Disentangling soil microbiome functions by perturbation

Environmental Microbiology Reports, vol. 13, pp. 582–590

Abstract

Soil biota contribute to diverse soil ecosystem services such as greenhouse gas mitigation, carbon sequestration, pollutant degradation, plant disease suppression and nutrient acquisition for plant growth. Here, we provide detailed insight into different perturbation approaches to disentangle soil microbiome functions and to reveal the underlying mechanisms. By applying perturbation, one can generate compositional and functional shifts of complex microbial communities in a controlled way. Perturbations can reduce microbial diversity, diminish the abundance of specific microbial taxa and thereby disturb the interactions within the microbial consortia and with their eukaryotic hosts. Four different microbiome perturbation approaches, namely selective heat, specific biocides, dilution-to-extinction and genome editing are the focus of this mini-review. We also discuss the potential of perturbation approaches to reveal the tipping point at which specific soil functions are lost and to link this change to key microbial taxa involved in specific microbiome-associated phenotypes.

Authors 3

1. Adam Ossowicki corresponding

   Czech Academy of Sciences · Czech Academy of Sciences, Biology Centre · Netherlands Institute of Ecology

   Affiliation as printed

   Department of Microbial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Droevendaalsesteeg 10 Wageningen PB 6708 Netherlands

   Soil and Water Research Infrastructure (SoWa) Biology Centre CAS České Budějovice Czech Republic

   Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, PB, 6708 Netherlands

2. Jos M. Raaijmakers Aachen Institute of Biology, Leiden University Leiden Netherlands Institute of Biology, Leiden University

   Leiden University · Netherlands Institute of Ecology

   Affiliation as printed

   Department of Microbial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Droevendaalsesteeg 10 Wageningen PB 6708 Netherlands

   Institute of Biology, Leiden University Leiden Netherlands

   Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, PB, 6708 Netherlands

   Institute of Biology, Leiden University, Leiden, Netherlands

3. Paolina Garbeva

   Netherlands Institute of Ecology

   Affiliation as printed

   Department of Microbial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Droevendaalsesteeg 10 Wageningen PB 6708 Netherlands

   Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, PB, 6708 Netherlands