FEMS microbiology ecology最新文献

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.

Recent studies have identified the environment as a key reservoir from which antibiotic resistance genes (ARGs) can be acquired and transmitted to pathogens. However, our knowledge about the presence of ARGs in high-flow river sediments is still limited. We analyzed the resistome of sediment bacterial communities along the Swedish river Göta Älv and investigated the potential dissemination of ARGs and antimicrobials from effluents of wastewater treatment plants (WWTPs). While we detected nine different antimicrobials in the effluent water from the WWTPs through HPLC-MS, their presence was not observed in river surface water. Analysis by qPCR revealed that the genes sul1 and ermB were the most dominant ARGs among sediment, sludge, and effluent samples. Shotgun metagenomics revealed unique differences between the sludge resistomes of the WWTPs. Moreover, our findings show that ARGs increase downstream of the Göta Älv and their diversity differs from the upstream sites. Efflux pump resistance-related genes were most abundant in sediment samples, and beta-lactams and tetracyclines were the most common antibiotic classes targeted by ARGs. Our study emphasizes the importance of urban river sediments as a reservoir of ARGs, as tracking ARGs in WWTPs and their receiving environments improves our understanding of their spread and characteristics.

Sapronotic pathogens are constituents of complex trophic networks, such as those that structure aquatic and soil ecosystems. In such habitats, sapronotic pathogens live and reproduce among microbial consortia; they also may occasionally infect hosts and cause sapronotic disease (sapronosis). Sapronotic pathogens regroup almost all fungal microparasites and about a third of the bacterial pathogens infecting humans, including for instance non-tuberculous mycobacteria. Even though sapronotic agents are naturally present in the environment, their population dynamics are unknown. Despite growing rates of sapronotic disease incidence among humans, wild and domestic animals, very few studies have examined sapronotic transmission and dynamics in the context of spatially implicit trophic networks. Patterns of sapronotic pathogen transmission arise from complex interactions, including pathogen natural history, non-host and host environments, and spatial and temporal scales of the system. In order to infer and ultimately predict how environmental disturbances affect trophic interactions and influence sapronotic ecology, we analyzed host and non-host species interacting as prey and as micro- and macropredators within a metacommunity context. Using a set of differential equation models, we assessed responses of environmental load dynamics of a sapronotic disease agent, i.e., a mycobacterial pathogen, within a general framework of environmental disturbance. We show that variation in top-down and horizontal interactions mediated sapronotic pathogen abundance and dynamics in the environment. Our findings indicate that habitat change and trophic interactions within these host-pathogen relationships may strongly affect sapronotic pathogen ecology through both synergistic and opposing mechanisms. This work provides for the first time an understanding of environmental disturbance consequences on trophic webs that include major sapronotic pathogens. In addition, the results provide a basis for interpreting the development of sapronotic epidemics and epizootics in the context of ecosystem modifications, particularly that of agriculture and land-use transformation. Further research of this type will provide a better understanding of the complex dynamics of sapronotic pathogens in animals and humans responding to global change.

The reductive dehalogenation of halogenated benzenes by anaerobic bacteria is of great environmental and biotechnological importance; however, the role of specific reductive dehalogenases in the dehalogenation of different isomers has not been studied in detail. Here, we cultivated the obligate organohalide-respiring Dehalococcoides mccartyi strain CBDB1 with either 1,2,3- or 1,2,4-trichlorobenzene (TCB) as electron acceptor and investigated the transcription of its 32 reductive dehalogenase (rdhA) genes using RNA-sequencing. The chlorobenzene reductive dehalogenase gene cbrA, and rdhA cbdbA80 were the two most highly expressed rdhA genes with 1,2,3-TCB. In the presence of 1,2,4-TCB, cbrA was the most highly expressed rdhA followed by rdhA cbdbA1588, encoding an orthologue of the tetrachloroethene reductive dehalogenase PceA of D. mccartyi strain 195. RNA-sequencing also allowed for the detection of small RNAs and an unannotated protein. Proteomics confirmed the synthesis of RdhA CbdbA1588 during respiration with 1,2,4-TCB and also with hexachlorobenzene, which is dehalogenated via 1,2,4-TCB. Dehalogenase activity assays with cell extracts from 1,2,4-TCB-grown cultures indicated a higher activity towards 1,2,4-TCB and a ten-fold higher activity towards 2,3-dichlorophenol compared to that in extracts from 1,2,3-TCB-grown cultures. These findings demonstrate the functionality of RdhA CbdbA1588 and further support a role in 1,2,4-TCB dechlorination by strain CBDB1.

Isoprene, a highly reactive biogenic volatile organic compound (VOC) emitted by terrestrial vegetation, influences atmospheric chemistry but its microbial degradation remains poorly understood. Aerobic degradation begins with isoprene monooxygenase (IsoMO), a multicomponent di-iron monooxygenase encoded by the isoABCDEF cluster, with isoGHIJ supporting downstream steps. We analysed iso gene clusters from eleven confirmed isoprene degraders, reconstructed amino acid sequence phylogenies and generated structural models of IsoMO components using mainly AlphaFold2. IsoA, IsoE, and IsoB formed a highly conserved α₂β₂γ₂ monooxygenase core (IsoMO core) whose predicted architecture and closely resembled the soluble methane monooxygenase (sMMO) hydroxylase, revealing a shared di-iron catalytic framework adapted to distinct hydrocarbon substrates. IsoA was the most conserved subunit and remains a reliable molecular marker for isoprene degradation. This work presents the first detailed structural model of an IsoMO core and reveals its deep relationship to other soluble di-iron monooxygenases. Together these results provide a molecular foundation for future mechanistic, ecological and inhibitor-based studies linking enzyme-level specificity to microbial control of isoprene turnover under changing climate conditions.

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.