Disentangling soil microbiome functions by perturbation

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.

Diverse responses ofpqqC‐ andphoD‐harbouring bacterial communities to variation in soil properties of Moso bamboo forests

“…The PMB communities at these sites strongly correlated with activities of various soil enzymes, especially urease and ALP. These suggests that the effects of PMB may be a set of actions orchestrated by different functions (Ossowicki et al ., 2021 ), and in turn, the PMB communities can be affected by their functional attributes derived by various soil properties. Our findings extend the current understanding of how soil properties influence entire PMB communities, with implications for the biotechnological application of PMB to alleviate P limitation in agricultural and forest ecosystems.…”

Coupling Circularity With Carbon Negativity in Food and Agriculture Systems

“…Perturbations in microbiome composition have been identified as a barrier to maintaining stability in designing microbiomes (Toju et al, 2018). Ossowicki et al (2021) highlighted the sensitivity to perturbations and the resultant instability that soil microbiomes encounter naturally. Controlled perturbations revealed how microbiomes react and the functional changes that occur (Ossowicki et al, 2021).…”

“…Ossowicki et al (2021) highlighted the sensitivity to perturbations and the resultant instability that soil microbiomes encounter naturally. Controlled perturbations revealed how microbiomes react and the functional changes that occur (Ossowicki et al, 2021). Perturbations included gene editing, dilution, biocide application, and selective heat.…”

Diversity and distribution of sediment bacteria across an ecological and trophic gradient

“…In the past decade, studies into the microbiomes of human organs, plants, soils, waters, and even space station astronauts have enhanced our understanding of how microbiota protect us from pathogens, increase agricultural production, and ultimately cycle nutrients in and throughout the natural environment [ 1 – 4 ]. Microbiomes are connected to the biogeochemical cycling of nutrients at both local and global levels, and as a result, disturbances or variations in their community composition can result in gains or losses of functional attributes, changes in nutrient availability, and shifts in ecosystem adaptability [ 5 – 7 ]. Understanding the selective pressures on microbiome community composition can provide insight into an environment’s ability to support higher trophic levels and respond to anthropogenic change.…”