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

Senka Čaušević, Manupriyam Dubey, Marian Morales, Guillem Salazar, Vladimir Sentchilo, Nicolas Carraro, Hans-Joachim Ruscheweyh, Shinichi Sunagawa and Jan Roelof van der Meer ()
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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

Nature Communications, 2024, vol. 15, issue 1, 1-19

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-46933-1

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