Search Results (22)

Hibernation in mammals entails profound physiological changes that are known to impact host-associated microbial communities, yet its effects on the gut microbiota of synanthropic bats remain underexplored. In this study, we investigated the gut bacterial composition and diversity of Nyctalus noctula before and during hibernation using high-throughput 16S rRNA amplicon sequencing. Fecal samples from individually banded bats were collected under controlled conditions at a rehabilitation center and analyzed for alpha and beta diversity, as well as differential taxonomic abundance. Hibernation was associated with a marked reduction in microbial diversity according to the Shannon and Simpson indices and a distinct restructuring of gut communities based on the Bray–Curtis dissimilarity index. Active bats exhibited a diverse microbiota enriched in facultative anaerobes, including Lactococcus, Enterococcus, and Escherichia–Shigella, while hibernating individuals were dominated by obligate anaerobes, such as Romboutsia and Paeniclostridium. These findings suggest a contraction and functional specialization of the gut microbiota during torpor, potentially reflecting adaptations to fasting, hypothermia, and reduced gut motility. Our results demonstrate that the bat’s gut microbiome is highly responsive to physiological status and underscore the importance of microbial ecology for understanding the host’s energy balance and health under seasonal contexts. Full article

Lake Urmia is one of the world’s most unique and hypersaline aquatic ecosystems. The aim of this study was to investigate the diversity, abundance and frequency of these microorganisms in water samples from the eastern regions of the lake over four seasons. Amplicon sequencing for the 16S rRNA gene was performed to examine bacterial communities in the samples. The study revealed significant seasonal variations in water quality parameters and their influence on the microbial communities. Majority and rarity analyses showed that winter and spring had higher core abundance and higher Gini index values, indicating a greater dominance of certain genera, while autumn and summer had a more balanced distribution. Analysis of beta diversity using the Bray–Curtis dissimilarity index emphasized that bacterial communities diverge most strongly in summer and winter, reflecting the significant changes in the environment with the season. Overall, understanding the seasonal variation in water chemistry and bacterial communities is critical for effective ecosystem management and conservation efforts. Full article

Synthetic microbial community (SynCom) application is efficient in promoting crop yield and soil health. However, few studies have been conducted to enhance pepper growth via modulating rhizosphere microbial communities by SynCom application. This study aimed to investigate how SynCom inoculation at the seedling stage impacts pepper growth by modulating the rhizosphere microbiome using high-throughput sequencing technology. SynCom inoculation significantly increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll content, leaf number, root vigor, root tips, total root length, and root-specific surface area of pepper by 20.9%, 36.33%, 68.84%, 64.34%, 29.65%, 27.78%, 117.42%, 35.4%, 21.52%, and 39.76%, respectively, relative to the control. The Chao index of the rhizosphere microbial community and Bray–Curtis dissimilarity of the fungal community significantly increased, while Bray–Curtis dissimilarity of the bacterial community significantly decreased by SynCom inoculation. The abundances of key taxa such as Scedosporium, Sordariomycetes, Pseudarthrobacter, norankSBR1031, and norankA4b significantly increased with SynCom inoculation, and positively correlated with indices of pepper growth. Our findings suggest that SynCom inoculation can effectively enhance pepper growth and regulate root morphology by regulating rhizosphere microbial communities and increasing key taxa abundance like Sordariomycetes and Pseudarthrobacter, thereby benefiting nutrient acquisition, resistance improvement, and pathogen resistance of crops to ensure sustainability. Full article

Fires play a significant role in shaping the Miombo woodlands. Understanding how fire affects the Miombo region’s resilience is crucial for ensuring its sustainability. This study evaluated plant composition and structure across different fire frequencies in the Miombo woodlands of the LevasFlor Forest Concession (LFC), central Mozambique. Fire frequency clusters-high (HFF), moderate (MFF), and low (LFF)-were identified using a 21-year remote-sensing dataset. In each cluster, 90 random sampling plots were established (30 per cluster). In each plot, the diameter at breast height (DBH) and total height of the saplings and trees were measured. Subplots were used to count and identify seedlings, herbs, climbers, and grasses. Plant species richness, evenness,—diversity, the importance value index (IVI), and similarity were computed to assess plant composition. For the structure, stem density, biomass, basal area, diameter, and height were assessed. A total of 124 plant species-including trees, saplings, seedlings, herbs, climbers, and grasses-were identified across the three clusters. The Bray-Curtis Dissimilarity Index, tested with an ANOSIM similarity test, revealed significant differences in plant species composition among clusters (p < 0.0003), with an overall average dissimilarity of 71.98%. In the HFF cluster, fire-tolerant species were among the five species with the highest IVI, while fire-sensitive species predominated in the LFF. Additionally, the Kruskal-Wallis test indicated significant differences in seedling stem density (p < 0.005) between the LFF and other clusters. However, overall, the composition and structure attributes suggested that current fire regime does not significantly compromise the plant species resilience of the Miombo woodlands in the LFC. Still, it is essential to concentrate management and conservation efforts on seedlings of some key Miombo species, such as Brachystegia spiciformis, whose ecology is particularly affected by fire. Full article

Background: Human activities such as agriculture are known to markedly affect natural ecosystems, including plant communities and soil properties. Biological activities are reduced in hot, hyper-arid ecosystems compared to temperate and tropical climatic conditions. Anthropogenic disturbances therefore have greater impacts on the ecosystem’s recovery potential. This study aimed to assess the diversity and recovery of post-agriculture plant communities in the Sharaan Nature Reserve (SNR), located in northern Saudi Arabia. Methods: Three types of habitats representative of different disturbance situations were identified in the reserve and sampled through 103 floristic and pedological surveys. The floristic composition was recognized and relative quantification of soil atomic elements was performed. The obtained data were processed using different statistical treatments such as the Shannon index and Bray–Curtis dissimilarities, non-metric multidimensional scaling (NMDS), Kruskal–Wallis tests and Redundant analysis (RDA). Results: Investigations led to the identification of 48 plant species belonging to 24 genera and 22 botanical families. Specific plant community structures were correlated with each habitat, and bioindicator plant species were identified. Polycarpaea repens and Stipagrostis plumosa were linked with natural habitats, while Atriplex leucoclada was specific to disturbed habitats. In contrast, Asteriscus graveolens and Haloxylon salicornicum were found to be ubiquitous species. Conclusions: The presence of bioindicator species was closely associated with the different soil properties measured in each habitat. Restoration strategies related to the overall dynamic plant community succession pattern observed in the Sharaan Nature Reserve are discussed. Active ecological restoration strategies based on targeted active ecological restoration interventions should facilitate the recovery and restoration of disturbed plant communities in hyper-arid areas. Full article

The gut microbiota plays a critical role in immune system function, with dysbiosis linked to systemic inflammation, contributing to conditions like psoriasis and depression. Although biological treatments for severe psoriasis are known to impact gut bacteria, less is understood about their effects on fungi. This study aims to investigate fungal gut microbiota changes in psoriasis patients transitioning from TNF-α inhibitors to brodalumab. Fecal samples from 20 patients were analyzed using Illumina MiSeq sequencing of the ITS2 region of 18S rRNA. Microbial diversity was assessed through Bray–Curtis dissimilarity and the Shannon–Wiener index. Clinical outcomes were measured using clinical scores for psoriasis and depression severity, with statistical analysis performed via Wilcoxon signed-rank tests and PERMANOVA. Results showed that Ascomycota was the dominant fungal phylum in both treatment groups, with Saccharomyces, Penicillium, Candida, and Debaryomyces as prevalent genera. No significant changes occurred at the phylum level after switching to brodalumab, though minor genome-level variations were observed. Beta diversity analysis highlighted inter-patient variability, with no significant correlation between fungal composition and clinical outcomes. Despite improved clinical scores, the fungal gut microbiota remained largely stable, suggesting that brodalumab does not significantly alter fungal communities in psoriasis patients. Further research is needed for a comprehensive understanding. Full article

Steelmaking slags are prospective base materials for seaweed beds, resulting from a continuous process of biofouling, starting from biofilm formation and leading to growing algae. While focusing on biofilm formation, we investigated specific features of steelmaking slags when utilized as a base for seaweed beds by comparing the bacterial communities in marine biofilms between steelmaking slags and artificially produced ones. Genomic DNA was extracted from the biofilms collected on days 3 and 7, and partial 16S rRNA libraries were generated and sequenced by second-generation next-generation sequencing. The read sequences were analyzed using QIIME 2™, then heatmaps and non-metric multidimensional scaling based on the Bray–Curtis dissimilarity index in the R program. Rhodobacteraceae and Flavobacteriaceae were the most dominant family members in all samples on both days 3 and 7. However, Mariprofundus, comprising iron-oxidative bacteria, was predominantly detected in the samples of steelmaking slags on day 7. This suggested that the growth of Mariprofundus was dependent on Fe(II) ion concentration and that steelmaking slags eluted Fe(II) ions more easily than artificial slags. In contrast, Sulfurovaceae, sulfur-oxidizing bacteria, were dominantly present in all samples on day 3, but decreased by day 7, regardless of the sulfur content. It was supposed that engine oil-derived sulfur compounds strongly influenced Sulfurovaceae growth, whereas slag-derived sulfur compounds did not. Heatmap analysis indicated that the submersion period significantly influenced the bacterial communities, regardless of the differences in the main slag content ratios. Summarizing these results, the elution characteristics of steelmaking slags have the potential to influence the formation of marine biofilms, and this formation is significantly influenced by environmental conditions. Full article

Montes de María is the best-preserved tropical dry forest fragment in the Colombian Caribbean, making it an ideal location for studying the impacts of human disturbance on local ecosystems. In this study, we analyzed the community structure of diurnal butterflies in both forested and disturbed areas using 16 circular plots to identify relationships between alpha and beta diversity, and the geographic distance between disturbed areas and native forests, using a range of metrics, including range–abundance and rarefaction curves, nonlinear models, and the Bray–Curtis dissimilarity index. The results revealed three distinct species assemblages associated with forests, intermediate disturbed areas (IDAs), and disturbed areas (DAs). Nonlinear models show that IDAs are more diverse than forests and DAs. However, forests have more beta diversity in plots than IDAs and DAs. Indicator species for each butterfly assemblage were also identified. Thus, although new butterfly species assemblages emerge from a new human landscape, it is clear that species that only occur within dry forest fragments are lost when forest fragments disappear. Overall, these findings have important implications for conservation efforts and understanding how human disturbance affects biodiversity in tropical ecosystems. Full article

Afforestation of former agricultural land poses a real challenge for foresters because soil life is often severely limited by the loss of natural soil fungal diversity. In addition, former agricultural soils have low levels of fungal species typical of forest soils, which have a unique microbiome that plays a protective role (antagonists, plant growth promoters, mycorrhizal fungi, etc.). This study aimed to determine the effect of using organic material in the form of bark compost, wood waste, and sawdust to improve the soil mycobiome of soils that have been damaged by their agricultural use. This study used experimental plots established 20 years ago, and we compared the biodiversity of the treated soils with that of the control soils by analysing soil samples with powerful molecular methods. Next-generation sequencing analysis of DNA extracted from soil samples and subsequent analysis of their species composition and biodiversity showed that the mycobiome of soil fungi has been altered by the addition of various forms of organic material. The proportion of fungi belonging to the Ascomycota decreased in favour of species from the Basidiomycota and Mucoromycota. The dominant fungal groups in the soil of the control area were Sagenomella, Wilcoxina, Oidiodendron, Meliniomyces, and Penicillium. Enrichment with organic matter by adding bark compost under the roots led to an increase in Penicillium, Inocybe, and Amphinema. The application of bark compost on the surface led to an increase in the dominance of Inocybe fungi in the soil. The mycobiome of the plant to which woody debris was applied was characterised by a marked dominance of fungi of the genera Russula, Oidiodendron, and Penicillium. Similar ratios were found in the plant to which sawdust was applied, where the fungi Meliniomyces, Penicillium, Oidiodendron, and Russula dominated. A comparative analysis of fungal diversity with the Shannon diversity index showed that the most diverse fungal communities were found in the sawdust plant (6.56), while the control sample (a soil sample from an agricultural area where no organic material was applied) had an index of 5.71. After the treatments, more potential antagonists against pine pathogens and mycorrhizal fungi were found to form beneficial symbiotic relationships with them. In our opinion, the results of this study show that it is worthwhile to introduce different forms of organic matter to post-agricultural land to improve soil biodiversity and mycorrhizal associations of pine roots with fungi to ensure the sustainability of the first generation of forests created. Full article

Background: The present study aimed to evaluate microbial diversity, taxonomic profiles, and fecal short chain fatty acid (SCFA) in female patients with fibromyalgia syndrome (FMS). Methods: Forty participants (19 patients with FMS and 21 controls) were included in the study, and the diagnosis of FMS was made based on the revised American College of Rheumatology criteria. DNA extraction from fecal samples and 16S rRNA gene sequencing were conducted to estimate microbial composition. To compare alpha diversity, the Shannon index accounting for both evenness and richness, Pielou’s evenness, and Faith’s phylogenetic diversity (PD) were calculated. Unweighted and weighted UniFrac distances, Jaccard distance, and Bray–Curtis dissimilarity were used to calculate beta diversity. Furthermore, stool metabolites were analyzed using gas chromatography-mass spectrometry, and a generalized regression model was used to compare the SCFA of stools between FMS and healthy controls. Results: Compared with the control, patients with FMS had lower observed OTU (p = 0.048), Shannon’s index (p = 0.044), and evenness (p < 0.001). Although patients with FMS had a lower PD than did controls, statistical significance was not reached. We observed significant differences in unweighted (p = 0.007), weighted UniFrac-based diversity (p < 0.005), Jaccard distance (p < 0.001), and Bray–Curtis dissimilarity (p < 0.001) between the two groups. Although the FMS groups showed lower propionate levels compared with those of the control group, only marginal significance was observed (0.82 [0.051] mg/g in FMS vs. 1.16 [0.077] mg/g in the control group, p = 0.069). Conclusions: The diversity of the microbiome in the FMS group was lower than that in the control group, and the reduced stool propionate levels could be associated with the decreased abundance of propionate-producing bacteria. Full article

Idiopathic granulomatous mastitis (IGM) is a rare and benign inflammatory breast disease with ambiguous aetiology. Contrastingly, lactational mastitis (LM) is commonly diagnosed in breastfeeding women. To investigate IGM aetiology, we profiled the microbial flora of pus and skin in patients with IGM and LM. A total of 26 patients with IGM and 6 patients with LM were included in the study. The 16S rRNA sequencing libraries were constructed from 16S rRNA gene amplified from total DNA extracted from pus and skin swabs in patients with IGM and LM controls. Constructed libraries were multiplexed and paired-end sequenced on HiSeq4000. Metagenomic analysis was conducted using modified microbiome abundance analysis suite customised R-resource for paired pus and skin samples. Microbiome multivariable association analyses were performed using linear models. A total of 21 IGM and 3 LM paired pus and skin samples underwent metagenomic analysis. Bray−Curtis ecological dissimilarity distance showed dissimilarity across four sample types (IGM pus, IGM skin, LM pus, and LM skin; PERMANOVA, p < 0.001). No characteristic dominant genus was observed across the IGM samples. The IGM pus samples were more diverse than corresponding IGM skin samples (Shannon and Simpson index; Wilcoxon paired signed-rank tests, p = 0.022 and p = 0.07). Corynebacterium kroppenstedtii, reportedly associated with IGM in the literature, was higher in IGM pus samples than paired skin samples (Wilcoxon, p = 0.022). Three other species and nineteen genera were statistically significant in paired IGM pus–skin comparison after antibiotic treatment adjustment and multiple comparisons correction. Microbial profiles are unique between patients with IGM and LM. Inter-patient variability and polymicrobial IGM pus samples cannot implicate specific genus or species as an infectious cause for IGM. Full article

Ecological communities change because of both natural and human factors. Distinguishing between the two is critical to ecology and conservation science. One of the most common approaches for modelling species composition changes is calculating beta diversity indices and then relating index changes to environmental changes. The main difficulty with these analyses is that beta diversity indices are paired comparisons, which means indices calculated with the same community are not independent. Mantel tests and generalised dissimilarity modelling (GDM) are two of the most commonly used statistical procedures for analysing such data, employing randomisation tests to consider the data’s dependence. Here, we introduce a Bayesian model-based approach called BetaBayes that explicitly incorporates the data dependence. This approach is based on the Bradley–Terry model, which is a widely used approach for modelling paired comparisons that involves building a standard regression model containing two varying intercepts, one for each community involved in the beta diversity index, that capture their respective contributions. We used BetaBayes to analyse a famous dataset collected in Panama that contains information on multiple 1 ha plots from the rain forests of Panama. We calculated the Bray–Curtis index between all pairs of plots, analysed the relationship between the index and two covariates (geographic distance and elevation), and compared the results of BetaBayes with those from the Mantel test and GDM. BetaBayes has two distinctive features. The first is its flexibility, which allows the user to quickly change it to fit the data structure; namely, by adding varying effects, incorporating spatial autocorrelation, and modelling complex nonlinear relationships. The second is that it provides a clear path for performing model validation and model improvement. BetaBayes avoids hypothesis testing, instead focusing on recreating the data generating process and quantifying all the model configurations that are consistent with the observed data. Full article

Transgenic Bacillus thuringiensis (Bt) maize has broad prospects for application in China. Before commercialization, it is necessary to assess possible ecological impacts, including impacts on non-target arthropods (NTAs) in the field. In the present study, transgenic Bt maize expressing cry1Ab/2Aj and its corresponding non-transformed near isoline were planted under the same environmental and agricultural conditions, and arthropods in the field were collected during the three main growth stages of maize. In a one year trial, the results showed the composition of NTA communities in the transgenic and control maize fields were similar. There were no significant differences for community-level parameters of species richness (S), Shannon–Wiener diversity index (H′), evenness index (J) and Simpson’s dominant concentration (C) between the two types of maize fields. Likewise, a Bray–Curtis dissimilarity and distance analysis showed that Cry1Ab/2Aj toxin exposure did not increase community dissimilarities between Bt and non-Bt maize plots and that the structure of the NTAs community was similar on the two maize varieties. Furthermore, planting of the transgenic cry1Ab/2Aj maize did not affect the density or composition of non-target decomposers, herbivores, predators, parasitoids and pollinator guilds. In summary, our results showed that planting of Bt maize producing Cry1Ab/Cry2Aj proteins do not adversely affect population dynamics and diversity of NTAs. Full article

The structure and distribution patterns of Himalayan vegetation are poorly explored, and research on species composition along the elevation gradient in these mountain ranges is still deficient. The current study was undertaken to analyze the variation and pattern of plant species composition along a vertical gradient in northwestern Himalaya, India. A total of 18 sites were selected along an elevation gradient ranging from 2200 to 3900 m asl positioned at an interval of 100 m. The Renyi diversity profile, non-metric multidimensional scaling based on the Bray–Curtis dissimilarity metric and beta diversity components among the elevation belts were calculated. Furthermore, to study the influence of altitude on species richness and diversity, a generalized additive model was created. Two hundred and ten plant species representing 66 families and 147 genera were recorded. The Renyi diversity profiles show that the lower and mid-altitudes had rich species diversity. The results of the non-metric multidimensional scaling analysis show a considerable variation in the total plant species composition among the studied elevation belts. The observed multiple-site Sorensen dissimilarity index across the studied elevation belts was very high. The contribution of species replacement or the turnover component to the observed dissimilarity was much higher than the nestedness component. Furthermore, the herbaceous and tree richness showed a significant decrease with increase in elevation; however, the richness of shrubs showed a bimodal pattern. The present study increases our understanding of the trends and patterns of species richness along the vertical gradient in the Himalayan region. Full article

Environmental short amplicon sequencing, or metabarcoding, is commonly used to characterize the bacterial and fungal microbiota of cheese. Comparisons between different metabarcoding studies are complicated by the use of different gene markers. Here, we systematically compare different metabarcoding molecular targets using V3–V4 and V6–V8 regions of the bacterial 16S rDNA and fungal ITS1 and ITS2 regions. Taxonomic profiles varied depending on the molecular markers used. Based on data quality and detection capacity of the markers toward microorganisms usually associated with the dairy environment, the ribosomal regions V3–V4 and ITS2 were selected and further used to evaluate variability in the microbial ecosystem of terroir cheeses from the province of Quebec in Canada. Both fungal and bacterial ecosystem profiles were described for 32 different ready-to-eat bloomy-, washed- and natural-rind specialty cheese varieties. Among them, 15 were studied over two different production years. Using the Bray–Curtis dissimilarity index as an indicator of microbial shifts, we found that most variations could be explained by either a voluntary change in starter or ripening culture composition, or by changes in the cheesemaking technology. Overall, our results suggest the persistence of the microbiota between the two years studied—these data aid understanding of cheese microbiota composition and persistence during cheese ripening. Full article