Chapter 31 : An Overview of Methodologies in Aquatic Microbial Ecology

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This chapter reflects the integrative nature of aquatic microbial ecology. It has been structured around areas that influence the role of the microbial community in ecosystem function such as diversity and community structure of primary and secondary producers, growth and grazing of primary and secondary producers, the role of bacteria in geochemical cycling, and specialized environments. The field of aquatic microbial ecology is being revolutionized by genetic and genomic approaches. Pioneering work in the late 1980s, which started with community analysis based on the PCR amplification of the 16S rRNA gene from many different types of bacteria, has expanded to encompass the analysis of multiple genomes from many individuals in many populations in the community (metagenome). Tringe et al. used environmental gene tags (EGTs), or short sequences that contain fragments of functional genes from whole genome shotgun libraries, to compare the microbial communities from three different ecosystems. In general, there are two approaches to measuring bacterial community activity in aquatic systems: (i) the direct tracer approach, which measures the conversion of a labeled substrate to a product of interest, and (ii) isotope dilution methods, in which the product pool is labeled and the dilution of the labeled product pool by new unlabeled product formation gives an estimate of the rate of production. Direct tracer methods have been employed for organic carbon, inorganic carbon, sulfur, nitrogen, phosphorus, and metal cycling. The future challenge is going to be to integrate activity and community structure measurements with ecosystem measurements of physicochemical fluxes.

Citation: Hullar M. 2007. An Overview of Methodologies in Aquatic Microbial Ecology, p 393-398. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch31

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Microbial Ecology
Environmental Microbiology
Reverse Transcriptase PCR
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