James M. Tiedje

Livestock manure is a prominent One Health setting for antimicrobial resistance (AMR), yet the contribution of viruses to resistome assembly remains unresolved. Here we compile the Livestock Manure Virus Database (LMVD), a global catalog of 1,330,372 viral operational taxonomic units reconstructed from 4,017 metagenomes. Livestock manure viral communities exhibit restricted biogeographic distributions, and antibiotic use and farming scale show the highest relative predictive importance for viral diversity. Viral genomes contained 78 antibiotic resistance gene (ARG) subtypes, representing 9.1% of resistome diversity in livestock manure, but virus-encoded ARGs were infrequent. Bacteriophages instead showed extensive predicted links to bacterial hosts, with nearly all antibiotic-resistant bacteria linked to viruses, predominantly temperate viruses, and enrichment in pathogenic antibiotic-resistant bacteria. Together, these findings place bounds on the contribution of viruses to direct ARG dissemination and indicate that lysogenic interactions with resistant hosts may shape AMR risk.

Deep soils represent one of Earth’s largest yet most enigmatic microbial habitats, where survival strategies under extreme oligotrophy remain poorly understood. Here, we report the Aridivitia group, a globally distributed bacterial lineage enriched in oligotrophic soils and thriving down to 22 m depth across sites in the United States and China. Despite its genome reduction (average size ~2.9 Mb), Aridivitia exhibits high metabolic flexibility in utilizing diverse carbon and energy sources. Cellular, genomic, and metatranscriptomic evidence, including small cell and genome sizes, host-associated metabolism, and the active expression of attachment- and attack-associated surface structures such as Tad pili and pore-forming toxins, indicate a predatory lifestyle in Aridivitia. Ancestral genome reconstruction reveals that Aridivitia originated as free-living mixotrophs, but subsequently lost the ability to fix carbon as they evolved a predatory lifestyle. Collectively, Aridivitia exemplifies a unique evolutionary strategy that reconciles genome reduction with functional versatility, expanding our understanding of microbial adaptation and evolution at the energetic limits of life.

As droughts become increasingly severe and prolonged worldwide, understanding how belowground biodiversity changes over time under water limitation is critical for assessing ecosystem resilience. However, long-term and continuous observations of soil microbial responses to drought remain rare. Here, using a 6-y experimental drought in a tallgrass prairie ecosystem, we showed that experimental drought reshaped the community compositions of soil bacteria, fungi, and protists, accompanied by progressive declines in microbial diversity and biomass. Analyses of time-decay relationships and paired community differences between drought and ambient conditions revealed increasingly divergent successional trajectories of soil microbiota under drought. Although stochastic processes dominated community assembly overall, their relative importance declined over time, particularly for bacteria in drought-treated soils, suggesting increasingly strong deterministic environmental filtering imposed by drought. In addition, drought reduced microbial network size but increased the complexity and stability of bacterial networks by favoring drought-tolerant taxa. Furthermore, drought-driven shifts in microbial community compositions significantly altered functional genes and associated ecosystem functioning. These findings suggest that microbial communities may become less variable but more vulnerable, and the detrimental effects of biodiversity loss on ecosystems could be more severe in an increasingly drought-prone world.

Cobamides are essential nutrients for most organisms but are only biosynthesized by a limited number of taxa through aerobic and anaerobic pathways. Although the origin of these widespread shared cofactors changed ecosystems and the metabolisms of living organisms, little evolutionary information is available about the biosynthetic genes and the producers. Here, we established a timeframe for the emergence of cobamide biosynthesis genes and producers, using a series of Bayesian molecular clock analyses combined with phylogenetic reconciliation. We revealed the partial producers of tetrapyrrole precursor and corrin ring were earlier than the oldest cobamide producer, suggesting the possibility that cobamide-like compounds may have existed before the emergence of their de novo producers. We also found that the anaerobic de novo producers and corrin ring producers emerged first ( Pelobacter , around 2458 Mya), and that the Great Oxidation Event postdated emergence of aerobic producers ( Kribbella , around 1784 Mya). These findings reveal the chronology of cobamide biosynthesis, which greatly changed global ecological frameworks and resulted in the current biosphere, and can guide the exploration of cross-feeding and the origin of diverse organisms on the planet.

Crop succession involving soybean and maize is the predominant grain production system in many regions, while crop rotation is often recommended to enhance sustainability. However, the specific effects of these practices on plant disease dynamics and soil microbial diversity remain insufficiently understood. This study evaluated bacterial community diversity and the presence of Fusarium verticillioides fumonisin-producing strains (fum1) under monoculture and rotational systems. Maize stalks were used to assess the influence of land use on pathogen persistence in crop residues. Metagenomic sequencing (16S rRNA, V3–V4 region) was conducted across four growing seasons (2016/2017 to 2019/2020). Results showed that a three-year rotation did not significantly increase soil bacterial diversity compared to continuous maize or soybean cultivation. Precipitation was a major driver of community composition during the first three seasons, with Actinobacteria dominating in the driest year. Both bulk soil and rhizosphere microbial communities were shaped by prior land use, with continuous soybean showing the highest diversity indices. Community composition differed most between continuous soybean and rotational systems. The abundance of fum1 decreased in soils under crop rotation but remained lower in maize stalks under continuous maize. Interestingly, continuous maize cultivation appeared to suppress some diseases, suggesting that not all pathogens respond equally to rotation. While crop rotation generally reduces disease incidence, it may promote others, highlighting the need for integrated management strategies, particularly those targeting pathogen survival in crop residues.

Soils are major reservoirs of antimicrobial resistance genes. Understanding how remediation strategies influence the specific bacteria responsible for antibiotic degradation remains both critical and challenging. Here, we use DNA stable-isotope probing to identify the active sulfadiazine-degrading microbiome and show that a biochar-biofilm composite carrying Arthrobacter D2 modulates resistance dynamics. In a less fertile Ultisol, the composite accelerated the removal of extractable sulfadiazine from bulk soil and reduced the total abundance of antimicrobial resistance genes and virulence factors. The more fertile Mollisol showed overall community resilience; however, targeted analysis of active sulfadiazine degraders revealed reduced diversity of resistance determinants in both soils. Importantly, distinguishing active sulfadiazine degraders from the total community uncovered resistance dynamics that bulk soil analyses failed to detect. These findings demonstrate that biochar-biofilm strategies can suppress resistance potential among key antibiotic-degrading bacteria, thereby potentially enhancing ecosystem safety in low-fertility soils.

The rhizosphere microbiome plays a crucial role in the resistance to soilborne plant diseases. However, the principles needed to explain and predict which microbiota will be effective against soilborne pathogens are still lacking due to the complexity of the soil microbial community. We hypothesized that, independent of particular microbial strains, a high diversity is associated with, or increases the probability of, effective suppression. We tested this hypothesis by demonstrating that random combinations of rhizosphere microbial isolates, with the same bacterial diversity, had an equal impact on suppressing root diseases. The incidence of root rot was significantly reduced when soil bacterial diversity was high. We further investigated how high-diversity bacterial communities suppress root rot by constructing synthetic bacterial communities (SynComs). The results suggest that high bacterial diversity suppresses pathogens through mechanisms potentially including nutrient competition and the formation of physical barriers on the root surface. Our study highlights that high bacterial diversity is beneficial for suppressing soilborne plant diseases, offering a nonchemical and sustainable approach for crop disease management.

The movement of exogenous chemicals through cell membranes using transport proteins and causing functional impairments to organisms is an important issue of molecular ecology. Per- and polyfluoroalkyl substances (PFAS) receives intensive concern by their global contamination and a limited understanding of their biological effects. Energy-coupling factor (ECF) transporters are critical to the absorption of vital micronutrients by bacteria and archaea, playing a significant role in maintaining microecological health. Our study found perfluorooctane sulfonate (PFOS) as an inhibitor on folate ECF transporter through competitive binding with folate and conformational alterations in ATP-binding domains, resulting in reduced folate absorption and ATPase activity. Molecular dynamics simulations depicted the process of PFOS internalization into plasma membrane prior to contact with ECF transporter. Using cryogenic electron microscopy (cryo-EM), we observed the conformational alterations caused by PFOS. The interaction mechanism between PFOS and folate ECF transporter was finally revealed though the combined approaches of cryo-EM and molecular simulation and elucidated as three critical pathway: membrane perturbation, competitive binding, and conformational changes. These findings reveal the functional impairments of exogenous chemicals on ECF transporters and advance the knowledge of ecotoxicity of PFAS.

Graphical Comparative genomic analysis revealed that I-F3 CASTs serve as important mobile genetic elements mediating horizontal transfer of functional genes associated with defence, resistance and electron transfer in Shewanella. The transposition function of a new I-F3 CAST variant carried by strain ANA-3 was assessed both endogenously and heterologously.

Livestock farming consumes more than 70% of global antibiotics annually, making livestock manures an important vector of anthropogenically influenced antibiotic resistance genes (ARGs). The global pattern of the livestock resistome, its driving mechanisms, and transmission potential to the clinic are not well assessed. We analyzed 4017 livestock manure metagenomes from 26 countries and constructed a comprehensive catalog of livestock ARGs and metagenome-assembled genomes. Livestock resistome is a substantial reservoir of known (2291 subtypes) and latent ARGs (3166 subtypes) and is highly connectable to human resistomes. We depicted the global pattern of livestock resistome and prevalence of clinically critical ARGs, highlighting the role of farm and human antibiotic stewardship in shaping livestock resistome. We developed a risk-assessment framework by integrating mobility potential, clinical significance, and host pathogenic relevance, and prioritized higher risk livestock ARGs, producing a predictive global map of livestock resistome risks that can help guide research and policy.