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

微生物群落的新特性是其组成不同成员的功能潜力的结果。根际的特定条件选择微生物，一方面支持植物生长，从根际沉积中获得能量丰富的碳源，另一方面与植物根竞争生长养分，特别是土壤氮(N)和磷(P)。这可以认为是植物与根际微生物群落之间的正反馈和负反馈。这项研究的目的是阐明根际微生物群落的功能网络对根际特性和土壤条件的响应，后者包括干旱、压实和根-土接触面积。在S伙伴P17，PP2089的第一阶段，我们成功地建立了从单个聚集体中提取DNA的方法，并基于16S rRNA聚合酶链式反应扩增片段DNA测序鉴定了细菌群落组成。用聚合DNA获得的细菌群落成员之间的网络表明，根毛的强烈影响在阿尔法多样性测量中是看不到的。在第二阶段，我们将进一步采用这种方法，在微生物功能潜力的水平上表征团聚体，基于对土壤N转化和P动员的微生物关键功能的替代遗传版本的多样性研究。我们将把我们的分子微生物群落结果与SPP合作伙伴提供的关于聚集体的3D结构和其他物理化学聚集体属性的信息结合起来。由于聚合酶链式反应的方法总是依赖于现有的遗传多样性知识，并受到引物设计的内在限制，我们还通过包括一种与聚合酶链式反应无关的鸟枪式元基因组DNA测序方法来扩展到未知的功能，从而揭示了存在于单个土壤团聚体中的几乎完整的遗传程序。我们在此SPP中与不同的合作伙伴合作，在不同的工作包内进行土柱和土壤小区田间试验的联合试验，从而获得将微生物群落信息与根系特性、根基因表达、土壤孔隙结构和水流等参数联系起来的新方法。因此，我们的研究开发的团聚体特有的微生物功能网络将为阐明根际作为一个受根和土壤性质影响的自组织系统做出重要贡献。我们对N转化和P动员的关注将使我们能够深入了解根际自组织如何在植物、土壤和微生物群落之间施加正反馈和/或负反馈。

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.