FEMS microbiology ecology最新文献

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.

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 nontuberculous 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, nonhost 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 analysed host and nonhost 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.

Plant species shape soil microbiome composition through species-specific interactions. However, it is less clear how these interactions vary across populations that diverged a long time ago. In this study, we explore the influence of host genetic composition and edaphic factors on the soil microbiome of Populus tremuloides, one of North America's most widespread tree species. Using 16S, 18S rRNA gene, and ITS2 region metabarcoding on soils from natural stands and potting mix, rhizosphere, and root samples from a greenhouse common garden, we examined prokaryotic and fungal communities in two aspen genetic groups. The Eastern Canada group represents boreal and cold temperate ecoregions, and the one from Northwestern Mexico represents warm temperate ecoregion. Variation in microbial community structure correlated with soil properties but results from common gardens indicated that the host genetic makeup may also play a role. The ecoregions showed functional divergence: warm temperate sites hosted a higher abundance and diversity of nitrogen-fixing bacteria, while boreal stands exhibited stronger associations with ectomycorrhizal fungi. Our findings highlight how local adaptations to climate and soil conditions in aspen extend to their microbial partners, emphasizing the potential role of host-microbe interactions in shaping tree resilience and susceptibility to future climate changes.

The globally distributed genus Methylobacter plays a crucial role in mitigating methane emissions from diverse ecosystems, including freshwater and marine habitats, wetlands, soils, sediments, groundwater, and landfills. Despite their frequent presence and abundance in these systems, we still know little about the genomic adaptations that they exhibit. Here, we used a collection of 97 genomes and metagenome-assembled genomes to ecogenomically characterize the genus. Our analyses suggest that the genus Methylobacter may contain more species than previously thought, with >30 putative species clusters. Some species clusters shared >98.65% sequence identity of the full-length 16S rRNA gene, demonstrating the need for genome-resolved species delineation. The ecogenomic differences between Methylobacter spp. include various combinations of methane monooxygenases, multigene loci for alternative dissimilatory metabolisms related to hydrogen, sulfur cycling, and denitrification, as well as other lifestyle-associated functions. Additionally, we describe and tentatively name the two new Methylobacter species, which we recently cultured from sediment of a temperate eutrophic fishpond, as Methylobacter methanoversatilis, sp. nov. and Methylobacter spei, sp. nov. Overall, our study highlights previously unrecognized species diversity within the genus Methylobacter, their diverse metabolic potential, versatility, as well as the presence of distinct genomic adaptations for thriving in various environments.

The gut microbiome of preterm infants is highly vulnerable to perturbations. Members of the class Clostridia are among the first anaerobes colonizing the preterm gut, yet their ecological roles and antimicrobial resistance (AMR) properties remain poorly understood. We characterized 98 Clostridia isolates from fecal samples of preterm infants, spanning 17 species and 11 genera. Isolates were identified by MALDI-TOF and 16S rRNA sequencing, colonization levels were quantified, and antimicrobial susceptibility was assessed by disk diffusion and E-test. Resistance determinants were screened by PCR and sequenced. We focused on Clostridia that were present at low colonization levels (mean 5.3 log10 CFU g-1 of feces). While most isolates were susceptible to amoxicillin-clavulanic acid, imipenem, and metronidazole, resistance to tetracycline (12%), clindamycin (35%), and cefotaxime (35%) was observed. Distinct species-specific resistance included linezolid (Clostridium argentinense), chloramphenicol (Clostridium innocuum), and tigecycline (Paeniclostridium sordellii), and one Robinsonella peoriensis isolate displayed vancomycin resistance. The detection of tet and erm genes corresponded with phenotypic resistance, while β-lactamase activity was uncommon. Although colonizing at low levels, these findings highlight the ecological significance of rarely studied commensal Clostridia and their contribution to the neonatal resistome, acting as underappreciated reservoirs of AMR genes during a critical window of microbiome assembly.

The human gastrointestinal (GI) ecosystem is a highly dynamic environment and provides diverse microbial habitats for the gut microbiota, which are shaped by environmental factors, metabolic processes, and immune responses. The host-microbiota interactions in the gut form a balanced yet adaptable network. When invading microorganisms enter the GI tract, they deploy multiple strategies to overcome both host defences and competition from the resident microbiota. In turn, the host and native microbiota have evolved sophisticated mechanisms to prevent the colonization of invading organisms, collectively termed colonization resistance. Deciphering the mechanisms of interplay in the host‒microbe and microbe‒microbe relationships in the gut offers crucial insights into therapeutic interventions aimed at restoring or maintaining gut microbial homeostasis.

The biomass, pH changes, and chemotaxis of Enterobacter cloacae (E. cloacae) DJ strain were assessed under various conditions using liquid culture and semi-solid agar plate. Concurrently, GABA concentration, GAD activity, and chemotactic gene expression were measured. The results demonstrated that DJ strain exhibited adaptability to saline-alkaline environments. After 4 h of culture, the pH value decreased, with more pronounced pH changes observed in the saline-alkaline groups. Semi-solid agar plate assays revealed that the DJ strain exhibited the strongest chemotaxis toward the saline-alkaline environment. The average migration radius of the DJ strain reached 1.64 ± 0.09 cm in the saline-alkaline environment after a 24-h cultivation, significantly exceeding the control group's value of 0.88 ± 0.097 cm. The DJ strain exhibited strong positive taxis toward the saline-alkaline environment. Na+ concentration was identified as the primary factor influencing the chemotactic behavior of DJ strain. The GABA content in the saline-alkali group and salt group was 13±0.38 µmol/l and 10.5±1.12 µmol/l, respectively. GAD enzyme activity peaked after 4 h of cultivation, then decreased progressively. qPCR results indicated that the expression of tsr and che-Y genes was up-regulated under saline-alkaline conditions. We propose a model whereby environmental Na+ activates GAD enzyme activity in the DJ strain, leading to increased GABA production that alters the bacterial microenvironment. In response, the DJ strain up-regulates chemotaxis-related gene expression, thereby modifying its behavior to adapt to the saline-alkaline environment.

The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin, it is still unclear which species transcribe the respective genes. Here, we systematically analysed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized cooccurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although ~60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.

Climate is a major determinant of fungal diversity on both large and small spatial scales. However, little is known about the combined effects of regional temperature, microclimate, and dispersal vectors on fungal diversity. We studied the effect of microclimate and wood-inhabiting beetles serving as potential dispersal vectors on the diversity of wood-inhabiting fungi in general-and of brown- and white-rot fungi in particular-along a regional temperature gradient. This focus is motivated by the critical role that different rot types play in wood decomposition and carbon cycling. Beetle and fungal communities were sampled in 243 logs of Norway spruce (Picea abies), which were placed along a 1200 km latitudinal gradient in Sweden (i.e. regional temperature gradient) and under different shading conditions (i.e. microclimatic gradient). Species richness of brown-rot fungi increased with beetle abundance in both the south and the north, whereas shade level markedly limited their species richness only in the north. In contrast, white-rot fungi were unaffected by either factor. These findings highlight that fungal responses to microclimate and dispersal vectors may differ between regions and suggest that species richness of brown-rot fungi may increase with a warming climate, especially in the north.