Microbial Ecology最新文献

Alpine plants in nitrogen-deficient environments can acquire nitrogen by associating with endophytic nitrogen-fixing microorganisms that inhabit their roots and leaves to form symbiotic relationships. However, research is limited on nitrogen-fixing bacterial communities in the roots and leaves of alpine grassland plants, especially regarding the differences between various plant parts. In this study, we compared the root and leaf bacterial communities of four alpine plant families (Asteraceae, Leguminosae, Poaceae, and Rosaceae) in the alpine meadow ecosystem of Naqu, Tibet, using culture-based methods, 16S rRNA, and nifH gene pyrosequencing. The results showed greater bacterial diversity in the root compared to the leaf, and Fabaceae plants harbored a higher abundance of nitrogen-fixing bacteria. Interestingly, the roots and leaves of non-Fabaceae plants (Kobresia, Festuca ovina, and Leontopodium) also harbored abundant nitrogen-fixing communities such as Microbacterium, Curtobacterium, and Rhodococcus. Compared with subtropical environments, Cyanobacteria are important symbiotic nitrogen-fixing bacteria in plants of alpine ecosystems. These findings indicate that plant species and plant parts strongly influence the selection of bacterial populations. Understanding these microbial ecological functions in alpine grasslands provides scientific insights for optimizing agricultural practices and ecosystem management.

Dutch elm disease (DED) was originally caused by the ascomycete Ophiostoma ulmi, which has been replaced by a more virulent species, O. novo-ulmi, divided into subsp. novo-ulmi and subsp. americana. Permeable reproductive barriers, a period of co-occurrence of O. ulmi and O. novo-ulmi, and the current overlap of O. novo-ulmi subspecies have been important in shaping the present O. novo-ulmi populations in Europe, which were initially clonal, predominantly of the MAT-2 type. This study confirmed the persistence of O. novo-ulmi in Croatia over the years, although at some forest sites, the diseased elms were not detected. The methodology used to assess changes in O. novo-ulmi populations was based on the col1 and cu genes, which have subspecies-specific nucleotide differences, analysis of MAT idiomorphs, and temperature-growth responses. The col1 and cu gene sequencing did not reveal a change in the number of isolates with the recombinant col1/cu genotype over 10 years (2012-2022). At both sampling times, approximately one-fourth of all analyzed isolates had recombinant col1/cu genotypes. However, the frequency of MAT-1 isolates, which all have MAT-1 genes originating from O. ulmi, increased during this period. Differences in growth rate at 20, 26, and 30 °C revealed variations in the temperature response of isolates, which were affected by sampling time and mating type. The MAT-1 isolates were shown to grow more slowly than MAT-2 at the three temperatures tested. The advantage of MAT-2 was reflected in temporal differences in growth rate at resampled sites, particularly at lower temperatures. These results suggest that changes in the frequency of mating types in Croatia occurred between 2012 and 2022, accompanied by modifications in the pathogen's response to temperature at the population level.

Death is a natural process present in all ecosystems; however, mass mortality events are instances of larger than average numbers of animals dying in a relatively short period of time. These events are increasing in frequency and magnitude, and the effects of mass mortalities - especially their long-term effects - are understudied. To better understand the long-term effects of mass mortalities in terrestrial ecosystems, we conducted experimental mass mortality events to determine if key ecosystem properties remained affected after 4 years. The experiment crossed three types of input treatments (control, carrion, and nutrient additive) with scavenger access (open plots versus fenced plots). To evaluate how increasing carrion biomass affected the ecosystem, sites were randomly assigned biomass (25, 59, 182, 363, 726 kg total (20m² plots)). Biomasses consisted of feral swine carcasses or the equivalent amount of N, phosphorus, and K nutrients. After 4 years, we found that while soil N did not differ among treatments, soil K and Ca significantly increased with biomass. Microbial communities significantly differed at the 182 kg biomass treatments compared to others and indicated significant effects between carrion and nutrient additive treatments. These results demonstrate that large die-offs, such as mass mortality events, can have long-lasting effects on soil composition through increased soil nutrients and alter soil microbial community (i.e., reduced Bacilliaceae, etc.). These long-lasting impacts can permanently alter the soil community, which can lead to cascading bottom-up effects that can alter the entire ecosystem structure.

Growing evidence suggests that the gut microbiota is closely intertwined with life-history evolution in a wide range of species, including well-studied model organisms like Drosophila melanogaster. Although recent studies have explored the relationship between gut microbiota and female life-history, the link between gut microbiota and male life-history remains relatively unexplored. In this study, we investigated how gut microbiota changes with male age as well as the associations between gut microbiota composition and male life-history traits in D. melanogaster. Using 22 isolines from the Drosophila melanogaster Genetic Reference Panel (DGRP), we measured lifespan, early/late-life reproduction, and early/late-life physiological performance. We characterized the gut microbiota composition in young (5 days old) and old (26 days old) flies using 16S rDNA sequencing. We observed substantial variation in both male life-history traits and gut microbiota composition across isolines and age groups. Using machine learning, we show that gut microbiota composition could predict the chronological age of the organisms with high accuracy. The most important species contributing to machine learning prediction belonged to the Acetobacter and Ralstonia genera. Associations between gut microbiota and life-history traits were also notable, particularly involving different species from the Acetobacter genus. Our findings suggest that taxa such as Acetobacter may be relevant to the evolutionary ecology of host-microbe interactions in male fruit flies.

Non-Dikarya fungi remain poorly characterized due to their cryptic morphology, cultivation difficulties, and limited representation in reference databases. To investigate their diversity and environmental distribution at a global scale, we reanalyzed over 6000 environmental samples using metabarcoding targeting the V4 region of the 18S rRNA gene, encompassing marine, freshwater, soil, hypersaline, polar, and other habitats. We constructed reference phylogenetic trees based on near full-length 18S rRNA gene sequences to enable accurate placement of short-read amplicon sequence variants (ASVs). This approach yielded robust classification at the phylum level and provided finer-scale clade resolution within major non-Dikarya groups. We delineated precise clades within Chytridiomycota, Microsporidia, Rozellida, and Aphelidea, and unveiled several novel ones. Our results show strong ecological structuring of fungal communities across habitats, with inland systems harboring greater fungal abundance and broader phylogenetic diversity than marine systems. Non-Dikarya fungi were consistently detected across diverse environments, including extreme habitats such as hypersaline lakes, deep sediments, and polar regions, where they were often the dominant fungal taxa. Although most ASVs tended to occur in a limited number of ecologically related habitats, phylogenetically related ASVs within the same clade were often adapted to different environments, indicating ecological diversity within clades. Our findings underscore both the ecological relevance and the cryptic diversity of non-Dikarya fungi in globally distributed environments, including extreme ones. Improved taxonomic resolution and broader reference dataset coverage are required to fully integrate these newly characterized lineages into fungal systematics and environmental surveys.

Hospitals are particularly sensitive environments where immunosuppressed patients might acquire invasive fungal infections. Therefore, it is necessary to carry out periodical environmental microbiological assessments that evaluate the fungal bioburden in air and surfaces from different hospital zones. Current microbiological monitoring protocols at healthcare settings are mostly based on cultivation, while environmental DNA (eDNA) assessments are still scarce and should be further evaluated. To fill this gap, this study combines a large sampling scheme, comprising > 200 samples (air, surface, dust and soil) collected from four zones at three Spanish hospitals in two campaigns (winter and autumn), with two eDNA approaches (DNA metabarcoding and quantitative PCR) to characterize the hospital mycobiomes (diversity, community composition and airborne load), compared to a parallel culture-dependent study. DNA metabarcoding revealed a much more comprehensive inventory of hospital fungi compared to culturing; however, both approaches found similar dominant taxa including a variety of potentially opportunistic human pathogens. Hospital mycobiomes were affiliated to 4 phyla (mostly Ascomycota and Basidiomycota), 35 classes, 114 orders, 305 families, 643 genera and 535 species. The dominant genera, in both air and surfaces from the three hospitals, were Cladosporium, Alternaria, Aureobasidium, Penicillium, Neodidymelliopsis, Aspergillus, Pseudopithomyces and Stemphylium. The yeasts Candida and Clavispora were particularly abundant on high-touch surfaces indoors. The most important explanatory factors for the variance in community composition were the hospital and zone where samples were collected, the type of sample and the sampling campaign. DNA metabarcoding can assist hospital managers by providing an in-depth characterization of the baseline hospital mycobiome during normal operating conditions, as well as identifying and controlling community imbalances and associated health risks under demanding situations such as construction works or reported clinical outbreaks.

Members of the phylum Verrucomicrobiota are abundant yet relatively understudied soil bacteria that play key roles in biogeochemical cycling and plant-microbe interactions. They participate in the carbon (C) and nitrogen (N) cycles through the degradation of complex organic polymers such as cellulose, pectin, and starch - via the production of hydrolytic enzymes (e.g., cellulases, xylanases, chitinases), and through nitrogen transformations including denitrification, ammonification, and nitrogen fixation. Methanotrophic representatives (Methylacidiphilum, Methylacidimicrobium) oxidise methane under acidic or thermophilic conditions, thereby contributing to greenhouse gas mitigation. The ecological distribution and activity of Verrucomicrobiota are strongly influenced by nutrient availability, particularly of C, N, phosphorus (P), and potassium (K). Their variable responses to these elements reflect diverse life-history strategies, encompassing both copiotrophic (r-strategist) and oligotrophic (K-strategist) taxa. While Spartobacteria (e.g., Ca. Udaeobacter) are typically oligotrophic, classes such as Opitutia and Verrucomicrobiae exhibit mixed strategies. Beyond nutrient cycling, several members of the phylum function as plant growth-promoting and stress mitigating bacteria. They produce phytohormones (e.g., indole-3-acetic acid) and siderophores, increase the availability of nitrogen and solubilise phosphate. Some taxa exhibit antioxidant activity and can suppress phytopathogens such as Fusarium oxysporum through secondary metabolite production. These traits suggest a significant potential in soil health improvement. Overall, Verrucomicrobiota represent a functionally diverse and ecologically significant bacterial phylum whose metabolic versatility, adaptive life strategies, and plant-associated traits underscore their central role in sustainable agricultural ecosystems.

The ecological mechanisms governing gut microbial community stability during Alzheimer's disease (AD) progression remain poorly understood. This study employed an ecological network to investigate microbial interactions and stability across cognitively normal controls (CK), individuals with mild cognitive impairment (MCI), and AD patients. We observed a stepwise decline in network complexity across groups, characterized by reduced clustering coefficients and average degree, from CK to AD. While the MCI group exhibited intermediate structural complexity, it displayed the highest vulnerability and lowest robustness, indicating a critical transitional state. Keystone taxa analysis revealed a significant shift in microbial community, with the CK network was enriched with diverse, potentially beneficial keystone taxa, whereas the AD network retained only connector species, and the MCI network showed a complete absence of keystone taxa. Cohesion analysis revealed a non-linear trajectory of microbial interactions, with negative cohesion peaking in MCI. Our findings demonstrate that cognitive decline is associated with a fundamental reorganization of the gut microbial ecosystem. This reorganization pattern reveals a resilient state in health, a vulnerable phase in MCI, and a stable yet dysbiotic configuration in AD, with keystone taxa serving as pivotal regulators of community stability. Community assembly analysis showed a shift from deterministic to stochastic processes during cognitive decline, with weakened host regulatory mechanisms. These findings advance our understanding of the gut microbial ecology in neurodegenerative disease and reveal the mechanism by which microbial communities reorganize network to maintain stability in different cognitive states.

Microbial community dynamics in relation to mesoscale hydrographical features are almost unknown particularly in the pelagic Central-Southern Tyrrhenian Sea. To get a more comprehensive view of phytoplankton community structure and microbial community functioning, datasets of phytoplankton abundance, composition and some microbial enzyme activities (leucine aminopeptidase, LAP, beta-glucosidase, GLU and alkaline phosphatase, AP) from six cruises carried out twenty years ago were analyzed. Hydrographic characteristics identified the presence of both Atlantic Waters (AW) and Tyrrhenian Intermediate Waters (TIW). Size structure of phytoplankton biomass showed an unexpected high contribution of the pico-phytoplankton to the total primary production (> 60%) determining a predominant microbial food web. Phytoplankton distribution patterns varied more significantly on a seasonal rather than spatial scale. Autumn assemblages were characterized by the highest abundance and carbon content, with species mainly belonging to dinoflagellates whose growth was supported by intense microbial activities. In contrast, in the summer diatoms developed in unstable TIW where microbial activity was declining. Enzymatic activities varied in the different water masses and seasons, with high LAP activity in summer AW (s-AW) as well as in deep TIW (d-TIW), while AP and GLU reached their maximum in autumn AW (a-AW), suggesting quick organic matter recycling. Coupled primary production and hydrolysis in mixed AW (m-AW) and in a-AW indicated synchronized autotrophic and heterotrophic processes, while in TIW organic matter was only partially recycled. Overall, microbial metabolism was closely shaped by hydrographic and seasonal dynamics, confirming its key role in biogeochemical cycles. Our data could provide a baseline study for future research dealing with the microbial functioning in this Mediterranean region.

The formation of biofilms in industrial environments poses a significant challenge because of their ability to degrade materials, contaminate products, and harbour pathogenic microorganisms. In the automotive industry, surface treatment systems (STS) used to prepare car bodies can provide a favourable environment for microbial development, driven by the presence of water, organic matter, and variable physicochemical conditions. In this context, the microbial diversity present in the different STS baths of an automotive plant, as well as in the process water, was analysed. Through culture-based methods and molecular analysis, 33 bacterial and 6 yeast species were identified. The results revealed a constant presence of bacteria at all sampling points, whereas yeasts were detected less frequently and in more localized areas (Industrial and Dechromatized Water, E2, Conversion stage, E4 and Passivation stage). This study underscores the importance to enhance cleaning and disinfection protocols in STS, as high bacterial counts persisted even after rinsing stages, in order to prevent economic losses, product degradation and health risks. Furthermore, it highlights the potential use of certain microorganisms in biotechnology and bioremediation applications.