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Abstract Growing concerns about the global antimicrobial resistance crisis require a better understanding of how antibiotic resistance persists in soil and how antibiotic exposure impacts soil microbial communities. In agroecosystems, these responses are complex because environmental factors may influence how soil microbial communities respond to manure and antibiotic exposure. The study aimed to determine how soil type and moisture alter responses of microbial communities to additions of manure from cattle treated with antibiotics. Soil microcosms were constructed using two soil types at 15, 30, or 45% moisture. Microcosms received biweekly additions of manure from cattle given cephapirin or pirlimycin, antibiotic-free manure, or no manure. While soil type and moisture had the largest effects on microbiome structure, impacts of manure treatments on community structure and individual ARG abundances were observed across varying soil conditions. Activity was also affected, as respiration increased in the cephapirin treatment but decreased with pirlimycin. Manure from cattle antibiotics also increased NH₄⁺and decreased NO₃⁻availability in some scenarios, but the effects were heavily influenced by soil type and moisture. Overall, this work demonstrates that environmental conditions can alter how manure from cattle administered antibiotics impact the soil microbiome. A nuanced approach that considers environmental variability may benefit the long-term management of antibiotic resistance in soil systems. 

Abstract Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 unique genomes). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data and quantified the prevalence of flagellar motility across four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations. 

Abstract Ecosystem functions and services are under threat from anthropogenic global change at a planetary scale. Microorganisms are the dominant drivers of nearly all ecosystem functions and therefore ecosystem-scale responses are dependent on responses of resident microbial communities. However, the specific characteristics of microbial communities that contribute to ecosystem stability under anthropogenic stress are unknown. We evaluated bacterial drivers of ecosystem stability by generating wide experimental gradients of bacterial diversity in soils, applying stress to the soils, and measuring responses of several microbial-mediated ecosystem processes, including C and N cycling rates and soil enzyme activities. Some processes (e.g., C mineralization) exhibited positive correlations with bacterial diversity and losses of diversity resulted in reduced stability of nearly all processes. However, comprehensive evaluation of all potential bacterial drivers of the processes revealed that bacterial α diversity per se was never among the most important predictors of ecosystem functions. Instead, key predictors included total microbial biomass, 16S gene abundance, bacterial ASV membership, and abundances of specific prokaryotic taxa and functional groups (e.g., nitrifying taxa). These results suggest that bacterial α diversity may be a useful indicator of soil ecosystem function and stability, but that other characteristics of bacterial communities are stronger statistical predictors of ecosystem function and better reflect the biological mechanisms by which microbial communities influence ecosystems. Overall, our results provide insight into the role of microorganisms in supporting ecosystem function and stability by identifying specific characteristics of bacterial communities that are critical for understanding and predicting ecosystem responses to global change.