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Microorganisms 2016, 4(2), 19; doi:10.3390/microorganisms4020019

New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment

GEOMAR Helmholtz-Zentrum für Ozeanforschung, Düsternbrooker Weg 20, D-24105 Kiel, Germany
Academic Editor: Senjie Lin
Received: 8 March 2016 / Revised: 20 May 2016 / Accepted: 20 May 2016 / Published: 24 May 2016
(This article belongs to the Special Issue Diversity and Dynamics of Marine Microbial Communities)
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Abstract

During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria. View Full-Text
Keywords: marine habitats; hypersaline lakes; hydrothermal vents; soda lakes; phototrophic bacteria; ammonia oxidation; denitrification; sulfate reduction; sulfur oxidation; methane oxidation marine habitats; hypersaline lakes; hydrothermal vents; soda lakes; phototrophic bacteria; ammonia oxidation; denitrification; sulfate reduction; sulfur oxidation; methane oxidation
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Imhoff, J.F. New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment. Microorganisms 2016, 4, 19.

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