Bray-Curtis Dissimilarity Research Articles

Intensive grazing confounds the patterns of plant compositional change along a soil pH gradient, not an aridity gradient, in the Mongolian steppe

AbstractAridity, edaphic variables and livestock grazing are major drivers of plant community composition across arid rangelands. Accumulated knowledge exists on the impact of each driver on community composition. Although previous studies have demonstrated changes in direct grazing impacts on ecosystem functions and community composition at different aridity levels, ranging from mesic to arid grasslands, whether a regional‐scale and continuous spatial pattern of plant compositional change along a gradient of aridity or edaphic variables is altered by grazing remains controversial. We compared the determinants and patterns of compositional changes with/without highly intensive grazing in the semi‐arid/arid regions of Mongolia. The compositional changes based on Bray–Curtis dissimilarity were investigated using generalized dissimilarity modeling, including geographic distance, aridity, soil pH and soil texture as independent variables. Aridity consistently had a significant impact on community composition, regardless of the region and presence/absence of grazing. However, a difference in response patterns was observed between the regions. The compositional change was steeper at the upper (drier) limit of aridity than at the lower limit in the arid region. This pattern indicates the vulnerability of plant communities to aridity shifts owing to future climate change, especially in the desert steppe of Mongolia, although the predictions of shifts in aridity are not accurate. In addition, regardless of the region, the effects of soil pH on the community composition were eliminated by the presence of grazing. Grazing may homogenize community composition by not reflecting the spatial heterogeneity of soil pH or nutrient availability via selective herbivory. Despite the potential indirect impacts of climate change on community composition via soil pH, the observations for only plant communities under intensive grazing might overlook regional biodiversity changes caused by global change drivers.

Assessing the conservation status of Mediterranean coastal ponds: Checklist, ecological and functional diversity of diatom communities

Coastal ponds are peculiar and threatened habitats, considered biodiversity hotspots. In many ecosystems ponds can be a valuable resource for the conservation of freshwater biodiversity. The Castelporziano Presidential Estate is a Mediterranean protected area hosting numerous ponds which are suffering severe droughts and a general decline in number and hydroperiod length. Hydroperiod changes can be particularly relevant for biodiversity inhabiting ponds, in particular diatom communities. Here, for the first time, we evaluate the conservation status of Mediterranean ponds inside the Castelporziano Reserve. The aims of this research are to i) investigate the influence of environmental variables on diatom communities of ponds; (ii) analyse diatom community structure in function of species richness and competitive interactions; (iii) highlight the potential and effectiveness of diatom ecological guilds in supporting the interpretation of the ecological status of threatened small waterbodies. Overall, 122 diatom taxa in the 29 ponds were described. Nitzschia (18 species) was the most species-rich genus, followed by Gomphonema (14) and Navicula (13). 17 species were included in the Red List of endangered species. Intra-pond distance and anthropogenic impacts didn't influence diatom assemblages. On the contrary, diatom communities were influenced by altitude and the distance from the sea. Furthermore, temporary ponds showed the lowest values for Shannon, evenness and Simpson indexes Considering Beta-diversity, both Bray-Curtis and Jaccard dissimilarity matrices highlighted a large dissimilarity between sampling sites. Inter-variability between sites and intra-variability within the sites resulted both very low. Our results highlight that diatom species are not influenced by hydroperiod length. Moreover, a structured diatom community emerged, where segregation processes predominating over aggregation ones. Finally, the average water quality of the ponds, calculated using the EPI-D index, was described as “good”. This study represents the most complete checklist of diatom communities inside coastal ponds of Castelporziano, providing valuable insights into the effects of natural and anthropogenic influences on ponds conservation and management activities. However, spatial-temporal changes and anthropogenic impacts should be deeply investigated.

Aggregate Size Mediated the Changes in Soil Microbial Communities After the Afforestation of a Former Dryland in Northwestern China

Although the afforestation of former arable lands is a common global land-use conversion, its impact on soil microbial communities at the aggregate scale has not been adequately addressed. In this study, soil samples were categorized into large macroaggregates (LM, >2 mm), small macroaggregates (SM, 2–0.25 mm), and microaggregates (MI, <0.25 mm) to assess the changes in microbial composition, diversity, network complexity, and network stability within soil aggregates after the afforestation of a former dryland in northwestern China. The results revealed that afforestation enhanced the relative abundance of Actinobacteriota, Chloroflexi, Ascomycota, and Mortierellomycota within the soil aggregates, suggesting that these phyla may have greater advantages in microbial communities post-afforestation. The Shannon–Wiener and Pielou indices for bacterial communities showed no significant differences between land-use types across all aggregate fractions. However, the alpha diversity of fungal communities within the LM and SM significantly increased after afforestation. Bray–Curtis dissimilarity indices showed that afforestation altered bacterial beta diversity within the LM and MI but had a minimal impact on fungal beta diversity across all three aggregate fractions. The topological features of cross-kingdom microbial co-occurrence networks within the soil aggregates generally exhibited a decreasing trend post-afforestation, indicating a simplification of microbial community structure. The reduced robustness of microbial networks within the LM and SM fractions implies that afforestation also destabilized the structure of microbial communities within the macroaggregates. The composition of the soil microbial communities correlated closely with soil carbon and nitrogen contents, especially within the two macroaggregate fractions. The linkages suggests that improved resource conditions could be a key driver behind the shifts in microbial communities within soil aggregates following afforestation. Our findings indicate that the impact of afforestation on soil microbial ecology can be better understood by soil aggregate fractionation.

Salivary microbiome signatures of Poles and Serbians and its potential for prediction of biogeographic ancestry

Biogeographical ancestry analysis is valuable in forensic investigations, especially in missing person cases or crimes without eyewitnesses, as it helps to infer geographic origins from genetic markers. This approach enhances forensic efforts by providing essential clues for identifying individuals with limited direct evidence. Slavic-speaking populations are poorly distinguishable based on human genome variability. However, recent studies show that even populations with close biogeographic origin could be differentiated based on salivary microbiomes. Nevertheless, the salivary microbiomes of Slavs have not been characterized yet. Therefore, this study aimed to compare the composition of the salivary microbiomes of Western and Southern Slavs’ representatives. 16S rRNA libraries from salivary microbiomes of 40 Poles (Western Slavs) and 40 Serbians (Southern Slavs) were prepared via PCR and sequenced on the MiSeq FGx platform (Illumina), giving approximately 100,000 reads per sample. Bioinformatic and statistical analyses were performed to assess the alpha and beta diversity of microbiomes and determine the differences in the abundance of bacterial genera between the groups studied. Analyses of alpha (ACE, Chao1, Shannon, and Simpson) and beta (Jaccard and Bray-Curtis dissimilarity) diversities in the salivary microbiomes clearly distinguished between Poles and Serbians. Alpha and beta diversity metrics were significantly higher in the Serbian population. Fusobacterium, Lautropia, Porphyromonas, Actinobacillus, Capnocytophaga, and Kingella were the most significantly increased genera in Serbians, whereas Veillonella, Selenomonas, Megasphaera, and Atopobium were more prevalent in Poles. In summary, our study identified significant differences in the salivary microbiomes of Poles and Serbians, with distinct microbial signatures associated with each population. These findings highlight the potential of salivary microbiome analysis as a tool for predicting biogeographic ancestry. Nevertheless, further analysis extended to other Slavic-speaking populations is necessary to clarify this issue.

Deciphering the microbial communities in ticks of Inner Mongolia: ecological determinants and pathogen profiles

BackgroundTicks are vectors of numerous pathogens, with their bacterial composition, abundance, diversity, and interaction influencing both their growth and disease transmission efficiency. Despite the abundance of ticks in Inner Mongolia, China, comprehensive data on their microbial communities are lacking. This study aims to analyze the microbial communities within ticks from Inner Mongolia to inform innovative control strategies for interrupting pathogen transmission.MethodsTick samples were collected from animals and vegetation in multiple locations across Inner Mongolia and stored at − 80 °C. Ticks were identified using morphological keys and molecular biology methods. Full-length 16S rRNA gene sequencing was performed on collected samples. Bacterial community composition and diversity were mainly analyzed using bioinformatic tools such as QIIME, phyloseq, and DESeq2. Alpha diversity was assessed using Chao1, ACE, and Shannon indices, while beta diversity was evaluated using Bray-Curtis dissimilarity matrices. LEfSe analysis was applied to identify taxa associated with ecological and biological variables.ResultsA total of 5,048,137 high-quality read counts were obtained, forming an average of 789.3 OTUs per sample. Proteobacteria, Firmicutes, and Bacteroidetes were the most dominant phyla. Bacterial community composition varied significantly with geography, with Dermacentor nuttalli showing a higher abundance of Rickettsia in Xilingol League, while other regions had different dominant genera. The microbial community also differed based on the feeding status of ticks. Additionally, the microbiota of engorged ticks showed organ specificity. Pathogen detection efforts revealed the presence of nine pathogens across all three tick species. D. nuttalli was found to carry a significantly higher burden of pathogenic bacteria, making it the most potentially threatening tick species in Inner Mongolia.ConclusionsThe study highlights significant variations in tick microbiomes influenced by geographic location, feeding status, and tick species. It underscores the importance of enhancing tick and tick-borne disease surveillance in Inner Mongolia for early detection and control of emerging pathogens.Graphical

Features of the oropharyngeal microbiota of healthy children and those with acute respiratory infections. A prospective single-center randomized study

Background. The oropharyngeal microbiota is involved in the development of colonization resistance, affecting viral adhesion and metabolism. Any deviations in the stability of the environmental microbial niches of the oropharynx alter the local immune response and can trigger severe chronic somatic disorders. Aim. To compare the composition of the microbiota of children during an episode of respiratory infection and healthy volunteers examined in different periods of convalescence. The obtained data can be used to predict the course of the disease, analyze the risk of complications, and assess the frequency of the diseases in the future. Materials and methods. From 20.01.2022 to 23.12.2022, an open-label prospective single-center randomized comparative study was conducted, which included 120 children aged 5-10 who presented with symptoms of acute respiratory infection. The control group consisted of 15 asymptomatic children examined at different periods of convalescence. The study compared changes in the oral microbiota composition of patients and healthy children. The evaluation was performed using complete 16S rRNA gene sequencing on the Oxford Nanopore platform. Taxonometric analysis at the species and genera level was performed using the Knomics-Biota platform. The R programming language was used for statistical processing. In addition, the parameters of α- and β-diversity of the microbiota were assessed. The Chao1 and Shannon indices were calculated to assess α-diversity (diversity within one community). The Chao1 index is based on the number of species found in the sample and also rare species that are found only 1 or 2 times, thus preventing underestimation of diversity. The Shannon index includes both the number of species and their uniformity in the community. A change in the index indicates the dominance of one or more species. The following indicators were used to assess the β-diversity describing the differences between two microbiota samples at the species and genera level: Bray–Curtis dissimilarity (characterizing the ratios of common and different microorganisms between the samples) and the Aitchison distance (reflecting the differences in the proportions of microorganisms). In addition, the balance between the two groups of microorganisms was evaluated using the NearesBalance method, which characterizes the differences between the microbiota of the main and control groups. Results. The results of our study show that during respiratory infection, the state of the oropharyngeal microbiota is characterized by an increase in α-diversity, which is associated with an increase in the proportion of species of Streptococcus salivarius, Streptococcus pneumoniae, Streptococcus pseudopneumoniae, Streptococcus pyogenes, Streptococcus thermophilus and A12 versus the proportion of Streptococcus mitis, Streptococcus oralis, Streptococcus gwangjuense, Streptococcus sanguinis, Streptococcus gordonii and FDAARGOS_192. In the control group, the oropharyngeal microbiota was divided into two clusters. The dominance of streptococci was observed in the first group (control), while the second group had a more uniform representation. Analysis of the changes in microbial communities in the main and control groups can show the stages of oral microbiota recovery after an acute respiratory infection episode. Conclusion. More research is needed in the field of the oropharyngeal microbiome on a larger sample of healthy children, to standardize the communities of the oropharyngeal microbiota, to study the interaction within communities and with the body as a whole. Analysis of the impact of the microbiota on the frequency and course of respiratory infections and the rate of complications opens up new prospects in treating, rehabilitating, and preventing diseases. These research areas can contribute to improving children's health and quality of life and introducing new approaches into clinical practice.

The influence of temperature and river runoff on phytoplankton community diversity in Beibu Gulf: insight from 18 S rDNA metabarcoding analysis

BackgroundSanniang Bay (SNB) and Dafeng River (DFR), located in the northern Beibu Gulf, is well-known as one of the eight habitats for humpback dolphins in China. This region is representative of typical estuarine and bay ecosystems and produce complex hydrodynamic seawater conditions. Moreover, anthropogenic pressure, such as eutrophication and large-scale infrastructure projects, have caused ongoing habitat deterioration and loss. It is urgent to know the phytoplankton community and their relationships with environmental factors in this region.ResultsIn this study, we assessed the diversity and assembly mechanisms of phytoplankton communities, as well as their relationship with the physicochemical characteristics of seawater in SNB and DFR region using 18 S rDNA metabarcoding analysis. The results showed that seasonal changes markedly impacted the alpha diversity of the phytoplankton community. From March to July, with the average temperature increasing from 25.2℃ to 28.1℃,the Shannon or Species Richness were negatively correlated with temperature. During hot season (in Sep, average temperature 32.1℃), phytoplankton diversity was negatively correlated with nutrients (NH4 +, NO3−, PO43−, TN). Additionally, during the rainy season, the Bray-Curtis similarity of the phytoplankton community was significantly lower than during the dry season. In March, the distance among the sampling sites was most strongly and positively correlated with the Bray-Curtis dissimilarity. Stochastic processes, specifically dispersal limitation and ecological drift, are the primary drivers of community assembly, while deterministic assembly processes (mainly heterogeneous selection) contribute a relatively minor portion (< 17%).ConclusionsRising temperature diminished the diversity of phytoplankton in SNB and DFR, and nutrient inputs and eutrophication in estuarine areas will aggravate the loss of phytoplankton diversity.

Effects of simulated low-temperature thermal remediation on the microbial community of a tropical creosote contaminated soil.

In the search for more sustainable remediation strategies for PAH-contaminated soils, an integrated application of thermal remediation and bioremediation (TEB) may allow the use of less impacting temperatures by associating heating to biological degradation. However, the influence of heating on soil microbiota remains poorly understood, especially in soils from tropical regions. This work investigated the effects of low-temperature heating on creosote-contaminated soil bacteria. We used culture-dependent and 16S rRNA sequencing methods to compare the microbial community of soil samples heated to 60 and 100 oC for 1h in microcosms. Heating to 60°C reduced the density of cultivable heterotrophic bacteria compared to control soil (p < 0.05), and exposure to 100°C inactivated the viable heterotrophic community. Burkholderia-Caballeronia-Paraburkholderia (BCP) group and Sphingobium were the predominant genera. Temperature and incubation time affected the Bray-Curtis dissimilarity index (p < 0.05). At 60°C and 30 days incubation, the relative abundance of Sphingobium decreased and BCP increased dominance. The network of heated soil after 30 days of incubation showed fewer nodes and edges but maintained its density and complexity. Both main genera are associated with PAH degradation, suggesting functional redundancy and a likely potential of soil microbiota to maintain biodegradation ability after exposure to higher temperatures. We concluded that TEB can be considered as a potential strategy to bioremediate creosote-contaminated soils, allowing biodegradation in temperature ranges where thermal remediation does not completely remove contaminants. However, we recommend further research to determine degradation rates with this technology.

Microbiome of the Middle Meatus, Tonsils, and Adenoids in Pediatric Chronic Rhinosinusitis.

Pediatric chronic rhinosinusitis (PCRS) is a common condition with a significant impact on quality of life. This study compares the microbiome of pediatric patients with and without chronic rhinosinusitis. Single-center, prospective, quantitative case-control. Metropolitan. Patients undergoing adenoidectomy for PCRS (subjects, n = 20) or obstructive sleep apnea (controls, n = 20) were recruited. 16S ribosomal RNA sequencing was performed on the right middle meatus (MM), adenoid, and palatine tonsil samples from each patient. Alpha diversity was measured by the Simpson's diversity index, beta diversity was measured by the Bray-Curtis dissimilarity index, and the differential abundance of bacteria genera was analyzed. There were 40 adenoid, 40 tonsil, and 37 MM samples analyzed. There was no significant difference in alpha diversity between controls and subjects. Tonsils were significantly more diverse than the adenoids, which were more diverse than the MM (P < .001). There was no difference in bacterial composition between controls and subjects, but the composition of the 3 sites were significantly different (P < .001). The dissimilarity in bacterial composition between the adenoid and MM sites was larger in the control group than in the subject group. There were significant differences in alpha diversity and bacterial composition between the anatomic 3 sites; however, there was no difference between the controls and subjects. The larger dissimilarity in bacterial composition between adenoid and MM sites in controls compared to subjects suggests there may be colonization of the MM by the adenoid in PCRS patients.

Microbial diversity in primary endodontic infections: demographics and radiographic characteristics.

To analyze if the microbiome community composition in primary endodontic infections is associated with clinical or radiographic factors. Seventy-one patients with primary endodontic infections were evaluated for percussion tenderness, presence of a sinus tract, presence of caries, sex, probing depth > 4mm, and age. Samples from the root canals were obtained and the microbiome was subsequently characterized by 16S rRNA amplicon sequencing. For the radiographic analysis, a subset of 12 samples with a periapical index (PAI) ≤ 2 were compared with 19 samples with PAI of 5. The Shannon and Chao1 indices were used to measure alpha diversity. Differences in abundances of genera were evaluated using the Kruskal-Wallis test with Bonferroni's correction. Differences in community composition were evaluated using analysis of similarity (ANOSIM) with Bray-Curtis dissimilarity matrices. No significant differences in microbiome composition relative to clinical factors were found using ANOSIM. Teeth within the two categories of periapical index showed a similar number of species richness, and alpha diversity values P > 0.05. Community composition was significantly affected by the periapical index (ANOSIM P = 0.039, R = 0.10). Larger radiographic lesions demonstrated significant increase in Prevotellaceae, Olsenella, and the motile bacteria Oribacterium, Selenomonadaceae spp., and Treponema. Clinical factors associated with apical periodontitis have a limited impact on the root canal microbiome composition. Community composition appears to be affected in teeth with large apical lesions.

Gut Microbiota Alterations in Alzheimer's Disease: Relation with Cognitive Impairment and Mediterranean Lifestyle.

Recently, an association between dysbiosis of the gut microbiota (GMB) and the development of several diseases, such as Alzheimer's disease (AD), has been proposed. Dysbiosis involves changes in microbial diversity influenced by environmental factors, like diet or lifestyle. In this study, we investigated the role of GMB parameters in Spanish AD patients, assessing the impact of adherence to the Mediterranean lifestyle (ML), as well as to characterize these parameters in relation to neuropsychological, neuropsychiatric, emotional, and functionality parameters. A case-control study was conducted to investigate the association between the composition of the GMB and cognitive, emotional, neuropsychiatric, and functionality status in Spanish AD patients, along with a shotgun metagenomics approach. Richness and alpha-diversity were significantly lower in the AD group compared to the controls. PERMANOVA and ANOSIM tests of Bray-Curtis dissimilarity, Aitchison distance, and Jaccard similarity did not showed significant differences in beta-diversity between the two groups. Moreover, associations between various phyla of the AD group and orientation performance, food consumption, and activities of daily living were identified. Dysbiosis observed in Spanish AD patients is characterized by reductions in richness and alpha-diversity, alongside alterations in GMB composition, which may be linked to adherence to the ML and cognitive and functionality symptoms.

Divergent Importance and Geographic Patterns in Threats to Birds and Mammals in China

ABSTRACTAimWildlife populations are continuing to decrease worldwide. Understanding the ranking and distribution of drivers of species declines is crucial to enable targeted actions to counteract major threats. However, few studies have assessed the relative importance and geographic distribution of threats to biodiversity in China, even for high‐profile groups such as birds and mammals. Therefore, this study aims to rank and map the distribution of threat to birds and mammals in China, which could provide novel insight into biodiversity conservation in China.LocationChina.MethodsA database of different threats for 147 threatened bird species and 176 threatened terrestrial mammal species was obtained from China's Red List of Biodiversity published in 2021. We collated information on the distribution and threat categories for birds and mammals in China, aiming to classify, rank and map threats. We used Bray–Curtis dissimilarity index to examine the correlations of threats occurring simultaneously, and compared the distribution of habitat of threatened birds and mammals. In addition, we conducted threat ranking analyses of threatened birds and mammals between different orders and traits (body mass and clutch/litter sizes).ResultsThe results showed that the most common threats to birds were habitat loss, hunting, human disturbance, agriculture, pollution and logging, while the most common threats to mammals were hunting, agriculture, logging, habitat loss, human disturbance and livestock farming or ranching. These threats showed different geographic patterns, and some threats frequently co‐occur as threat syndromes. Forests were the primary habitat for most threatened species, and orders formed by larger species with small clutch or litter sizes were more likely to be threatened.Main ConclusionsWe highlight the most common threats and key areas for conservation. Furthermore, focusing on clusters of co‐occurring threats may be the most effective way to aid recovery of threatened species, and targeted actions are needed to counter ongoing population declines in many groups. These actions should not be limited to the protection of regions where species are at risk of multiple significant threats, but should also include the maintenance and restoration of native forests and strategic planning of afforestation through planted forests.

The Effects of Brodalumab on the Fungal Microbiome in Patients with Psoriasis.

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.

Comparison of Stool Antigen and PCR-Based Diagnostics for Helicobacter pylori Infection and Associated Gut Dysbiosis in Wad-Medani City, Sudan

Background: The development of stomach illnesses has been linked, in part, to Helicobacter pylori (H. pylori) infection; in clinical practice, accurate identification of Helicobacter pylori infection is crucial, H. pylori infection was associated with a decrease in microbial diversity and an increase in pathogenic taxa, indicating its role in gut dysbiosis. Objectives: We tested a noninvasive method using immunochromatography to detect the presence of the H. pylori antigen in stool specimens. PCR was used to validate the presence of H. pylori by identifying the bacteria's ureC gene in the DNA extracted from stool specimens. Additionally, gut microbiome changes were assessed, understanding the link between H. pylori infection and gut dysbiosis is vital for public health interventions. Method: A total of 100 stool samples obtained from dyspeptic patients (46 men and 54 women, average age 46.1) were assessed using these methods. The results were then compared between the PCR-based technique and the SAT technique. Results: The results showed that 35 (35%) out of 100 samples were positive by the PCR-based technique, compared to 33 (33%) positive by the SAT technique and The PCR method demonstrated a sensitivity of 95% and specificity of 92% in detecting H. pylori. Beta diversity was assessed using Bray-Curtis dissimilarity, revealing significant variations in microbial composition among samples. Conclusion: These data suggest that the techniques used in this study are valuable for studying the molecular epidemiology of H. pylori infection in dyspeptic patients. Stool, as a non-invasive sample, has the potential to be a good replacement for the detection of H. pylori. Additionally, we found that infection with this bacterium contributes to gastric microbial dysbiosis, while no statistically significant differences were observed.

Seasonal dynamics of environmental heterogeneity augment microbial interactions by regulating community structure in different trophic lakes

Understanding how environmental heterogeneity drives microbial communities in lakes is essential for developing effective strategies to manage and restore aquatic ecosystems. However, the mechanisms by which environmental heterogeneity influences microbial community structure, network patterns, and interactions remain largely unexplored. To bridge this gap, we collected 84 water samples from four typical lakes in China (Fuxian, Tianmu, Taihu, and Xingyun) representing a range of trophic levels, across wet and dry seasons. We assessed environmental heterogeneity using 14 water quality parameters, analyzed community structure with Jaccard and Bray-Curtis dissimilarity indices, and developed a comprehensive index to elucidate microbial network complexity. Our study reveals three key findings: (1) Environmental heterogeneity was significantly greater in dry season compared to wet season across all lakes (P < 0.05). (2) Increased environmental heterogeneity led to higher bacterioplankton community dissimilarity, with greater β-diversity observed in dry season (P < 0.05). (3) Shifts in community structure due to increased environmental heterogeneity further enhanced microbial interactions, as evidenced by more complex and interconnected co-occurrence networks in the dry season. In summary, our study demonstrates that environmental heterogeneity significantly impacts bacterioplankton community structure and subsequently enhances microbial interactions. These findings underscore the importance of considering environmental heterogeneity in lake ecosystem management, as it plays a crucial role in regulating microbial community dynamics and interactions.

Prokrustean Graph: A substring index for rapid k-mer size analysis.

Despite the widespread adoption of -mer-based methods in bioinformatics, understanding the influence of -mer sizes remains a persistent challenge. Selecting an optimal -mer size or employing multiple -mer sizes is often arbitrary, application-specific, and fraught with computational complexities. Typically, the influence of -mer size is obscured by the outputs of complex bioinformatics tasks, such as genome analysis, comparison, assembly, alignment, and error correction. However, it is frequently overlooked that every method is built above a well-defined -mer-based object like Jaccard Similarity, de Bruijn graphs, -mer spectra, and Bray-Curtis Dissimilarity. Despite these objects offering a clearer perspective on the role of -mer sizes, the dynamics of -mer-based objects with respect to -mer sizes remain surprisingly elusive. This paper introduces a computational framework that generalizes the transition of -mer-based objects across -mer sizes, utilizing a novel substring index, the Prokrustean graph. The primary contribution of this framework is to compute quantities associated with -mer-based objects for all -mer sizes, where the computational complexity depends solely on the number of maximal repeats and is independent of the range of -mer sizes. For example, counting vertices of compacted de Bruijn graphs for can be accomplished in mere seconds with our substring index constructed on a gigabase-sized read set. Additionally, we derive a space-efficient algorithm to extract the Prokrustean graph from the Burrows-Wheeler Transform. It becomes evident that modern substring indices, mostly based on longest common prefixes of suffix arrays, inherently face difficulties at exploring varying -mer sizes due to their limitations at grouping co-occurring substrings. We have implemented four applications that utilize quantities critical in modern pangenomics and metagenomics. The code for these applications and the construction algorithm is available at https://github.com/KoslickiLab/prokrustean.

From Skin to Gut: Understanding Microbial Diversity in Rana amurensis and R. dybowskii.

Amphibians face the threat of decline and extinction, and their health is crucially affected by the microbiota. Their health and ecological adaptability essentially depend on the diverse microbial communities that are shaped by unique host traits and environmental factors. However, there is still limited research on this topic. In this study, cutaneous (C) and gut (G) microbiota in Rana amurensis (A) and R. dybowskii (D) was analyzed through 16S amplicon sequencing. Groups AC and DC significantly differed in alpha diversity, while the gut groups (AG and DG) showed no such differences. Analyses of Bray-Curtis dissimilarity matrix and unweighted UniFrac distances showed significant differences in cutaneous microbiota between groups AC and DC, but not between groups AG and DG. Stochastic processes significantly influenced the assembly of cutaneous and gut microbiota in amphibians, with a notably higher species dispersal rate in the gut. The predominant phyla in the skin of R. amurensis and R. dybowskii were Bacteroidetes and Proteobacteria, respectively, with significant variations in Bacteroidota. Contrarily, the gut microbiota of both species was dominated by Firmicutes, Proteobacteria, and Bacteroidetes, without significant phylum-level differences. Linear discriminant analysis effect size (LEfSe) analysis identified distinct microbial enrichment in each group. Predictive analysis using phylogenetic investigation of communities by reconstruction of unobserved states 2 (PICRUSt2) revealed the significant functional pathways associated with the microbiota, which indicates their potential roles in immune system function, development, regeneration, and response to infectious diseases. This research underscores the critical impact of both host and environmental factors in shaping amphibian microbial ecosystems and emphasizes the need for further studies to explore these complex interactions for conservation efforts.

Succession in abandoned fields: Chronosequence data verified by monitoring of semi‐permanent plots

AbstractQuestionsIs there a similarity between successional patterns in abandoned fields identified (a) through analysis of differently aged sites examined at one point in time (chronosequence) and (b) those derived from a limited set of semi‐permanent plots? What is the rate of succession on dry and mesic abandoned fields and how is the participation of different functional groups changing during succession?LocationBohemian Karst, the Czech Republic, Europe.MethodsThis study utilises data collected from dry and mesic abandoned fields between 1975 and 2019. A data set of 129 chronosequence vegetation samples (54 dry and 75 mesic plots) and 26 samples from six semi‐permanent plots (11 dry and 15 mesic) with different repetitions were analysed. Plot age (since abandonment) varied from 1 to 91 years for chronosequences and up to 99 years for semi‐permanent data. Moreover, we compared the rate of succession between dry and mesic series using Bray–Curtis dissimilarity. We used a generalised linear mixed model to study the relationship between the cover of different functional groups and the age of abandoned fields.ResultsThe successional patterns observed on abandoned fields were consistent between the chronosequence and semi‐permanent plots. Both on dry and mesic fields, the early stages of succession transitioned from open annual to perennial herbal vegetation. In mesic fields, the succession led to woodland stands within approximately 25–30 years. Conversely, succession slowed down in dry fields and has persisted for several decades in a stage dominated mostly by perennial graminoids accompanied by scattered shrubs and trees. The trends detected with the chronosequence approach for the different functional groups corresponded to those found in semi‐permanent dry and mesic series plots.ConclusionsThe plots using a chronosequence approach can reliably reveal general successional patterns comparable to those obtained from semi‐permanent plots. Observing a higher number of plots at one time may better illustrate the variability of succession at the landscape scale than a detailed, long‐lasting study of a low number of semi‐permanent plots. In the studied area, the dry abandoned fields host a long‐persisting non‐forest state of succession under the current climatic conditions, while succession in mesic abandoned fields continues further towards woodland.

Beta diversity subcomponents of plant species turnover and nestedness reveal drivers of community assembly in a regenerating subtropical forest.

Secondary forests represent a significant proportion of global forest cover, with over 70% of forests in East Asia classified as regenerating. While succession has been studied extensively in temperate systems, trajectories of subtropical succession remain poorly characterized in highly disturbed, urban-adjacent forests. Investigating the additive beta diversity components of turnover and nestedness may reveal community assembly mechanisms driving secondary succession. The present study investigates plant community assembly along a successional gradient from 7 to 70 years following the onset of succession in secondary subtropical forests in Hong Kong, China. Plant survey data for 28 plots were analysed, generating additive Simpsons turnover and nestedness beta diversity metrics. Dissimilarity matrices were generated and modelled as a function of environmental matrices including forest plant community age (years following onset of secondary succession), inter-community distance (metres), and soil moisture saturation (%) across three elevational bands using generalized dissimilarity models. Nonmetric multidimensional scaling of plant communities was conducted with Bray-Curtis dissimilarity matrices. Inter-community distance and successional age differentially influenced plant species turnover between lowland and Montane forest types. Models of nestedness found that plot age and soil moisture saturation were significant drivers of nestedness patterns in plant communities across elevational classes. Turnover represented a higher proportion of Sorensen beta diversity than nestedness, while ANOSIM found significant differentiation between plant communities at different successional stages. Turnover patterns suggest a deterministic model of community assembly, with strong patterns of species replacement between communities at fine spatial scales and successional stages, as well as clear compositional shifts between lowland and montane forest types. NMDS analysis and functional compositional assessments suggested a transition from early successional communities with a high proportion of shrub species, to later successional communities with a higher proportion of tree species, with an increase in species turnover with greater age dissimilarity.

Deciphering the role of rhizosphere microbiota in modulating disease resistance in cabbage varieties

BackgroundCabbage Fusarium wilt (CFW) is a devastating disease caused by the soil-borne fungus Fusarium oxysporum f. sp. conglutinans (Foc). One of the optimal measures for managing CFW is the employment of tolerant/resistant cabbage varieties. However, the interplay between plant genotypes and the pathogen Foc in shaping the rhizosphere microbial community, and the consequent influence of these microbial assemblages on biological resistance, remains inadequately understood.ResultsBased on amplicon metabarcoding data, we observed distinct differences in the fungal alpha diversity index (Shannon index) and beta diversity index (unweighted Bray–Curtis dissimilarity) within the rhizosphere of the YR (resistant to Foc) and ZG (susceptible to Foc) cabbage varieties, irrespective of Foc inoculation. Notably, the Shannon diversity shifts in the resistant YR variety were more pronounced following Foc inoculation. Disease-resistant plant variety demonstrate a higher propensity for harboring beneficial microorganisms, such as Pseudomonas, and exhibit superior capabilities in evading harmful microorganisms, in contrast to their disease-susceptible counterparts. Furthermore, the network analysis was performed on rhizosphere-associated microorganisms, including both bacteria and fungi. The networks of association recovered from YR exhibited greater complexity, robustness, and density, regardless of Foc inoculation. Following Foc infection in the YR rhizosphere, there was a notable increase in the dominant bacterium NA13, which is also a hub taxon in the microbial network. Reintroducing NA13 into the soil significantly improved disease resistance in the susceptible ZG variety, by directly inhibiting Foc and triggering defense mechanisms in the roots.ConclusionsThe rhizosphere microbial communities of these two cabbage varieties are markedly distinct, with the introduction of the pathogen eliciting significant alterations in their microbial networks which is correlated with susceptibility or resistance to soil-borne pathogens. Furthermore, we identified a rhizobacteria species that significantly boosts disease resistance in susceptible cabbages. Our results indicated that the induction of resistance genes leading to varied responses in microbial communities to pathogens may partly explain the differing susceptibilities of the cabbage varieties tested to CFW.-meKq2qaHpqpKck3NvZ8m1Video