Multispecies toxicity evaluation of extractable chemicals from commercial biodegradable plastic products.

The present essay attempts to stimulate interest and provide insight into the dynamics of internal conflicts, kin selection, and ecological interactions in multicellular, metabolically gifted microorganisms and how these processes may affect biosynthetic gene cluster (BGC) diversity. The multicellular antibiotic-producing soil bacterium Streptomyces provides a useful model for exploring how internal conflicts emerge and are resolved in biology. These organisms must balance two resource-intensive processes that can create internal conflicts-natural product biosynthesis and sporulation. In Streptomyces, there is potential to mitigate these internal conflicts through division of labour, phenotypic specialisation, and extensive gene duplication and diversification, enabling colonies to optimise both natural product production and reproductive success. Horizontal gene transfer further expands gene families and BGCs, introducing new metabolic capabilities while generating opportunities for functional divergence to reduce internal conflict and potentially promote kin selection. Natural product BGCs also possess features that could identify them as 'greenbeards' (kin selection by trait), promoting cooperation among producers and harming non-producers. The coexistence of multiple natural product BGCs and resistance mechanisms in Streptomyces is discussed in the context of the diverse eco-evolutionary processes occurring in structured natural environments, competition among close relatives, recurrent BGC acquisition, and regulatory compatibility encountered by Streptomyces.

Volatile organic compounds (VOCs) emitted by soil bacteria influence interactions with other soil microbes and plants. While their potential as plant growth promoters is well recognized, their role in promoting plant resilience to abiotic stress and the underlying molecular mechanisms remain poorly understood. Here, we investigate the role of Pseudomonas VOCs in enhancing plant resilience to drought stress Arabidopsis seedlings were exposed to VOCs emitted by Pseudomonas strains under control and osmotic stress conditions. Plant biomass and root architecture were evaluated. Root transcriptomics analysis was performed and validated using Arabidopsis mutants and metabolomics. Volatile organic compounds effects were also tested on soil-grown Brassica oleracea and on its rhizosphere microbiome. Pseudomonas VOCs promoted plant growth under both axenic and soil conditions in A. thaliana and in B. oleracea, and under control and drought conditions. Transcriptomics, metabolomics, and functional analysis revealed interactions between Pseudomonas VOCs, glucosinolates, and ABA signalling, as well as a positive association between VOC exposure and coumarin biosynthesis. VOC treatment also reshaped the rhizosphere microbiome under drought, leading to a community composition more similar to that of well-watered plants. Overall, Pseudomonas VOCs promote plant growth under drought conditions, linked to root transcriptional reprogramming and direct or indirect microbiome modulation.

Angelica dahurica var. formosana is a medicinal and edible plant. Higher abundance of Proteobacteria is an excellent characteristic of its rhizosphere bacterial community. Aspergillus niger ZJ-17 (AN17) significantly improved plant yield and quality while reducing fertilizer input application in both pot and field experiments. However, the impact of inoculants on resident soil bacteria directly determines their field application. Therefore, to systematically analyze how AN17 remodels host rhizosphere bacterial communities, we inoculated AN17 into the roots of A. dahurica var. formosana. The rhizosphere bacterial communities and root exudates were investigated at the harvest stage. Rhizosphere bacteria were isolated for in vitro experiments to elucidate the reasons for the changes in the rhizosphere bacterial community. AN17 promoted nutrient utilization and absorption in rhizosphere soil and increased the accumulation of IAA and JA in plant roots. In the microbiome, the relative abundance of rhizosphere Proteobacteria increased after inoculation. A total of 832 bacterial strains were isolated from the rhizosphere of the host for in vitro experiments. In in vitro experiments, AN17 induced the enrichment of Proteobacteria through microbial interactions and the modulation of host root exudates. These root exudates promoted the proliferation of bacterial genera with higher abundance and diversity. In the metabolome, host root activity increased following AN17 inoculation. According to the KEGG analysis of root exudates, AN17 upregulated microbial metabolism in diverse environments, the biosynthesis of alkaloids derived from the shikimate pathway and tryptophan metabolism. Correlation analysis and in vitro tests revealed that AN17 regulated the secretion of phenolic acids (4-chlorophenol, 2-oxoadipic acid, pyrogallol, and vanillic acid) from roots, which serve as crucial components driving the enrichment of Proteobacteria. In both plate and pot experiments, these bacteria promoted the growth of A. dahurica var. formosana and activated nutrient availability. We supplemented multiple growth-promoting strategies by which AN17 improves rhizosphere bacterial communities. Phenolic acids in root exudates were recognized during the stimulation of rhizosphere bacterial proliferation by AN17. The interaction relationships among plants, beneficial fungi and rhizobacteria were explored and revealed. This result provides a sustainable approach for rhizosphere bacterial optimization and chemical fertilizer reduction in agricultural production.

Artificial grassland establishment alters soil metabolomes by reshaping multi-domain microbial networks.

Microbially induced calcium carbonate precipitation (MICP) holds potential for soil stabilization and carbon sequestration efforts, with the overall efficiency of the process being a major determinant for its use in many environmental and civil engineering applications. While the biogeochemical pathways and enzymes driving MICP are known, the microbial metabolic networks and community dynamics underlying such processes remain poorly characterized. To address this gap, we interrogated a MICP-capable four-member consortium of soil bacteria (Curtobacterium flaccumfaciens, Rhodococcus qingshengii, Bacillus toyonensis and a Microbacterium species), termed carbon storing consortium - A (CSC-A). Prior work shows that CSC-A yields carbonate at a higher quantity compared to the sum of carbonate individually produced by each member, suggesting MICP is driven by community dynamics. To that end we applied a multi-omic integration approach of genomics, transcriptomics, and metabolomics to investigate potential inter-species interactions that may influence the MICP phenotype. Genomic life history characterizations identified evidence of specialization by B. toyonensis and Microbacterium, while metatranscriptomic perturbation was almost ten times greater in the absence of R. qinshengii than C.flaccumfaciens, suggesting that R. qingshengii is a keystone species when grown in urea, a molecule key to the MICP process. By comparing individual species' metabolomes to the metabolic profile of a shared well, we identified over 200 metabolites predicted to be produced or consumed by CSC-A members. Integrating both data types and mapping them to the KEGG reactome highlighted over 20 different enriched pathways with reactions related to glutamate metabolism, succinate metabolism, and branched chain amino acid biosynthesis. As succinate metabolism was a major node in this network we applied laboratory assays to confirm that additional added succinate led to increased carbonate precipitation by CSC-A, a critical validation of our modeling approach. By isolating and identifying the interconnected metabolic components underlying MICP in CSC-A, we identified keystone taxa, metabolites, and pathways important for future optimization of the application of this consortium to carbonate precipitation.

The evolutionary genomics of novel endosymbiosis in wild rhizobia bacteria.

Iterative precursor rebalancing improves phenazine-1-carboxylic acid production in engineered Pseudomonas chlororaphis.

The role of cover crops in promoting the abundance of beneficial soil microbes is increasingly gaining attention in tree crops. However, soil fungi remain comparatively understudied despite their roles in nutrient cycling and soil organic matter turnover, functions that are directly influenced by cover crops and may, in turn, affect the cash crop. This study compared the effects of cover crop mixtures to a weedy control on soil bacterial and fungal communities in young (< 10 years) and old (> 20 years) citrus orchards-with different lengths of cover cropping-across three soil depths over 2 years. Soil fungi responded to cover crops, whereas soil bacteria showed minimal changes in both orchards. In the young orchard, non-legume cover crop mixtures altered soil fungal communities three months after planting and after 2 years, both cover crop mixtures resulted in distinct community shifts relative to the control. In the old orchard, soil depth shaped fungal communities, with the strongest cover crop effects in the topsoil and subsurface soil. In both orchards, cover crops enriched potentially plant-beneficial microbial taxa, including arbuscular mycorrhizal fungi, highlighting the importance of cover crops as a management tool for driving fungal-mediated ecological processes and soil health benefits in orchard systems.

Agriculture alters protein evolution of respiratory nitrate reductase in soil bacteria at a global scale.

In Myxococcus xanthus, a predatory soil bacterium, cell polarity and motility are regulated by MglA (a small GTPase) and its regulators, MglB (a potential GAP) and RomRX (a previously proposed GEF), but their precise roles remain unclear. Using fluorescent nucleotides suitable for fluorescence anisotropy measurements, we show that RomRX does not function as a GEF but instead acts as an effector binding MglAGTP. We further find, using an enzymatic model, that MglB exhibits both GAP and GEF properties depending on the local MglAGDP concentration. Additionally, RomRX, specifically RomR, effectively dissociates the MglA-MglB complex by sequestering MglB. This low-affinity interaction permits GAP activity while still partitioning the proteins in vivo, as shown by a biomimetic oil-emulsion droplet assay in a cell-sized system. A minimal mathematical model incorporating these interactions and previous findings recapitulates how dynamic interactions between these three players form an invertible polarity axis in the M. xanthus cell.

A study was conducted during the summer season of 2025 at the College of Agriculture, University of Kufa, with the aim of biologically treating groundwater. This experiment included the sequential addition of two types of bacteria and one type of fungus (Control, Providencia rettgeri, Bacillus amyloliquefaciens and Rhizoctonia solari) to saline groundwater, as well as adding them to squash seedlings irrigated with two types of water (saline and fresh). The bacteria were isolated from multiple locations in the College of Agriculture soil, and sites clearly affected by salinity were selected. The experiment was then carried out, which included adding treatments B1, B2, F, and C to a field planted with squash seedlings irrigated with two types of irrigation water (saline and fresh). Their role in reducing the effects of salinity, pH, and the total number of soil bacteria was monitored. The addition of Rhizoctonia solari achieved superiority, recording the lowest soil electrical conductivity using fresh and saline water, reaching 79.7 and 184.7 ds m-1 , respectively, compared to the control treatment, which recorded the highest electrical conductivity, reaching 154.7 and 620.3 ds m-1 , respectively. The same treatment also achieved superiority by raising the acidity from 6.333 to 5.833 . The bacteria Providencia rettgeri, using fresh and saline water, demonstrated significant superiority in increasing the total bacterial count in the soil, recording the highest count of 89,000,000 and 61,000,000 CFU g-1 dry soil, respectively, compared to the control treatment, which recorded the lowest count of 26,000,000 and 3,300,000 CFU g-1 dry soil, respectively.

Region-specific patterns of soil bacterial communities' adaptation to hexachlorocyclohexane contamination.

Wild plants are periodically exposed to nutrient flushes, whereas modern cultivars are acclimated to regular nutrition from fertilizers. Phosphorus (P) fertilizers, however, convert into unavailable forms in soil. Here, we assessed plant growth, rhizosphere microbiome, and root exudation of a wild and modern tomato to determine how a wild crop relative responds to a flush of P fertilization. We found that the modern tomato relatively lacked P-mineralizers and grew quickly, depleting soil P. Conversely, wild tomato continued growth and promoted an array of beneficial soil bacteria, resulting in higher bioavailable soil P across development. This microbial strategy was driven by its root exudates, which were subsequently found to be enriched in trehalose and glycerol compounds. In vitro testing showed that these compounds promoted microbial P solubilization. Finally, we grew modern tomato in P-fertilized soils following a previous planting of either wild or modern tomato. Modern tomato grown in wild tomato-conditioned soils increased biomass compared to those grown in modern tomato-conditioned soils. The change may be associated with residual soil P as the wild-induced microbial community changes diminished. The root exudate driven strategy of wild tomato helps maintain soluble soil P and may be utilized in agriculture to prevent fertilizer loss.

Exposure to arsenic and cadmium promotes conjugative transfer of plasmid-borne antibiotic resistance genes among soil microbiota.

Dimethyl sulfide is a central volatile sulfur intermediate in the global sulfur cycle, traditionally associated with marine ecosystems. However, despite significant advances, important gaps remain in our understanding of its metabolism in terrestrial environments. Here, we elucidate a complete dimethyl sulfide catabolic pathway for sulfur utilization in the soil bacterium Acinetobacter baylyi ADP1 using an integrative approach combining targeted metabolomics, genetic knockouts, and in vitro enzyme assays. The pathway consists of a series of oxidation reactions catalyzed by two-component monooxygenases, including newly identified enzymes responsible for the sequential conversion of dimethyl sulfide to dimethyl sulfoxide and then dimethyl sulfone. These steps are followed by previously reported downstream enzymes that form methylsulfinate and methanesulfonate, ultimately yielding sulfite for cysteine biosynthesis. Functional redundancy and substrate promiscuity characterize these monooxygenases, all of which are powered by a single flavin reductase. A genomic survey revealed that this pathway is widespread among plant-associated and soil-dwelling Proteobacteria, including Pseudomonas putida and Rhodococcus opacus, which were experimentally confirmed to grow on DMS. Our findings reveal a widespread terrestrial DMS metabolic route that may represent a significant, yet previously unrecognized, component of the global sulfur cycle.

Traditionally, determination of explosives and their decomposition products in soil samples involves a 24-hour ultrasonic solid-liquid extraction (SLE) using acetonitrile followed by a "salting out" liquid-liquid extraction (LLE). Alternatively, aqueous extracts of soil can undergo solid-phase extraction to isolate target analytes prior to liquid chromatography. Although well suited for environmental analysis and standardized by the Environmental Protection Agency (EPA), these methods can be overly labor- and time-intensive for a forensic chemist working a post-blast investigation. This highlights the need for rapid, simple, and effective alternatives. In addition, the extent to which the post-blast residues of explosives can biodegrade due to soil bacteria is not fully characterized. In this study, we introduce total vaporization-solid phase microextraction (TV-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) as an alternative to traditional methods for environmental and forensic samples. To benchmark TV-SPME, more established methods including modified-immersion SPME GC-MS and immersion-SPME GC-MS were evaluated for their ability to identify TNT in both spiked and post-blast soils. Three soils with varying composition and organic matter content were spiked with TNT and analyzed to assess the impact of matrix on TNT recovery. In addition, three different storage temperatures (freezer, fridge, and room temperature) were examined to understand TNT degradation in post-blast soil. The chemical kinetics of the TNT degradation process were also explored. TV-SPME showed the greatest response for TNT present in soil. Among the spiked soils, those with higher organic content exhibited greater degradation over time. There is clear evidence of microbial degradation of TNT in post-blast soil over several weeks, which argues for immediate analysis of such samples or their storage at temperatures of at least -18 °C. These findings emphasize the importance of soil composition, extraction methodology and storage conditions when analyzing explosives in forensic and environmental samples.

Legume nodulation is initiated when soil bacteria rhizobia infect root hairs and is tightly regulated by host-derived mechanisms that restrict nodule numbers to balance the benefits of symbiotic nitrogen fixation with the plant's growth and metabolic demands. However, how plants actively promote the initiation of nodulation to counterbalance these restrictive mechanisms and maintain an optimal level of nodulation remains largely unknown. Here, we report a systemic regulatory mechanism through which soybean (Glycine max) promotes rhizobial infection. We show that inoculation of soybean roots with rhizobia suppresses the biogenesis of microRNA miR4416-5p in shoots, a mobile microRNA that is transported from shoots to roots. The resulting reduction of miR4416-5p levels in roots enhances the expression of a vegetative lectin gene Lectin 3 (GmLe3), which promotes rhizobial infection, thereby enhancing nodule formation and improving plant productivity under low nitrogen conditions. We further demonstrate that suppression of miR4416-5p biogenesis in shoots is triggered by the root-derived C-TERMINALLY ENCODED PEPTIDE 7 (GmCEP7), establishing a long-distance GmCEP7-miR4416-5p-GmLe3 regulatory loop that is critical for desirable symbiotic synergy and plant productivity. Comparative genomic analysis reveals that this miR4416-5p-mediated regulatory module is absent in the model legumes Medicago truncatula and Lotus japonicus but appears to be conserved in economically important legume crops common bean (Phaseolus vulgaris) and pigeonpea (Cajanus cajan), suggesting an evolutionary innovation in nodulation control. These findings uncover a systemic mechanism that promotes rhizobial infection and highlight an evolutionary innovation in regulation of nodulation with potential implications for improving legume crop productivity under nitrogen-limited conditions.

Streptomyces GMR22 exhibits anti-Porphyromonas gingivalis activity and binding affinity toward gingipain K and dipeptidyl aminopeptidase IV

Chemotaxis of bacterial swimmers that move in a run-and-turn pattern is well studied in uniform bulk fluid. It is primarily based on modulating the run time in dependence on the swimming direction with respect to the source of chemoattractant (run-time bias). Here, we provide evidence that the lophotrichously flagellated soil bacterium Pseudomonas putida may also perform chemotaxis in porous media where the free path length is severely restricted. Besides the classical run-time bias, we identify a second chemotaxis strategy, the turn-angle bias: the change in swimming direction upon a turn event is adjusted so that the orientation of the subsequent run phase is more likely to be directed toward the source of chemoattractant. We show that the resulting directional preference of runs arises from active, motor-induced turning events. Passive mechanical trapping in the porous matrix, in contrast, weakens the resulting preference of run orientations. Agent-based simulations, which rely on experimentally observed statistical properties of swimming patterns, indicate that the turn-angle bias is the predominant chemotaxis strategy of bacteria in porous environments.