterns

“…Furthermore, 6.48 is also higher than the p I of a Methanosarcinaceae sp. genome isolated from the same Pond R1, which had a mean p I of 5.90 [ 24 ], similar to Salinibacter ruber . As with p I , GC contents of the Marivita MAGs (~62%) were also similar to the other Marivita genomes and are in the range of other reported halophilic organisms [ 65 ].…”

“…Elevated methane (CH 4 ) emissions were measured from both cores in the field (R1 = 1347, R2 = 1607 µmol CH 4 m −2 d −1 ) [ 15 ]. The metagenomic sequencing, processing, and binning has been described previously [ 15 , 24 ]. For these two draft genomes, we began with MAGs constructed with MetaBAT [ 25 ], with a completeness of 99.05% and 96.29% and contamination of 0.74% and 3.17%, for M. sp.…”

“…We used Geneious version 2021.1.1 [ 30 ] (Biomatters Ltd., Auckland, New Zealand) to remap paired-end reads to each scaffold and extend using reads partially overlapping the ends of the scaffolds as described elsewhere [ 24 , 31 ]. Performing two rounds of these steps improved the completeness of M. sp.…”

Perspective on the use of methanogens in lithium recovery from brines

“…Methanosalis sp. SBSPR1A , a closely related taxon in the Methanolobus and Methanomethylovorans genera, is a methylotrophic methanogen tolerating up to 3.6 M of salinity and performing methanogenesis only from dimethylamine and trimethylamine ( Bueno de Mesquita et al, 2021 ). Methylated amines, particularly trimethylamines, originate from glycine betaine fermentation ( Welsh, 2000 ).…”

Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils

“…There are several reports exploring the microbial and metabolic diversity of various hypersaline ecosystems. In 2021, Bueno de Mesquita and colleagues uncovered a new genus, Methanosalis , during their investigation of the salt pond in San Francisco ( 12 ). In addition, the research group of Chakraborty and Kurth delved into the xenobiotic-degrading and carbon fixation capabilities of Lonar Lake in India and La Brava and Tebenquiche lakes in Salar de Atacama, Chile, respectively ( 13 , 14 ).…”