For more than four decades, the catechol route has been the only genetically resolved aerobic pathway for aniline biodegradation. The genetic basis of aniline degradation via 2-aminophenol is relatively unexplored. In this study, Pseudomonas sp. ANNB1 degraded aniline aerobically with trace accumulation of 2-aminophenol, phenylhydroxylamine, nitrosobenzene and nitrobenzene. The ANNB1 genome encodes a dmp gene cluster and two nbz operons, consistent with the degradation ability of this strain towards phenol and 2-aminophenol. During aniline degradation, the transcription levels of both dmp and nbz genes were significantly elevated. Deletion of nbzCaCb caused 2-aminophenol accumulation and a 79.5% reduction in aniline removal, whereas loss of dmpMNOP abolished aniline degradation. Compared to previously characterised aniline-degradative gene clusters, the dmp operon has a broader phylogenetic distribution. Moreover, co-cultures of phenol- and 2-aminophenol-degraders showed synergistic aniline degradation in the presence of additional carbon and nitrogen sources. In conclusion, phenol hydroxylase can initiate aniline degradation by catalysing it to 2-aminophenol. Furthermore, this work provides a genetic framework for engineering synthetic consortia targeting multiple pollutants.

Petroleum refining activities exert substantial contamination pressure on soil ecosystems, yet the corresponding microbial response mechanisms remain insufficiently understood. This study integrates source apportionment, high-throughput sequencing and co-occurrence network analysis to elucidate microbial adaptations along a petroleum exposure gradient. Source analysis confirmed that all soils were predominantly influenced by petroleum-derived inputs, with hydrocarbon concentrations increasing significantly across gradients. Under contamination levels of 422.35-621.21 mg/kg, petroleum pollution not only reduced soil total organic carbon (TOC) but also induced coupled C-N interactions and altered soil physicochemical properties, resulting in complex environmental effects. The soil quality index (SQI) exhibited a nonlinear trend, first decreasing and then increasing, with moderate overall levels (0.40-0.45). Functional diversity analyses indicated functional convergence rather than loss under contamination stress. At the metabolic level, low exposure primarily stimulated naphthalene degradation and detoxification pathways, whereas high exposure shifted microbial functions towards oxidative stress resistance and membrane structural remodelling. Meanwhile, microbial networks transitioned from densely connected but disturbance-sensitive structures at low exposure to simplified yet more stable and robust configurations at high exposure. These findings provide mechanistic insights into microbial adaptation in petroleum-contaminated soils and offer theoretical support for bioremediation strategies.

Bacterial bioremediation involves bacterial strains and communities and their complex interactions with the environment, aiming to restore ecological balance by degrading contaminants in natural systems (soil, water, air). These processes rely on coordinated gene clusters encoding catabolic pathways. Many xenobiotic-catabolic gene clusters (XGCs) reside on mobile genetic elements (MGE), enabling horizontal gene transfer (HGT) and genome rearrangements that drive rapid microbial adaptation to anthropogenic contaminants. Here we review the evolutionary and ecological roles of HGT and genome restructuring in assembling and optimising biodegradative functions. We introduce the concept of metabolic HGT hubs-microbial taxa, mobile elements, and ecological features that serve as central nodes for gene exchange-facilitating metabolic innovation and cooperation within microbial consortia. These processes enhance ecosystem resilience and pollutant degradation efficiency by promoting functional redundancy and metabolic division of labour. Understanding these dynamics informs strategies for engineering microbial communities and genetic bioaugmentation to improve bioremediation outcomes. Our perspective highlights bioremediation as an extension of metabolic network evolution under anthropogenic selection, emphasising both its potential and the need to consider ecological and biosafety implications.

Sulfur is a vital macroelement for soil fertility and crop growth, and its bioavailability is converted with electron flux. To determine the effect of biological electron transfer on the sulfur cycle in soil, a microbial electrochemical system (MES) was established to amplify the efficiency of extracellular electron transfer. Results showed that biocurrent obviously promoted the reduction of water-soluble SO4 [2-] to S[2-], and afterward reoxidised to fulvic acid sulfur (FAS, 32% increment) instead of humic acid sulfur (HAS, 77% decrement). The δ[34]FAS values (12‰ to 24‰) were consistent with the typical isotopic signatures of dissimilatory sulfate reduction, while the δ[34]HAS values (-40‰ to -60‰) matched the assimilatory sulfate reduction. Meanwhile, the assimilatory SO4 [2-] reduction to cysteine improved with a 30%-33% increase for the NAD[+]/NADH and secretion of cytochrome c to support robust redox. Essentially, the precursor-product pairs of desulfonation were enhanced by 26%-93%. Compared to a 6% contribution of HAS, the formation of cysteine accounted for 55% of the electron transport flux. According to screening 32 sulfur-transforming genes, 609 genera were identified, especially 31%-84% proliferation for Desulfatitalea. This study reveals ways of organic sulfur conversion mediated by electron transfer, which can assist the biological amendment of sulfur bioavailability in soil.

D-amino acids (DAAs), once considered minor enantiomers, are now recognised as abundant and dynamic components of marine and terrestrial organic matter. While they do not participate in ribosomal protein synthesis, they play crucial roles in microbial physiology, particularly in bacterial cell wall structure. This review systematically synthesises the current understanding of DAA sources, distribution and fate, with a central focus on the microbial catabolic pathways that drive their recycling in marine and terrestrial environments. We show that, despite differences in DAA distribution and bioavailability between marine and terrestrial ecosystems, the core catabolic strategies adopted by bacteria-conversion to α-keto acids, L-amino acids (LAAs) or Gly-are largely conserved. We also evaluate limitations in current studies and major knowledge gaps, including the unclear role of marine fungi in DAA turnover and the relative lack of systematic studies on DAA-catabolising taxa and pathways in terrestrial microbial communities. This review highlights the ecological significance of microbial-mediated DAA recycling in marine and terrestrial environments, offering a better understanding of the global biogeochemical cycling of DAAs.

Selecting between axenic strains and microbial consortia remains a key challenge in microbial remediation. Here, we established a systematic quantitative framework to compare their degradation performance and biological traits across six pollutant classes: petroleum hydrocarbons, antibiotics, pesticides, polycyclic aromatic hydrocarbons (PAHs), heavy metals, and plastics, under comparable experimental contexts. For complex substrates requiring sequential transformation and mineralisation, especially petroleum hydrocarbons and PAHs, microbial consortia generally showed higher degradation efficiency through metabolic division of labour, biofilm enrichment, and functional redundancy. Reported efficiency improvements ranged from approximately 17% to 73%, with selected cases reaching up to 200%. In contrast, for certain antibiotics and pesticides, consortium performance was inconsistent and sometimes inferior to acclimated or engineered axenic strains due to interspecific antagonism, metabolic inhibition, or unstable functional coordination. Based on the assembled evidence, we propose a decision-making framework for remediation strategy selection: microbial consortia are preferable for complex, multi-step substrates, whereas axenic strains are more suitable for highly toxic contaminants or scenarios requiring strong operational controllability. This study provides quantitative evidence and practical guidance for rational microbial strategy selection, system design, and scale-up in bioremediation engineering.

Microbial communities in natural environments are consistently challenged by toxic compounds, such as polycyclic aromatic hydrocarbons (PAHs). The capacity for rapid phenotypic diversification is key to survival in these dynamic and often hostile niches. Here, we report a mechanism by which Escherichia coli (E. coli) generates immediate phenotypic heterogeneity in response to a model PAH, perylene. Utilising single-cell techniques, we revealed unexpected efflux phenotypic switches occurring in a single division event by examining the asymmetric distribution of perylene, a TolC-related efflux system substrate. Contrary to gradual changes in many generations, the phenotypic switch we observed is abrupt, resulting in daughter cells with distinct efflux phenotypes and asymmetric viability. We ruled out uneven efflux pump distribution and suggested the switch is linked to asymmetric proton motive force. Furthermore, we found a correlation between the age of the inherited pole during division and the propensity for phenotypic switching. New pole cells are identified as more prone to this switch. Our findings reveal a rapid division-based strategy for generating phenotypic diversity that could enhance the adaptive potential and resilience of bacterial populations facing fluctuating environmental toxins.

Viruses are the most abundant biological entities on Earth. Metagenomic data indicates a higher viral abundance of viruses of unicellular eukaryotes in the polar regions, information still not matched by broad isolation efforts using samples collected in these regions. Here we describe a prospection effort using diverse samples collected above the Arctic circle, including freshwater and marine samples from urban areas, deep-sea hydrothermal vents and sea ice samples from the Nansen Basin. We isolated 10 giant viruses capable of infecting Acanthamoeba spp., five representing the Marseilleviridae family and five representing the Mimiviridae family. These viruses are the northernmost isolates found so far in the Nordic countries and consist of a unique cohort of Arctic viruses that differs geographically and temporarily from a cohort already described from the Siberian permafrost. Despite an apparent viral diversity in the samples, the uniqueness of the samples themselves and the use of additional non-amebozoan strains as hosts, our viruses are still representatives of known viral families. In conclusion, here we show the isolation of giant viruses in Northern Norway and highlight the potential host bias towards Acanthamoeba in giant virus prospection, indicating the need to break this bias to diversify the isolation of environmental viruses.

Symbiotic partnerships have opened new ecological niches and contributed to the remarkable diversification of insects. The leafhopper Scaphoideus titanus, a phloem-feeding insect known to be the primary vector of Flavescence dorée phytoplasma, harbours two primary endosymbionts: the bacterium 'Candidatus Karelsulcia muelleri' and a yeast-like symbiont (YLS). While most studies on insect-associated microorganisms have focused on obligate bacterial symbionts, fungal endosymbionts, although documented for almost a century, are only now gaining renewed attention for their evolutionary and ecological significance. In this study, we integrated genomic and proteomic data with phylogenetic analyses to elucidate the functional and evolutionary features of the YLS associated with S. titanus. Using a data-independent proteomic approach supported by a newly sequenced symbiont genome, we defined the proteins expressed by the YLS that may contribute to host physiology. Comparative analyses across the five currently available YLS genomes enabled a proteome-wide phylogenetic reconstruction within the genus Ophiocordyceps, refining the evolutionary placement of these symbioses. Finally, large-scale mining of NCBI transcriptomic Sequence Read Archive datasets using a novel computational workflow, combined with an extensive literature survey, identified several new candidate insect hosts and provided a comprehensive inventory of species harbouring these fungal partners.

Understanding the transport and fate of glacier-originating microorganisms along glacier-fed stream (GFS) gradients is critical for elucidating their downstream impacts. Yet, how glacier-originating microbes contribute to downstream communities across the GFS continuum and over the melt season remains poorly understood. Using 16S rRNA gene sequencing, we integrated spatial and temporal sampling to characterise bacterial communities along the hydrologic continuum of the Longxiazailongba (LXZLB) Glacier in the Tanggula Mountains, spanning supraglacial, glacier terminal and proglacial streams. Alphaproteobacteria, Gammaproteobacteria, Bacteroidia and Actinobacteria dominated communities. Bacterial diversity varied along the continuum, with higher alpha diversity in proglacial than in supraglacial and glacier terminal waters, driven by environmental variables including water temperature, pH and conductivity. Glacier-originating bacteria accounted for a substantial proportion of downstream communities but declined in relative contribution with distance from the glacier. Melt-season variability modulated the downstream representation of glacier-originating ASVs, reflecting changes in meltwater-driven hydrologic connectivity and transport intensity. Taxa exhibiting distinct downstream distributions responded differently to environmental gradients, leading to shifts in community structure along the stream. These findings indicate that spatial environmental gradients and melt-season hydrologic variability jointly shape the downstream contribution and persistence of glacier-originating bacteria, with implications for how continued glacier retreat may restructure microbial communities downstream.

Polyphosphate (polyP) is an inorganic biopolymer of orthophosphate (Pi) that plays roles in many central biochemical processes in microorganisms, including acting as a cellular reservoir of phosphorus. The microbial metabolism of polyP is considered limited to its intracellular cycling by kinases and exopolyphosphatases. However, little is known about polyP metabolism in the Archaea. Notably, many haloarchaea, including Haloferax volcanii, encode homologues of bacterial polyP-synthesising genes, but lack the corresponding genes for its catabolism. Here, we show that H. volcanii possesses a novel polyP-degrading enzyme with characteristics distinguishing it from currently known enzymes. This activity also enabled H. volcanii to grow on exogenous polyP as its sole source of phosphorus. Activity was localised to a discrete protein band by native-PAGE zymography and enzyme assays of cell-free extracts from cells grown on polyP revealed the enzyme was halophilic, required Mn[2+] or Co[2+] and released Pi from polyP. No activity was observed in the extracellular medium of cells grown on polyP, suggesting the enzyme is either membrane-bound or intracellular. These findings thus broaden our understanding of the potential ecological roles of polyP in the biogeochemical cycling of phosphorus, and our understanding of the enzymes and pathways involved in archaeal polyP metabolism.

Gut microbiota and metabolites have been increasingly implicated in the pathogenesis of immune inflammation, which may be affected by environmental factors. This study aimed to explore the influence of co-exposure to high humidity and temperatures (low, normal or high) on biomarkers of immune inflammation and potential mechanisms. We established C57BL/6J mice models (with equal numbers of males and females) of high humidity and low temperature (HH-LT), normal temperature (HH-NT) or high temperature (HH-HT) co-exposure environments to observe the impact of high humidity and different temperature co-exposure environments for 28 and 56 consecutive days. Following exposure, results showed that all six combined exposure conditions significantly increased pro-inflammatory cytokines (TNF-α, IL-1β, IL-12p70), decreased anti-inflammatory cytokines (IL-4, IL-10) and elevated the Teff/Treg ratio in the spleen. Gut microbiota analysis revealed reduced Akkermansia and increased Desulfovibrio and Enterorhabdus. Serum metabolomics identified widespread disturbances enriched in pathways including protein digestion and absorption, lysine degradation, phenylalanine metabolism and unsaturated fatty acid biosynthesis. Pearson correlation analysis confirmed significant associations among microbial shifts, immune-inflammatory dysregulation and metabolic perturbations-suggesting that high humidity combined with different temperatures correlated with immune imbalance, likely mediated by gut dysbiosis and serum metabolic disruption.

Pseudogymnoascus destructans (Pd), the causative agent of bat white-nose syndrome, persists in cave soils and acts as a chronic source of infection, yet the environmental processes governing this reservoir remain unclear. We performed seasonal sampling of bat cave soils in Northeast China and combined metagenomic, untargeted metabolomic and physicochemical analyses to identify drivers of Pd loads. Pd abundance tracked strong seasonal gradients in temperature, soil water content, electrical conductivity and nitrogen availability. The microbial community structure exhibited pronounced seasonal variation, primarily associated with pH, and was governed predominantly by stochastic ecological processes. Nitrogen-cycling genes showed a switch from nitrogen fixation and nitrification in summer to denitrification and nitrate reduction in winter. Antibiotic resistance genes and mobile genetic elements covaried with core bacterial taxa, while antifungal metabolites such as tetracycline, glycitin and chrysin were positively associated with putatively antagonistic genera (e.g., Rhodanobacter, Pseudomonas, Streptomyces, and Bacillus), indicating a microbe-metabolite defence network. Structural equation modelling revealed a temperature-driven cascade linking nutrient cycling, microbial communities, metabolite profiles and Pd loads. Our results show that seasonal dynamics of Pd in cave soils emerge from interactions between climate-regulated soil processes and microbe-metabolite feedbacks, with implications for environmental control of pathogenic fungi.

We investigated the development of a new, hybrid catabolic pathway for m-cresol utilization in Pseudomonas putida strain PaW1-T, a subline of TOL plasmid pWW0-possessing strain PaW1 carrying xyl catabolic operons for utilization of toluene and its methyl derivatives (xylenes) as carbon sources. The ability to hydroxylate m-cresol to methyl catechol was horizontally transferred within a broad-host-range plasmid expressing the phenol monooxygenase PheA. We observed that using m-cresol as a new carbon source required genetic rearrangements associated with elevated expression of meta-pathway enzymes encoded by the xyl lower operon with concomitant inactivation of the xyl upper operon. Analysis of DNA sequencing data from four m-cresol-selected (Cre[+]) strains revealed substantial heterogeneity in the populations of these strains and differences among individual Cre[+] strains. The DNA samples of Cre[+] strains Cre1 and Cre2 yielded sequencing reads consistent with separately existing circular forms of transposons Tn4653 and Tn4651, respectively, with inversions that could inactivate the xyl upper operon. Thus, our results indicated that in addition to conventional transposition events, increasing gene dosage by forming circles of catabolic transposons Tn4651 and Tn4653 could also facilitate bacterial adaptation for growth on new carbon sources.

Trichoderma is a genus of beneficial fungi widely used in agriculture disease suppression, plant growth promotion, and soil health improvement. Although some studies have shown that Trichoderma spp. can be seed-borne, albeit at low frequency, no specific study has so far focused on the diversity of Trichoderma isolates capable of adapting to this particular environment. Over 2 years of routine seed health analyses, we isolated 107 Trichoderma strains associated with seeds from 32 cultivated plant species, and we investigated the diversity of this specific library using multi-locus analysis. These isolates are distributed among 18 different species, but Trichoderma atroviride is by far the most frequent. Representative strains of each species all have the ability to parasitise damping-off agents, although the intensity of parasitism can vary greatly from one strain to another and depending on the targeted plant pathogens. For two isolates of T. atroviride, we showed that these fungi can be transmitted from fruit to seed and limit the transmission of the plant pathogen Alternaria brassicicola. Furthermore, these strains stimulated seedling growth and provided protection against Globisporangium ultimum. Together, these findings support the benefits of focusing on certain selected seed-borne Trichoderma which seem particularly well suited to improving seed health.