Microbial Ecology最新文献

Despite the known influence of climate change on high-altitude ecosystems, the long-term response of prokaryotic communities in Mediterranean high-mountain lakes remains poorly understood. Here, we investigate the temporal dynamics of prokaryotic communities over the past ~ 430 years in a Mediterranean high-mountain lake, utilizing sedimentary ancient DNA (sedDNA). By examining a sediment core from Borreguil Lake in the Sierra Nevada (Spain), we evaluated bacterial and archaeal abundance, diversity, and community composition (β-diversity) in relation to paleoenvironmental and climate data. Our findings revealed a significant restructuring of prokaryotic communities, particularly since ca. 1960. A Random Forest model identified dissolved organic carbon, organic nitrogen, Saharan atmospheric dust inputs, and temperature as key drivers of the abundance, diversity, and composition of prokaryotic communities, particularly in the modern era. Notably, the abundance and diversity of bacterial communities increased in response to increased dissolved organic carbon, elevated temperatures, and dust deposition, while archaea demonstrated a more nuanced response linked to organic nitrogen availability and dust inputs. The temporal shifts in microbial community composition point to broader ecological changes within the lake, shaped by climate-driven environmental variations. For example, the increased relative abundance of Cyanobacteria and other taxa linked to higher nutrient availability indicates ongoing eutrophication processes, likely intensified by climate warming. This study highlights the importance of high-mountain lakes as indicators of climate change, contributing valuable insights into microbial ecology's response to long-term environmental change. Our findings offer a foundational understanding for predicting microbial responses in sensitive ecosystems under future climate scenarios.

The anaerobic ammonium oxidation (anammox) process offers a sustainable and energy-efficient alternative for nitrogen removal in wastewater treatment, but its performance at low temperatures remains a major challenge. This study investigated the role of zero-valent iron (ZVI) in enhancing anammox activity across a temperature range of 10-30 °C using both synthetic and municipal wastewater (MWW). Short-term batch tests demonstrated that low-dose ZVI (5-10 mg/L) stimulated specific anammox activity (SAA) particularly at 13-20 °C, while ZVI increasing concentration (1-10 mg/L) enhanced the enzymatic activity of HDH and decreased NIR activity, as well as modulated oxidative stress (ROS and GSH balance). In contrast, the long-term operation of the anammox process in sequencing batch reactors (SBR) showed that while ZVI (5 mg/L) improved SAA and microbial stability under synthetic conditions at 13 °C in compared to control (without ZVI), these benefits diminished once real municipal wastewater was introduced, most likely due to biomass stress and organic load. Metataxonomic analysis confirmed that ZVI selectively promoted genera such as Candidatus Brocadia, Denitratisoma, Micavibrionales_unclassified, while reducing overall microbial diversity. These results indicate that low-dose ZVI can temporarily enhance anammox resilience at suboptimal temperatures. However, its long-term application in MWW requires further optimization to mitigate potential inhibitory effects and iron passivation.

The 17-year Periodical cicadas (Magicicada spp.) are long-lived insects that emerge in mass synchronized events after 17 years underground. Their survival and ecological success depend heavily on their microbiomes, which include obligate bacterial symbionts essential for nutrient acquisition, as well as occasional pathogens such as the behavior-altering fungus Massospora cicadina. While the periodical cicada lifecycle is well studied, little is known about how cicada microbiomes vary across species and environments during a single emergence event. During the 2024 emergence of Brood XIII in northern Illinois, 17-year cicadas were sampled from four ecologically distinct forest preserves. Cicadas were identified by species and sex; their microbiomes were assayed using 16S rRNA gene sequencing and tested for the presence of the fungal pathogen M. cicadina DNA in asymptomatic individuals. Sampling sites were characterized by plant community composition, historical disturbance, and potential presence of the antifungal compound juglone. Microbiome composition differed significantly by cicada species and site, but not by sex. The obligate symbionts Hodgkinia cicadicola and Sulcia muelleri dominated microbiome profiles, though other bacteria-including Pantoea agglomerans, a potential pheromone producer-were variably abundant. Cicada species distributions were non-random across sites and correlated with local plant diversity. M. cicadina DNA was detected in 23% of otherwise asymptomatic cicadas, with infection rates varying by location and negatively correlated with microbiome diversity. This study highlights complex interactions between cicada species, their microbial communities, and environmental variables such as plant diversity, soil chemistry, and land use history.

Vicatia thibetica de Boiss is a unique medicinal and edible plant endemic to Xizang, China. It is one of the five primary root medicines in Tibetan medicine due to its high content of flavonoids. However, the community composition of endophytic bacteria in its various tissues and their potential role in flavonoid accumulation remain unclear. We employed high-throughput sequencing to compare the diversity of endophytic bacteria in the rhizosphere soil and various tissues of V. thibetica collected from three sampling sites in Nyingchi, Xizang. Concurrently, we assessed the types and concentrations of flavonoids present in the roots. Finally, we investigated the relationship between root endophytic bacteria and flavonoid accumulation through correlation analysis. The results indicated that the diversity and abundance of bacterial communities in the rhizosphere soil exceeded those of the endophytic bacterial communities of V. thibetica. Proteobacteria is the dominant phylum, and Sphingomonas is the dominant genus. Each tissue of a plant exhibits its dominant genus. PICRUSt predictive analysis revealed that RNA processing and modification were the predominant functions among related species. Targeted metabolomics analysis has revealed that the roots of the plants contain 14 flavonoid compounds. Correlation analysis revealed that the concentrations of flavonoids in the roots, including apigenin, rutin, astragalin, quercetin 3-glucoside, L-epicatechin, kaempferol, and luteolin, are associated with the distribution and abundance of specific bacterial genera, such as Lactobacillus, Kurthia, Bradyrhizobium, Phenylobacterium, Novosphingobium, and Mycobacterium, among others. This finding suggests that these bacterial genera may directly influence the production and accumulation of flavonoids in the plant. Our findings will enhance the understanding of plant-microbe interactions and provide crucial insights into the role of endophytes in the production of V. thibetica and its significant secondary metabolites.

How land-use history-particularly in contrasting systems such as rotational shifting cultivation (RSC) and continuously fallow (CF) fields-influences soil microbial communities and their biogeochemical functions remains insufficiently understood. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition and functional gene profiles of soils under RSC and CF systems in Northern Thailand. The results revealed distinct microbial assemblages and metabolic potentials shaped by land-use legacy. RSC soils were characterized by a higher abundance of nitrifiers and nitrogen-fixing taxa, including Nitrosocosmicus and Streptomyces, along with enriched genes involved in nitrification (e.g., amoC_B, nxrB) and nitrogen fixation (nifD, nifK), reflecting an enhanced potential for nitrogen acquisition and retention. In contrast, CF soils showed enrichment in Bradyrhizobium, Halobaculum, and Russula, and exhibited higher expression of denitrification-related genes (norB, narJ), suggesting increased nitrogen loss via gaseous emissions. Functional genes related to phosphate metabolism (phoX, glpQ) and nutrient signal transduction were more abundant in RSC soils, indicating active nutrient cycling in response to recent disturbance. Conversely, CF soils demonstrated broader metabolic capabilities, including genes for sulfur oxidation and redox regulation, suggesting microbial adaptation to more stable but nutrient-limited conditions. These findings demonstrate that land-use legacies strongly influence microbial composition and function, with important implications for nutrient cycling and soil fertility restoration in shifting cultivation landscapes.

The gut microbiome is an important factor in animal health and can be influenced by factors such as age, diet, stress, environmental conditions, and farming practices. Bacterial communities of the gut microbiome in many species have been extensively studied, but research on the fungal microbiota remains limited and underrepresented in the literature. The objective of this study was to characterize the fecal mycobiota of swine raised under two different production systems: outdoor pasture-based or conventional indoor systems. Fecal samples from nursery, growing-finishing, and sow pigs from both farming systems were collected, and the mycobiota was profiled using PCR amplification and sequencing of the universal fungal internal transcribed spacer 1 (ITS1) region. A significant difference in fungal community structure was observed between the conventionally raised and pasture-raised pigs, as well as among all three production phases. Four species, Arthrographis kalrae, Enterocarpus grenotii, Pseudallescheria angusta, and Sagenomella oligospora, were differentially abundant between the two farms, all of which had higher relative abundance in the pasture-raised pigs. Additionally, pasture-raised pigs hosted a more diverse fungal community with higher species richness in their gastrointestinal tract. In summary, farming practices and pig age influenced the pig fecal mycobiota.

Schoolchildren from the Galapagos and the Andean region present the worst indices of malnutrition in Ecuador and are exposed to distinctive food and water insecurity. We compared the nutritional status, the fecal microbiota composition of schoolchildren from the Galapagos (n = 51; 8.88 ± 2.15 years) and the Andean region (n = 114; 8.69 ± 1.83 years). Children had a nutritional evaluation and provided fecal samples for microbiota analysis by 16S rRNA gene sequencing. Excess weight was more prevalent in Galapagos (41.18%) than in the Andes (24.5%). Additionally, intestinal parasitosis was more prevalent in children from the Andes (76.4%) than in Galapagos (13.0%). Species richness was lower in fecal samples of children from the Galapagos than those from the Andes (Chao1 index p = 0.001). Beta-diversity metrics also showed significant differences between these samples. Bacteroidota and Proteobacteria were enriched in the microbiota of Galapagos children, whereas Firmicutes A and Cyanobacteria were enriched in the Andean children. At the genus level, the top 3 genera present in schoolchildren from the Galapagos were Bacteroides, Phocaeicola, and Escherichia, while in children from the Andes were Cryptobacteroides, Prevotella, and Clostridium. Cyanobacteria were inversely associated with BMI z-score in the Galapagos region (q = 0.009), while, Firmicutes D had a direct relationship with BMI z-score in children from the Andes (q = 0.05). At the genus level, only Butyrivibrio was inversely associated with BMI z-score in children of the Galapagos (q = 0.04). We conclude that schoolchildren with different degrees of malnutrition from two distinct geographical areas have dissimilar fecal microbiota characteristics.

The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski's gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.

The host-microbiome association is considered a coevolutionary process, in which the microbiome provides important functions for host development, physiology and health. However, the ecological and evolutionary forces shaping the diversity and structure of the bacterial communities that form the microbiome are still being elucidated. We assessed the composition of gut microbiota in six rodent species from three geographic regions across the Yucatán peninsula, Mexico. We evaluated the contribution of host species identity, phylogenetic relationships, and geography to the rodents' gut microbiota, using 16S rRNA V4 sequences. We performed a comprehensive set of analytical approaches, including Hill numbers, machine learning, and phylogenetic comparative frameworks. Our results show that phylosymbiosis is one of the main mechanisms driving microbiota dissimilitude across species and specific microbiota diversity traits. Additionally, the microbial pool in each region was geographically differentiated, shaped by the rodent community ensemble, while ecological filtering rendered a microbial pool characteristic of each species. The environment also played a significant role for some species like Heteromys gaumeri, while dietary habits showed a stronger signal for Oryzomys couesi. Rodents with more specialized habits like Ototylomys phyllotis (semi-arboreal, folivorous) had higher bacterial diversity. The abundance of eight bacterial families determined key differences of the gut microbiota which, in addition to phylogeny and geography, are associated with distinct diet and metabolic functions among rodents. Distinct metabolic functions were related, among others, to toxins metabolism and digestion of complex food components. Overall findings show that both evolutionary and ecological drivers influence these rodents gut microbial structure and composition.

Tebuconazole is a widely used triazole fungicide to control fungal diseases. While there have been reported side effects on non-target arthropods, its ecological risks to natural enemies remain poorly understood. In this study, we evaluated the developmental toxicity and symbiotic microorganism responses of the wolf spider Pardosa pseudoannulata, an important predator in rice ecosystems, following exposure to tebuconazole. The results indicated that tebuconazole did not significantly increase the mortality rate of spiderlings; however, it did lead to a significant decrease in spiderling body weight, as well as the length and width of the carapace. High-throughput sequencing of the 16S rRNA gene V3-V4 regions and the ITS region revealed that tebuconazole significantly reduced bacterial diversity indices in the short term, with a gradual recovery over time. In contrast, the impact on the fungal community was continuous and irreversible, with a significant decrease in the Shannon index observed after 15 days. At the genus level, the relative abundances of Cupriavidus and Staphylococcus in the bacterial community decreased significantly after tebuconazole exposure, while Stenotrophomonas increased. In the fungal community, Fungi_gen_Incertae_sedis decreased significantly, and Simplicillium increased. Our findings highlight the ecological risks of fungicide exposure to beneficial predators and underscore the importance of considering symbiotic microbiota in pesticide risk assessments.