Reference Work Entry

Handbook of Hydrocarbon and Lipid Microbiology

pp 2231-2244

The Meta-Methanoxgenome

  • M. TauppAffiliated withDepartment of Microbiology and Immunology, University of British Columbia, Life Sciences Centre, Health Sciences Mall
  • , S. J. HallamAffiliated withDepartment of Microbiology and Immunology, University of British Columbia, Life Sciences Centre, Health Sciences Mall

Abstract:

Although the vast majority of microbes in nature resist laboratory cultivation, they represent an almost limitless reservoir of genomic diversity and biological innovation. The development of cultivation-independent tools to explore the genomic potential of naturally occurring microbial communities illuminates their hidden enzymatic powers and provides direct insight into the metabolic networks underlying fundamental biogeochemical processes. Microbial mediated anaerobic oxidation of methane (AOM) is a prime exemplar of this paradigm. AOM acts as a biological methane filter beneath the sea, stimulates subsurface metabolism and supports thriving chemosynthetic communities that derive energy from one of its by-products, hydrogen sulfide. Recent environmental genomic surveys of DNA sequences recovered from AOM communities in the Eel River Basin, Hydrate Ridge and Black Sea have identified numerous gene sequences typically associated with canonical methanogenic pathways, including the terminal step, mediated by methyl coenzyme M reductase. Combined nucleotide composition, read density, and linkage analyses have enabled the separation of this sequence information into phylogenetic bins representing the genomic repertoires of anaerobic methane-oxidizing archaeal (ANME) subgroups opening a functional genomic window into the metabolic networks underlying AOM. The following chapter reviews theoretical and pragmatic aspects of environmental genomic library construction and sequence analysis of AOM communities focusing on carbon and energy metabolism. We consider how ANME ecotype variation contributes to adaptation, or niche partitioning at the genotypic level and present a series of experimental recommendations for pathway validation and composite genome assembly.