Spatiotemporal organization of the rhizosphere microbiome shaped by external drivers

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The rhizosphere microbiome plays an important role for soil ecosystem functions and plant growth and health. Self-organization of the rhizosphere arises from feedback loops between root, microbiome and soil. In phase I of the SPP2089 we aimed to unravel major external drivers shaping the spatial and temporal rhizosphere microbiome patterns. We investigated the microbiome associated with the rhizosphere of two maize genotypes (wild type (WT) and root hair defective mutant (rth3)) in two distinct soil substrates (loam (L) and sand (S)) in central soil column experiments in a growth chamber (SCE) and a soil plot experiment in the field (SPE). Sequence analysis of 16S rRNA gene and ITS amplicons from total community (TC)-DNAs revealed that the soil substrate was the strongest driver shaping the maize rhizosphere microbiome followed by soil depth and maize genotype (SCE and SPE). Unexpectedly, the presence of maize root hairs had only minor effects on the rhizosphere microbiome, in SCE and SPE. In phase II we will continue to address the hypotheses 1 and 4 and novel questions II, III and IV of the SPP2089 in more detail, to unravel spatial organization of the rhizosphere microbiome of maize depending on the soil texture and the presence of external drivers (inoculation of a consortium of beneficial microorganisms [BMs], drought conditions). We will participate in the central experiments performed both at lab (SCE_Drought) and field (SPE_BBCH19) scale, and will carry out central satellite experiments using pots and rhizoboxes (RB_Drought_BM). We hypothesize that the presence of root hairs and the inoculation of a consortium of BMs will be more important for maize growth performance and rhizosphere/rhizoplane microbiome under drought conditions. The role of root hair and spatial pattern (root tip, root base and different soil depths) of the rhizosphere microbiome of maize affected by drought and/or inoculated BMs will be investigated in a polyphasic and interdisciplinary approach (MiSeq sequencing of amplicons from TC-DNAs, qPCR, CLSM, selective plating and Winrhizo performed by our group). For the SPE_BBCH19, we will participate in the complex sampling to test the following hypotheses: (i) After four years of maize growth under field conditions soil substrate, depth and plant genotype will still be the main drivers shaping the rhizosphere microbiome and (ii) Maize root residues and deposits resulting from previous cropping will be degraded in a soil substrate-dependent manner and result in a build-up of taxa contributing to replant depression and microbial dysbiosis, using the MisSeq amplicon sequencing and qPCR. Applying the concept of self-organization to the rhizosphere and unique interdisciplinary approaches used to investigate the central experiments will enable us to gain a better understanding of the spatiotemporal rhizosphere microbiome patterns and how they are influenced by external drivers.