Subterranean estuaries (STEs) are key bioreactors regulating the quantity and chemical composition of groundwater-derived nitrogen (N) reaching coastal ecosystems. Yet, the microbial controls on N-cycling within these groundwater-seawater mixing zones remain poorly understood. We investigated the spatio-temporal variations in microbial communities and their N-cycling potential within an alluvial Mediterranean STE with high N concentration. We explored changes in microbial abundance, heterotrophic activity, taxonomic composition, and the abundance of N-cycling genes across groundwater samples collected at several depths and distances from the shoreline in winter and summer. Microbial abundance, activity, and diversity varied strongly across hydrochemical zones according to physicochemistry and aquifer depth but showed limited seasonality. Functional predictions suggested a complex, spatially structured suite of N pathways encoded by diverse taxa occupying different STE zones, and quantitative-PCR revealed niche partitioning between ammonia-oxidizing archaea, prevalent in fresh-groundwater, and bacterial denitrifiers enriched in deep-saline layers. Multiple linear model predictions showed a stronger fit for NO2 [-] and NH4 [+] concentrations when using microbial properties than when using environmental variables, highlighting their importance for understanding N cycling in STEs. Our results suggest that the functional potential of the STE microbiome is complex and spatially structured across hydrochemical zones, explaining spatial variations in STE N-cycling.

Reptile microbiotas remain poorly understood despite their importance for host ecology and evolution. This study investigated how diet, climate and evolutionary history shape the gut microbiota of 234 Australian freshwater turtles spanning 10 species, four climatic zones and contrasting trophic strategies. It was found that turtles' microbiotas were dominated by Pseudomonadota, Actinobacteriota and Bacteroidota. Microbial richness and evenness varied significantly among species, diets and climates. Carnivorous turtles exhibited greater bacterial diversity than omnivores, while individuals from oceanic and humid subtropical zones had higher diversity than those from semi-arid and Mediterranean regions. Canonical Correspondence Analysis confirmed diet and climate as significant predictors of community composition, together explaining 2.76% of total variation. Omnivorous turtles were enriched in Bacteroidota, Myxococcota, Cyanobacteriota and Bacillota, whereas climatic effects drove distinct phylum-level signatures across habitats. Host phylogeny showed a weak but significant signal of phylosymbiosis, indicating an evolutionary imprint on microbial structure. Collectively, these findings reveal that turtle microbiotas are shaped by a complex interplay between ecological and evolutionary forces, underscoring the importance of integrating microbial data into conservation strategies for Australia's increasingly threatened freshwater turtles.

Microplastics (MPs) have established complex bidirectional interactions with bacteria, encompassing both mutualism and antagonism. This review advances a unified 'Stress-Habitat-Degradation' triangular model that systematically integrates three interconnected dimensions: (1) MPs-induced biotoxic stress on bacterial communities in water, soil, guts and plant tissues; (2) the plastisphere as a colonisation substrate that enriches pathogens and facilitates ARG spread; and (3) enzymatic biodegradation by functional taxa like Pseudomonas via specific enzymatic pathways. This framework explicitly links microbial community dynamics to functional outcomes, demonstrating that the same MPs-bacteria interplay simultaneously drives toxicity/pathogen enrichment and beneficial degradation. Environmental factors (temperature, oxygen, soil organic matter) profoundly shape these interactions by regulating gene expression and community succession. Crucially, we identify and resolve apparent contradictions-such as differential Gram-positive/Gram-negative responses and conflicting diversity trends-by attributing them to variations in polymer type, particle size, concentration, exposure time, host species and test conditions. Overall, this synthesis provides a critical integration of MPs-bacterial interactions and proposes a novel pollution control strategy centred on these interactions, redefining environmental risk assessment and bioremediation approaches.

Ester-containing pesticides, such as diphenyl ether herbicides, aryloxyphenoxypropionate herbicides, and strobilurin fungicides, are widely applied in agriculture, but their residues pose significant risks to ecosystems. Functional microorganisms can degrade ester-containing pesticides in the natural environment. However, the microbial mechanisms responsible for their degradation in soils remain unclear. A novel hydrolase gene triS from the strain S113 encoded a broadly active carboxylesterase that hydrolyzes a wide range of ester-containing pesticides. TriS exhibited a maximum sequence similarity of 34.92% to proteins in the Swiss-Prot (UniProt) database. Gene redundancy was observed in strain S113, with TriS showing higher catalytic activity than its homologues. The enzyme contains a conserved Ser226-Glu346-His456 catalytic triad, and its substrate-binding pocket can accommodate complex substrates, which contributes to its broad substrate spectrum and enhanced catalytic efficiency. Genomic analyses revealed that triS resides in a conserved locus, whereas related paralogs occupy more variable regions, suggesting potential horizontal dissemination. Bioinformatics-based taxonomic profiling showed widespread occurrence of TriS homologues, mainly in agricultural soils, and also in forests and wetlands, indicating spread beyond pesticide-treated fields. This study elucidated the function and distribution pattern of triS, enhancing our understanding of microbial ester-containing pesticide degradation in the environment.

Coastal environments are increasingly recognised as reservoirs of known antibiotic resistance genes (ARGs), but are less frequently identified as sources of novel ARGs. Here, we investigated class A β-lactamases circulating in European coastal environments used for oyster farming. We examined their diversity, function, and the ecological factors associated with their geographic distribution and environmental dynamics. A high diversity of carbenicillinases was detected in the culturable microbiome of European oysters. The Harveyi and Splendidus clades were key Vibrio lineages structuring the geography of carbenicillinase diversity. The Harveyi clade was primarily associated with the circulation of known carbenicillinases in Mediterranean samples, whereas the Splendidus clade contributed previously uncharacterized carbenicillinase sequences across all Europe. A one-year seasonal monitoring revealed that Vibrio alginolyticus drives the circulation of blaCARB-42 in the Mediterranean Thau lagoon, with dynamics strongly associated with seawater temperature. blaCARB-42 conferred intrinsic resistance to both carboxypenicillins and aminopenicillins in V. alginolyticus, which was found in most other species of the Harveyi clade with additional resistances to aztreonam, third-generation cephalosporins and aminoglycosides. Since the Harveyi clade includes major human pathogens, these findings have direct implication for environmental and One Health surveillance, as rising seawater temperatures may increase coastal exposure to antibiotic-resistant Harveyi clade Vibrio.

Bacterial species that inhabit diverse nutritional niches, such as plants, the human gut, and aquatic environments, exhibit common and unique molecular mechanisms for acquiring nutrients from plant polysaccharides like xylan. The oligotrophic bacterium Caulobacter vibrioides (Syn. Caulobacter crescentus) shows unique adaptations for growth in low-nutrient conditions and codes for a repertoire of genes that facilitate xylan utilisation as a carbon source. Investigation of xylan and xylan-derivative utilisation by C. vibrioides shows membrane-bound xylanase-mediated xylan deconstruction on the cell surface and further deconstruction of the xylo-oligosaccharides in the periplasm by xylosidases and other accessory enzymes. Proton motive force disruption studies suggest involvement of TonB-dependent transporters, Major Facilitator Superfamily transporters, or ATP-Binding Cassette transporters in the transport of xylo-oligosaccharides and other xylan-derivatives across the membranes of C. vibrioides. Results from our studies using enzyme assays and chromatographic analyses suggest that bacteria deconstruct xylan in a surface-bound manner leading to efficient uptake of xylo-oligosaccharides across the outer membrane, without loss of nutrients to the environment. This proposed model for C. vibrioides xylan utilisation highlights both unique and similar mechanistic features found in gut and plant pathogenic bacteria, advancing the molecular understanding of nutrient acquisition in oligotrophic Gram-negative bacteria.

Biodegradation of benzene is most challenging among the plethora of hydrocarbons due to its high chemical stability. While aerobic bacteria employ O2-dependent oxygenases to overcome the high energy barrier, anaerobic benzene degradation remains enigmatic. Here we achieve an anaerobic enrichment, which is clonal with respect to the benzene-degrading, sulphate-reducing, marine bacterium BzS1, from a previously reported enrichment culture. We investigate this clonal enrichment culture by metabolite and proteogenomic analyses. BzS1 has a tailor-made catabolic network for utilising benzene, toluene, and acetate. Concerning the initial reaction of anaerobic benzene degradation, labelling experiments render previously suggested direct carboxylation (to benzoate) or methylation (to toluene) unlikely. Accordingly, a benzoate-CoA ligase is not encoded in the genome and proteins of anaerobic toluene degradation are not detectable in benzene-utilising cells. Rather, detection of labelled 3-phenylpropanoate hints at addition of benzene to a C3-cosubstrate. Moreover, a presumptively heterotrimeric flavoprotein is present at remarkably high abundance (~⅕ of covered proteome) during anaerobic growth with benzene. This protein is related to glycolate oxidase and flavoproteins of the VOA/PCMH family. Taken together, these findings open the possibility of considering flavin cofactor involvement for the initial reaction using, for example, enolpyruvate (central metabolite) or glutaconyl-CoA (intermediate of benzoyl-CoA pathway) as cosubstrate.

Microplastic pollution in terrestrial environments has emerged as a growing threat to agricultural sustainability. Earthworms and their gut microbiota have recently attracted attention as potential nature-based agents for microplastic mitigation. This study systematically synthesizes empirical evidence on the role of earthworm intestinal microorganisms in the transformation and potential biodegradation of microplastics. A literature synthesis was conducted using Scopus-indexed, peer-reviewed publications published between 2018 and 2025 that examined interactions among microplastics, earthworms, and gut microbiota. The synthesis indicates that microplastic degradation within the earthworm digestive system is a multifactorial process involving mechanical fragmentation, selective microbial enrichment, and biological and metabolic activity. Across different earthworm species and polymer types, the phyla Actinobacteria, Proteobacteria, and Firmicutes consistently dominated the gut microbiome. Several genera, including Bacillus, Paenibacillus, Rhodococcus and Streptomyces, were repeatedly associated with microplastic transformation. Earthworm activity may also improve nutrient availability, stabilize soil microbial communities and enhance plant tolerance to microplastic-induced stress. However, major gaps remain in quantifying biodegradation rates, determining microbial removal efficiency and identifying enzymes directly involved in plastic degradation. Overall, this synthesis positions vermiremediation as a promising strategy for managing terrestrial microplastic contamination, while underscoring the need for stronger mechanistic evidence to support practical application.

Climate change intensifies drought in several regions. Here, we assess how water availability and air humidity regulate photosynthesis in epiphytic cyanobacterial biofilms on Jacaranda mimosifolia. We combined field measurements with controlled laboratory experiments, exposing biofilms to hydration-dehydration cycles and assessing, by chlorophyll fluorescence: potential quantum yield (Fv/Fm), relative electron transport rate (rETRmax), and photosynthetic photon flux density at saturation (PPFDsat). Historical precipitation and relative humidity (RH) data from the last six decades were analysed. Biofilms were completely inactive under dry conditions (Fv/Fm = 0), but rapidly recovered photosynthesis (Fv/Fm≈0.5) within two hours of rehydration. A bark water content of approximately 16% was sufficient to restore 50% of Fv/Fm, whereas higher water availability (> 30%) was required to recover rETRmax and PPFDsat. Air humidity influences the duration of water availability, whereas photosynthetic reactivation depends primarily on liquid water. Climate analyses (1961-2024) revealed an increase in the local frequency of drier days (RH < 60%; Vapour Pressure Deficit > 1; rainfall = 0 mm). This trend suggests that these biofilms are increasingly exposed to prolonged water stress, potentially compromising their ecological functioning and associated ecosystem services. Overall, our findings highlight the vulnerability of epiphytic cyanobacterial biofilms to ongoing climatic drying.

Deciphering the intrinsic coexistence mechanisms of generalists and specialists is crucial for maintaining biodiversity. However, how these taxa seasonally turn over to sustain the stability of bacterial communities remains poorly understood in river sediments. Here, we employed 16S rRNA gene amplicon sequencing and statistical analyses to investigate the diversity, assembly processes, and ecological state conversion of bacterial generalists and specialists in river ecosystems. Our results revealed that generalists exhibited significantly higher phylogenetic species variability (p < 0.001), whereas specialists demonstrated a stronger phylogenetic signal in ecological preferences (p < 0.05). Specialists were mainly shaped by stochastic processes (wet season: 91%; dry season: 86%), while the impact of stochasticity on generalists was distinct across different seasons (wet season: 65%; dry season: 35%). Co-occurrence network analysis revealed that generalists played a more important role than specialists in maintaining the stability of bacterial communities, with generalist communities (robustness: 0.46; vulnerability: 0.0059) themselves exhibiting higher stability than specialist communities (robustness: 0.34; vulnerability: 0.13). Nevertheless, ecological state conversion from specialists to generalists (conversion rate: 43.01) ensured the maintenance of stable biodiversity. Collectively, these findings underscore the importance of dynamic trade-offs between generalists and specialists in sustaining the stability of bacterial communities in river ecosystems.

Ferromanganese (Fe-Mn) concretions are porous accumulations of iron and manganese (hydr)oxides. While recent studies suggest that microbes contribute to metal accumulation in Baltic Sea concretions, the detailed composition of microbial communities and their impact on metal enrichment across different concretion morphotypes remain unexplored. We investigated how microbes influence the accumulation and release of trace metals and rare-earth elements in Fe-Mn concretions from the Gulf of Finland through 15-week microcosm incubation experiments with biotic and abiotic treatments, focusing on three main concretion morphotypes: crust, discoidal, and spheroidal. Elemental analysis showed that microbes enhanced metal incorporation in discoidal and spheroidal morphotypes. Characterisation of microbial composition revealed that all three morphologies host distinct communities. Discoidal and spheroidal morphotypes had a higher relative abundance of Gammaproteobacteria and sulfate-reducing bacteria, and a lower abundance of Entotheonellaeota, compared to crusts. In all morphotypes, the bacterial phylum Pseudomonadota dominated, with several genera of Fe- and Mn-oxidisers and reducers. Fe-Mn concretions also host communities involved in methane oxidation and nitrogen cycling, consistent with decreased methane and increased nitrous oxide, nitrite, and nitrate concentrations in the microcosms. Our findings underscore that distinct microbial communities are associated with different concretion morphotypes, potentially influencing nutrient and metal cycling on the seafloor.

Methanol derived from pectin degradation is common in oxic and anoxic sediments and is used by various aerobic and anaerobic microorganisms such as acetogenic bacteria or methanogenic archaea as a carbon and energy source. Acetogens use the Wood-Ljungdahl pathway to disproportionate methanol to CO2 and acetate. Methanol metabolism has been studied primarily in mesophilic acetogens such as Acetobacterium woodii and Eubacterium callanderi, that do not have cytochromes or quinones. Moorella thermoacetica, the model organism for elucidation of acetogenesis, is a thermophilic, cytochrome- and quinone-containing acetogen which is commonly found in terrestrial soil. Here, we elucidated the physiology and bioenergetics of M. thermoacetica growing on methanol by performing physiological and biochemical experiments as well as genome-wide transcription analysis. Thereby, we identified genes and enzymes involved in acetogenesis from methanol. We will present a comprehensive model for carbon and energy flow from methanol to acetate and line out the bioenergetics of methanol-based acetogenesis in M. thermoacetica. Furthermore, we show that in the presence of DMSO as an alternative electron sink, no acetate is produced from methanol.

Quorum quenching (QQ) is an effective biological strategy for mitigating membrane biofouling in membrane bioreactors (MBRs), yet the persistence of QQ bacteria under harsh industrial wastewater conditions remains poorly understood. Here, the induction, resuscitation and functional recovery of the viable but nonculturable (VBNC) state in the efficient QQ bacterium Brucella sp. ZJ1 was investigated under salinity and combined phenol-salinity stress. Combined stress markedly accelerated VBNC formation (36 h vs. 10 days under salinity alone) and caused greater oxidative damage, metabolic suppression, structural deterioration and loss of QQ activity. Salinity-induced VBNC cells recovered following stress removal, whereas phenol-salinity-induced cells required resuscitation-promoting factor (Rpf) for efficient revival. Rpf-mediated resuscitation substantially restored both QQ activity and biofilm inhibition capacity. Transcriptomic analysis revealed that VBNC formation was accompanied by coordinated repression of genes involved in central metabolism, DNA replication and protein biosynthesis, together with activation of osmotic adaptation, membrane transport, quorum sensing and oxidative stress response pathways. These findings demonstrate that the VBNC state is an active adaptive strategy that preserves the potential for functional recovery and provides new insights for improving the antifouling performance of QQ-based MBR systems treating high-strength industrial wastewater.

Lactococci are best known to thrive in acidic conditions. While their physiology in an acidic environment is well researched, their stress response towards an alkaline environment remains to be explored. In this study, we habituated Lactococcus lactis FM03 to pH 6, 7 and 8 in chemostats with a fixed dilution rate of 0.2 h[-1] and defined the alkaline-induced stress proteome. Based on an enrichment analysis of GO-terms, we identified key physiological adaptations, including cell wall reinforcement, an increase in the uptake and metabolism of peptides and amino acids, as well as elevated levels of translation-related proteins. Transmission electron microscopy revealed a doubling in cell wall thickness at pH 8 compared with pH 6, and we measured higher release of multiple amino acids in the supernatant at pH 8. Further, the compatible solute uptake system for glycine betaine (OpuA) was upregulated, indicating osmotic stress conceivably linked to low cyclic-di-AMP levels. Selected global stress proteins were upregulated at pH 8 (GroEL, HtrA, FtsH), and RelA increased, suggesting the activation of the stringent response, whereas acid resistance systems (F0F1-ATPases, ADI, GAD) decreased. Together, this work defined a distinct alkaline stress remodelling of the proteome in L. lactis FM03 under sustained alkaline growth.

Fluoride is abundant in the Earth's crust but is rarely used by biological systems and is toxic inside cells. Most prokaryotic genomes contain genes encoding fluoride export channels, known as CrcB, or fluoride/proton antiporters, known as CLC[F]. Prokaryotes rely on one type only. In this study, Pseudomonas putida ATCC 12633 that natively expressed a chromosomally-encoded CrcB was engineered with plasmids containing a CLC[F] exporter gene. The addition of CLC[F] and subsequent adaptive evolution made the cells resistant to > 500 mM sodium fluoride and able to degrade 150 mM 2-fluoropropionic acid and export 150 mM fluoride. In the absence of CLC[F] and adaption, only 1 mM 2-fluoropropionic was degraded and culture density decreased. The adaption of multiple cell lines occurred uniformly. All increased their CLC[F] gene copy and incurred mutations in the native CrcB. Two of those point mutations and a designed deletion were introduced into the unadapted wild-type strain and confirmed as CrcB knockouts. In total, the CLC[F] antiporter was selected for under the conditions used and was necessary for biodegrading high concentrations of an organofluorine compound. Sustaining viability at high fluoride levels is relevant for engineering prokaryotes to biodegrade fluorinated chemicals and installing fluoride into compounds by biosynthesis.