Environmental Microbiology Reports最新文献

Cyanobacteria play a key role in the biomineralisation of carbon dioxide into solid carbonates, a critical process in the global carbon biogeochemical cycle that links atmospheric CO₂ to lithospheric carbonate reservoirs. While photosynthetic carbon fixation by these microorganisms has been extensively studied and is relatively well understood, the biomineralisation pathway remains much less explored, likely leading to an underestimation of its global relevance. This review summarises current findings and highlights the ecological and cellular factors that contribute to cyanobacterial biomineralisation. In particular, the need to cope with fluctuating environmental conditions has played a central role in enabling cyanobacteria to develop rapid metabolic adaptations together with the evolution of a complex cell wall architecture. Within this framework, biomineralisation emerged as a tangible and effective adaptive strategy. Particular attention is given to the metabolic processes and related ion trafficking mechanisms across the cell envelope, which are instrumental in facilitating mineral nucleation and growth.

The specific fermented matrices influence microbial diversity and proteomic adaptations being crucial for optimising fermentation efficiency and effective microbial identification. Therefore, the study aimed to investigate the impact of plant-based fermentation matrices and their physicochemical composition on microbial diversity and MS-protein profiles. Microbial communities were characterised using MALDI-TOF MS and 16S rRNA sequencing. Physicochemical analyses were conducted on the 10 fermentation matrices. The sequencing verified low-confidence MALDI identifications and assessed species-level microbial diversity. Combined MALDI-TOF MS and 16S rRNA gene sequencing confirmed the presence of 24 species across five taxonomic classes and revealed strong matrix-dependent variation in the lactic acid bacteria composition. A significant positive correlation was observed between Lactiplantibacillus pentosus abundance and pH, with the presence being negatively associated with Ca and Mg levels in the fermented products. Furthermore, the concentration of carbohydrates and Fe was positively correlated with Corynebacterium amycolatum and Micrococcus luteus. MALDI−TOF MS spectra obtained for the key lactic acid bacteria species revealed differences in protein profiles depending on the type of fermented matrices. The study provides new insights into the interactions between microbial communities and fermentation substrates, emphasising the role of physicochemical properties of plant-based matrices in shaping microbial diversity and proteomic adaptations.

The growing demand for sustainable medical applications has sparked interest in the valorisation of agro-industrial waste for bioactive compounds. Compost teas (CTs) from agrifood waste, rich in phenolics and lignin derivatives, offer promising biological properties. This study analysed CTs from bell pepper (CT-BP) and citrus (CT-C) composted waste, assessing their antioxidant, antiviral, and antimicrobial activities. NMR spectroscopy and thermochemolysis revealed that CT-BP had more oxidised lignin derivatives, while CT-C contained intact lignin structures. Both CTs effectively inhibited Gram-positive bacteria (Staphylococcus aureus and Enterococcus faecalis), with CT-BP showing greater efficacy. However, Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) were more resistant. CT-BP also exhibited potent antiviral effects against enveloped viruses like herpes simplex virus type 1 (HSV-1) and respiratory syncytial virus (RSV). These findings support the use of compost-derived extracts as sustainable bioactive agents, offering natural alternatives to conventional treatments. Further research could enhance the extraction and scalability of these materials for biomedical applications, aligning with principles of the circular economy.

Temperature and salinity are key environmental drivers that constrain growth and distribution of marine cyanobacteria, yet their combined physiological effects remain unexplored. We analysed the physiological and transcriptional responses of two Synechococcus strains, the marine RS9907 and euryhaline WH5701, across a salinity gradient (18–50 PSU) under optimal (28°C–30°C) and low temperature conditions (15°C–20°C). Growth and photosynthetic efficiency (F_V/F_M) declined under salinity stress (18 PSU for RS9907 and 50 PSU for WH5701), relative to typical marine conditions (36 PSU). RS9907 maintained the photosynthetic electron transport rate under salt stress and the F_V/F_M under cold conditions more effectively than WH5701. Salinity induced a stronger regulatory response in WH5701 (71% genes differentially expressed, compared to only 6% in RS9907). Both strains shared a core response, upregulating carbon fixation genes under cold stress, and glycogen degradation and osmolyte synthesis genes at high salinity (42–50 PSU). Conversely, some photosynthetic genes (psbCD, psaC) showed increased expression at low salinity, but temperature-dependent regulatory differences were observed. WH5701 uniquely upregulated genes related to membrane transporters, fatty acid desaturases and the pentose phosphate pathway within salinity, potentially contributing to their broader tolerance to salt fluctuations. Collectively, our results reveal contrasting strategies of thermohaline acclimation in Synechococcus strains adapted to different salinities.

Microbial communities are widely recognised as indicative of ecosystem health. Changes in the microbial community composition of seagrasses and their environment could act as an important bio-indicator for stress factors affecting the submerged aquatic plants that make up the Ruppia community in the Coorong. Here, we explored prokaryotes associated with surface biofilms of the leaves and roots of the seagrasses to determine the microbiota composition of the Ruppia community, and their link to the surrounding sediment and water. Ruppia was recorded growing at 55% of the sites surveyed, and all collected samples showed a high diversity of prokaryotes. Turbidity was the main driver of the fluctuations in microbiota composition of the Ruppia community. Water and sediment microbial communities were correlated with the presence/absence of the seagrasses. Seagrass health indicators were assessed, allowing for a clear distinction between the various states of the Ruppia community identified in this study. This study provides key baseline insights into the composition and possible functions of these biofilm microbiota, as well as identifying potential health bio-indicators for the Ruppia community. Furthermore, it identifies specific beneficial bacteria that could be selected to enhance seagrass restoration efforts as well as inhibit detrimental algal blooms in the Coorong.

Medium chain length polyhydroxyalkanoates (mcl-PHA) are elastomeric biodegradable bioplastics produced by a few bacteria. The large-scale mcl-PHA production remains limited by the low yield of bacterial strains and biomass reduction due to prolonged nutrient limitation in the media. In the present study, Pseudomonas aeruginosa MCC 5300 produced mcl-PHA copolymer of about 39.4% cell dry weight (CDW) at a short duration of 24 h of growth in tryptic soy broth media containing oleic acid and the PHA content was enhanced up to 66.4% CDW in the presence of azide. The production of mcl-PHA at such a short duration was not reported previously in nutrient-enriched conditions. The application of azide enhanced mcl-PHA production in the bacteria. Oleic acid shifted the electron transport chain (ETC) from the cytochrome c pool to the ubiquinol pool. The inhibition of bo₃-oxidase by azide increased electron flux towards bd-oxidase to maintain proton gradient for oxidative phosphorylation, causing depletion of cellular reduced-redox cofactor levels. The increased mcl-PHA accumulation in bacteria compensated for the loss of reduced-redox cofactors, thus maintaining cellular redox homeostasis. Hence, the study invokes a novel link between the ETC and mcl-PHA production.

A total of 1347 Escherichia isolates from water, soil, sediment, biofilm, and faecal samples (n = 413) across five pristine (native forest) and five impacted (pastoral or urban) sites were subtyped into E. coli phylotypes and non-E. coli Escherichia spp. (Escherichia marmotae, Escherichia ruysiae and Escherichia whittamii). Impacted sites showed a higher prevalence of E. coli, particularly the ruminant-associated phylotype B1, across water, biofilm, sediment, and mammalian faeces. In contrast, E. marmotae (189 isolates) were more common in pristine sites and avian faeces, with a prevalence of 28.7%. Metabarcoding of the hypervariable gene gnd further revealed that Escherichia population diversity was greatest in aquatic environments (water, sediment, biofilm). Escherichia population diversity was also associated with elevated freshwater E. coli concentrations, increased prevalence of pathogenic E. coli virulence factors (stx1, stx2 and eae), and higher livestock numbers. In contrast, diversity measures for Escherichia populations were lowest in avian faeces and soil samples, and samples obtained from pristine sites with fewer faecal sources. These findings highlight the ecological role of birds as reservoirs of E. marmotae and their contribution to microbial diversity in New Zealand's freshwater ecosystems.

Actinobacteria of the genus Frigoribacterium were isolated from adelgid Adelges (Aphrastasia) pectinatae collected from a Korean fir tree. Genomic analyses revealed that these bacteria encode a range of factors that may be involved in the interactions among Frigoribacterium strains, adelgids and/or conifers. Secreted carbohydrate-active enzymes were identified in the genomes, which allow these bacteria to degrade plant polysaccharides such as cellulose, xylan, pectin and mannan, the main hemicellulose component of softwood. The degradation potential of insect cuticles was investigated, and secreted chitinases belonging to the GH18 family were predicted to be present in the genomes. However, no phenotypic chitinolytic activity was detected. The potential interactions between these bacterial strains and either plants or insects were assessed, resulting in a few high-scoring hits. The related Frigoribacterium genomes were compared, revealing several unique features, such as numerous orthologous gene clusters specific to these strains and five biosynthetic gene clusters. Ten genomic islands were predicted in the genomes of the adelgid-associated strains, which contained genes responsible for adapting to environmental changes, resisting heavy metals and expanding metabolic capabilities. We propose a new species, Frigoribacterium adelgis, belonging to the genus Frigoribacterium, based on these results.

Microplastics (MPs) impact soil microorganisms by altering habitats and community structures. However, generalising these effects across polluted environments is challenging, particularly concerning soil carbon's role in biodegradation. This review aims to address crucial knowledge gaps regarding the relationship between soil carbon availability and microbial preferences for MP-derived polymers. It highlights that, despite being carbon-based, the unique structures of MPs prevent them from functioning like natural organic matter in the soil. This limitation affects both the degradation process and the ability of soil microorganisms to utilise MPs effectively as a carbon source. Notably, even polymers that are not directly assimilated after MP biodegradation can be transformed by other soil microorganisms into more readily exploitable forms through vital microbial interactions within the soil food web, which play a key role in carbon cycling. Moreover, this review emphasises attention on understanding how the microbial preferences for substrates derived from MPs are influenced by more readily available organic carbon in the soil. Evaluating carbon use efficiency among these communities reveals intricate responses of soil microorganisms to various carbon sources, including those from MPs. Overall, this review underscores the complex interplay between soil microorganisms, carbon sources, and MP pollution.

UV light is a well-studied environmental DNA damaging agent. Bacterial cells respond to UV exposure by upregulating several pathways to repair and tolerate the lesions induced by this agent. The SOS response is the primary pathway activated during genotoxic stress that can shift the balance between mutagenesis and genome integrity. However, in Pseudomonas aeruginosa, the canonical SOS response is not the only pathway activated after DNA damage. This opportunistic pathogen also activates the production of pyocins (Prt regulon) and an autolysis pathway controlling the alp genes (Alp regulon) in response to DNA damage. This study aims to characterise gene expression changes in response to UV-C damage. We performed RNA sequencing analysis to determine the set of differentially expressed genes, and qRT-PCR to track the course of expression of representative genes from each regulon. Our results show that the canonical LexA-regulated SOS response is the earliest activated one, while the Alp regulon displays a delayed induction. We also investigated the contribution of the Alp and Prt regulons to UV-induced cell death and found that the predominant mechanism varies between PAO1 sublines.