Environmental Microbiology Reports最新文献

Enhancing plant resilience is crucial for sustainable agriculture and ecosystem health in an era of climate change and the global spread of plant pathogens. The strategic exploitation of diverse ecological niches to isolate microorganisms that promote plant growth, suppress pathogens and tolerate abiotic stress conditions is paramount. Here, 21 bacterial strains were isolated from three distinct sources: digestate produced from straw feedstock, Quercus ilex roots mycorrhised with Tuber aestivum, and a peperino stone fountain. These isolates were assigned to eight genera, Bacillus, Pseudomonas, Stenotrophomonas, Burkholderia, Acinetobacter, Aeromonas, Exiguobacterium and Sphingobacterium, all linked to plant growth promotion, stress mitigation and pathogen control. Tests for plant-growth-promoting and biocontrol activities included indole acetic acid, siderophores, hydrogen cyanide, cellulase and chitinase and phosphate/potassium solubilisation. Efficacy against Phytophthora infestans and tolerance to salinity, pH and drought were also assessed. Functional patterns varied by isolation source, suggesting niche-specific adaptation. Although all isolates displayed metabolic versatility, peperino stone strains exhibited higher tolerance to acidity and drought, while isolates from straw digestate and mycorrhizal roots tolerated alkalinity. Most isolates are promising for P. infestans control. These findings highlight the importance of targeted microbial sourcing in developing effective biofertilisers and biopesticides, offering sustainable solutions to agricultural and environmental challenges.

As Arctic shipping increases due to climate change, characterised by rising temperatures and decreasing sea-ice coverage, the risk of oil spills through the Northwest Passage in this fragile ecosystem grows, necessitating effective bioremediation strategies. Research on bioremediation using Arctic coastal sediment bacteria has gained attention, particularly Rhodococcus species that play key roles in hydrocarbon degradation under extreme conditions. This study investigates the hydrocarbon degradation capabilities of a novel cryophilic Arctic Rhodococcus sp. strain R1B_2T isolated from Canadian high Arctic beach sediment in Resolute Bay, exposed to ultra-low sulphur fuel oil for 3 months at 5°C. Comparative transcriptomics analyses revealed dynamic responses and metabolic plasticity, with upregulation of genes for aliphatic, aromatic, and polycyclic aromatic hydrocarbons, biosurfactant production (e.g., rhamnolipid), cold adaptation, and stress responses. The strain possesses several key alkane degradation genes (alkB, almA, CYP153, ladA), with co-expression network analysis highlighting synergistic mechanisms between alkB and CYP153 that target different chain-length alkanes (alkB: ~C5–C20; CYP153: ~C5–C12 and > C30), demonstrating complementary degradation strategies. The findings reveal adaptive mechanisms and degradation kinetics of native Arctic bacteria, highlighting the potential of Arctic cryophilic and halotolerant Rhodococcus species for oil spill remediation in polar marine environments.

Peritrichs are widely studied ciliates; however, their eukaryotic epibionts have not yet been examined in detail. Our study investigates the colonisation patterns and seasonal dynamics of peritrich ciliates and their epibionts in lotic environments over 14 sampling periods. In the early stages of colonisation, settlement was likely characterised by random establishment, consistent with the lottery model of Chesson and Warner. In later stages, the autogenic, ecosystem-engineering role of peritrich species facilitated the settlement of additional organisms on the substrate. During warmer months, the structurally complex surface of peritrichs hosted a greater abundance of epibionts—particularly choanoflagellates. Colonisation of the peritrich stalks by attached filter feeders and other functional groups increased the filtration-capable surface area, thereby enhancing biofilm function. Additionally, the presence of predatory ciliates such as Trachelius ovum can alter biofilm structure by consuming colonial peritrichs. These findings highlight the crucial role of peritrichs in biofilm dynamics and their contribution to community complexity in lotic ecosystems.

The English Channel features a wide range of ecological habitats that host numerous biodiversity resources and are submitted to natural and/or anthropogenic pressures. During the ‘EcoPel’ oceanographic campaigns (spring and summer 2018) in French waters of the English Channel and North Sea, a variety of coastal pelagic habitats were sampled for analysing environmental variables and bacterial communities. Results of PCA suggest that main environmental variables were SPM, POM, PIM, salinity and NO₂⁻/NO₃⁺ in spring and salinity, SPM, Si and Chl-a in summer. The Shannon index suggested summer alpha diversity had higher richness and equitability compared to spring. A clear seasonality in the bacterial community structure was also revealed by hierarchical cluster analysis. Most of the spring communities had a higher proportion of Bacteroidetes while most of the summer communities had a higher proportion of Proteobacteria, Actinobacteria, Verrucomicrobia and Planctomycetes. Based on distance correlations and statistical significance, the spring taxonomic composition was correlated with Chl-a, PO₄, POM, SPM and PIM, while the summer composition was correlated with salinity. According to hierarchical cluster analyses, both environmental variables and bacterial communities seem to be clustered in parallel with the coast, evidencing the main influence of coastal-offshore gradients and implying possible links with river inputs and phytoplankton/algae dynamics.

Bacterial infections in aquatic organisms pose a significant threat to shrimp aquaculture, often leading to production losses. In Pangandaran Regency, early shrimp harvesting is frequently practiced as a response to outbreaks. Previous studies have documented Vibrio and non-Vibrio bacteria in pond water and sediments at five stations, but infections in shrimp tissues remain less explored. This study aimed to identify pathogenic Vibrio species in vannamei shrimp (Litopenaeus vannamei) and wild black tiger shrimp (Penaeus monodon), examine toxin genes, and quantify bacterial abundance. Samples were collected from five stations and analyzed using culture media, Gram staining and Polymerase Chain Reaction (PCR). Vibrio parahaemolyticus and Vibrio alginolyticus were detected at Stations 1 and 5, whereas only V. alginolyticus appeared at Stations 2, 3 and 4. Station 1 showed the highest Vibrio abundance (1.3767 × 10⁶ CFU/g), while Station 3 recorded the lowest (0.009 × 10⁶ CFU/g), with significant differences (p < 0.05). Non-Vibrio bacteria dominated most stations, except at Station 1 where Vibrio species were predominant. Toxin gene analysis revealed toxR in some isolates, while tdh, trh, pirA and pirB were absent. These findings emphasize the importance of bacterial and genetic monitoring to improve disease surveillance and support sustainable shrimp aquaculture.

Insects of the suborder Auchenorrhyncha harbour multiple ancient endosymbionts that jointly produce essential nutrients lacking from the host's diet. Compared to cicadas, leafhoppers, and spittlebugs, our understanding of the multipartite symbioses among planthoppers, an extremely diverse insect group, is still very limited. Herein, we assembled the genomes of the primary endosymbionts of two planthopper species from the Cixiidae family, Cixius wagneri and Pentastiridius leporinus, both vectors of phytopathogenic Arsenophonus in Europe. Each species harboured a different tripartite endosymbiont consortium: while P. leporinus carried the well-known combination ‘Candidatus Karelsulcia muelleri’, ‘Ca. Vidania fulgoroideae’, and ‘Ca. Purcelliella pentastirinorum’, C. wagneri harboured a yet unknown Gammaproteobacterium in addition to Karelsulcia and Vidania. This new endosymbiont ‘Ca. Mirabilia symbiotica’ is likely much older than Purcelliella, considering its extremely reduced genome. In both species, Karelsulcia and Vidania jointly produce the 10 essential amino acids, whereas Purcelliella and Mirabilia provide the non-essential amino acid cysteine and slightly different gene sets encoding B vitamins. Our findings confirm the functional stability of multipartite planthopper endosymbiont consortia despite changing partners over evolutionary time. In addition, we describe a new Rickettsia strain from the Meloidae group colonising P. leporinus, highlighting the diversity of bacterial endosymbionts associated with planthoppers.

In freshwater lakes, protistan and fungal communities play crucial roles in the microbial loop as bacterivorous consumers, facilitating nutrient cycling and maintaining microbial balance by controlling bacterial populations. However, understanding of their functional roles and community assembly across varying environmental gradients in different lake ecosystems remains limited. In this study, we used 18S rRNA gene amplicon sequencing and multivariate statistical analyses to investigate the spatiotemporal and biogeographical patterns of protistan and fungal communities in the water column of two different lake systems in Croatia. Our results revealed that these complex communities were dominated by Chlorophyta, Ciliophora and Cryptophyta as well as Ascomycota, Basidiomycota and Chytridiomycota. Null model analysis showed that stochastic processes dominated most of the prokaryotic and fungal communities across sampled lakes and fractions, with seasonally salty Lake Crniševo having more prominent variable selection due to the presence of a salinity gradient. Also, it was discovered that salinity had a negative influence on the stability of both protistan and fungal communities in Lake Crniševo, acting as a major selective pressure. These results provide valuable insights into the community stability and assembly mechanisms of protistan and fungal communities in lake ecosystems and their responses to environmental changes.

Dysbiosis is associated with shifts in the diversity or relative abundance of beneficial versus harmful bacteria, leading to health issues in organisms. This study investigated gut bacterial dysbiosis associated with larval quality using 16S rRNA gene sequencing. The gut microbiome of gilthead sea bream and European sea bass, key commercial species and vertebrate models, was examined in high- and low-quality larvae batches from several European hatcheries. Larval quality, hatchery site and species influenced bacterial diversity in the gut. Individuals from larval batches that performed well had higher microbial diversity in the gut and individuals from batches that performed poorly had a gut microbiota dominated by pathogenic Vibrio (e.g., V. aestuarianus and V. cortegadensis). The bacterial dysbiosis index revealed a notable predominance of Fusobacteriota and Firmicutes phyla, Thermoanaerobacteria class and Lactobacillaceae, Moritellaceae, Clostridiaceae, Thiotrichaceae and Shewanellaceae families in good-quality larvae batches, and a prevalence of the Proteobacteria phylum, Gammaproteobacteria class, Sphingomonadaceae and Vibrionaceae families in the gut of individuals from poor-quality larvae batches. A positive dysbiosis index (cutoff > 0.4) was associated with a high risk of decreased larval performance and quality. Additionally, the abundance of Clostridium_sensu_stricto_15, Shewanellaceae_unclassified, Cetobacterium, Psychrilyobacter, Moritella and Latilactobacillus genera in the gut of good production batches, and the Vibrio genus in the gut of poor production batches, identified these genus as potential markers for diagnosing and mitigating bacterial dysbiosis in fish and potentially other vertebrates.

Diarrheal diseases remain a significant public health concern worldwide, particularly among children under five. Surveillance is primarily focused on clinical samples. However, environmental reservoirs, particularly rivers, are increasingly recognised as critical sources of enteric pathogens. This study used whole-genome sequencing (WGS) to characterise Escherichia coli isolates from the Jukskei River in Johannesburg, South Africa. Twenty-seven E. coli isolates were subjected to pathotype-specific PCR and WGS for characterisation. Diarrheagenic E. coli accounted for 44% (12/27) of the isolates, including enterotoxigenic, atypical enteropathogenic and a hybrid enterotoxigenic-enteroinvasive E. coli. Most isolates (63%, 17/27) were O16:H48, and fimbrial typing revealed nine Fimtypes, with fimH27 being the most prevalent at 56% (15/27). Resistance to ciprofloxacin, sulfamethoxazole and azithromycin was noted in 11% (3/27) of the isolates. The most prevalent virulence-associated genes were fimH, csgA, gad, terC, ompT, iss and yehA-D, associated with adhesion, invasion and stress response. Phylogroup A dominated the collection (70%, 19/27), and phylogenetic analysis revealed diversity among the river isolates. Some genetic links between human and livestock strains were noted, suggesting cross-environmental transmission. These findings highlight the Jukskei River as a potential vehicle for E. coli transmission and underscore the importance of integrated surveillance across the environmental, human and animal sectors.

Fusarium oxysporum is a widespread phytopathogenic fungus that affects a variety of crops worldwide. This study evaluated the independent effects of three species of Trichoderma (T. harzianum, T. viride, and T. longibrachiatum) and the springtail Folsomia candida on the suppression of F. oxysporum under laboratory conditions. We conducted separate in vitro assays to assess fungal antagonism and feeding preferences of the springtail. The results demonstrated that all Trichoderma species significantly inhibited F. oxysporum growth, whilst F. candida showed a marked preference for consuming F. oxysporum mycelium over that of the tested Trichoderma species. These findings suggest that both organisms may contribute to the reduction of F. oxysporum independently. This preliminary work lays the foundation for future studies investigating potential interactions and combined biocontrol applications under more complex and ecological settings.