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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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Community structure of microbes in natural environments

Community structure of microbes in natural environments

(p.157) Chapter 9 Community structure of microbes in natural environments
Processes in Microbial Ecology

David L. Kirchman

Oxford University Press

Community structure refers to the taxonomic types of various microbes and their relative abundance in an environment. Traditional methods for identifying microbes rely on biochemical test of phenotype observable in the lab. Even for cultivated microbes and larger organisms, the traditional, phenotype approach has been replaced by comparing sequences of specific genes, those for 16S rRNA (archaea and bacteria) or 18S rRNA (microbial eukaryotes). Cultivation-independent approaches based on 16S rRNA gene sequencing have revealed that natural microbial communities have a few abundant types and many rare ones. These organisms differ substantially from those that can be grown in the lab using cultivation-dependent approaches. The abundant types of microbes found in soils, freshwater lakes, and oceans all differ. The phylum Actinobacteria is abundant in soils and lakes, not in the oceans. Alphaproteobacteria are abundant in the oceans, while Betaproteobacteria are more common in lakes. Once thought to be confined to extreme habitats, Archaea are now known to occur everywhere, but are particularly abundant in the deep ocean, where they make up as much as 50 per cent of total microbial abundance. The same environmental properties known to affect the total community at the bulk level are known to affect community structure, more or less. Salinity and temperature are very important, for example, as is pH especially in soils. In addition to bottom-up factors, both top-down factors, grazing and viral lysis, also shape community structure. According to the Kill the Winner hypothesis, viruses select for fast-growing types, allowing slower-growing defensive specialists to survive.

Keywords:   rare biosphere, plankton, species problem, Bass Becking hypothesis, morphospecies

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