Microbial Ecology最新文献

Acid mine drainage (AMD) generated during coal mining activities is characterized by low pH, high concentrations of dissolved metals and metalloids, and elevated sulfate levels, all of which significantly impact surrounding ecosystems. Scaling up biochemical passive reactor (BPR) systems represents a promising approach for the in situ bioremediation of AMD. While numerous laboratory-scale studies have described the taxonomic and functional composition of microbial communities in BPRs, typically dominated by (ligno)cellulolytic organisms and sulfate-reducing bacteria (SRB), it remains unclear whether this composition is maintained at the field-pilot scale under environmental conditions. To address this gap, 16S rRNA gene metabarcoding and shotgun metagenomics analyses were performed to characterize the taxonomic and functional diversity of microbial communities in the BPRs within a multi-unit field-pilot system. The results revealed that bioremediation effectiveness was driven by syntrophic interactions among hydrolytic, fermentative, and sulfate-reducing bacteria, aligning with laboratory-scale observations. While community composition shifts altered specific taxa, core operational dynamics remained preserved.

Soil fatigue, well documented in various crops, presents a significant challenge to banana production by causing fast and then gradual declines in plant growth and yield over years of cultivation. Despite its impact on profitability, the underlying mechanisms driving soil fatigue remain poorly understood; however, a strong link to shifts in the soil microbiome has been suggested. We investigated the dynamics of microbial communities in relation to soil fatigue, using a novel semi-controlled outdoor experimental system. Soil at different stages of fatigue (0 to 42 months of banana cultivation) was generated in large containers filled with initially healthy soil. Banana plants grown in these soils were replaced with new plants which showed soil age-dependent growth. Three months postplanting, soil and root samples were collected for analyses of soil parameters and microbial community composition using bacterial (16S) and fungal (ITS) amplicon sequencing. We identified minor age-related shifts in mainly pH, potassium, and organic matter in the soil. While alpha diversity remained unchanged, significant shifts in bacterial and fungal community composition were observed in fatigued soils. Notably, the relative abundance of bacterial families such as Flavobacteriaceae, Pseudomonaceae, and Acidibacter increased, as did some fungal taxa (many from groups with known pathogens)-Ceratobasidiaceae (including Rhizoctonia), Dothideomycetes, and Stachybotryaceae. Simultaneously, the relative abundance of bacterial families with known beneficial members, including Gemmatimonadaceae, Moraxellaceae, Sphingomonadaceae, and Azospirillaceae, as well as symbiotic fungal taxa such as Glomeraceae and Lasiosphaeriaceae, declined. Thus, soil fatigue may be correlated to the proliferation of pathogenic populations and a loss of beneficial microorganisms.

Cycads are ancient gymnosperms that play a crucial role in the soil health of scarp forests through their symbiotic associations with nutrient-cycling bacteria. However, the abundance of cycads in scarp forests has been decreasing at an alarming rate, highlighting the importance of determining the role of these species in nutrient cycling, microbial dynamics, and soil health. This study examined soil nutrient and microbial dynamics associated with Encephalartos villosus across four scarp forest sites in KwaZulu-Natal, South Africa. Soil samples were collected from the rhizosphere and non-rhizosphere zones (3-5 m away from the canopy) of mature plants. Results show that collection point did not influence soil nutrient and properties statistically; however, site-level variation was evident, with Hlathikhulu showing higher pH and nutrient concentrations, while Vernon Crookes exhibited lower pH and nutrient availability. Rhizosphere soils supported a greater diversity of nutrient-cycling bacteria, particularly taxa from the genera Bacillus, Burkholderia, Enterobacter, Luteibacter, and Pseudomonas with N-fixing, P-solubilizing, and N-cycling functions. Non-metric multidimensional scaling (NMDS) revealed that site differences, mainly driven by Mg, Ca, K, Zn, pH, and total cations, were stronger predictors of soil nutrient and microbial community variation than collection point alone. Enzyme assays showed that glucosaminidase and acid phosphatase were associated with community differences. These findings indicate that E. villosus enhances soil nutrient enrichment and microbial functional diversity in scarp forests, although the strength of these effects depends on local site conditions. Conservation of E. villosus is therefore critical, not only for species survival but also for sustaining soil fertility and ecosystem functioning in nutrient-limited scarp forest habitats.

The role of gut microbiota in shaping host fitness is already well established. However, it remains unclear to what extent the gut microbiota influences host fitness in the presence of environmental stressors. Here, we tested the hypothesis that responses of water flea Daphnia to the heavy metal nickel are mediated by gut microbiota. Germ-free D. magna exhibited somewhat lower fitness than did those with gut microbiota transplant. Among germ-free Daphnia, those that were exposed to heavy metals did not differ in fitness from unexposed Daphnia. In contrast, when incubated with their donors' gut microbiota, initially germ-free D. magna continuously exposed to nickel for 21 days showed a significantly lower survival rate than those not exposed to nickel. We detected a reduced set of microbes in the formerly germ-free Daphnia in the presence of nickel. Transcriptomic analysis of Daphnia showed that expression/regulation of genes related to oxygen transport, chitin metabolism, and detoxification changed in response to the reduced gut microbiomes acquired in the presence of nickel. Our findings show that the toxic effects of heavy metal led to a reduced diversity of gut microbiota in Daphnia and can thus affect host fitness.

Heat stress poses a significant global challenge to sustainable livestock production, leading to detrimental impacts on animal production and welfare. Reduced appetite and increased body temperature further disrupt the gastrointestinal microbial ecosystem of heat-stressed animals, altering nutrient digestion and affecting host production. However, reported heat-stress-associated microbes have varied across studies, partly due to inconsistencies in microbiota analysis pipelines and taxonomic levels reported. In this study, to identify consistent rumen microbial taxa influenced by heat stress and evaluate potential of rumen microbiota in heat stress prediction, we collected publicly available raw 16S rRNA gene amplicon sequencing data of rumen fluid samples from lactating Holstein cattle housed in thermoneutral or heat stress condition from eight studies, analyzed their microbial composition using a consistent bioinformatic pipeline, and built machine learning models with the rumen microbiota profile to predict heat stress. Important rumen microbial taxa were selected using Boruta (a feature selection algorithm to identify important features) as potential biomarkers to predict heat stress, such as lactate-producing bacteria Lactobacillales, fiber-degrading bacteria Ruminococcaceae UCG-001, and methanogenic archaea Methanomicrobium. Additionally, the random forest model using the available animal factors and relative abundance of rumen microbial taxa showed a much higher performance for heat stress prediction, compared to the model without rumen microbiota profile (Area Under the Curve: 0.851 vs. 0.440). This study confirmed a distinct rumen microbiota signature in heat-stressed lactating Holstein cattle and identified specific rumen microbial taxa as potential biomarkers that could be targeted to mitigate heat-stress responses in dairy cows.

The unintended spread of genetically modified (GM) crops and introgression into wild relatives raises concerns about ecological impacts. In South Korea, CP4-EPSPS-containing Brassica juncea hybrids (GM-hybrid B. juncea) have been detected in natural ecosystems. However, the impact of these GM crops on ecology remains unclear. In this study, we aimed to investigate the potential effects of GM-hybrid B. juncea on the gut and fecal microbiomes of Armadillidium vulgare, a dominant decomposer in natural habitats and an ideal model organism for assessing the ecological impact of GM plant material. Leaf litter from wild-type and GM-hybrid B. juncea was collected from the field, and feeding experiments were conducted using A. vulgare under controlled conditions. Although no significant differences in survival rates or growth were observed between groups, microbiome analysis revealed significant changes in both bacterial and fungal community composition and functional profiles in the gut and feces of the GM-hybrid-fed group. Specifically, in the GM-hybrid-fed group, the proportion of intestinal Plectosphaerella (Glomerellales) increased. Additionally, the bacterial Shannon index decreased, whereas the fungal Shannon index increased. Microbial network analysis revealed distinct interaction patterns and GM-hybrid-specific modules. GM-hybrids may influence decomposer-associated microbiomes through indirect pathways. Such influences could affect ecosystem-level processes such as decomposition and nutrient cycling. This experimental framework can be extended to other crop-derived hybrids or applied to different ecological contexts, providing a valuable basis for future assessments of transgene impacts on ecosystem functions.

Microbial inoculation is a commonly applied approach in composting to enhance organic matter biodegradation and reduce odor emissions. However, the different characteristics of bacteria in terms of temperature can be considered to optimize their effect during different phases of composting. A mesophilic bacterium, namely Aquamicrobium lusatiense NLF 2-7, was evaluated to mitigate odor emissions and enhance the bacterial community under mesophilic composting. Two different treatments were designed: treatment 1 with a single inoculation on the initial day and treatment 2 with split inoculation at the initial and after 2 weeks. Results show that the treatments improve organic matter decomposition by 17.7-28.6% and significantly reduce volatile sulfur compound emissions, especially dimethyl sulfide (DMS) and hydrogen sulfide (H₂S) during the initial phase of composting. DMS emissions were mostly emitted in the first week, with reduction rates of 60.3% and 61.5% in both treatments, respectively. Additionally, mean phenol emissions were reduced by 7.9% in treatment 1 and 11.7% in treatment 2. The dominant bacterial phyla during composting were Bacillota, Pseudomonadota, Bacteroidota, and Actinomycetota, comprising 74 to 95% of the total population. This experiment suggests that A. lusatiense NLF 2-7, which is known for reducing sulfur emissions, can also enhance organic matter decomposition. Split inoculation appears more beneficial, with an initial inoculation managing sulfur emissions early on, followed by a second inoculation after the thermophilic phase to control phenol emissions throughout the composting process.

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.