Environmental Microbiology Reports最新文献

Microbial communities in the deep basaltic aquifers of Iceland remain poorly characterized, despite their relevance for understanding subsurface biogeochemical processes, including silicate weathering. Here, we used 16S rRNA gene metabarcoding to investigate bacterial and archaeal diversity in 22 geothermal wells spanning broad gradients in temperature (30°C–110°C), pH (7.0–11.0), and bedrock age (0.01–15 Myr). We observed highly variable microbial assemblages, with several dominant taxa affiliated with known deep biosphere lineages, including hydrogenotrophs and sulfate reducers. Archaeal communities were less diverse and displayed domain-specific patterns, distinct from bacterial assemblages. Beta diversity was primarily structured by temperature and pH, and, to a lesser extent, by bedrock age. Thermodynamic and kinetic parameters derived from groundwater chemistry—including redox potential and silicate dissolution rates—also accounted for significant fractions of the variation in microbial beta diversity, although it cannot be ruled out that their influence primarily reflected underlying correlations with temperature and pH. Our results suggest that both environmental gradients and host-rock reactivity shape microbial diversity in these systems. This highlights the importance of considering geochemical context when designing subsurface microcosm experiments, and identifies candidate taxa for future studies exploring links between microbial composition and silicate weathering processes.

The maintenance and manipulation of the beneficial plant microbiome is a new frontier in ecofriendly disease management, particularly during post-harvest storage. However, the fruit microbiome is highly variable and can be influenced by both biotic and abiotic factors. A comprehensive understanding of how these factors influence microbial communities is necessary in order to unlock the microbiome for sustainable disease management. In this study, we demonstrate the impacts of the growing season and management strategy on the composition and structure of the bacterial microbiome of ‘Honeycrisp’ apples at harvest from seven different orchards in the Atlantic Maritime Ecozone, over the course of two growing seasons. We show that the bacterial communities associated with core and peel tissues respond differently to changes in external environmental conditions, underscoring the need to include multiple tissue types in future fruit microbiome research. Finally, we characterize the microbial cooperation networks of apple core and peel tissues and identify key microbial taxa influencing these networks.

Climate change poses significant challenges to forest ecosystems, particularly influencing processes such as deadwood decomposition and carbon sequestration. This study explores the impact of decaying spruce wood on soil properties, enzymatic activity and microbial structure across an altitudinal gradient in mountain ecosystems dominated by spruce monocultures. In the Babia Góra Massif (Poland), we analysed soils beneath highly decomposed spruce logs (600–1200 m a.s.l.), focusing on soil chemistry, enzymatic activity and microbial composition. Decaying wood enriches soil with carbon and nitrogen, boosting β-glucosidase and phosphatase activities. Increased soil moisture content under decaying wood promotes decomposition and microbial activity. Interestingly, microbial community composition under deadwood exhibited biodiversity changes compared to control soils, and metabolic activity was notably higher, suggesting shifts in microbial function rather than community diversity. The study highlights the significant role of decaying spruce wood in shaping soil properties and microbial processes in mountain ecosystems, emphasising its contribution to carbon and nitrogen enrichment and enhanced enzymatic activities. These findings underscore the ecological importance of deadwood in forest ecosystems, particularly in the context of carbon cycling and climate change adaptation. Sustainable forest management practices should prioritise the retention of deadwood to maintain vital ecosystem functions, particularly in the context of global climate change. Future studies should broaden this approach by including different tree species and additional environmental factors, in order to better understand the variability and resilience of deadwood-driven soil processes across forest ecosystems.

Climate change poses significant challenges to forest ecosystems, particularly influencing processes such as deadwood decomposition and carbon sequestration. This study explores the impact of decaying spruce wood on soil properties, enzymatic activity and microbial structure across an altitudinal gradient in mountain ecosystems dominated by spruce monocultures. In the Babia Góra Massif (Poland), we analysed soils beneath highly decomposed spruce logs (600–1200 m a.s.l.), focusing on soil chemistry, enzymatic activity and microbial composition. Decaying wood enriches soil with carbon and nitrogen, boosting β-glucosidase and phosphatase activities. Increased soil moisture content under decaying wood promotes decomposition and microbial activity. Interestingly, microbial community composition under deadwood exhibited biodiversity changes compared to control soils, and metabolic activity was notably higher, suggesting shifts in microbial function rather than community diversity. The study highlights the significant role of decaying spruce wood in shaping soil properties and microbial processes in mountain ecosystems, emphasising its contribution to carbon and nitrogen enrichment and enhanced enzymatic activities. These findings underscore the ecological importance of deadwood in forest ecosystems, particularly in the context of carbon cycling and climate change adaptation. Sustainable forest management practices should prioritise the retention of deadwood to maintain vital ecosystem functions, particularly in the context of global climate change. Future studies should broaden this approach by including different tree species and additional environmental factors, in order to better understand the variability and resilience of deadwood-driven soil processes across forest ecosystems.

The maintenance and manipulation of the beneficial plant microbiome is a new frontier in ecofriendly disease management, particularly during post-harvest storage. However, the fruit microbiome is highly variable and can be influenced by both biotic and abiotic factors. A comprehensive understanding of how these factors influence microbial communities is necessary in order to unlock the microbiome for sustainable disease management. In this study, we demonstrate the impacts of the growing season and management strategy on the composition and structure of the bacterial microbiome of ‘Honeycrisp’ apples at harvest from seven different orchards in the Atlantic Maritime Ecozone, over the course of two growing seasons. We show that the bacterial communities associated with core and peel tissues respond differently to changes in external environmental conditions, underscoring the need to include multiple tissue types in future fruit microbiome research. Finally, we characterize the microbial cooperation networks of apple core and peel tissues and identify key microbial taxa influencing these networks.

Shale oil reservoirs are typically characterised by elevated temperatures, confined spaces and oligotrophic conditions. Understanding the role of microorganisms in shale oil reservoirs is essential for elucidating biogeochemical cycles and the origins of life. However, the composition and metabolic functions of microbial communities in shale oil reservoirs remain elusive. In this study, shale core samples were collected from the HY1-1 and HY7 wells in the Jiangsu Oilfield. A combination of X-ray fluorescence, powder X-ray diffraction and scanning electron microscope analyses revealed that the samples contained various transition metals, abundant clay minerals and numerous pores with diameters greater than 1 μm. Fractionation of extracted crude oil fractions revealed that HY1-1 and HY7 contained 60% and 74% saturated hydrocarbons, primarily comprising C₁₁–C₃₅ n-alkanes. Various hydrocarbon-degrading microorganisms, including Marinobacter, Alcanivorax, Alkanindiges and Nocardioides were present in HY1-1 or HY7 samples. Metagenomic analysis showed the presence of genes associated with aerobic hydrocarbon degradation, denitrification and DNRA in the HY7 sample, suggesting that microorganisms may utilise crude oil for growth and participate in the subsurface carbon and nitrogen cycle. This study elucidates the microbial community structure and functional gene profiles in shale core samples, providing critical insights for harnessing in situ microorganisms in shale oil reservoir development.

Shale oil reservoirs are typically characterised by elevated temperatures, confined spaces and oligotrophic conditions. Understanding the role of microorganisms in shale oil reservoirs is essential for elucidating biogeochemical cycles and the origins of life. However, the composition and metabolic functions of microbial communities in shale oil reservoirs remain elusive. In this study, shale core samples were collected from the HY1-1 and HY7 wells in the Jiangsu Oilfield. A combination of X-ray fluorescence, powder X-ray diffraction and scanning electron microscope analyses revealed that the samples contained various transition metals, abundant clay minerals and numerous pores with diameters greater than 1 μm. Fractionation of extracted crude oil fractions revealed that HY1-1 and HY7 contained 60% and 74% saturated hydrocarbons, primarily comprising C₁₁–C₃₅ n-alkanes. Various hydrocarbon-degrading microorganisms, including Marinobacter, Alcanivorax, Alkanindiges and Nocardioides were present in HY1-1 or HY7 samples. Metagenomic analysis showed the presence of genes associated with aerobic hydrocarbon degradation, denitrification and DNRA in the HY7 sample, suggesting that microorganisms may utilise crude oil for growth and participate in the subsurface carbon and nitrogen cycle. This study elucidates the microbial community structure and functional gene profiles in shale core samples, providing critical insights for harnessing in situ microorganisms in shale oil reservoir development.

Octocorals such as Corallium rubrum are key components of temperate Marine Animal Forests (MAFs), providing three-dimensional habitats that support diverse marine life. However, C. rubrum faces growing threats from overexploitation and climate stressors such as ocean warming. While the coral's bacterial microbiome is well-documented and stable across spatial and temporal scales, the associated microeukaryotes, collectively referred to as the coral eukaryome, remain poorly characterised. In this study, we used 18S rRNA gene metabarcoding to explore the eukaryome of 46 C. rubrum colonies collected from five sites (~44,670 km²) in the northwestern Mediterranean. We identified a limited set of core microeukaryotic families, including Licnophoridae and Dino-Group I Clade 1, which were present at all sampling locations. Despite sharing core taxa, eukaryome composition showed high variability between sampling sites, seasons and years. This suggests the red coral eukaryome is strongly influenced by local environmental factors. Given the increasing frequency of marine heatwaves and habitat degradation, further research is needed to understand the ecological roles of key eukaryotic taxa and their contribution to coral holobiont resilience. Clarifying the function of the eukaryome is essential for predicting how C. rubrum and other habitat-forming octocorals will respond to future climate scenarios.

Vibrio parahaemolyticus (VP) is a major bacterial species that causes early mortality syndrome (EMS) in shrimps. EMS can be classified into two groups based on histological signs of hepatopancreatic tissues, i.e., acute hepatopancreatic necrosis disease (AHPND) and non-AHPND. To investigate how toxin-producing AHPND and toxin-lacking non-AHPND VP could lead to EMS, growth characteristics and transcriptomic analyses of the representative strains, 5HP and 2HP, were compared. Non-pathogenic VP represented by strain S02 was also used. Two types of growth media included rich medium represented by tryptic soy broth plus 1.5% NaCl (TSB) and depleted media represented by artificial seawater (SW) and spent seawater (SSW). SSW refers to a sterile used-SW medium from healthy shrimp rearing or shrimp-conditioned SW. Growth characteristics under these media indicated that TSB and SSW supported better growth than SW, suggesting shrimp-conditioned SW is sufficient to support normal VP growth. Transcriptomic analyses revealed that both EMS isolates shared overall expression patterns. Metabolic stress adaptation systems of non-AHPND strain 2HP under SW and SSW were more upregulated than in AHPND strain 5HP. Specific virulence genes (i.e., zot1 [zonula occludens toxin] and vopS [type III secretion effector]) and a general stress response gene (i.e., rpoS [stress response sigma factor]) were upregulated in strain 2HP under both SW and SSW. These expression profiles of strain 2HP suggest higher persistence, which might be useful for cell survival and non-AHPND pathogenesis even without toxin production. We proposed that these genes encode virulence factor ‘candidates’ in non-AHPND VP.

Playgrounds are a common feature in modern cities. Although guidelines addressing safety requirements for playground equipment have been established worldwide, none include recommendations concerning microbiological safety. Given the potential public health implications, there is a growing need to develop strategies for mitigating the risk of exposure to antibiotic-resistant pathogens in playgrounds. The objective of this paper is to present the current state of knowledge through a systematic review of the literature, regarding microbiological safety in urban playgrounds, including an overview of the most commonly used research methodologies, the types of pathogens identified, the extent of antimicrobial resistance, and geographic differences. The review revealed significant gaps in knowledge on this topic: targeted empirical studies have been conducted relatively infrequently and only in a few countries worldwide. Even less frequently has the issue of antibiotic resistance in playground-isolated bacteria been addressed. At the same time, antibiotic-resistant strains represent an increasingly significant global public health concern, underscoring the need to develop global strategies to better protect playgrounds from resistant pathogens. Based on the findings, we present and discuss various factors that may influence microbiological safety in playgrounds, as well as strategies that can be implemented to address this critical issue.