Environmental Genomics of Methylotrophs
The Microbial Observatory in Lake Washington was initially funded in 2002, and subsequently renewed in 2006. The goals of the original project have been uncovering the diversity of C1-metabolizing populations in Lake Washington sediment, as a model for global estimates for C1 utilizers in the environment, and obtaining insights into the evolution of metabolic pathways enabling methylotrophy, with a focus on the pathway for formaldehyde oxidation linked to tetrahydromethanopterin (H4MPT). As part of this project, significant progress has been achieved in understanding the diversity, the distribution, the evolution and environmental significance of the H4MPT-linked pathway in bacteria. Comparative genomics have been employed to build and expand the databases of relevant genes, and novel tools for environmental detection of the pathway have been developed. These have been employed to describe the diversity of C1-metabolizing populations in Lake Washington and in other environments. Phylogenetic analyses of the newly acquired gene and protein sequences revealed a broad distribution of the genes for H4MPT-linked C1 transfer reactions within Proteobacteria, Planctomycetes and other, yet unidentified major phyla. A variety of C1-utilizing bacteria have been isolated from Lake Washington in pure cultures, and a number of novel species have been formally described. Community members actively metabolizing C1 compounds in situ have been detected using rRNA or functional gene mRNA and also using the stable isotope probing approach (SIP). From these analyses, extensive knowledge on the presence, diversity and divergence of C1-utilizing populations in Lake Washington and other environments has emerged, pointing toward the existence of multi-tired microbial food webs involved in environmental C1 cycling.
The major goals of the recently renewed Microbial Observatory project are the three interconnected parts of a systems approach towards the knowledge on the microbial populations involved in degradation of C1 compounds in Lake Washington, as a model for understanding other functional communities. These include functional metagenomics, functional metatranscriptomics and functional metaproteomics. All these approaches focus on a fraction of the total population in Lake Washington sediment that is involved in C1 metabolism, by the means of specific enrichments. The first objective, functional metagenomcs, has been met as a result of close collaboration of the MO team and the Joint Genome Institute (JGI) metagenomics team. Community DNA labeled with 13C was obtained from microcosms that were exposed to five different 13C-C1 compounds (methane, methanol, methylamine, formaldehyde, formate) in conditions mimicking in situ conditions. 13C-DNA from each microcosm (expected to be enriched in the sequences of community members actively metabolizing the C1 substrates) was sequenced, assembled and automatically annotated at JGI. The MO team has performed manual analyses of the metagenome. We are now concentrating on the objectives of functional metatranscriptomics and metaproteomics. The former is approached using expression arrays manufactured by Combimatrix. And the second via mass spectrometry.
The project provides a high value outreach to the Pacific Northwest community. High school and undergraduate students are involved in research activities and are educated in microbial diversity, genomics and environmental science.