In Situ Non-Destructive Temporal Measurements of the Rhizosphere Microbiome ‘Hot-Spots’ Using Metaproteomics

Richard Allen White,James J Moran,Colin J Brislawn,Joshua Rosnow,Paul D Piehowski

doi:10.3390/agronomy11112248

Abstract

Rhizosphere arguably embodies the most diverse microbial ecosystem on the planet, yet it is largely a functional ‘black box’ of belowground plant-microbiome interactions. The rhizosphere is the primary site of entry for subsurface injection of fixed carbon (C) into soil with impacts on local to global scale C biogeochemistry and ultimately Earth’s climate. While spatial organization of rhizosphere is central to its function, small scale and steep microbial and geochemical gradients within this dynamic region make it easily disrupted by sampling. The significant challenge presented by sampling blocks elucidation of discreet functions, drivers, and interactions within rhizosphere ecosystems. Here, we describe a non-destructive sampling method linked to metaproteomic analysis in order to measure temporal shifts in the microbial composition and function of rhizosphere. A robust, non-destructive method of sampling microbial hotspots within rhizosphere provides an unperturbed window into the elusive functional interactome of this system over time and space.

Highlights

Rhizosphere microbiomes inhabits the narrow (~2–4 mm) zonal interfaces between soil and plant roots, representing the most diverse microbiomes on Earth, containing up to 1011 microbial cells and ~30,000 bacterial species per gram of root [1]
The rhizosphere microbiome exists through an interwoven tapestry of bacteria, viruses, archaea, protists, fungi, nematodes, and small arthropods interacting directly with plant roots and each other
Increased anthropogenic C cycling is manipulating the global climate with resulting differential moisture extremes, rising temperatures, and pathogen migrations that are undoubtedly impacting the function of the rhizosphere microbiome and shifting its overall functional capacity

Summary

Introduction

Rhizosphere microbiomes inhabits the narrow (~2–4 mm) zonal interfaces between soil and plant roots, representing the most diverse microbiomes on Earth, containing up to 1011 microbial cells and ~30,000 bacterial species per gram of root [1]. Plant functional traits are influenced by the rhizosphere microbiome, which includes impacts on plant metabolism, hormonal pathways, nutrition, stress tolerance (e.g., drought), and enhancement of biosynthetic capacities [2]. The rhizosphere is fundamentally essential for multiple ecosystem processes including recycling and storage of plant fixed. Increased anthropogenic C cycling is manipulating the global climate with resulting differential moisture extremes, rising temperatures, and pathogen migrations that are undoubtedly impacting the function of the rhizosphere microbiome and shifting its overall functional capacity. Warming is causing increased global soil respiration and the resulting CO2 fluxes driven by microbial heterotrophic metabolism. The impact of these microbes ‘breathing harder’ results in net C losses and likely the overall reduction in

Methods

Discussion

Conclusion