Microbiome engineering – the targeted manipulation of microbial communities – is considered a promising strategy to restore ecosystems, but experimental support and mechanistic understanding are required. Here, we show that bacterial inoculants for soil microbiome engineering may fail to establish because they inadvertently facilitate growth of native resident microbiomes. By generating soil microcosms in presence or absence of standardized soil resident communities, we show how different nutrient availabilities limit outgrowth of focal bacterial inoculants (three Pseudomonads), and how this might be improved by adding an artificial, inoculant-selective nutrient niche. Through random paired interaction assays in agarose micro-beads, we demonstrate that, in addition to direct competition, inoculants lose competitiveness by facilitating growth of resident soil bacteria. Metatranscriptomics experiments with toluene as selective nutrient niche for the inoculant Pseudomonas veronii indicate that this facilitation is due to loss and uptake of excreted metabolites by resident taxa. Generation of selective nutrient niches for inoculants may help to favor their proliferation for the duration of their intended action while limiting their competitive loss.

微生物组工程——对微生物群落的有针对性的操纵——被认为是恢复生态系统的一种有前景的策略，但需要实验支持和机制理解。在这里，我们表明，用于土壤微生物组工程的细菌接种剂可能无法建立，因为它们无意中促进了本地微生物组的生长。通过在存在或不存在标准化土壤居民群落的情况下生成土壤微观世界，我们展示了不同的养分有效性如何限制焦点细菌接种剂（三种假单胞菌）的生长，以及如何通过添加人工的、接种剂选择性的养分生态位来改善这一点。通过琼脂糖微珠的随机配对相互作用测定，我们证明，除了直接竞争之外，接种剂还通过促进常驻土壤细菌的生长而失去竞争力。使用甲苯作为接种剂维氏假单胞菌的选择性营养位的宏转录组学实验表明，这种促进作用是由于常驻类群对排泄代谢物的损失和吸收造成的。为接种剂生成选择性营养位可能有助于在其预期作用期间促进其增殖，同时限制其竞争损失。