FEMS microbiology ecology最新文献

Metabarcoding is a powerful tool to simultaneously identify multiple taxa within a habitat. However, its application to host-associated microbiomes is challenged by substantial co-amplification of host DNA. Here we developed a host-exclusive primer design workflow, to selectively generate amplicons from target taxa while excluding the host. This workflow is centered around a new computational tool, mbc-prime, that can generate a list of discriminative candidate primers and score them. We showcase the use of this tool in the design of primers for long-read metabarcoding of endophytic fungi in Vinca minor. Mbc-prime streamlines the design of fungus-specific primers, enabling efficient and plant-free amplification of fungal rDNA from mixed DNA samples. Our workflow can be used to study the composition of complex host-associated microbiomes. It should be universally applicable for the design of discriminative primers in a user-friendly and practical manner and thus be of use for various researchers in microbiome research.

Under low-nutrient conditions, nematode-trapping fungi (NTFs) can differentiate their mycelia into specialized trapping devices for capturing prey. Using energy-dispersive X-ray spectroscopy in conjunction with transmission electron microscopy, together with a series of bioassay, we identified that the characteristic electron-dense bodies in trapping devices contained more iron than vacuoles and mitochondria, functioning as an unrecognized iron storage organelle. Genomic analysis revealed that all NTFs lack the Ccc1-mediated vacuolar iron detoxification mechanism conserved in most fungi. Heterogenous expression of yeast-derived Ccc1 gene in Arthrobotrys oligospora significantly reduced trapping device formation and nematicidal activity. Mapping key factor fluctuations onto Bayesian relaxed molecular clock analysis indicated that the loss of Ccc1-mediated vacuolar iron storage occurred during Late Paleozoic Ice Age, whereas the emergence of trapping devices and the acquisition of desferriferrichrome were closely associated with elevated temperatures. Temperature bioassays showed that trap formation is highly temperature-dependent, with free iron levels inversely correlated with temperature, consistent with the temperature sensitivity of A. oligospora, which cannot grow above 30°C. Our findings demonstrated that global temperature fluctuations serve as a critical driver of the evolution of NTFs and act as a catalyst for the emergence of trapping devices, novel phenotypic indicator of eukaryotic iron overload.

Arctic warming has coincided with dramatic changes in plant cover, but the impact that aboveground biomass shifts have on soil microbial communities and processes remains poorly understood. To address this, we investigated spatial patterns of soil microbes in relation to vegetation changes using a space-for-time approach in the high Arctic region of Longyearbyen, Svalbard. We collected and characterized 31 topsoil samples from three sites that differed in nutrient input, CO2 flux, soil chemistry, and plant cover. Pronounced vegetation differences were observed at fine spatial scales, including a highly localized graminoid-dominated hotspot within areas of mixed plant communities. This graminoid-rich hotspot coincided with locally elevated soil fertility and exhibited particularly high CO2 fluxes. In areas that transitioned from dwarf shrub- to graminoid-dominated vegetation, we observed an increase in estimated fungal abundance, a shift from heterogeneous to Ascomycota-dominated fungal communities, and a greater abundance of r-strategist prokaryotes. Multiple regression on biotic and abiotic distance matrices revealed that soil fungi may be especially sensitive to changes compared to prokaryotes and plants. These findings highlight the need for future experiments investigating fungi in high Arctic tundra to better understand feedback between biotic and abiotic factors under warming.

Soils in northern latitudes are warming, resulting in changes to soil abiotic and biotic processes. We conducted a laboratory study of boreal forest soils from Finland where we manipulated temperature and moisture while measuring respiration. The temperature and moisture reflected field data collected during the summer. Microbial respiration and potential extracellular enzyme activity (EEA) both significantly increased with warming. The nitrogen-degrading potential EEA values were significantly affected by both temperature and moisture conditions, with peak activity occurring at -10 kPa. Both bacterial and fungal community composition shifted with incubation temperature with more fungal families than bacterial families decreasing in relative abundance with increasing temperature. Overall, microbial activity increased with temperature and the changes in community composition were driven by temperature. The effect of matric potential was stronger for the fungal communities. These results suggest potential increases in the rate of microbial respiration and increased seasonal nutrient cycling as boreal forest regions experience warmer and wetter climate regimes.

This study investigated the persistence and control of S. enterica serovar Newport on garden cress under warming temperature scenarios (15°C, 17°C, 19°C, 21°C), simulating climate change-relevant conditions. Two contamination routes-seed and irrigation-were tested with irrigation applied at different plant growth stages to assess the impact of contamination timing too. In addition, the study evaluated the effectiveness of preharvest bacteriophage irrigation applied at various intervals prior to harvest. Results showed that both contamination routes supported long-term survival, with the greatest persistence at 15°C. Late-stage contamination through irrigation resulted in higher bacterial loads at harvest, posing greater food safety risks. While a washing step significantly reduced Salmonella levels, especially in later contamination scenarios, it was insufficient to fully remove strongly attached bacterial populations across all cases. Bacteriophage irrigation achieved up to 2.2 log MPN/g reduction when applied close to harvest, particularly when combined with washing. Beyond expanding the mechanistic understanding of Salmonella-plant interactions, these findings illustrate how temperature dynamics, contamination timing, and exposure routes collectively influence bacterial persistence under warming scenarios relevant to climate change, while also demonstrating the potential of a targeted preharvest intervention strategy with significant control efficacy.

Artificial lakes formed from past mining activities represent unique but underexplored ecosystems that support diverse microbial communities. This study examined how seasonal variation and depth influence bacterial, archaeal, and microeukaryotic assemblages in the stratified water column of the Blackburn mine (Outaouais, Quebec, Canada). Water and biofilm samples were collected by technical divers from the surface to 52 m during spring, summer, and autumn of 2021-2022, and analysed by 16S/18S rRNA gene sequencing. Seasonal changes had little effect on physicochemical parameters but strongly shaped microbial community composition, together with depth. Archaeal taxa displayed greater stability across depths compared to bacteria and eukaryotes. Oxygen profiles defined three ecological zones: an oxic layer dominated by Actinobacteria and the methanogen Methanosarcina; a transition zone enriched in Chlorobium and methanogens such as Methanospirillum and Methanosaeta; and an anoxic layer containing sulfur-reducing (Desulfomonile and Desulfobacca), sulfur-oxidizing (Sulfuricurvum), and methane-cycling archaea. Eukaryotic communities included algae, particularly Chrysophyceae, and diverse protists. These findings suggest that microbial communities in the mine are integral to sulfur and carbon cycling, emphasizing the ecological significance of such stratified, mining-associated aquatic systems. The Blackburn mine provides valuable insight into how anthropogenic legacies shape microbial diversity and ecosystem functioning in artificial aquatic environments.

Novel cutting-edge technologies for plastid genetic engineering have a great potential in agriculture. Genetic engineering of the plastid genome (plastome) can be performed using both conventional homologous recombination vectors, and novel episomal platforms that rely on synthetic plastomes (minisynplastomes) to express transgenes from a nonintegrating plasmid. Evaluating the potential risk of horizontal gene transfer (HGT) is an important step for regulatory approval of environmental release of these novel genetic engineering tools. In particular, the endosymbiotic origin of plastids from a prokaryotic progenitor may increase the probability of HGT to the environmental microbial community. In this study, the naturally competent soil bacterium Acinetobacter baylyi has been used to test the probability of plant-to-bacterium HGT under laboratory conditions. While plant-to-bacterium HGT can be detected in vitro as a low probability event, the minisynplastome does not show an increased HGT compared to conventional transformation platforms. After a comprehensive evaluation of minisynplastome elements affecting plasmid persistence in bacteria (plastid origin of replications, plastomic regions containing rRNA genes, and regulatory elements for transgene expression), optimized minisynplastome (Gen3) platforms with no residual activity in bacteria and with undetectable HGT were characterized. This study represents a valuable resource for designing minisynplastome transformation platforms with improved environmental biosafety in agriculture.

During terrestrial vertebrate decomposition, host and environmental microbial communities work together to drive biogeochemical cycling of carbon and nutrients. These mixed communities undergo dramatic restructuring in the resulting decomposition hotspots. To reveal the succession of the active microbes (bacteria, archaea, and fungi) and the metabolic pathways they use, we generated metatranscriptomes from soil samples collected over 1 year from below three decomposing human bodies. Soil microbes increased expression of heat shock proteins in response to decomposition products changing physiochemical conditions (i.e. reduced oxygen, high salt). Increased fungal lipase expression identified fungi as key decomposers of fat tissue. Expression of nitrogen cycling genes was phased with soil oxygen concentrations: during hypoxic soil conditions, genes catalyzing N-reducing processes (e.g. hydroxylamine to nitric oxide and nitrous oxide to nitrogen gas during reduced oxygen conditions) were increased, followed by increased expression of nitrification genes once oxygen diffused back into the soil. Increased expression of bile salt hydrolases implicated a microbial source for the high concentrations of taurine typically observed during vertebrate decomposition. Collectively, microbial gene expression profiles remained altered even after 1 year. Together, we show how human decomposition alters soil microbial gene expression, revealing both ephemeral and lasting effects on soil microbial communities.

Alpine catchments encompass heterogeneous soil habitats with varying roles in nutrient cycling. While undeveloped till soils in scree areas are hotspots for nitrate and phosphate leaching, vegetated alpine meadow soils rather efficiently retain nutrients. This study examines the role of microbial communities in nutrient mobilization and retention, beyond the effects of abiotic soil properties. We compared the chemical, microbial, and functional characteristics of scree and meadow soils in four high-elevation catchments of the Tatra Mountains in Central Europe. Despite their lower organic matter content and microbial biomass, scree soils exhibited high concentrations of mobile nitrate and phosphate, low phosphate sorption ability, and significantly greater phosphorus leaching. Their microbiomes were distinct and enriched with pioneer taxa, including lichenized fungi, oligotrophic bacterial lineages (e.g. AD3 and Eremiobacteria), and saprotrophic fungi that specialize in the recycling of microbial necromass. These microbiomes exhibited high biomass-specific activities related to nutrient mobilization. In contrast, meadow soils supported larger microbial communities dominated by fungi with strong plant associations and functional traits that enhance nutrient retention. Our findings demonstrate that soil microbiota actively control nitrogen and phosphorus mobility by acting as either accelerators (in vegetation-free scree areas) or buffers (in meadows) of nutrient leaching from alpine soils.