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Processes in Microbial Ecology$
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David L. Kirchman

Print publication date: 2011

Print ISBN-13: 9780199586936

Published to Oxford Scholarship Online: December 2013

DOI: 10.1093/acprof:oso/9780199586936.001.0001

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Genomes and metagenomes of microbes and viruses

Genomes and metagenomes of microbes and viruses

(p.177) Chapter 10 Genomes and metagenomes of microbes and viruses
Processes in Microbial Ecology

David L. Kirchman

Oxford University Press

The sequencing of entire genomes of microbes grown in pure cultures is now routine. Sequencing studies have found that bacterial genomes range from 0.18 Mb (intracellular symbiont) to 13 Mb (a soil bacterium), whereas genomes of eukaryotes are much bigger. One fungus has a 40 Mb genome. While bacteria and their small genomes often grow faster than eukaryotes, there is no correlation between genome size and growth rates among the bacteria examined so far, although one of the slowest-growing bacterium in the lab, Pelagibacter ubique, has one of the smallest genomes (1.3 Mb) among free-living bacteria. Genomic studies have also highlighted the importance of genes exchanged (‘lateral gene transfer’) between organisms seemingly unrelated, as defined by rRNA gene sequences. Microbial ecologists use new technology to sequence all microbes in a community. This metagenomic approach has revealed unsuspected physiological processes in microbes, such as the occurrence of a light-driven proton pump, rhodopsin, in bacteria (dubbed proteorhodopsin). Metagenomic studies contributed to establishing that archaea in the deep ocean are capably of chemoautotrophy fuelled by ammonia oxidation, and other studies suggest the occurrence of sulfide oxidation by chemoautotrophic bacteria in oxic surface waters. Metagenomic studies have been even more important in identifying viruses and in showing their huge diversity.

Keywords:   environmental genomics, ecological genomics, shot-gun cloning, horizontal gene transfer, acid mine drainage, metatranscriptomics, metaproteomics

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