Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies

Abstract

Microorganisms have evolved various life-history strategies to survive fluctuating resource conditions in soils. However, it remains elusive how the life-history strategies of microorganisms influence their processing of organic carbon, which may affect microbial interactions and carbon cycling in soils. Here, we characterized the genomic traits, exometabolite profiles, and interactions of soil bacteria representing copiotrophic and oligotrophic strategists. Isolates were selected based on differences in ribosomal RNA operon (rrn) copy number, as a proxy for life-history strategies, with pairs of “high” and “low” rrn copy number isolates represented within the Micrococcales, Corynebacteriales, and Bacillales. We found that high rrn isolates consumed a greater diversity and amount of substrates than low rrn isolates in a defined growth medium containing common soil metabolites. We estimated overlap in substrate utilization profiles to predict the potential for resource competition and found that high rrn isolates tended to have a greater potential for competitive interactions. The predicted interactions positively correlated with the measured interactions that were dominated by negative interactions as determined through sequential growth experiments. This suggests that resource competition was a major force governing interactions among isolates, while cross-feeding of metabolic secretion likely contributed to the relatively rare positive interactions observed. By connecting bacterial life-history strategies, genomic features, and metabolism, our study advances the understanding of the links between bacterial community composition and the transformation of carbon in soils.

Reproducible growth ofBrachypodium distachyonin fabricated ecosystems (EcoFAB 2.0) reveals that nitrogen form and starvation modulate root exudation

“…5A) . This is consistent with a recent study that showed that coumaric acid is generally not a preferred microbial substrate by soil bacterial isolates in vitro ( 49 ). Our data suggest that concentrations of 500 µM and higher can have phytotoxic activity on Brachypodium seedlings and may negatively impact crop productivity ( Fig.…”

Low and high nucleic acid content bacteria play discrepant roles in response to various carbon supply modes

“…Within these, only the order Micrococcales had a significantly higher relative abundance in LNA bacteria. Their isolates had the potential to compete with others for substrates (Wang, Wilhelm, et al, 2022).…”

Life history strategies and niches of soil bacteria emerge from interacting thermodynamic, biophysical, and metabolic traits

“…In particular, for senescing roots that have ceased exudation, microbial investment in extracellular polymer breakdown will further increase resource-based niche partitioning [42]. Further, positive interactions between rhizosphere bacteria may contribute to a more efficient microbial stabilization route via cross-feeding of metabolic byproducts [67], although the stability of microbially-derived carbon is likely impacted by the mechanism and kinetics of microbial mortality [60].…”

“…Due to their metabolic diversity, bacteria with larger genomes may be more ecologically successful where resources are scarce but diverse, and where there is little penalty for slow growth [13]. In contrast, bacteria found to be resource generalists in culture have higher rRNA copy numbers, indicative of copiotroph lifestyles, than bacteria with low rRNA copy numbers that were associated with a higher degree of specialization [67]. These mixed results question whether evolutionary trade-offs between power and yield can be generalized from genomes alone.…”