DOI: 10.5061/dryad.gb5mkkwkk
title: Transient invaders can induce shifts between stable states of microbial communities

description: Microbial dispersal often leads to the arrival of outsider organisms into
 ecosystems. When their arrival give rise to successful invasions, outsider
 species establish within the resident community, which can dramatically
 alter the ecosystem. Seemingly less influential, the potential impact of
 unsuccessful invaders that interact only transiently with the community
 has remained largely ignored. Here, we experimentally demonstrate that
 such transient invasions can perturb the stability of microbial ecosystems
 and induce a lasting transition to an alternative stable state, even when
 the invader species itself does not survive the transition. First, we
 develop a mechanistic understanding of how environmental changes caused by
 such transient invaders can drive a community shift in a simple, bistable
 model system. Beyond this, we show that transient invaders can also induce
 switches between stable states in more complex communities isolated from
 natural soil samples. Our results demonstrate that short-term interactions
 with an invader species can induce lasting shifts in community composition
 and function.
description: The data corresponds to the 16S amplicon sequencing of samples
 taken from the laboratory experiments described in Amor, Ratzke and Gore
 2019. These laboratory communities were originated through inoculation of
 soil samples. The soil was sampled from a lawn in
 Cambridge Massachusetts, at depth ~15 cm. About 20 grains of soil (~0.5g)
 were diluted into 20 ml of PBS, vortexed at intermediate speed for 30s and
 then incubated on shaker at 250rpm. After 30 minutes, the sample was
 allowed to settle for 5 minutes and the supernatant was transferred to a
 new Falcon tube. 7mL aliquots of this supernatant were then transferred
 into a 96-deepwell plate, thus generating the initial condition
 for multiple replicate communities of soil origin. The DNA extractions were
 performed using Agencourt DNAdvance A48705 extraction kit (Beckman
 Coulter, Indianapolis, IN, USA) following the provided protocol. The
 obtained DNA was used for 16S amplicon sequencing targeting the V4-V5
 region. The sequencing was done on an Illumina, MySeq by CGEB - Integrated
 Microbiome Resource at the Dalhousie University, Halifax, NS,
 Canada. We used the R package DADA2 to obtain the Amplicon Sequence Variants (ASV) as described Callahan <i>et al</i>. 2016. Taxonomic identities were assigned to the ASVs by using the GreenGenes Database Consortium (Version 13.8, DeSantis 2006) as reference database. References: B. J. Callahan, K. Sankaran, J. A. Fukuyama, P. J. McMurdie, and S. P. Holmes, “Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses,” <i>F1000Research</i>, vol. 5, p. 1492, Nov. 2016.  T. Z. DeSantis <i>et al.</i>, “Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.,” <i>Appl. Environ. Microbiol.</i>, vol. 72, no. 7, pp. 5069–72, Jul. 2006
description: The ReadMe.txt file contains:  - Description
 of the workflow to obtain the Amplicon Sequence Variants and their
 taxonomic identities from the fastaq files. - List of
 samples used to generate Figure 3C in the main text, and Supplementary
 Figures 9 and 11.