title: A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.
abstract: 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".
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America.
authors.forename: Scott W
authors.identifier: 0000-0001-5400-4945
authors.initials: SW
authors.lastname: Olesen
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America.
authors.forename: Suhani
authors.initials: S
authors.lastname: Vora
authors.affiliation: Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States of America.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Techtmann
authors.affiliation: Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States of America.|Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America.
authors.forename: Julian L
authors.initials: JL
authors.lastname: Fortney
authors.affiliation: Institute Centre for Water and Environment (iWater), Masdar Institute of Science and Technology, Abu Dhabi, UAE.
authors.forename: Juan R
authors.initials: JR
authors.lastname: Bastidas-Oyanedel
authors.affiliation: Institute Centre for Water and Environment (iWater), Masdar Institute of Science and Technology, Abu Dhabi, UAE.
authors.forename: Jorge
authors.initials: J
authors.lastname: Rodríguez
authors.affiliation: Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States of America.|Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States of America.
authors.forename: Terry C
authors.initials: TC
authors.lastname: Hazen
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Alm
mesh_terms: D044822:Biodiversity; D004463:Ecology