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Front. Microbiol. | doi: 10.3389/fmicb.2017.02321

Parallelized, aerobic, single carbon-source enrichments from different natural environments contain divergent microbial communities

  • 1Biosciences Division, Argonne National Laboratory (DOE), United States

Microbial communities that inhabit environments such as soil can contain thousands of distinct taxa, yet little is known about how this diversity is maintained in response to environmental perturbations such as changes in the availability of carbon. By utilizing aerobic substrate arrays to examine the effect of carbon amendment on microbial communities taken from six distinct environments (soil from a temperate prairie and forest, tropical forest soil, subalpine forest soil, and surface water and soil from a palustrine emergent wetland), we examined how carbon amendment and inoculum source shape the composition of the community in each enrichment. Dilute subsamples from each environment were used to inoculate 96-well microtiter plates containing triplicate wells amended with one of 31 carbon sources from 6 different classes of organic compounds (phenols, polymers, carbohydrates, carboxylic acids, amines, amino acids). After incubating each well aerobically in the dark for 72 hours, we analyzed the composition of the microbial communities on the substrate arrays as well as the initial inocula by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Comparisons of alpha and beta diversity in these systems showed that, while the composition of the communities that grow to inhabit the wells in each substrate array diverges sharply from that of the original community in the inoculum, these enrichment communities are still is strongly affected by the inoculum source. We found most enrichments were dominated by one or several OTUs most closely related to aerobes or facultative anaerobes from the Proteobacteria (e.g. Pseudomonas, Burkholderia, and Ralstonia) or Bacteroidetes (e.g. Chryseobacterium). Comparisons within each substrate array based on the class of carbon source further show that the communities inhabiting wells amended with a carbohydrate differ significantly from those enriched with a phenolic compound. Selection therefore seems to play a role in shaping the communities in the substrate arrays, although some stochasticity is also seen whereby several replicate wells within a single substrate array display strongly divergent community compositions. Overall, the use of highly parallel substrate arrays offers a promising path forward to study the response of microbial communities to perturbations in a changing environment.

Keywords: carbon cycling, Soil Microbiology, Microcosm, enrichment culture, microbial ecology

Received: 17 Jul 2017; Accepted: 10 Nov 2017.

Edited by:

Jorge L. Rodrigues, University of California, Davis, United States

Reviewed by:

Steven Singer, Lawrence Berkeley National Laboratory, United States
Lucas William Mendes, University of São Paulo, Brazil  

Copyright: © 2017 Flynn, Koval, Greenwald, Owens, Kemner and Antonopoulos. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Theodore M. Flynn, Argonne National Laboratory (DOE), Biosciences Division, 9700 S. Cass Ave., 9700 S. Cass Ave., Lemont, 60439, IL, United States,
Dr. Dionysios A. Antonopoulos, Argonne National Laboratory (DOE), Biosciences Division, 9700 S. Cass Ave., 9700 S. Cass Ave., Lemont, 60439, IL, United States,