Environmental microbiology最新文献

The height profile of Bacillus subtilis biofilms exhibits complex fractal morphology shaped by cellular behaviour and environmental factors. While phenotypic differentiation relates to biofilm spatial patterns, the mechanisms regulating upper surface morphology remain unclear. This study combines experiments with an agent-based model to explore how nutrient-driven phenotypic switches affect the morphological complexity (fractal dimension D) and heterogeneity (roughness Ra) of the biofilm upper surface. We analyse biofilm images at different nutrient concentrations to quantify morphology. The model incorporates Monod kinetics, with phenotypic transition probabilities and mechanical interactions depending on substrate availability. The results show that nutrient conditions regulate phenotypic ratios, and matrix-producing cells promote anisotropic biofilm growth, enhancing surface heterogeneity and morphological complexity. Spores fill vacancies created by heterogeneous cell growth, and this behaviour, in coordination with isotropic growth of motile cells, reduces the morphological complexity and heterogeneity of biofilm morphology. When the populations of matrix-producing cells and the other two phenotypes balance, the biofilm's morphological complexity and heterogeneity peak. The model accurately predicts experimental trends, revealing that phenotypic transitions mediated by metabolic dependence and nutrient diffusion drive biofilm morphogenesis. This work links cell differentiation to biofilm upper surface morphology, advancing our understanding of biofilm adaptation in dynamic environments.

Sea ice is a crucial, yet declining, habitat in high latitude ecosystems. Here we present a high-temporal resolution amplicon sequence data set collected during the spring ice-algal bloom near Utqiaġvik, Alaska in 2021 to study sea-ice microbial dynamics. The ice-algal bloom peaked on May 8th, reaching 46.6 mg chlorophyll a m⁻² and thereafter became limited by nitrate availability. A massive bloom of the oil-degrading bacterium, Oleispira (> 80% relative abundance), coincided with the algal bloom raising questions about hydrocarbon exposure. The sea-ice algal bloom was dominated by diatoms, particularly, Nitzschia spp. and transitioned into a flagellate-dominated postbloom community which aligned with melt-associated changes to the physicochemical environment. We explored the relationship between putative parasitoids, Chytridiomycetes, Thecofilosea (Cercozoa), Oomycetes, Syndiniales (Dinoflagellata) and Labyrinthulomycetes (Bigyra) and potential microalgal hosts. Chytrids peaked periodically suggesting synchronised infections and Cryothecomonas (Thecofilosea) was observed parasitizing Nitzschia spp. for the first time in Arctic sea ice. Co-occurrence analysis suggested that diatoms, especially Nitzschia, were the primary hosts of Pacific-Arctic parasitoids and that top-down parasitoid control may dramatically alter community composition over short timescales, such as days. These results provide important insights into the drivers of spring bloom timing and maintenance of microalgal diversity in sea ice.

Endosymbionts play pivotal roles in driving ecological and evolutionary diversification of many insects, yet the morphogenesis and evolutionary origin of their specialised symbiotic organs (e.g., bacteriomes) remain poorly understood. Here we investigated the bacteriome morphogenesis in Cicadidae using microscopy-based methods. We revealed that bacteriomes originate either from both the original bacteriocytes that emerged after anatrepsis and the novel bacteriocytes that appeared during katatrepsis, or solely from the latter. Bacteriomes expand via “budding” proliferation to increase the bacteriome unit number, and bacteriome developmental patterns closely correlate with the presence/absence of the yeast-like fungal symbionts (YLS) and their colonisation dynamics. The obligate endosymbiont Karelsulcia and YLS, coexisting in bacteriomes during early stages of host ontogeny, may compete for ecological niches, potentially resulting in translocation of YLS into fat bodies. This indicates that bacteriomes may have initially functioned as immune organs like fat bodies, but evolved specifically for accommodating bacterial endosymbionts. The translocation of YLS from bacteriomes to fat bodies during the later development of host cicadas indicates that immune-mediated regulation occurs in such symbiotic organs as host insects mature. This study sheds light on how symbiont-host interactions shape the symbiotic organogenesis, which provides insights into adaptive evolution of specialised symbiotic organs in plant sap-feeding insects.

Microbial communities play pivotal roles in ocean biogeochemistry, yet linking their composition to ecosystem functions remains a significant challenge. In this study, we demonstrate the predictive power of bacterioplankton taxonomic composition in explaining oxygen consumption during dissolved organic matter (DOM) degradation. Using 4 years of experimental data, we integrated ‘omics with statistical modeling, applying feature selection and dimensionality reduction to develop high-performance linear regression models with strong predictive accuracy. Our framework also identifies key microbial groups driving oxygen consumption, including taxa known for their differential capabilities in DOM processing and recently shown to exhibit distinct respiration rates. Flavobacteriales emerge as central contributors to oxygen consumption, underscoring their ecological importance in nutrient-rich, highly productive coastal systems often referred to as ‘green seas’. Their consistent dominance across varying oxygen consumption categories highlights their pivotal role in sustaining ecosystem functions in these environments. Beyond oxygen consumption, this framework provides a versatile tool for investigating microbially driven biogeochemical processes. By linking community composition with ecosystem functions, our study advances predictive microbial ecology. These findings deepen our understanding of microbial contributions to the ocean's carbon and oxygen cycles, improving our ability to anticipate their responses to environmental change.

Viruses play essential roles in shaping the structure and function of microbial communities, including those inhabiting extreme environments. The Qaidam Basin is a unique Mars-analog desert characterised by hyperaridity, oligotrophy and high soil salinity. We hypothesise that viruses contribute to microbial adaptability and biogeochemical cycling through virus-host interactions in desert ecosystems. Here, we investigated viral diversity, biogeography, life strategies and interactions with soil microbiomes across the Qaidam Basin. Soil properties, such as water content, pH and mineral assemblages, significantly influenced the distribution patterns of both viral and prokaryotic communities. Broad host range may confer fitness advantages for viruses in deserts where host biomass is limited. Most viruses were characterised as lytic and infected dominant microbial phyla, supporting the “Kill-The-Winner” model, which suggests viral regulation in microbial community diversity and stability. We identified over 32,000 potential viral auxiliary metabolic genes (AMGs), including key genes involved in carbohydrate metabolism, carbon fixation, photosynthesis and phosphorus cycling. Moreover, AMGs related to the biosynthesis of antibiotics, pigments and alkaloids may enhance the adaptability of hosts under extreme conditions. This study unveils the enigmatic virosphere of the Mars-analog Qaidam Basin and underscores the roles of viruses in promoting microbial adaptability and driving biogeochemical cycling.