PDF(Pubmed)
Abstract：
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.
摘要：
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有希望的策略，但是需要实验支持和机械理解。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天然常驻微生物组的生长。通过在存在或不存在标准化土壤居民社区的情况下产生土壤微观世界，我们展示了不同的营养素可用性如何限制局灶性细菌接种剂(三种假单胞菌)的生长，以及如何通过添加人工来改善这一点，接种剂选择性营养生态位。通过琼脂糖微珠中的随机配对相互作用测定，我们证明，除了直接竞争,接种剂通过促进土壤细菌的生长而失去竞争力。用甲苯作为接种物veronii假单胞菌的选择性营养生态位的超转录组学实验表明，这种促进作用是由于常驻分类群的排泄代谢物的损失和吸收。接种剂的选择性营养生态位的产生可能有助于在其预期作用的持续时间内促进其增殖，同时限制其竞争性损失。
