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Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions

Author

Listed:
  • Senka Čaušević

    (University of Lausanne)

  • Manupriyam Dubey

    (University of Lausanne)

  • Marian Morales

    (University of Lausanne)

  • Guillem Salazar

    (ETH Zurich)

  • Vladimir Sentchilo

    (University of Lausanne)

  • Nicolas Carraro

    (University of Lausanne)

  • Hans-Joachim Ruscheweyh

    (ETH Zurich)

  • Shinichi Sunagawa

    (ETH Zurich)

  • Jan Roelof van der Meer

    (University of Lausanne)

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.

Suggested Citation

  • Senka Čaušević & Manupriyam Dubey & Marian Morales & Guillem Salazar & Vladimir Sentchilo & Nicolas Carraro & Hans-Joachim Ruscheweyh & Shinichi Sunagawa & Jan Roelof van der Meer, 2024. "Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46933-1
    DOI: 10.1038/s41467-024-46933-1
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