Restoring degraded microbiome function with self-assembled communities

FEMS Microbiology Ecology, vol. 96

Abstract

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.

Authors 4

1. Carlos Fernando Gutiérrez

   Universidad del Valle

   Affiliation as printed

   Environmental Microbiology and Biotechnology Laboratory, Engineering School of Environmental and Natural Resources, Engineering Faculty, Universidad del Valle, 760032, Cali, Colombia

2. Janeth Sanabria

   Universidad del Valle

   Affiliation as printed

   Environmental Microbiology and Biotechnology Laboratory, Engineering School of Environmental and Natural Resources, Engineering Faculty, Universidad del Valle, 760032, Cali, Colombia

3. Jos M. Raaijmakers Aachen Institute of Biology, Leiden University

   Leiden University · Netherlands Institute of Ecology

   Affiliation as printed

   Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands

   Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands

4. Ben O. Oyserman corresponding

   Netherlands Institute of Ecology · Wageningen University & Research

   Affiliation as printed

   Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1,6708 PB, Wageningen, The Netherlands

   Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands