The Expanded Diversity of Methylophilaceae from Lake Washington through Cultivation and Genomic Sequencing of Novel Ecotypes

Abstract

We describe five novel Methylophilaceae ecotypes from a single ecological niche in Lake Washington, USA, and compare them to three previously described ecotypes, in terms of their phenotype and genome sequence divergence. Two of the ecotypes appear to represent novel genera within the Methylophilaceae. Genome-based metabolic reconstruction highlights metabolic versatility of Methylophilaceae with respect to methylotrophy and nitrogen metabolism, different ecotypes possessing different combinations of primary substrate oxidation systems (MxaFI-type methanol dehydrogenase versus XoxF-type methanol dehydrogenase; methylamine dehydrogenase versus N-methylglutamate pathway) and different potentials for denitrification (assimilatory versus respiratory nitrate reduction). By comparing pairs of closely related genomes, we uncover that site-specific recombination is the main means of genomic evolution and strain divergence, including lateral transfers of genes from both closely- and distantly related taxa. The new ecotypes and the new genomes contribute significantly to our understanding of the extent of genomic and metabolic diversity among organisms of the same family inhabiting the same ecological niche. These organisms also provide novel experimental models for studying the complexity and the function of the microbial communities active in methylotrophy.

Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions

“…The methanotrophic strain M. tundripaludum 31/32 (35) and the nonmethanotrophic methylotrophic strains M. mobilis 13 (33) and M. mobilis JLW8 (34) were isolated within the last few years from Lake Washington sediment. In addition, we used the MDH mutants xoxF1 (mmol_1170), xoxF2 (mmol_2048), and xoxF12 (mmol_1770, mmol_2048) of M. mobilis JLW8, which were created in an earlier study (38).…”

“…We first verified that it is possible to establish cocultures of a methanotroph from Lake Washington, Methylobacter tundripaludum 31/32 (35), and nonmethanotrophic methylotrophs from Lake Washington, Methylotenera mobilis 13 and JLW8 (33), in the laboratory using a microcosm model system with methane as the sole carbon source (Fig. 1).…”

“…4A), but in the absence of lanthanum methanol and a shift to mxaF gene expression, methanol was clearly detected with a concentration of 1.24 mM at the end of the incubation (Fig. 4 B and C); this level is sufficient to support growth of the nonmethanotrophic methylotrophs (33 cocultures grown without lanthanum, increased expression of the MxaF-type MDH occurs in the methanotroph, and the cooccurring nonmethanotrophic methylotroph increases in abundance (Fig. S3).…”

Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

“…Its presence has been detected in all Methylophilaceae described so far (7,31,56), and its role in methanol oxidation has also been demonstrated in members of this family, such as Methylotenera mobilis JLW8, and even in more divergent model methylotrophs, such as Methylobacterium extorquens AM1 (49,50). The predicted XoxF protein from the Red Sea strain MBRS-H7 is 86% identical (amino acid sequence level) to that in M. mobilis and is 84%, 88%, 90%, and 97% identical to those in MMS-10A-171, MMS-2-53, HTCC2181, and KB13, respectively.…”

“…The evolutionary relationship of the OM43 clade was determined based on single marker genes such as rRNA genes, the internal transcribed spacer (ITS), and the genes encoding xanthorhodopsin (XR) and on a concatenated alignment of 764 conserved singlecopy genes (CSCG) shared with other representative Methylophilaceae members with sequenced genomes (see Table S1 in the supplemental material), complementing previous phylogeny analyses (31).…”