Noninvasive analysis of the soil microbiome: Biomonitoring strategies using the volatilome, community analysis, and environmental data

Kelly R. Redeker*, Leda L. Cai, Alex J. Dumbrell, Alex Bardill, James P.J. Chong, Thorunn Helgason

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Within soils there are microorganisms that act to break down complex substrates (saprophytes), microorganisms that actively aid nutrient delivery (mycorrhizal fungi and nitrogen-fixing bacteria), and others that hijack the system to their own benefit (parasitic bacteria and fungi). The complex interaction between plants, these microbes, and the soil determines how effectively nutrients will be recycled, with a significant impact on regional productivity and biodiversity. Each microbe plays a role in overall soil function but, despite the critical role they play, soil microbial communities and their functions remain challenging to accurately quantify. The functional behaviour of soils is difficult to quantify, in part due to the effects of disturbance when sampling. This suggests that noninvasive analytical tools are necessary to diagnose current soil function and to predict changes in soil behaviour with changing climate or land use. Microbial communities, the drivers of soil function, are diverse, and their individual metabolisms are often tightly coupled, such that the microbial community in aggregate may be considered to have a “net” metabolism. This net metabolism can be described by the volatile signatures that propagate from the soil into the atmosphere and, by proxy, allowing a noninvasive analysis of the microbial community active in the subsurface. Here, we detail the complexities of the soil volatile metabolism, propose a “fingerprint” strategy to describe this complex community that uses trace gas fluxes combined with environmental data, and describe the promising outcomes from an initial foray using this method.

Original languageEnglish
Title of host publicationAdvances in Ecological Research
EditorsDavid A. Bohan, Alex J. Dumbrell, Guy Woodward, Michelle Jackson
PublisherAcademic Press Inc.
Chapter4
Pages93-132
Number of pages40
Volume59
ISBN (Print)9780128143179
DOIs
Publication statusPublished - 10 Sep 2018

Publication series

NameAdvances in Ecological Research
Volume59
ISSN (Print)0065-2504

Keywords

  • dimethyl sulphide
  • isoprene
  • methyl halides
  • microbial community
  • microbiome
  • salt marsh
  • volatile metabolites
  • volatilome

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