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

Abstract

Background Conventional 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. Results Metabarcoding 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. Conclusions The 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.

Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome

“…The other dominant phyla are Basidiomycota and Chytridiomycota (5-15% each; Table 1). At genus level, Mortiella (phylum Mucoromycota), Verticillum (Ascomycota), Donn et al, 2015;Rascovan et al, 2016;Mahoney et al, 2017;Fan et al, 2018;Tkacz et al, 2020;Prudence et al, 2021 Acidobacteria 0.5 (Gundibinyal, Australia; k)…”

“…11.5 14 (a, b, c, d, e, f, g, h, i, j, k, l, NS) 5 Turner et al, 2013;Donn et al, 2015;Rascovan et al, 2016;Mahoney et al, 2017;Fan et al, 2018;Tkacz et al, 2020;Prudence et al, 2021 Actinobacteria 1.0 (Villa Saboya, Argentina; l) 26.0 (Gundibinyal, Australia; k)…”

“…12.9 14 (a, b, c, d, e, f, g, h, i, j, k, l, NS) 5 Turner et al, 2013;Donn et al, 2015;Rascovan et al, 2016;Mahoney et al, 2017;Fan et al, 2018;Tkacz et al, 2020;Prudence et Min and Max correspond to minimum and maximum occurrences observed for each phylum in the specified references, after combining data from all replicate plants of one genotype (indicated between parentheses), at one growth stage, for one treatment in one soil of one geographic location (indicated between parentheses). For each phylum, the mean is calculated from all the values obtained from the different geographic locations and T. aestivum genotypes.…”

“…The bacterial community of the root endosphere of T. aestivum, in contrast with that of the rhizosphere, is dominated by Actinobacteria (Tkacz et al, 2020;Prudence et al, 2021).…”

“…They are followed by Proteobacteria (about 30%), and then Bacteroidetes, Acidobacteria and Verrucomicrobia (each at 5-10%). At family level, the Streptomycetaceae (Actinobacteria) dominates the endophytic community, followed by Chitinophagaceae (Bacteroidetes) and Polyangiaceae (Proteobacteria) (Prudence et al, 2021), whereas at genus level Streptomyces, Microbispora, Micromonospora, and Nocardioides (all in the Actinobacteria phylum) are prevalent (Coombs and Franco, 2003). Root archaeal endophytes consist mainly of Thaumarchaeota (about 60% of the community) and Euryarchaeota (about 30%) (Table 3; Tkacz et al, 2020).…”