Methylotrophy in a Lake: from Metagenomics to Single-Organism Physiology

Abstract

This review provides a brief summary of ongoing studies in Lake Washington (Seattle, WA) directed at an understanding of the content and activities of microbial communities involved in methylotrophy. One of the findings from culture-independent approaches, including functional metagenomics, is the prominent presence of Methylotenera species in the site and their inferred activity in C 1 metabolism, highlighting the local environmental importance of this group. Comparative analyses of individual genomes of Methylophilaceae from Lake Washington provide insights into their genomic divergence and suggest significant metabolic flexibility.Metabolism of organic C 1 compounds (compounds containing no carbon-carbon bonds) is an important part of the global carbon cycle. Methane is recognized as one of the major C 1 compounds in the environment and a major contributor to the greenhouse effect, emitted at approximately 600 Tg year Ϫ1 (29, 44). Methanol emissions into the atmosphere are estimated on a similar scale, 82 to 273 Tg year Ϫ1 (16). Methylated amines are known to be abundant in marine and freshwater environments, representing dynamic constituents of not only carbon but also nitrogen global cycles (37). Other environmentally important C 1 compounds are halogenated methanes and methylated sulfur compounds (4, 43). Methylotrophic bacteria play an important role in maintaining the balance of C 1 compounds in aerobic environments, major niches being oceans, soils, and freshwater lakes (17,30). Each of these types of environments potentially hosts a variety of methylotrophs with different substrate preferences and different metabolic capabilities. However, aside from a few well-established groups, such as type I (gammaproteobacterial) and type II (alphaproteobacterial) methanotrophs, the composition and specific activities of such communities remain poorly characterized. As part of the Microbial Observatories project funded by the National Science Foundation, we have been studying the methylotroph community in Lake Washington sediment in a comprehensive fashion, applying a variety of culture-independent approaches in addition to traditional cultivation approaches. Some of the findings resulting from this project, including insights into the important role of Methylotenera species in freshwater habitats, are featured in this review. METHYLOTROPHS IN LAKE WASHINGTONMany methylotrophic bacteria are available in culture, including a number of isolates from Lake Washington (3,20,21,23,28,35). These organisms provide useful models for studying the distinguishing features of methylotrophic metabolism (1, 33). However, it is a widely accepted fact that most microbes in the universe remain uncultivated (40), and this is very likely true for methylotrophs. Therefore, knowledge gained from studying model laboratory methylotrophs may not accurately reflect the composition and the diversity of methylotrophs in natural environments. In addition, genomic content, metabolic activities, and substrate specificities may differ distinctly...

Methylamine Utilization via the N -Methylglutamate Pathway in Methylobacterium extorquens PA1 Involves a Novel Flow of Carbon through C 1 Assimilation and Dissimilation Pathways

“…Of late, though, the NMG pathway is going through a phase of rediscovery, in light of its importance in several environmental regimes (7,51,52). While various studies with different model systems FIG 6 (A) Red, blue, and green arrows represent the deletion of fae, fae2, and fae3, respectively, in the genomic background from which the arrow originates.…”

Insights into Denitrification in Methylotenera mobilis from Denitrification Pathway and Methanol Metabolism Mutants

“…We also mutated a gene predicted to encode a nitric oxide dioxygenase (Nod; mmol_1063) and each of two xoxF genes (mmol_1770 and mmol_2048) that encode homologs of the large subunit of methanol dehydrogenase (11,14,19,20). In addition, a double mutant lacking both XoxF proteins was generated.…”

“…Methylotenera species represent a recently described novel genus within the family Methylophilaceae (11). Apart from genomic divergence (12), one of the main properties that distinguishes the described species of Methylotenera from species representing three other genera within this family (Methylophilus, Methylobacillus, and Methylovorus) is extremely poor growth on methanol and the lack of genes for the classic (MxaFI) methanol dehydrogenase (11).…”

“…Apart from genomic divergence (12), one of the main properties that distinguishes the described species of Methylotenera from species representing three other genera within this family (Methylophilus, Methylobacillus, and Methylovorus) is extremely poor growth on methanol and the lack of genes for the classic (MxaFI) methanol dehydrogenase (11). However, Methylotenera appears to thrive in a variety of environments (12), and these organisms appear to be one of the major species that consume methanol in situ (13).…”

Pyrroloquinoline Quinone Ethanol Dehydrogenase in Methylobacterium extorquens AM1 Extends Lanthanide-Dependent Metabolism to Multicarbon Substrates

“…Studies have provided evidence for the physiological role of a second type of PQQ-dependent MDH, XoxF, which has ϳ50% amino acid identity to MxaF from MxaFI-type MDHs (17). Metagenomic and environmental proteomics studies have demonstrated that xoxF is more widespread than mxaF in environmental samples (18)(19)(20)(21). Phylogenetic analysis of putative PQQ-containing MDHs has shown that XoxF-type MDHs are genetically diverse with at least five distinct clades, and it has been suggested that MxaFI-type MDHs represent a minor fraction of these MDHs (8,22).…”