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Inhibitions Dominate but Stimulations and Growth Rescues Are Not Rare Among Bacterial Isolates from Grains of Forest Soil

  • Soil Microbiology
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Abstract

Soil is a complex environment made of multiple microhabitats in which a wide variety of microorganisms co-exist and interact to form dynamic communities. While the abiotic factors that regulate the structure of these communities are now quite well documented, our knowledge of how bacteria interact with each other within these communities is still insufficient. Literature reveals so far contradictory results and is mainly focused on antagonistic interactions. To start filling this gap, we isolated 35 different bacterial isolates from grains of soil assuming that, at this scale, these bacteria would have been likely interacting in their natural habitat. We tested pairwise interactions between all isolates from each grain and scored positive and negative interactions. We compared the effects of simultaneous versus delayed co-inoculations, allowing or not to a strain to modify first its environment. One hundred fifty-seven interactions, either positive or negative, were recorded among the 525 possible one’s. Members of the Bacillus subtilis, Pseudomonas and Streptomyces genera were responsible for most inhibitions, while positive interactions occurred between isolates of the Bacillales order and only in delayed inoculation conditions. Antagonist isolates had broad spectral abilities to acquire nutrients from organic and inorganic matter, while inhibited isolates tended to have little potentials. Despite an overall domination of antagonistic interactions (87%), a third of the isolates were able to stimulate or rescue the growth of other isolates, suggesting that cooperation between bacteria may be underestimated.

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Acknowledgements

The authors wish to thank Anthony Gauthier (DynAMic lab) and Yoann Guignet (IAM lab) for the assistance in the laboratory procedure.

Funding

This work was supported by the French National Research Agency through the Laboratory of Excellence ARBRE (ANR-11-LABX 0002 01) and Agreenium (Agreenskills grant). M.G. was supported by a CJS (Contrat Jeune Scientifique) grant from INRA.

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Author notes

  1. Aurélie Deveau and Bertrand Aigle contributed equally to this work.

Authors and Affiliations

  1. Université de Lorraine, INRAE, IAM, F-54000, Nancy, France

    Milena Gonzalo & Aurélie Deveau

  2. Université de Lorraine, INRAE , DynAMic, F-54000, Nancy, France

    Milena Gonzalo & Bertrand Aigle

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  1. Milena Gonzalo
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  2. Aurélie Deveau
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Correspondence to Aurélie Deveau or Bertrand Aigle.

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Supplemental Figure 3. Comparison of inhibition behaviours of isolates from grain 1 and grain 2. A. Distribution of intensities of inhibitions of isolates from grain 1 (black bars) and from grain 2 (white bars). B. Distribution of the receiver degree for inhibition of isolates from grain 1 (black bars) and from grain 2 (white bars). Differences among ditribution were tested with X2 tests (PDF 68.6 kb)

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Gonzalo, M., Deveau, A. & Aigle, B. Inhibitions Dominate but Stimulations and Growth Rescues Are Not Rare Among Bacterial Isolates from Grains of Forest Soil. Microb Ecol 80, 872–884 (2020). https://doi.org/10.1007/s00248-020-01579-6

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