The assembly of root-associated microbes during the seedling stage has strong impact on subsequent performance of crops. Major factors influencing this assembly are crop species identity and composition of potential root-colonizing microbes in the bulk soil. The latter can be modified by soil management, such as organic amendments. The incorporation of residues of cover crops before the start of the growing season of cash crops presents an interesting option for steering of root-associated seedling microbiomes as there is a wide range of cover crops species with different properties available for farmers.

In a greenhouse study, we examined the effect of soil amendments with milled shoot and root materials of seven cover crop species (niger seed, phacelia, rapeseed, radish, vetch, black oat and buckwheat) on the assembly of root-associated bacteria and fungi of seedlings of four cash crop species (asparagus, carrot, onion and sugar beet). Field-grown cover crops material used for the study was collected at two time points (before and after winter) which had strong impact on plant elemental composition. The soil used for the study was a mixture of sandy arable soils with a history of soil-borne fungal diseases (Fusarium and Rhizoctonia). Within the context of a strong selection of root-associated microbes by cash crop species, we found significant modifying effects by cover crop materials. We show that cover crop elemental composition had a stronger effect than cover crop species identity. High quality residues (with low C/N ratio) caused profound shifts within root-associated Proteobacteria and increases in relative abundance of certain microbial groups such as Bacillaceae and Mortierellomycetes. These changes coincided with differences in establishment and survival of cash crop seedlings. Tolerance of sugar beet seedlings against the fungal pathogen Rhizoctonia solani was correlated with residues causing increases of root-associated Oxalobacteraceae, Bacillaceae and Mortierellaceae. However, the same residues increased Fusarium-induced failure of asparagus seed germination. This indicates that fine-tuning of cover crops amendments for different cash crops is required to realize enhanced functioning of root microbiomes.

幼苗期根相关微生物的聚集对作物的后续性能有很大影响。影响这种组装的主要因素是作物物种特性和大块土壤中潜在根系定植微生物的组成。后者可以通过土壤管理进行修改，例如有机改良剂。在经济作物生长季节开始之前加入覆盖作物的残留物为引导与根相关的幼苗微生物组提供了一个有趣的选择，因为农民可以使用各种具有不同特性的覆盖作物物种。

在一项温室研究中，我们研究了土壤改良剂对七种覆盖作物物种（尼日尔种子、phacelia、油菜籽、萝卜、紫云英、黑燕麦和荞麦）的研磨芽和根材料对根相关细菌和真菌组装的影响四种经济作物（芦笋、胡萝卜、洋葱和甜菜）的幼苗。用于研究的田间覆盖作物材料是在两个时间点（冬季前后）收集的，这对植物元素组成有很大的影响。用于研究的土壤是具有土传真菌病史（镰刀菌和丝核菌）的沙质耕地的混合物）。在经济作物物种对根系相关微生物进行强烈选择的背景下，我们发现覆盖作物材料具有显着的修饰效果。我们表明，覆盖作物元素组成比覆盖作物物种特性具有更强的影响。高质量的残留物（低 C/N 比）导致根相关变形菌内发生深刻变化，并增加某些微生物群（如芽孢杆菌和被孢霉）的相对丰度。这些变化与经济作物幼苗的建立和成活的差异相吻合。甜菜幼苗对真菌病原体立枯丝核菌的耐受性与导致与根相关的草酸杆菌科、芽孢杆菌科和被孢霉属增加的残留有关。然而，相同的残留物增加了镰刀菌诱导的芦笋种子萌发失败。这表明需要对不同经济作物的覆盖作物修正进行微调，以实现根系微生物组的增强功能。