TY - JOUR
T1 - A novel analysis method for paired-sample microbial ecology experiments
AU - Olesen, Scott W.
AU - Vora, Suhani
AU - Techtmann, Stephen M.
AU - Fortney, Julian L.
AU - Bastidas-Oyanedel, Juan R.
AU - Rodríguez, Jorge
AU - Hazen, Terry C.
AU - Alm, Eric J.
N1 - Funding Information:
This material is based on work supported by BP Exploration/MIT Energy Initiative under Grant No. 6926835, the National Science Foundation under Grant No. 0821391, and the National Science Foundation Graduate Research Fellowship under Grant No. 1122374. The authors are grateful to BP and its partners for support in the sampling effort.
Publisher Copyright:
© 2016, Public Library of Science. All rights reserved. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
PY - 2016/5/1
Y1 - 2016/5/1
N2 - Many microbial ecology experiments use sequencing data to measure a community's response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method's validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of "bottle effects".
AB - Many microbial ecology experiments use sequencing data to measure a community's response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method's validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of "bottle effects".
UR - http://www.scopus.com/inward/record.url?scp=84968658894&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0154804
DO - 10.1371/journal.pone.0154804
M3 - Article
C2 - 27152415
AN - SCOPUS:84968658894
SN - 1932-6203
VL - 11
JO - PLoS ONE
JF - PLoS ONE
IS - 5
M1 - e0154804
ER -