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Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses
Authors:Steven J Blazewicz  Romain L Barnard  Rebecca A Daly  Mary K Firestone
Affiliation:1.The Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA;2.Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA;3.Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
Abstract:Microbes exist in a range of metabolic states (for example, dormant, active and growing) and analysis of ribosomal RNA (rRNA) is frequently employed to identify the ‘active'' fraction of microbes in environmental samples. While rRNA analyses are no longer commonly used to quantify a population''s growth rate in mixed communities, due to rRNA concentration not scaling linearly with growth rate uniformly across taxa, rRNA analyses are still frequently used toward the more conservative goal of identifying populations that are currently active in a mixed community. Yet, evidence indicates that the general use of rRNA as a reliable indicator of metabolic state in microbial assemblages has serious limitations. This report highlights the complex and often contradictory relationships between rRNA, growth and activity. Potential mechanisms for confounding rRNA patterns are discussed, including differences in life histories, life strategies and non-growth activities. Ways in which rRNA data can be used for useful characterization of microbial assemblages are presented, along with questions to be addressed in future studies.
Keywords:community rRNA   microbial activity   microbial growth   ribosomes   environmental samples   ecosystem processes
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