Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils

Abstract

<jats:title>Abstract</jats:title><jats:p>Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea, bacteria) and eukaryotic (fungi, protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 179 taxa (2 archaea, 104 bacteria, 41 fungi, 32 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our dataset. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.</jats:p><jats:sec><jats:title>Graphical Abstract</jats:title><jats:fig id="ufig1" position="float" fig-type="figure" orientation="portrait"><jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="777383v2_ufig1" position="float" orientation="portrait" /></jats:fig></jats:sec>

Defining the wheat microbiome: Towards microbiome-facilitated crop production

“… Type Factor Reference Anthropogenic Exogenous compounds (fungicide) [18] , [19] Exogenous compounds (glyphosate) [20] Exogenous compounds (insecticides) [21] Exogenous compounds (phosphine fumigation of stored wheat grains) [22] Exogenous compounds (plastic mulch film residues) [23] Fertilization [24] , [25] , [26] , [27] , [28] , [29] , [30] , [31] , [32] , [33] Inoculation of biocontrol agent [26] , [34] , [35] Land use [36] , [37] , [38] Management type [39] , [40] , [41] Overhead irrigation [42] Rotation [43] , [44] , [45] , [46] , [47] , [48] Tillage [40] , …”

“…The effect of different wheat genotypes has been thoroughly investigated [32] , [33] , [43] , [52] , [55] , [58] , [60] , [69] , [70] , [77] , [78] and those differences could be attributed to the differential root exudate chemistry [60] , [69] , [78] and disease susceptibility [70] , [77] . The use of genome-wide association studies (GWAS) will likely improve our understanding of the genetic basis of microbiome selection by host plants [58] .…”

“…In addition, it is important to consider the core microbiome, members being consistent features of a dataset that are hypothesized to reflect underlying functional relationships with the host [102] . Different approaches have been used to determine the core microbiome of plants such as the use of a theoretical framework [103] , abundance-occupancy distribution [102] , microbiome package in R [32] , [104] , network analyses [105] , DESeq2 [38] , QIIME 2 [37] , [106] , [107] . Although the term “core microbiome” has been widely used, there is disagreement surrounding its definition and to the method that should be deployed to define the core microbes which are associated with a given host [108] .…”

“…Attempts to define the core microbiome of wheat have utilized large datasets [38] . One study identified a core microbiome of 30 bacterial, 24 fungal and 10 taxa assigned to protists by utilizing data from three wheat genotypes grown in eight contrasting soils from Europe and Africa [32] . In another study, Rossmann et al [37] identified 22 bacterial and 13 fungal taxa and 3 taxa assigned to protists corresponding to the core microbiome of modern wheat cultivars.…”

“…

Fig. 2 Correlation plot showing 256 bacterial genera commonly associated to wheat from ten studies (A-J) (A-Simonin et al [32] ; B- Rossmann et al [37] ; C- Araujo et al [35] ; D- Mahoney et al [69] ; E- Kavamura et al [27] ; F- Kavamura et al [36] ; G- Kavamura et al [72] ; H- Schlatter et al [38] ; I- Schlatter et al [56] ; J- Mavrodi et al [42] ). Studies A and B determined the core microbiome using R microbiome package and QIIME, respectively.

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