ABSTRACT Microbiome‐mediated nitrate transformation is central to nitrogen cycling in agroecosystems, yet the governing principles linking microbial functional organization to ecosystem‐scale nitrogen outcomes remain poorly resolved. Here, combining 15 N tracing, high‐throughput quantitative PCR arrays and multi‐omics across a complete rice growth cycle with a tillering‐stage survey of 15 rice‐growing regions, we identify paddy‐field periphyton as a temporally dynamic dissimilatory nitrate reduction (DNR) system whose associated genes are geographically widespread. Under aerobic incubation (dissolved oxygen > 5 mg L −1 ), early‐stage communities are dominated by incomplete denitrifiers expressing norB/norC , producing transient N 2 O, whereas later‐stage communities shift towards taxa active in dissimilatory nitrate reduction to ammonium (DNRA) and expressing nirB/nirD–nrfA/nrfH , promoting ammonium production. This transition suggests a phenology‐associated redistribution of nitrate/nitrite‐reduction pathways, redirecting nitrate‐derived nitrogen from gaseous intermediate production towards ammonium retention. Metatranscriptomics confirms coordinated suppression of denitrification and activation of DNRA, indicating a microbiome‐level transition from nitrogen loss to retention. Across the surveyed regions, both pathways were widespread but latitudinally structured, with the DNRA balance index showing a broadly unimodal pattern peaking at mid‐latitudes. Together, these results identify periphyton as an important dual‐functional DNR system linking microbiome organization to nitrogen cycling outcomes in rice paddies.
ABSTRACT The ecological fate of human faecal bacteria entering hydrological networks remains poorly understood. We investigated bacterioplankton assembly across an urbanized stream network in the Buenos Aires Metropolitan Area (Argentina), distinguishing faecal from non‐faecal taxa by cross‐referencing 192 human gut microbiome samples from three South American countries; independent source tracking confirmed a predominantly human origin. Faecal taxa occurred throughout the watershed, but their abundance was not significantly associated with Escherichia coli (Spearman's ρ = 0.25; p > 0.05), regardless of the assembly process governing them. Homogeneous selection was the most frequent assembly outcome in both faecal and non‐faecal fractions, yet dispersal limitation separated them sharply: 38.2% of non‐faecal site pairs versus 1.8% of faecal ones. Accordingly, compositional similarity declined with hydrological distance in the non‐faecal fraction but not in the faecal one, where selection was strongest between sites of similar non‐vegetated surface cover. Nestedness contributed far more to faecal than non‐faecal dissimilarity (42.7% vs. 4.3%), consistent with an external inoculum progressively filtered along the network. Faecal and non‐faecal bacterioplankton are therefore shaped by different ecological processes, which single‐indicator monitoring cannot capture. Reducing sanitary inputs, while necessary, should be complemented by strategies enhancing the environmental filtering capacity of urban stream habitats.
ABSTRACT Water sustains all living systems, maintaining human, animal, and environmental health. However, as open systems, surface waters are highly exposed to microbial and chemical pollutants, including antimicrobials. These contaminants exert selective pressure on densely packed bacterial genomes and drive mutations leading to adaptation. This review explores the dynamics and key drivers underlying the emergence and persistence of antibiotic‐resistant bacteria (ARB) in aquatic environments. It delineates both classical and novel horizontal gene transfer (HGT) mechanisms, ranging from conjugation, transduction, and transformation to outer membrane vesicles, gene transfer agents, and intercellular nanotubes. These mechanisms promote the evolution, distribution, and stable persistence of antibiotic resistance genes (ARGs) in aquatic systems, including freshwater sources. Furthermore, the review outlines surface water contaminants and their biomagnification risks in the environment and through the consumption of food from freshwater food webs, drinking water, and animal products. Finally, the review discusses potential mitigation strategies, highlighting advanced treatment technologies, constructed wetlands, and biocontrol approaches using aquatic macrophytes (e.g., water hyacinth), microalgae, and phage‐based remediation, while addressing concerns regarding safety, applicability, and scalability. Stewardship programs aligned with One Health frameworks remain vital to mitigating these global risks.
ABSTRACT Plants shape their microbiota through root exudation to resist environmental constraints. These plant's exuded metabolites also serve as hatching signals for cyst nematodes, a major crop pest, to trigger their parasitic cycle. The “suicide hatching” strategy takes advantage of these exudates as a decoy, inducing hatching of juveniles in the absence of the host plant. We questioned here the effect of the soil microbiota on the suicide hatching induction. We used the carrot cyst nematode ( Heterodera carotae, Jones) and evaluated the impact of three rotation crops (leek, turnip, and barley) and their associated fungal and bacterial communities on the hatching efficacy of carrot exudates in two types of soil. Our results indicated that hatching induction is lower when leek was previously cultivated. By analysing the covariation between hatching and microbiota composition, we identified fungal ASVs, notably Fusarium equiseti, whose abundances correlate significantly with nematode hatching. We validated that diacetoxyscirpenol, a compound produced by this species, significantly reduces nematode hatching induction. Our results demonstrated that rotation crops modulate the composition of the soil microbiome and can promote the abundance of fungi modulating the suicide hatching success. These results provide insights into plant‐microbiota‐nematode interactions for optimizing pest biocontrol strategies.
ABSTRACT Microbially‐induced corrosion (MIC) driven by redox‐active metabolites has been well studied for iron‐bearing infrastructure, but whether such pathways solubilise economically critical cobalt is poorly understood. This study uses the model bacterium Pseudomonas chlororaphis subspecies aureofaciens to test if redox‐active phenazines corrode elemental cobalt. Mutants incapable of phenazine production corroded as much cobalt as wild‐type cells after one‐week incubations with Co(0) wires, and phenazines alone did not induce corrosion. Anoxic corrosion assays with cell‐free spent medium showed that phenazines can maintain Co(0) oxidation in the absence of oxidants like oxygen, but that oxygen and live cells strongly favour corrosion. Constraining metabolic pathways contributing to corrosion by creating a ∆ phz∆hcn mutant led to twice as much cobalt being solubilised compared to the wild type due to metabolic rerouting that could affect the production of putative metallophores. Geochemical and electrochemical analyses suggested these metal‐binding metabolites keep cobalt in solution and prevent the formation of a passivation layer that inhibits MIC. This study shows that complex interactions between abiotic and biotic pathways that control the solubility and bioavailability of cobalt govern MIC. Understanding these mechanisms is critical to mitigating concerns related to MIC damaging infrastructure and optimising sustainable cobalt recovery strategies for solid waste.
