Kinkel, L. L. | Search bioRxiv

bioRxiv2025

Incorporation of plant residue in corn monoculture selectively enriches antagonistic phenotypes among lignin-degrading vs non-degrading Streptomyces

Competition for limited carbon resources in the soil can drive complex microbe-microbe dynamics including selection for antagonistic resource competitors. Lignin, one of the main components of plant residue, is one source of carbon input into soil. However, the highly recalcitrant nature of lignin requires degrading organisms to invest in extracellular enzymes, whose breakdown products are susceptible to poaching by opportunistic competitors. Here, we tested two hypotheses: 1) lignin-degrading Streptomyces are more inhibitory than non-degrading isolates, and 2) competition for lignin contributes to the frequency and intensity of antagonistic phenotypes. We collected 134 Streptomyces from the soil of 55-year corn monocultures that had been managed in a +/- fertilizer by +/- residue removal factorial design. Using a subset of 24 lignin-utilizing and 24 non-utilizing isolates we measured the inhibition of each isolate against ten Streptomyces standards. Lignin-degrading Streptomyces had larger mean zones of inhibition than non-lignin-degrading populations, but only in plots where residue was retained, suggesting competition for lignin promotes the evolution or maintenance of antagonistic interactions when plant residues provide abundant lignin substrates. Among non-lignin-degrading Streptomyces, there was no difference in the frequency or intensity of antagonistic phenotypes with fertilizer or residue practices. Our results suggest that competition for byproducts of lignin degradation by lignin-degrading Streptomyces imposes selection for antagonistic phenotypes in habitats with regular residue inputs, but not in non-lignin-enriched soils. This work has potential implications for the development of antibiotic-mediated disease suppressive soils, the survival of plant pathogens within residue, and the structure and function of the soil microbial community.

microbiology↗

bioRxiv2025

Compost amendments to potato soils enrich yield-associated members of soil microbiomes across the continental US

Plant health is regulated by complex consortia of soil microbes with growth-promoting and pathogenic functions. In potato production, various soil management practices are undertaken to boost yields and suppress diseases, but connections between these practices, soil microbiomes, and tuber yields have not been characterized across diverse growing regions. To identify growing practices and microbes associated with increased yields, we established four-year field trials across eight US sites from Oregon to Maine that consisted of controls, fumigations, organic amendments, and mustard incorporations. Soil microbiomes consisted of 16S and ITS amplicon sequences from bacteria and microeukaryotes, respectively. While soil treatments influenced microbiomes differently across all field sites, eukaryotes were more sensitive than bacteria to all treatments. Soil treatments impacted proportions of distinct amplicon sequence variants (ASVs), and associations between ASVs and tuber yields varied within genus-level taxonomy and across field sites. Forty-five ASVs were identified as both treatment-impacted and yield-associated within any field site. Models identified three of thirteen compost amendment scenarios and one of thirteen fumigation scenarios that increased tuber yields by increasing proportions of these taxa within soil microbiomes. These ASVs were not influenced by treatment-associated changes in soil nutrients or organic matter, highlighting complex relationships within specific field sites that require further study to achieve the goal of implementing sustainable, microbiome-informed potato production techniques. ImportanceSoil microbes play diverse and interconnected roles in mediating plant health, growth, and disease, but understanding the specifics of how they work and applying them across different agricultural systems remains a challenge. To address this, we amassed a dataset from eight potato field sites across major US growing regions consisting of nearly two thousand soil bacterial and fungal microbiomes paired with soil chemical and tuber yield data. We describe how soil microbiomes are impacted by different soil treatments (compost amendments, chemical fumigation, and mustard incorporation), and identify treatments that boosted yields by up to 23% by increasing proportions of certain bacterial or fungal sequences. Compost amendments affected yield-associated taxa more often than other soil treatments, but these effects varied by rotation length and growing region. Changes to soil chemistry resulting from specific soil treatments did not influence abundances of yield-associated taxa, suggesting that the ways in which they may act to maintain plant vigor are field-specific and complex, calling for further study.

microbiology↗