Environmental Microbiology Reports最新文献

The area of fungal parasitism is attracting growing attention because of its great importance for aquatic organisms and their community dynamics. Despite increasing interest in this area, few studies have addressed baseline data on occurrence and environmental factors associated with chytrid parasite infections in natural ecosystems. This work provides insights into occurrence, prevalence, and dynamics of parasitic infections by studying three freshwater reservoirs over a period of 6 years. Chytrid infections were detected in each of the studied water bodies, infecting species of cyanobacteria, green algae and diatoms. However, recurring and prevalent infections were observed in only one water body, which is classified as a natural aquatic ecosystem. The recorded infection prevalence (IPC) ranged between 0% and 20%, while the mean infection severity remained low. Infection rates were highest in summer and most prominent during cyanobacterial blooms. Yet, the most infected group of phytoplankton consisted of green algae. GLM revealed a significantly positive correlation between IPC and water temperature and precipitation. Overall, these results demonstrate the dynamic nature of chytrid infections, which are shaped by multiple environmental factors across space and time.

The area of fungal parasitism is attracting growing attention because of its great importance for aquatic organisms and their community dynamics. Despite increasing interest in this area, few studies have addressed baseline data on occurrence and environmental factors associated with chytrid parasite infections in natural ecosystems. This work provides insights into occurrence, prevalence, and dynamics of parasitic infections by studying three freshwater reservoirs over a period of 6 years. Chytrid infections were detected in each of the studied water bodies, infecting species of cyanobacteria, green algae and diatoms. However, recurring and prevalent infections were observed in only one water body, which is classified as a natural aquatic ecosystem. The recorded infection prevalence (IPC) ranged between 0% and 20%, while the mean infection severity remained low. Infection rates were highest in summer and most prominent during cyanobacterial blooms. Yet, the most infected group of phytoplankton consisted of green algae. GLM revealed a significantly positive correlation between IPC and water temperature and precipitation. Overall, these results demonstrate the dynamic nature of chytrid infections, which are shaped by multiple environmental factors across space and time.

Candidatus Saccharimonadia is a class-level lineage of ultrasmall bacteria within the phylum Minisyncoccota (formerly Candidate Phyla Radiation or Ca. Patescibacteria), commonly found in activated sludge processes treating municipal wastewater. In this study, we aimed to elucidate the metabolic potential of Ca. Saccharimonadia by using shotgun metagenomic sequencing combined with a filtration-based size-fractionation approach for activated sludge from five wastewater treatment plants. A total of 65 high-quality metagenomic bins were recovered, belonging to four orders and 19 families of Ca. Saccharimonadia, including previously unreported lineages in activated sludge. These bins had small genomes (approximately 0.46–1.73 Mbp) with limited metabolic capabilities, indicating dependency on other microorganisms. Notably, the order Ca. Saccharimonadales retained a type IV secretion system and effector gene cluster for parasitic interactions with the hosts, suggesting that Ca. Saccharimonadales bacteria may exhibit a parasitic lifestyle. Co-occurrence network analysis showed that members of the order Ca. Saccharimonadales were significantly correlated with multiple lineages, including Actinobacteriota, for which a parasitic relationship has been previously demonstrated. Our results shed light on the potential ecophysiology of the diverse members of Ca. Saccharimonadia, providing a comprehensive understanding of Ca. Saccharimonadia in activated sludge.

Dryas octopetala is one of the most important botanical components of Arctic tundra. In parts of the Norwegian High Arctic Archipelago of Svalbard it can face strong grazing pressure, in particular of its flowers, by the Svalbard reindeer, whilst its production of mature viable seeds may be impacted by climate changes. Diverse organisms are associated with the habitat provided by flowering plants, some with the roots (rhizosphere) and others with the above-ground surface of a plant (phyllosphere). Climatic changes affecting Svalbard may lead to the local expansion or reduction of plant populations and their associated communities. In this study, we carried out an initial investigation of non-fungal eukaryotic communities associated with D. octopetala collected from four sampling locations at Vindodden on Svalbard using DNA metabarcoding. The diversity of organisms assigned based on the DNA sequences obtained was higher in the rhizosphere (6 phyla) than in the phyllosphere (11 phyla). The assignments included taxa that are common in Svalbard as well as some from various parts of the world but not recorded from the archipelago.

Swordfish (Xiphias gladius) is a large, migratory apex predator with a carnivorous diet, occupying a top position in the marine food chain. Although it is a valuable teleost pelagic fish with a significant commercial value, its gut microbiota has never been studied. The gut microbiota of 100 individuals was characterised by sequencing the V3–V4 region of the bacterial 16S rRNA gene. Gut microbiota findings were classified with consideration to diversity, taking into account their weight (10–20; 21–30; over 31 kg) and the FAO fishing areas in which they were caught (FAO 27, 34, 37.1.1 areas). Significant differences in the alpha diversity were observed among the weight categories for all metrics examined (except for the evenness index) and only by Shannon's index among the FAO fishing areas. Beta-diversity analysis revealed no significant differences. The phylum Pseudomonadota dominated the swordfish gut microbiota, followed by Fusobacteriota. Photobacterium was the most abundant genus across all weight categories and FAO fishing areas. Smaller fishes showed a less rich and diverse gut microbiota, dominated almost exclusively by Photobacterium. Conversely, Pseudoalteromonas, Psychrobacter, Psychrilyobacter, and Cetobacterium appeared to increase in abundance with fish weight. Although Photobacterium was dominant across the different FAO fishing areas, distinctive microbial community compositions were observed: Cetobacterium was more prevalent in FAO 27, while Pseudoalteromonas was more prevalent in the other areas. Unlike the gut microbiota of other marine fish species, Vibrio and Lactobacillus were largely absent. This study represents the first metataxonomic characterisation of the gut microbiota of swordfish using next-generation sequencing.

The establishment of native grassland species is widely implemented on abandoned land as a strategy to restore degraded soils. However, its effects on soil properties are highly species-specific, as plant-driven physicochemical changes subsequently reshape microbial community structure. The linkages between soil physicochemical properties and microbial communities following native grassland establishment remain poorly understood. To address this knowledge gap, we examined the effects of 11 native grassland species on soil physicochemical properties and fungal community structure. Using co-occurrence network analysis, we elucidate how plants drive fungal community reorganisation through soil-mediated trophic pathways. The results showed that soil aggregate stability, chemical properties, and fungal communities differed significantly among the 11 species. Soil chemical properties, such as pH and EC, correlated with symbiotic fungi dominated modules; both soil aggregate stability and chemical properties were linked to pathogenic fungi dominated modules, while saprophytic fungi dominated modules displayed no linkage to either soil aggregate stability or chemical properties. These findings establish that fungal trophic modes govern species-dependent restoration outcomes via modular soil–microbe linkages, thereby offering predictive frameworks for species-specific management of abandoned soils.

Bacteroid inorganic phosphorus (Pi) metabolism in the Rhizobium-legume symbiosis differs between indeterminate and determinate legume nodules. In contrast to alfalfa bacteroids, bean (Phaseolus vulgaris) bacteroids exhibit high levels of alkaline phosphatase (AP), the native reporter enzyme for the bacterial Pi stress response. ¹⁴C and ³²Pi whole plant labelling techniques were used in conjunction with diagnostic mutants (lacking AP or lacking high affinity Pi transport) to assess the relative importance of the Pi stress response in Rhizobium tropici bacteroids during symbiosis. The AP- mutant was not defective for symbiosis and did not differ from wildtype bacteroids for Pi acquisition. ¹⁴C-CO₂ feeding to host plants revealed ¹⁴C-carbon uptake and accumulation in AP- mutant bacteroids, and their nodules were increased relative to wildtype bacteroids, implying that organo-P compounds may account for meaningful levels of carbon exchange between symbionts. ³²Pi tracer experiments implied that the high affinity transporter is important to bacteroid Pi acquisition and symbiotic performance in determinate nodules, but that the symbiosome Pi concentration does not meet the capacity of the high affinity transporter. ³²P tracer work also illustrated that Pi taken up into the nodule does not remain in the nodule, but rather is redistributed to the host.

Due to limitations in disease management strategies and the impact of climate change, phytopathogenic bacteria are threatening global crop production. Xanthomonas hortorum pv. vitians, the causal agent of bacterial leaf spot of lettuce, remains difficult to manage due to the lack of efficient treatment options. As an alternative, phage-based biocontrol offers a promising solution, but its long-term efficacy depends on a thorough understanding of phage–host interactions and the potential development of bacterial resistance. In this study, we isolated and characterised the lytic bacteriophage ΦXhv-1, which defines a novel genus within the class Caudoviricetes. Using transposon insertion sequencing, we identified 36 bacterial genes essential for phage susceptibility, primarily involved in lipopolysaccharide biosynthesis and surface polysaccharide modifications. Targeted mutagenesis and fluorescence microscopy confirmed that ΦXhv-1 adsorbs onto specific residues of the LPS O-antigen side chains. Phage-resistant mutants exhibited a decreased motility in vitro and a significant reduction in virulence in planta. These findings reveal a strong evolutionary trade-off between phage resistance and bacterial fitness, suggesting that resistance emergence in the field may be naturally constrained. This study provides new insights into X. hortorum pv. vitians–phage interactions and supports the development of sustainable phage-based biocontrol strategies against bacterial leaf spot of lettuce.

Airborne fungi are ubiquitous microorganisms in the environment, and some of them are known opportunistic pathogens. In recent years, azole resistance, which can have a clinical or environmental origin, has become a critical issue. Four environmental samplings were performed to assess the prevalence and diversity of potentially azole-resistant fungi in three areas (hospital surrounding, rural and urban) from the Basque Country. The microbial concentration varied from 40 to 3670 CFU/m³, depending on the location and sampling. The CFU/m³ count on plates incubated with voriconazole at 37°C was only three times lower than that of plates incubated without the antifungal, suggesting many 37°C-growing fungi might be triazole-resistant. Three hundred and twenty one potentially resistant isolates were identified, belonging to 21 genera and 55 species. Alternaria (62.31%) and Talaromyces (18.69%) were the predominant genera, with Alternaria infectoria (47.19%) being the most abundant species. Overall, the two coastal provinces (Bizkaia and Gipuzkoa) showed the most similarity. The rural area exhibited the highest alpha diversity values for each province, whereas samples from this area were more alike in terms of beta diversity. PCoA analysis indicated that sampling points were clustered by samplings or provinces. This study provides the first characterisation of the outdoor environment from the Basque Country and highlights the importance of determining the prevalence of potentially azole-resistant isolates.

Little is known about virome changes in raw and drinking water over time, and differences between raw water sources and treatment technologies. This study used metagenomics to assess viruses prevalent in raw and drinking water samples over 1 year from six Swedish drinking water treatment plants (DWTPs) with varying treatment barriers and with different raw water sources. Sequences homologous to known viruses in the raw water samples were detected by amplification and next-generation sequencing and classified into 152 different virus species belonging to 76 virus families/orders. The majority were small bacteriophages. Other viral genomes were homologous to viruses infecting plants, invertebrates, vertebrates, mammals and giant viruses infecting amoeba or algae. Several virus species were simultaneously found in both raw and drinking water, indicating passage through the purification barriers, although reduced by 1–3 log₁₀ after treatment. Most viruses detected in water samples after ultrafiltration were small viruses, and other barriers appeared more effective at removing smaller viruses. To avoid detecting viruses possibly replicating within DWTPs, viruses were separated according to the possibility that the host could be found in the water sources or not. These results underscore the importance of monitoring both raw and drinking water for small viruses, especially when viral contamination of the source water is at risk, to ensure drinking water quality.