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The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet
Descriptions of some of the earliest metagenomics projects illustrating different approaches to characterizing microbial communities are presented later in this chapter.
SEQUENCING IS JUST ONE KIND OF METAGENOMICS
As with genomics, many early metagenomics projects concentrated on gathering enough sequence information to characterize complete genomes. For metagenomics projects, the assembly of complete genomes from samples that are not pure cultures requires the physical recovery of organism-specific clones from environmental-DNA libraries or the computational recovery from environmental-DNA sequence databases of overlapping target-organism-specific sequences (“contigs”). For environments of low complexity, such as the acid mine drainage described below, it is possible to assemble several genomes simultaneously from an environmental sequence database by using various sophisticated “binning” methods (see Box 3-1). Other early metagenomics efforts, including the ones that first applied the term metagenome, used the term to describe a resource (all the genes in a particular community) to be mined for specific genes by assessing biochemical functions performed by large-insert clones in suitable hosts (Rondon et al. 2000). This kind of project is now called functional metagenomics, but that term is also sometimes taken to have a meaning analogous to functional genomics. In functional genomics, the goal is to determine not just the sequence of the genome but each gene’s function in the organism in which it is found. The metagenomic analogue would assess functions of the genes found in a community (or a sampling thereof) rather than in an individual species.
Many other “omics” techniques can be borrowed across disciplines. DNA microarrays, when bearing multiple rRNA (or other phylogenetic marker) gene sequences as probes, can be used to track variations in population structure and thus (indirectly) in community function over time and space. Microarrays based on selected genes (and gene variants) involved in processes of particular interest can be used to assess a community’s ability to perform a collective function (such as biodegradation of contaminants) and monitor changes in it over relevant periods (for example, during bioremediation). Community transcriptomics and metabolomics are still subdisciplines in their infancy because of the lability of mRNA and the complexity of communities, but metaproteomics (separation and identification through mass-spectrometric methods of many of the proteins in an environmental sample) is surprisingly well-advanced. And in communities where several genomes are known, it is beginning to be possible to develop community-interaction maps. Meta-omic monitoring of microbial communities as they function and change with time—for instance, genetic,