ECOLOGY AND METAGENOMICS
As noted in the introduction, metagenomics research analyzes bacteria, viruses, and even simple gene creatures found within an environmental sample. The results obtained from metagenomic research have major potential for many different applications, including the study of ecology. Metagenomics techniques have been used to identify the entire genome sequence of symbiotic organisms. For example, Buchnera are symbiotic bacteria that live within aphids. These bacteria produce amino acids essential to the aphid, and in return, the aphids provide carbon and energy sources to the bacteria. The relationship is so intertwined that neither organism can live without the other. The bacteria have lost so many of their original functions that they are almost organelles. Because there is no possible way to culture the bacteria outside the aphid, a traditional genomic library cannot be established. Instead, a metagenomic library containing both aphid and Buchnera DNA was constructed and sequenced. Only when both genomes were examined was the true level of dependence deciphered.
The same scenario was used to sequence the entire genome of the bacteria that coexist within deep-sea tube worms. Tube worms live near thermal vents that are rich in sulfide and reach temperatures of 400°C. The worms lack mouths and digestive tracts and rely completely on symbiotic members of the Proteobacteria to provide nutrition. The bacteria live within a specialized structure called a trophosome where they oxidize hydrogen sulfide to make energy. The energy is used to manufacture amino acids that feed the worm. In return, the worm collects hydrogen sulfide, oxygen, and carbon dioxide and transports these to the bacteria. The metagenomic library contained both worm and bacterial genomes, but yielded information about the bacteria previously unknown. For instance, the bacterial genome had genes for flagella, suggesting that the bacteria may also have a motile phase. Indeed, other observations suggest that the bacteria move through the seawater to colonize juvenile worms.
Metagenomics can also help in understanding microbial competition and communication. This research may have far-reaching applications to all environments, whether they are within the digestive tract of humans or in the deep-sea vents in the oceans. Functional metagenomics can identify small molecules important to microbial survival, such as antibiotics. Metagenomic libraries can be assessed for antimicrobial activity using functional assays to identify new antibiotics. Additionally, sequence-based analysis of metagenomic libraries can identify synthases that make novel polyketides (antibiotics related to erythromycin and rifamycin;). Other functional metagenomic screens have been used to identify quorum-sensing molecules. These are indicators of bacterial population density. Because many bacteria only infect eukaryotic cells or make toxins when they are present in sufficient numbers, interference with quorum sensing provides a new approach to antibacterial therapy. Thus this area is of direct clinical importance. New quorum-sensing molecules were identified by coexpression of metagenomic clones with the reporter GFP. When clones express a quorum-sensing molecule, this activates the expression of GFP, making the bacteria fluorescent. The quorum-sensing metagenomic clone can then be isolated with FACS or microscopy, and then sequenced to determine the identity of the genes involved.
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