Functional microbial networks in soil aggregates and their adaptation to root properties and soil conditions

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Emerging properties of microbial communities are a result of the functional potentials of their constituting diverse members. The specific conditions in the rhizosphere select for microorganisms that, on one side, support plant growth in return for receiving energy rich carbon sources from rhizodepositions, and, on the other side, compete with plant roots for growth nutrients, especially soil nitrogen (N) and phosphorous (P). These can be considered as positive and negative feedbacks between the plant and the rhizosphere microbial community, respectively. The objective of the research proposed here is to elucidate the functional networks of microbial communities in the rhizosphere in response to root properties and soil conditions, the latter including drought, compaction, and root-soil contact areas. During the 1st phase of this S partners P17, PP 2089, we, successfully established a protocol for extracting DNA from individual aggregates and characterized the bacterial community composition based on 16S rRNA PCR amplicon DNA sequencing. Networks between bacterial community members obtained with aggregate DNA indicated a strong effect of root hairs not seen with alpha-diversity measurements. For the 2nd phase we will take this approach further and characterize the aggregates at the level of their microbial functional potentials, based on studying the diversity of alternative genetic versions of microbial key functions contributing to soil N transformation and P mobilisation. We will combine our molecular microbial community results with information on the aggregates’ 3D architecture and other physico-chemical aggregate properties, as provided from SPP partners. Because PCR approaches always rely on existing knowledge on genetic diversity and are intrinsically limited by primer design, we extend to the “unknown” functions by also including a PCR-independent shotgun metagenome DNA sequencing approach, thus unveiling the almost complete genetic program which exists in individual soil aggregates. We collaborate with different partners in this SPP in context of joint experiments with soil column and soil plot field experiments done within distinct work packages and thus obtain new means to link microbial community information to root properties, root gene expression, soil pore structure and waterflow and several other parameters. The aggregate-specific microbial functional networks developed by our research should thereby make an important contribution to elucidate the rhizosphere as a self-organized system under the influence of root and soil properties. Our focus on N transformation and P mobilization will allow for insight into how rhizosphere self-organization imposes positive and/or negative feedbacks between the plant, soils and microbial communities.