Strain-specific higher-order interactions break phylogenetic conservatism in microbial communities

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Whether strains of the same species sharing the same ecological role are truly interchangeable has not been directly tested experimentally in communities, where higher-order interactions govern outcomes. Using 79 co-occurring Bacillaceae isolates from the Cuatrocienegas Basin, we combined whole-genome analyses with systematic strain substitutions in BARS, a three-species community in which a resistant strain protects a sensitive strain from an antagonist. Trait conservatism strongly predicted pairwise antagonistic outcomes. Yet across 34 assembled triads, 13 showed rescue beyond pairwise expectations and five showed suppression; single-strain substitutions rarely restored protection, although protection was recovered in one fully reconfigured triad. These outcomes could not be inferred from taxonomic relatedness, pangenomic content or pairwise assays; phylogenetic conservatism thus reaches its limit at the transition from pairwise to higher-order interactions. To explain this limit, we propose that strains behave as non-equivalent biological tiles whose interaction edges must align, a dynamic biological tessellation .

Authors 9

1. Emmanuel Cordero-Martínez

   Instituto Politécnico Nacional

   Affiliation as printed

   Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional, Unidad Irapuato, Mexico;

2. Marisol Navarro-Miranda

   Instituto Politécnico Nacional

   Affiliation as printed

   Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional, Unidad Irapuato, Mexico;

3. Obed Ramírez‐Sánchez
   Affiliation as printed

   Department of Soil Genomics & Discovery, Solena Ag. Leon, Mexico;

4. Edder D. Bustos‐Díaz Aachen

   Naturalis Biodiversity Center

   Affiliation as printed

   Naturalis Biodiversity Center, Darwinweg 2, 2333CR, Leiden, the Netherlands; Aging Research Center, Cinvestav Sede Sur, Mexico City, Mexico;

5. Victor M. Higareda‐Alvear
   Affiliation as printed

   Department of Soil Genomics & Discovery, Solena Ag. Leon, Mexico;

6. Gabriel Moreno‐Hagelsieb

   Wilfrid Laurier University

   Affiliation as printed

   Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada;

7. Jorge Rocha

   Centro de Investigaciones Biológicas Margarita Salas

   Affiliation as printed

   Centro de Investigaciones Biologicas del Noroeste, Mexico;

8. Maribel Hernández-Rosales

   Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional

   Affiliation as printed

   CINVESTAV Unidad Irapuato: Centro de Investigacion y de Estudios Avanzados Unidad Irapuato

9. Gabriela Olmedo‐Álvarez

   Instituto Politécnico Nacional

   Affiliation as printed

   Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional, Unidad Irapuato, Mexico;