The natural microbial functions of many soils are severely degraded. Current state-of-the-art technology to restore these functions is through the isolation, screening, formulation and application of microbial inoculants and synthetic consortia. These approaches have inconsistent success, in part due to the incompatibility between the biofertilizer, crop, climate, existing soil microbiome and physicochemical characteristics of the soils. Here, we review the current state of the art in biofertilization and identify two key deficiencies in current strategies: the difficulty in designing complex multispecies biofertilizers and the bottleneck in scaling the production of complex multispecies biofertilizers. To address the challenge of producing scalable, multispecies biofertilizers, we propose to merge ecological theory with bioprocess engineering to produce ‘self-assembled communities’ enriched for particular functional guilds and adapted to a target soil and host plant. Using the nitrogen problem as an anchor, we review relevant ecology (microbial, plant and environmental), as well as reactor design strategies and operational parameters for the production of functionally enriched self-assembled communities. The use of self-assembled communities for biofertilization addresses two major hurdles in microbiome engineering: the importance of enriching microbes indigenous to (and targeted for) a specific environment and the recognized potential benefits of microbial consortia over isolates (e.g. functional redundancy). The proposed community enrichment model could also be instrumental for other microbial functions such as phosphorus solubilization, plant growth promotion or disease suppression.

中文翻译：

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通过自组装社区恢复降解的微生物组功能

许多土壤的天然微生物功能严重退化。恢复这些功能的当前最先进的技术是通过微生物接种剂和合成财团的分离，筛选，配制和应用。这些方法取得的成功不一致，部分原因是生物肥料，作物，气候，现有土壤微生物组和土壤的理化特性之间不兼容。在这里，我们回顾了生物肥料的最新技术现状，并确定了当前策略中的两个主要缺陷：设计复杂的多物种生物肥料的难度以及扩大复杂的多物种生物肥料产量的瓶颈。为了应对生产可扩展的多种生物肥料的挑战，我们建议将生态理论与生物过程工程相结合，以产生针对特定功能行会而丰富并适应目标土壤和寄主植物的“自组装社区”。我们以氮问题为锚点，回顾了相关的生态学（微生物，植物和环境），以及用于生产功能丰富的自组装社区的反应堆设计策略和操作参数。利用自我组装的社区进行生物施肥解决了微生物组工程学中的两个主要障碍：丰富特定环境（针对特定环境）的微生物的重要性以及公认的微生物群落优于分离株的潜在益处（例如功能冗余）。