Soil, senescence and exudate utilisation: characterisation of the\xa0Paragon var. spring bread wheat root microbiome

Samuel Mm Prudence,Michael C Macey,J Colin Murrell,Jake T Newitt†,Matthew I Hutchings,Sarah F Worsley,Laura E Lehtovirta-Morley

doi:10.1186/s40793-021-00381-2

Samuel Mm Prudence, Michael C Macey + Show 5 more

Open Access

https://doi.org/10.1186/s40793-021-00381-2

Copy DOI

Abstract

BackgroundConventional methods of agricultural pest control and crop fertilisation are unsustainable. To meet growing demand, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. The aim of the present work was to profile the community of bacteria, fungi, and archaea associated with the wheat rhizosphere and root endosphere in different conditions. We also aimed to use 13CO2 stable isotope probing (SIP) to identify microbes within the root compartments that were capable of utilising host-derived carbon.ResultsMetabarcoding revealed that community composition shifted significantly for bacteria, fungi, and archaea across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however, several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these were Streptomycetaceae and Burkholderiaceae. Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. Stable isotope probing showed that bacterial taxa within the Burkholderiaceae family, among other core enriched taxa such as Pseudomonadaceae, were able to use root exudates, but Streptomycetaceae were not.ConclusionsThe consistent enrichment of Streptomycetaceae and Burkholderiaceae within the endosphere, and their reduced abundance after developmental senescence, indicated a significant role for these families within the wheat root microbiome. While Streptomycetaceae did not utilise root exudates in the rhizosphere, we provide evidence that Pseudomonadaceae and Burkholderiaceae family taxa are recruited to the wheat root community via root exudates. This deeper understanding crop microbiome formation will enable researchers to characterise these interactions further, and possibly contribute to ecologically responsible methods for yield improvement and biocontrol in the future.

Highlights

Conventional methods of agricultural pest control and crop fertilisation are unsustainable
Paragon across starkly contrasting soil environments? (2) How does the community change as the plant enters developmental senescence, and which microbial taxa, if any, are unable to persist through senescence? (3) Do wheat roots select for specific archaeal lineages as they do for bacteria and fungi? (4) Which bacterial taxa utilise wheat root exudates? The results provide a significant advance towards understanding wheatmicrobiome interactions and establishing an understanding of the core microbial taxa in T. aestivum var
Paragon To gain initial insights into the microbial communities associated with wheat roots, we characterised the microbial community associated with field-grown wheat sampled during the stem elongation growth phase

Summary

Introduction

Conventional methods of agricultural pest control and crop fertilisation are unsustainable. Wheat is a staple crop for more than 4 billion people and globally accounts for more than 20% of human calorie and protein consumption [1] This means that farming wheat, and the accompanying use of chemical fertilisers and pesticides, has a huge environmental. One possible way to achieve this is to manipulate the microbial communities associated with wheat and other crop plants. These communities are commonly referred to as “microbiomes” and a healthy microbiome can enhance host fitness by providing essential nutrients [4], increasing resilience to abiotic stressors [5], and protecting against disease [4]. Each new generation of plants must recruit the microbial species (archaea, bacteria, fungi and other micro-eukarya) that make up its root microbiome from the surrounding soil, and this means that the soil microbial community is an important determinant of plant root microbiome composition [6]

Objectives

Methods

Results

Discussion

Conclusion