Freshwater wetlands in the Himalayan region are ecologically sensitive and microbiologically diverse ecosystems, yet their seasonal dynamics remain insufficiently characterised. This study investigated seasonal variations in physicochemical properties and bacterial diversity of two Ramsar wetlands in northwestern India, Renuka Ji Lake and Asan Conservation Reserve. Water samples were collected during pre-monsoon (June), monsoon (August) and post-monsoon (November) seasons. Physicochemical parameters were analysed using standardised IS:3025, APHA 24th Edition and SLS/SOP protocols. Bacterial isolation was performed by serial dilution-pour plating on nutrient agar, followed by Gram staining, biochemical characterisation and 16S rRNA gene sequencing. Both wetlands exhibited pronounced seasonal fluctuations in water chemistry. At both sites, dissolved oxygen (Renuka Ji), turbidity and dissolved oxygen (Asan Conservation Reserve) exceeded CPCB permissible limits during specific seasons. Eleven bacterial isolates were identified, predominantly representing freshwater associated genera. Agrobacterium cavarae was comparatively uncommon in freshwater environments. No bacterial colonies were recovered from Renuka Ji Lake during post-monsoon sampling within the tested dilution range (101-104). Overall, culturable bacterial communities showed seasonal variation and were dominated by a limited number of genera. These findings highlight the ecological sensitivity of Himalayan Ramsar wetlands and emphasise the need for continuous physicochemical and microbiological monitoring for effective conservation and sustainable management.
Aeromonas dhakensis has emerged as a significant pathogen affecting both aquatic animals and humans; however, genomic data for isolates from marine mammals remain scarce. In this study, we characterised the genome of A. dhakensis strain KDL-001, isolated from a fatal dolphin case, using whole-genome sequencing and comparative genomics. Taxonomic analyses, including MLST and average nucleotide identity (ANI), confirmed the isolate as A. dhakensis. Core-genome phylogeny further revealed that KDL-001 is closely related to strains derived from fish and aquatic environments. Notably, in silico screening of virulence-associated genes showed that the virulence-associated gene profile of the dolphin isolate was broadly comparable to those of other A. dhakensis strains, with no isolate-specific virulence-associated genes being identified within the limits of this analysis. These findings demonstrate that the dolphin-derived isolate is genomically comparable to previously described A. dhakensis strains and possesses conserved virulence-associated genes commonly found within the species.
Periphytic biofilms are key mediators of freshwater ecosystem processes but are increasingly exposed to anthropogenic stressors. We compared biofilms sampled upstream and downstream of a wastewater treatment plant (WWTP) effluent, two source communities presumed to differ in prior exposure to wastewater-associated press disturbance, to examine differences in tolerance to ciprofloxacin (CIP) exposure. We assessed biomass, photosynthetic pigments and fatty acid (FA) profiles as well as microbial community structure using qPCR and metabarcoding. Downstream-sourced biofilms exhibited higher biomass stability, reduced pigment and FA losses and fewer bacterial and eukaryotic community shifts under CIP exposure than upstream-sourced biofilms. Upstream-sourced communities, despite higher baseline pigment and FA contents, showed pronounced sensitivity to CIP, including biomass declines and reduced prokaryotic diversity. Taxon-specific responses revealed stress-tolerant Chlorophyceae, cyanobacteria and heterotrophic taxa, which may have contributed to higher functional stability under the tested conditions. Our findings show that biofilm responses to CIP varied with source site and community composition. While not a direct test of environmental filtering, the observed patterns are consistent with its predictions. The results further suggest that legacy effects and spatial heterogeneity may influence biofilm vulnerability to antibiotic exposure, although this requires validation across multiple WWTP-impacted and reference sites.
The need to include wildlife in surveillance programs for antibiotic resistance has been previously highlighted. In the present study, we explored the possibility of sampling Swedish wildlife in conjunction with ongoing monitoring programs for wildlife health and disease to evaluate the occurrence of antibiotic resistance. The animals included in the study represented different trophic levels and degrees of interaction with humans, namely bears, eagles, wolves, foxes, otters, and hares. Samples were screened for ESBL-, pAmpC-, and carbapenemase-producing Escherichia coli using selective media, and indicator E. coli was also isolated from each sample. All isolates were tested for antimicrobial susceptibility, and a subset of isolates was genome sequenced. Two samples from foxes were found to carry ESBL- or pAmpC-producing isolates, while no carbapenemase-producing E. coli could be detected. Geographical information on the samples and genetic characterization of the ESBL- and pAmpC-producing isolates suggest that proximity to anthropogenic settings could play a role in the occurrence of antibiotic resistance in wildlife. In addition, the study demonstrated that the use of ongoing wildlife surveillance programs presents a cost-efficient possibility to monitor antibiotic resistance in wild animals. However, future studies and monitoring programs should take careful consideration regarding selection of animal species and distribution.
Soil microbial communities exhibit strong sensitivity to environmental gradients, yet their distribution across depth and land-use types in hyper-arid environments remains poorly characterised. Using whole-genome shotgun metagenomics via Oxford Nanopore Technologies long-read sequencing, we profiled soil microbial communities across six contrasting land-use sites in Dubai, UAE: urban, industrial (two locations), marine, desert and agricultural, where each sampled at three depth intervals (0-25 cm, 25-50 cm and 50-100 cm). Marine soils exhibited extreme salinity (EC 23.7-30.7 dS m-1) and the highest organic matter content (1.19%-1.76%), while desert soils were nutrient-poor with minimal salinity. Actinomycetota and Pseudomonadota co-dominated across all sites, collectively accounting for 77%-96% of classified sequences. Actinomycetota prevailed in undisturbed desert horizons (up to 53.4%), while Pseudomonadota dominated nutrient-enriched environments, reaching 69.4% at industrial sites. A notable compositional reversal was observed in the desert deep horizon (50-100 cm), where Pseudomonadota increased to 56.8%, departing from the expected oligotrophic depth gradient. PERMANOVA confirmed land use as the primary driver of community composition (p = 0.001), with depth exerting a secondary but significant effect (p ≤ 0.01). NMDS ordination revealed strong site-specific clustering, with each environment harbouring a distinctive microbial fingerprint with promising forensic geolocation potential.
To promote sustainable use of marine resources, the United Nations Sustainable Development Goal 14 (SDG 14): Life Below Water aims to alleviate the threats of marine pollution, habitat degradation, unsustainable fishing and ocean acidification on ocean ecosystems. With the 2030 deadline approaching, much work remains, necessitating innovative solutions for ocean health and sustainability that can be upscaled and implemented globally. The metabolic versatility of microorganisms makes them powerful, yet currently underutilized tools that can be leveraged to advance SDG 14. Here, we synthesize current microbial technologies that align with primary targets of SDG 14: plastic reduction (14.1), nutrient removal (14.1), coastal restoration (14.2) and sustainable aquaculture (14.7). Diverse microbial groups are involved in these functions in natural and human-perturbed ecosystems, including plastic-degrading bacteria, denitrifying communities, host-associated microbes, biofloc and periphyton systems, as well as photosynthetic microorganisms. We emphasize the ways in which wide-scale implementation requires mechanistic and systems-level understanding of microbial applications, environmental testing in variable environments and the development of monitoring and deployment infrastructure. We also highlight the importance of protecting microbial biodiversity to preserve the ecosystem services that will maintain the outcomes of SDG 14. Integrating microorganisms into existing ocean management and policy structures represents a compelling pathway to accelerate progress towards SDG 14-a conceptual framework that can be applied to other SDGs.
Coastal ecosystems are vital for biodiversity but are increasingly threatened by urbanisation and pollution, which significantly alter local microbial communities. This study assessed bacterial diversity and functional profiles in urban and island beaches in Belém, Brazil. Urban beaches showed significantly higher microbial diversity and evenness, alongside functional plasticity due to pollutant input, while island beaches hosted more specialised and stable communities. Taxonomic analysis revealed the significant enrichment of opportunistic genera such as Comamonas, Clostridium and Paenibacillus in urban areas, and the massive dominance of Prochlorococcus and Candidatus Pelagibacter in island sites. Furthermore, shotgun metagenomics identified a robust genomic potential for xenobiotic degradation and antibiotic resistance in urban microbiomes, whereas island microbiomes were significantly enriched in genes for energy production and biosynthesis. These results underscore the ecological divergence between anthropogenically impacted and natural coastal environments, highlighting the importance of microbiome monitoring for sustainable coastal management.
The impact of plant microbiota on host is increasingly recognized, yet specific bacterial functions and genetic determinants in rhizosphere interactions remain largely unknown. Agrobacteria, common soil and rhizospheric bacteria, establish root interactions. The species Agrobacterium fabrum harbour seven specific-gene regions, whose annotation indicates a close connection with the plant. To evaluate the involvement of these specific regions in the plant-bacteria interaction, deletion mutant strains of each specific region were inoculated on Medicago truncatula roots. Root metabolite profiles were compared by UHPLC-UV/DAD-ESI-MS QTOF analyses, and the highlighted discriminating metabolites were annotated by tandem mass spectrometry. A. fabrum inoculation modulates the content of root phenolic compounds, in particular flavonoids. These root metabolite modulations appear to be linked to at least one of the A. fabrum-specific genes, as almost all specific regions showed an influence on one or more of these metabolites. Furthermore, our results suggested a putative cross-talk of the specific regions during the interaction of A. fabrum with M. truncatula, as all mutants except one induced similar modifications on flavonoids. These findings enhance our understanding of A. fabrum's ecological niche construction, highlighting the importance of specific genes in the establishment of this fine-tuned interaction.
Serratia marcescens is a gram-negative bacillus commonly found in aquatic environments. This opportunistic human pathogen can form biofilms and acquire resistance to multiple antimicrobial classes, raising public and environmental health concerns. The occurrence of antimicrobial-resistant S. marcescens in aquatic ecosystems is alarming, yet relatively few studies have addressed this topic in depth. To compile and analyse studies on the antimicrobial susceptibility profiles and resistance mechanisms of S. marcescens isolated from aquatic environments. A systematic search was performed in PubMed, Scopus, Web of Science and the Virtual Health Library for articles published between 2019 and 2024, using descriptors related to S. marcescens from aquatic sources. Studies evaluating susceptibility profiles of isolates from water samples were included. Thirteen articles met the inclusion criteria, encompassing 90 isolates from diverse water sources. Resistance to β-lactams was most prevalent, including carbapenems, the most recent compounds in this class. Identified mechanisms included plasmid-mediated genes blaOXA-48, blaTEM-1 and aac(6')-Ic. Aquatic environments can serve as reservoirs for resistant S. marcescens, posing risks of dissemination to humans and other ecosystems. Continuous monitoring, environmental contamination control and stronger microbiological surveillance policies are crucial to mitigate this emerging public health threat.
The physical and chemical properties of soil fundamentally shape its microbial communities. In a controlled 28-day microcosm experiment, we assessed bacterial community responses to imidacloprid in three soils with differing textures and classifications: a loamy sand (11 g/100 g clay; red Luvisol), a sandy loam (16 g/100 g clay; red Luvisol) and a clay soil (56 g/100 g clay, Vertisol). Analyses included 16S rRNA gene amplicon sequencing, indicator species analysis, co-occurrence network analysis and PICRUSt2-based functional prediction. Imidacloprid exposure elicited soil-specific shifts in bacterial community structure, primarily altering evenness rather than richness; however, overall diversity patterns were more strongly governed by soil texture and sampling time. Indicator species analysis identified distinct sensitive and tolerant taxa in each soil texture, with a core set of taxa remaining largely unchanged. Co-occurrence network analysis showed decreased network complexity and increased modularity under imidacloprid, particularly in loamy sand and clay soils, suggesting altered bacterial interaction patterns. Predicted functional profiles showed upregulation of stress-response pathways and downregulation of energy/nutrient metabolism pathways, implying a community-level shift toward stress adaptation. Although taxonomic richness remained relatively stable, these reorganisations of community interactions and functional potential suggest changes in bacterial resilience and biogeochemical cycling, which may have implications for long-term soil health.
Animal carcasses are common in natural environments and, owing to their high energy and nutrient content, support distinct microbial communities. However, little is known about how carcass-associated microbial communities vary among geographically distinct regions. To address this knowledge gap, we deployed sardine carcasses on surface sediments at seven tidal flats distributed along the Japanese archipelago and compared microbial communities in sediments with and without carcasses. We focused on the taxonomic composition of bacterial assemblages and their potential predators, ciliophorans. Both bacterial and ciliophoran communities associated with carcasses differed markedly among sites. However, the overall effect of carcass addition on community composition was superimposed on strong geographic and environmental patterns. These results suggest that carcass-associated microbial communities are shaped primarily by local species pools and environmental conditions rather than by a common carcass-driven effect across geographically distinct sites.
Pollen functions as a dynamic microbial habitat and the microbes living in pollen reserves play vital roles in pollinator health and nutrition. However, the microbiota composition of honeybee pollen reserves in biodiverse Neotropical regions remains largely unknown. This study provides the first comprehensive analysis of bacterial and fungal communities in honeybee pollen reserves across six ecosystems in the Amazonas region of Peru using high-throughput metabarcoding of the 16S rRNA gene and ITS2 markers. We found that ecosystem type is a primary driver of community structure, with bacteria and fungi responding differently to environmental changes. Despite high taxonomic heterogeneity and a limited number of shared core microbes, the main functions of these microbes were maintained, featuring enrichment of bacterial pathways involved in nutrient metabolism and saprotrophic fungal guilds. Lactobacillus and an unclassified Tremellomycetes fungus were dominant, yet their abundance varied with respect to floral resource diversity. The simplified Palm Swamp ecosystem showed significantly reduced microbial diversity, underscoring the vulnerability of these communities to habitat homogenization. Our results demonstrate that the pollen reserve microbiome is assembled through environmental filtering and pollinator-mediated selection, resulting in taxonomically flexible but functionally stable communities essential for hive processes. This work provides a foundation for understanding the microbial ecology of pollen in the Amazonas region.
Vibrio splendidus is an opportunistic pathogen widely distributed in marine environments, animal tissues and seabed sediments. It can infect various marine animals, resulting in high mortality and substantial economic losses. Exposure to high concentrations of tetracycline induces V. splendidus to form persister cells, which exhibit tolerance to multiple classes of antibiotics and pose a serious threat to aquaculture by promoting disease outbreaks. Previous studies have suggested that metabolic regulation is a key mechanism for maintaining the dormant and low-energy state of persister cells. In this study, we found that the accumulation of histidine-derived metabolites significantly reduced the susceptibility of V. splendidus to tetracycline. Transcriptomic analysis revealed a marked upregulation of genes involved in histidine metabolism and exogenous supplementation of histidine significantly increased the proportion of persister cells, suggesting that histidine plays a promotive role in persister formation. Furthermore, histidine enhanced the membrane potential and upregulated the expression of the efflux pump gene tolC, thereby contributing to the formation of tetracycline-induced persister cells. These findings reveal a previously unrecognized role of histidine metabolism in antibiotic tolerance and provide a theoretical basis for understanding persister cell formation in V. splendidus.
This study investigates the characteristics of AL (Anacamptis laxiflora flower)-doped carbon quantum dots (AL-CQDs), synthesised via a 7-h pyrolysis process and their effects on the growth of the Ceratobasidium sp. (AL5) fungus. AL-CQDs exhibited strong ultraviolet-visible absorption and a consistent spherical morphology. High-resolution transmission electron microscopy (HR-TEM) analysis revealed that the particles were homogeneously distributed, predominantly spherical or quasi-spherical in shape and ranged in size from 45 to 110 nm. In addition, the HR-TEM images showed localised ordered domains with an average interplanar spacing of approximately 0.113 nm, indicating the presence of graphitic or crystalline-like regions within the carbon dots. Fungal growth experiments demonstrated that nutrient media supplemented with CQDs significantly increased the growth rate and decreased hyphal diameter, suggesting more efficient nutrient uptake. The medium containing 2 g of CQDs promoted the fastest growth, reaching maximum levels by Day 5, whereas the 1 g CQD medium resulted in a more compact cell structure and steady growth. These findings suggest that AL-CQDs enhance fungal growth and may have promising applications in fungal biotechnology and nanobiotechnology.
Background: Soil fungal communities play vital roles in forest ecosystem functioning, yet their relationship with tree health remains insufficiently characterized in many endangered species. Aims: This study, investigated the composition and functional structure of soil fungi associated with symptomatic and asymptomatic individuals of Araucaria araucana in the Nahuelbuta Coastal Range, Chile. Materials and Methods: Using high-throughput ITS1 sequencing and trait-based annotation, we compared fungal assemblages across two forest sectors with contrasting edaphic conditions. Results: Marked differences in taxonomic and functional composition were observed between sites, with more even and functionally diverse communities in less restrictive soils. Within this site, where both tree health conditions co-occur, no significant differences in alpha or beta diversity were detected; nevertheless, species-level and functional guild analyses revealed shifts in composition. A shared core microbiome included taxa putatively identified as endophytes, including Cladophialophora minutissima, Fraxinicola europaea, Linnemannia hyalina, saprotrophs (Solicoccozyma terricola, Helicodendron conglomeratum, Pseudogymnoascus roseus) and a plant pathogen (Penicillium excelsum). Symptomatic trees harboured unique stress-tolerant taxa, including cold-adapted saprotrophs and ericoid mycorrhizal fungi, while asymptomatic trees supported lignocellulose decomposers, mutualists and early-successional symbionts. Discussion: The observed fungal shifts suggest that canopy dieback is associated with a functional reorganization of the rhizosphere microbiome rather than a simple loss of diversity. Conclusion: These findings provide new insights into the fungal ecology of A. araucana forest and contribute to understanding how soil microbiomes respond to forest decline under contrasting edaphic conditions.
Benthic cyanobacterial mats in flowing waters are complex communities typically composed of taxa from the orders Coleofasciculales and Oscillatoriales, many of which have unresolved taxonomic positions and poorly characterized toxic potential. We collected field mats of a benthic non-heterocytous filamentous cyanobacterium from the North and South Forks of the Shenandoah River in Northern Virginia (USA) that were dominated by a novel morphotype. Whole-genome and 16S rRNA gene phylogenetic analyses placed this cyanobacterium within the recently described genus Limnofasciculus (Coleofasciculaceae). Genome-based species delimitation metrics fell below accepted thresholds for bacterial species delineation relative to Limnofasciculus baicalensis, the only formally described species in the genus to date, supporting recognition of the cyanobacterium from Shenandoah River as a distinct species. Furthermore, the two Limnofasciculus species exhibited marked structural differences in the Box B helix of the 16S-23S ITS region. Comparative genomic analyses revealed a genome size similar to L. baicalensis and a conserved core gene repertoire alongside substantial divergence in biosynthetic gene cluster composition. Neither species contains biosynthetic gene clusters associated with the production of known cyanotoxins. Based on morphological, phylogenetic and genomic evidence, we describe Limnofasciculus delicatus sp. nov., supported by light microscopy and whole-genome characterization.
In hydroponic horticulture, where soil is replaced by a sterile artificial substrate, attention to microorganisms is primarily focused on the suppression of plant pathogens and the application of potentially beneficial organisms. This study examined the ecology of the root microbiome of tomato plants which were grown to maturity in a hydroponic rockwool system and then treated with a Trichoderma-based biocontrol product. The bacterial community was species-rich but was dominated by a small number of Alphaproteobacteria, Gammaproteobacteria and Bacteroidia species. The fungal community was less diverse and consisted almost exclusively of Ascomycota and Rozellomycota species. Biocontrol treatment did not have a significant effect on bacterial diversity, but the microbiome composition changed distinctly over the period of sampling in both treated and untreated plants. These results support the view that mineral substrates in a hydroponic system can support a complex and resilient root microbiome. Understanding the microorganisms that thrive in this unique environment may help identify effective biological treatments, and enable the development of rockwool-specific practices for monitoring, protecting and promoting plant health.
Deep-sea microorganisms adapt to extreme conditions by diverse metabolic strategies, yet their intracellular carbon fluxes remain largely unexplored. Here, we investigated the central carbon metabolic fluxes of four bacterial strains isolated from Pacific Ocean sediments and deep waters, including Stutzerimonas marianensis PS1, Shewanella piezotolerans WP3, Georhizobium profundi WS11 and Parasedimentitalea marina W43. Using 13C metabolic flux analysis with multiple 13C-labelled glucose isotopologues, all strains preferentially degraded glucose via the Entner-Doudoroff pathway (EDP) with fluxes accounting for 66.7%-94.0% of total glycolytic flux, indicating that EDP is a conserved and dominant glycolytic route among deep-sea heterotrophs. S. piezotolerans WP3 uniquely exhibited substantial flux through both oxidative and non-oxidative branches of the pentose phosphate pathway, suggesting heightened precursor and redox demands. The strains also displayed diverse anaplerotic strategies, engaging either phosphoenolpyruvate or pyruvate carboxylation to replenish tricarboxylic acid cycle intermediates and enhance carbon utilisation efficiency. Oxidative stress assays further revealed a link between intracellular energy status and tolerance to hydrogen peroxide. Collectively, these findings provide comparative fluxomic evidence for central carbon metabolism in deep-sea bacteria and highlight metabolic traits that support survival in carbon-limited, high-pressure marine environments.
Candida auris is an emerging fungal pathogen known to cause outbreaks in healthcare settings that are difficult to control. Here, data from 80 wastewater treatment plants were collected between December 2023 and November 2024 to compare C. auris seasonal detection rates across the four meteorological seasons. The mean C. auris seasonal detection rate communicated as a percentage (((# of detections per site/# test days per site)/# total sites)*100) was highest in the summer (7%), followed by fall (4%), spring (4%) and winter (2%). A Kruskal-Wallis test identified a significant difference between the seasons (H = 43.6, p < 0.0001) and a Dunn's post hoc test with Bonferroni correction identified pairwise differences between summer and each of the other seasons (p < 0.05). Statistical significance and 95% confidence intervals (CI) were further assessed by a bootstrapping analysis that also identified a significant difference between summer and all other seasons (p < 0.01). Proportionally, 39 (48%) sites had their highest seasonal detection rate in summer, followed by 21 (27%) in fall, 15 (18%) in spring and five (7%) in winter. These results collectively document elevated C. auris seasonal detection rates in summer, providing new context to apply C. auris wastewater surveillance.
Demodex mites inhabit the pilosebaceous unit despite harsh environmental conditions including UV radiation, variable salinity, and cosmetics. Their recently characterized endobacterium may contribute to this resilience. This study aimed to elucidate mechanisms of the microbe-host interaction that help mites withstand environmental stress. The genome of Corynebacterium kroppenstedtii subsp. demodicis was sequenced using PacBio technology and annotated via MicroScope. Metabolic and symbiotic traits were analyzed using KEGG and compared with the Demodex folliculorum secretome from published transcriptome data. The complete 2,456,075 bp genome contains 2034 coding sequences and exhibits reduced variable genes compared to other Corynebacterium species. Primary metabolism comprises an almost complete minimal gene set but lacks two tRNA synthetases and genes for phosphatidylethanolamine and NAD+ biosynthesis. Carbohydrate pathways are incomplete and fatty acid synthase I is absent. Secondary metabolism includes complete mevalonate and β-carotene biosynthetic pathways, while the methylerythritol phosphate pathway is missing. UV protection and oxidative stress tolerance are supported by β-carotene, ClpB, RecN, MsrA, KatA, SodA, and manganese transporter SitB. The secretome contains hydrolases likely aiding mite digestion. These findings provide genomic insights into mite-bacterium symbiosis and follicular adaptation. All functional inferences are based on genomic data and in silico predictions; experimental validation remains to be established.
