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Transient invaders can induce shifts between stable states of microbial communities

Citation

R. Amor, Daniel; Ratzke, Christoph; Gore, Jeff (2020), Transient invaders can induce shifts between stable states of microbial communities, Dryad, Dataset, https://doi.org/10.5061/dryad.gb5mkkwkk

Abstract

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.

Methods

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 et al. 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,” F1000Research, vol. 5, p. 1492, Nov. 2016. 

T. Z. DeSantis et al., “Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.,” Appl. Environ. Microbiol., vol. 72, no. 7, pp. 5069–72, Jul. 2006

Usage Notes

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.

Funding

NIH R01, Award: GM102311