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Sustainable strategies: Nature-based solutions to tackle antibiotic resistance gene proliferation and improve agricultural productivity and soil quality.

The issue of antibiotic resistance is now recognized by the World Health Organisation (WHO) as one of the major problems in human health. Although its effects are evident in the healthcare settings, the root cause should be traced back to the One Health link, extending from animals to the environment. In fact, the use of organic fertilizers in agroecosystems represents one, if not the primary, cause of the introduction of antibiotics and antibiotic-resistant bacteria into the soil. Since the concentrations of antibiotics introduced into the soil are residual, the agroecosystem has become a perfect environment for the selection and proliferation of antibiotic resistance genes (ARGs). The continuous influx of these emerging contaminants (i.e., antibiotics) into the agroecosystem results in the selection and accumulation of ARGs in soil bacteria, occasionally giving rise to multi-resistant bacteria. These bacteria may harbour ARGs related to various antibiotics on their plasmids. In this context, these bacteria can potentially enter the human sphere when individuals consume food from contaminated agroecosystems, leading to the acquisition of multi-resistant bacteria. Once introduced into the nosocomial environment, these bacteria pose a significant threat to human health. In this review, we analyse how the use of digestate as an organic fertilizer can mitigate the spread of ARGs in agroecosystems. Furthermore, we highlight how, according to European guidelines, digestate can be considered a Nature-Based Solution (NBS). This NBS not only has the ability to mitigate the spread of ARGs in agroecosystems but also offers the opportunity to further improve Microbial-Based Solutions (MBS), with the aim of enhancing soil quality and productivity.

Animals

Climate-Driven Niche Tracking and Genomic Resilience Shape Future Distribution of a Widespread Agricultural Weed.

Understanding how agriculturally important species respond to environmental change is critical for maintaining productivity, mitigating agroecosystem threats and sustaining resilience. While crops have traditionally been the focus in agroecosystems, agricultural weeds are integral components that often face even stronger selective pressures, making them powerful models for investigating ecological and evolutionary responses to climatic and human-mediated challenges. Insights from how weeds adapt rapidly under these pressures can inform strategies to improve agricultural outcomes, since both pests and crops evolve under the same multivariate selective pressures. Here, we integrate two centuries of distribution records with whole-genome sequencing from natural populations of the most damaging weed in Europe-Alopecurus myosuroides (blackgrass) - to examine its ecological and evolutionary responses in agroecosystems. Blackgrass largely maintained its historical climatic niche, expanding its range primarily by tracking environments analogous to those it historically occupied. Genome-wide analyses revealed a polygenic basis of environmental responses, with most loci linked to single environmental variables and a subset showing limited environmental pleiotropy, indicating modular adaptation to the complex selective pressures of managed agricultural landscapes. Coupling these genomic-environment relationships with projected climate change and genomic offset analyses indicated that most blackgrass populations will remain well aligned with future conditions. Our findings show that ecological niche tracking and polygenic adaptation allow agricultural weeds like blackgrass to persist under rapid environmental change, offering insights relevant not only for weed management but also for designing resilient cropping systems under future climates.

Plant Weeds

The impact of Triticum aestivum L. cultivation management on genomic polymorphism of Harpalus rufipes and Silpha obscura assessed by RAPD markers.

Beetle genetics is becoming increasingly important in research on agricultural ecosystems, not only from a basic biological perspective but also for practical applications in pest management, biodiversity, and agroecosystem sustainability. Our study analyzed the genetic variability of beetle populations (Harpalus rufipes and Silpha obscura) under two types of agricultural management systems-organic and conventional-using RAPD markers. Out of six tested markers (OPB 5, OPB 8, OPB 11, OPB 12, OPB 14, and OPB 18), three markers (OPB 11, OPB 14, and OPB 18) demonstrated clear genetic differentiation between beetle samples collected from organically and conventionally cultivated wheat. The results of DNA fingerprinting and t-SNE analysis confirmed the formation of two genetic clusters corresponding to the management type. Jaccard similarity coefficient values indicated moderate to strong genetic similarity within individual management systems, while similarity between systems was weaker. These findings suggest that agronomic practices influence the genetic structure of beetle populations, likely due to ecological and anthropogenic factors such as pesticide use and landscape modification. The study emphasizes the importance of molecular markers in assessing population-level responses to agroecosystem management and their contribution to sustainable agriculture.

Animals

Adaptation to Plant Defence in an Agricultural Insect Pest: Integrating Genome Scans and Gene Expression in the Soybean Aphid Reveals Multi-Genic Pathways.

In agroecosystems, intense selection pressures cause species to adapt and spread, often leading to the evolution and persistence of pests. Understanding how pests rapidly adapt can help develop sustainable strategies for their management and improve agroecosystem health. Pest adaptation involves stable variations in DNA sequence, as well as dynamic shifts in gene expression, often mediated by non-coding regulatory elements. We examined adaptation to plant defences in the soybean aphid, Aphis glycines, in which virulent aphids have overcome plant defences and avirulent aphids have not. Previous data with laboratory colonies suggested that virulent aphids have higher overall gene expression, including transposable elements, some of which influence gene regulation. However, we lack information on how genetic variation in natural populations impacts adaptation and potentially gene regulation. We integrated population genome scans of field-collected, soybean aphid populations with gene expression profiles of virulent and avirulent laboratory colonies to uncover connections between genetic differentiation and gene regulation for virulence. Genome scan methods found 2144 single nucleotide polymorphisms (SNPs) with significant genetic differentiation (i.e., outliers) in field-collected populations. These SNPs were near 1004 genes, representing 5.16% of the effective number of genes. Based on previous RNA-Seq data with laboratory colonies, we found 3160 genes and 147 long non-coding RNAs (lncRNAs) with differential expression among virulent and avirulent biotypes. By integrating both data sets, we identified 16 genes and 5 long non-coding RNAs with differential expression and that were associated with an outlier SNP (within 10 kbp). We validated SNPs with additional field collected aphids and found an aphid clone with stronger virulence than our laboratory virulent colony, surviving on 2 different aphid-resistant soybean varieties. This new virulent clone had fixed allele differences at 9 SNPs compared to our avirulent and other virulent colony. Field collected soybean aphids matching the phenotype of this new virulent clone had significant genetic differentiation with 3 outlier SNPs near genes related to zinc transport and lachesin compared to field collected avirulent aphids. Our entire data reinforced the importance of a potential multi-genetic response to overcome plant defence and generates new insights into complex genetic and regulatory mechanisms involved in insect-plant interactions.

Animals

Orchard netting impacts on biodiversity leading to cascading effects at the ecosystem level.

Agriculture must ensure food production without further compromising the ecosystem functions upon which it depends. Agricultural practices should therefore avoid harming farmland biodiversity, especially of taxa that supply the key ecosystem services (e.g. pollination, pest control and nutrient uptake) that ultimately support crop production. Orchards are among the largest permanent plantations worldwide and are increasingly characterised by the spread of plastic nets used to protect fruits/nuts from either abiotic (anti-hail, anti-rain, shade nets) or biotic (exclusion nets) hazards. Despite having received little attention to date, these nets may impact natural communities, acting both as physical barriers and as drivers of habitat changes to which biota must respond. Species-level responses to netting depend on the organism's ability to enter the netted environment and successfully exploit available resources. Net-mediated ecological filtering and plastic behavioural responses may alter species interactions, leading to cascading ecological impacts that may create species-poorer 'netted communities' with simplified ecological networks. Such changes may erode biological control potential, other ecosystem functions, and overall system stability. We conducted a systematic review on the effects of protection nets on biota, and reported novel empirical evidence on anti-hail nets' impacts on communities of orchard-dwelling birds, flower-visiting insects, and rodents. In total, we identified 48 studies from the literature, however this literature was strongly biased towards apple orchards, western countries, and pest taxa. Net deployment was highly effective in deterring target pest species, in some cases regardless of their original function, as even weather-protection nets limited pest populations. Side effects on non-target taxa were also often reported, such as decreases in pollinators and natural enemies, and/or increases in secondary pests or microbial diseases. However, most assessments largely disregarded non-pest taxa and the broader ecological consequences of netting. The few studies that addressed the effects of nets at the guild/community level, including our empirical study, confirmed that orchard netting resulted in species-poor assemblages, with possible ecosystem-level consequences. We propose that future assessments should pay more attention to the indirect effects of netting on non-target taxa, and on the supply of crop-supporting ecosystem services mediated by wild species occurring in agroecosystems. Due to the trade-offs between these services and net-mediated crop protection, integrated alternatives should be tested to improve the environmental sustainability of food production and biodiversity conservation in farmed landscapes.

Biodiversity

Isolation of rhizobia from Ontario soils that are effective at fixing nitrogen with common bean (Phaseolus vulgaris).

UNLABELLED: Common bean (Phaseolus vulgaris) is an important crop in Canada and globally. Like other legumes, common bean establishes symbiotic interactions with nitrogen-fixing bacteria called rhizobia. However, nitrogen fixation by rhizobia in association with common bean is often suboptimal, constraining its productivity and necessitating the application of nitrogen fertilizer. To support the development of high-performing, locally adapted rhizobial inoculants for Ontario common bean growers, we isolated 216 common bean-nodulating rhizobia from southern Ontario soils using a nodule trapping approach with four common bean cultivars. Whole genome sequencing followed by phylogenomic analyses of all rhizobial isolates revealed substantial diversity, assigning them to 11 Rhizobium species, including two novel species. Nearly all isolates belong to the symbiovar phaseoli, spanning the nodC γ-a, γ-b, and α alleles, with four isolates belonging to the symbiovar gallica. Soil origin had a significant impact on the species-level community composition recovered during the nodule trapping experiments. In contrast, host trapping cultivar had only a minor influence on the recovered Rhizobium population. Greenhouse assays demonstrated that one of the novel Rhizobium species exhibited the highest average symbiotic effectiveness, although high-quality isolates were found across multiple species. Together, these results revealed a diverse and genomically variable Rhizobium community capable of forming effective symbioses with common bean in southern Ontario soils. Importantly, our genome-sequenced Rhizobium collection will serve as a valuable resource for identifying competitive and high-quality strains for the development of inoculants tailored to Ontario common bean production. IMPORTANCE: Common bean is a globally important food crop, yet its productivity is often limited by suboptimal nitrogen fixation, forcing growers to rely on synthetic fertilizers. Consequently, identifying high‑performing, locally adapted inoculant strains is essential for reducing dependence on synthetic nitrogen fertilizers and improving the sustainability of temperate agroecosystems. Our study provides a genome‑sequenced collection of common bean-nodulating Rhizobium from southern Ontario, revealing substantial species and genomic diversity across sampling locations. Greenhouse studies allowed us to identify multiple isolates that consistently fix nitrogen with, and enhance the growth of, common bean plants. Our findings highlight strong biogeographical structuring of the effective and competitive subpopulations of rhizobial communities and demonstrate that Ontario soils already harbor strains with high symbiotic potential. In addition, our Rhizobium collection represents a foundational resource to support future inoculant development and enables future work on the ecology, evolution, and applied optimization of legume-rhizobium symbioses.

Nanopore

Identification of an antifungal lipopeptide from Bacillus amyloliquefaciens HAU3 inhibiting the growth of Fusarium graminearum using preparative chromatography and 2D-NMR.

UNLABELLED: The presence of fungal contamination and its mycotoxins in animal feed is pervasive, posing a significant threat to the well-being and performance of animals, as well as the safety of animal-derived food products. In this work, we screened a strain of Bacillus amyloliquefaciens (B. amyloliquefaciens) HAU3 that exhibits efficient antifungal activity against the growth of Fusarium graminearum (F. graminearum). The antifungal activity was detected in the supernatant, with 20% sterile supernatant demonstrating an impressive antifungal rate of 98.46% against F. graminearum. The antifungal activity of the strain was evaluated through spectrum analysis and silage trials, revealing its effective antifungal activity against multiple fungal species. Furthermore, the strain is capable of degrading ZEN and its derivatives. The targeted disruption of fungal mycelial membrane was observed using scanning electron microscopy and transmission electron microscopy. Additionally, staining with the reactive oxygen species (ROS)-sensitive fluorogenic dye DCFH-DA and propidium iodide (PI) revealed that the strain induces accumulation of ROS in fungal mycelia. The active compounds underwent further separation, purification, and detection. The prominent active peak was identified through mass spectrometry and magnetic resonance spectroscopy. The molecular structure of the active compounds was predicted to be lipopeptides composed of 8 amino acids known as fengycin. The whole genome sequencing and informatics analysis unveiled a total of 13 gene clusters responsible for the synthesis of secondary metabolites. The antifungal effects of B. amyloliquefaciens HAU3 are exerted through the synthesis of fengycin, which selectively targets and compromises the integrity of fungal mycelia membranes, thereby making it a potential biocontrol agent for mitigating mycotoxin contamination in feed. IMPORTANCE: Mycotoxin contamination in animal feed, predominantly driven by Fusarium graminearum, represents a persistent threat to livestock health and food chain integrity. Here, we report the isolation of a soil-derived Bacillus amyloliquefaciens HAU3, exhibiting potent and broad-spectrum antifungal activity alongside efficient biodegradation of zearalenone and its derivatives. Mechanistic dissection reveals that fengycin, the principal bioactive metabolite, compromises fungal membrane integrity and elicits intracellular oxidative stress, culminating in hyphal collapse. Genomic profiling uncovers a diverse repertoire of biosynthetic gene clusters underpinning secondary metabolite production. These findings establish strain HAU3 as a promising microbial chassis for the development of next-generation biocontrol strategies aimed at mitigating mycotoxin burden in agroecosystems.

Bacillus amyloliquefaciens

Genomic exploration of Bacillus paralicheniformis TB197: an agrobiotechnological tool from the Sonoran Desert.

Climate change and the harmful effects of extensive agrochemical use for plant nutrition and pest control on soils, the environment, and human health are driving the search for sustainable alternatives that reduce their use while increasing plant resilience. In regenerative agriculture, microorganisms have become valuable tools, acting as biological control agents or biostimulants, such as plant growth-promoting rhizobacteria, and/or to enhance plant performance under abiotic stress. The genus Bacillus is well known for its versatile interactions with plants. Specifically, Bacillus paralicheniformis TB197 has demonstrated high efficacy in controlling phytopathogenic nematodes and adapting to diverse soil and crop conditions. Based on these traits, we explored the agricultural potential of this strain through genomic analysis and in vitro and in vivo assays. Gene analysis identified functions related to three main areas: (i) stress resistance and plant colonization, (ii) plant growth promotion, and (iii) phytopathogen control. The strain showed high tolerance to salinity and temperature, promoted plant growth, and exhibited strong antifungal activity. These findings highlight the potential of the TB197 strain as a promising candidate for developing next-generation bioinoculants.IMPORTANCEThe use of beneficial microorganisms is a pivotal strategy for mitigating the environmental impacts of intensive agriculture while preserving crop productivity. Bacillus paralicheniformis TB197 is a native desert soil bacterium with genetic traits associated with stress tolerance, plant growth promotion, and suppression of plant pathogens. In this study, we employed a multifaceted approach integrating genomic analysis and functional assays to demonstrate the strain's multifunctional potential as an agricultural bioinoculant. The results of the study demonstrate that a singular bacterial strain can integrate multiple beneficial functions relevant to sustainable agriculture. This work contributes to the field of applied microbiology by expanding the understanding of how environmentally adapted bacteria can serve as biological alternatives to chemical inputs in agroecosystems.

Bacillus

Clinical and Microbiological Insights into Caseous Lymphadenitis in Sheep and Goats in Khorasan Razavi, Iran.

INTRODUCTION: Caseous lymphadenitis (CLA), a chronic bacterial disease caused by Corynebacterium pseudotuberculosis, significantly impacts small-ruminant health and productivity worldwide, causing economic losses through reduced wool and milk yields, reproductive issues, and carcass condemnation. Despite its importance, CLA prevalence and microbial dynamics remain under explored in Iran, where small ruminants are vital to rural economies. This study assessed the prevalence, clinical manifestations, and bacteriological profile of CLA in Khorasan Razavi Province, northeast Iran, to inform regional control strategies and address potential zoonotic risks. MATERIALS & METHODS: We examined 15 flocks totaling 4,733 animals (4,640 sheep, 93 goats) through clinical inspections and microbiological analysis of pus samples from affected lymph nodes. RESULTS: The results revealed a lymphadenitis prevalence of 11.59% (95% CI, 10.58%, 12.66%), with 8.62% of sheep (400/4640) and 8.60% of goats (8/93) affected, varying across flocks from 0% to 28.57%. Submandibular lymph nodes were most commonly affected (51.35%), followed by retropharyngeal (18.02%) and parotid (15.32%) nodes, with peak incidence in the 2-3-year age group (38.24%), likely linked to shearing practices. Bacteriological analysis of 102 pus samples identified C. pseudotuberculosis in 19.6% (20/102) of cases, characterized by small, dry, white colonies with β-hemolysis on Columbia blood agar. A diverse microbial profile included Actinobacillus spp. (7.8%), Trueperella pyogenes (3.9%), and novel isolates like Acinetobacter spp. and Yersinia spp. (1.0% each), with 43.14% of samples sterile, suggesting chronicity or sampling challenges. CONCLUSION: These findings indicate CLA etiology is complex, extending beyond a single pathogen and influenced by local husbandry practices. The study underscores CLA's economic burden and zoonotic potential, given rare but documented human cases. Integrated control measures-enhanced molecular diagnostics, recombinant phospholipase D (PLD) vaccine trials, and improved biosecurity-are urgently needed. Future research should prioritize genomic strain typing and environmental reservoir analysis to refine CLA management in Northeast Iran, offering insights applicable to similar agroecosystems globally.

Animals