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ISME J. 2016 May;10(5):1147-56. doi: 10.1038/ismej.2015.191. Epub 2015 Nov 13.

Decreases in average bacterial community rRNA operon copy number during succession.

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Department of Biology, Duke University, Durham, NC, USA.
Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, USA.
Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
U.S. Geological Survey, Canyonlands Research Station, Moab, UT, USA.
Department of Biological Sciences, St Edward's University, Austin, TX, USA.
School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.
Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France.
Nicholas School of the Environment, Duke University, Durham, NC, USA.


Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.

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