Differences In Community Composition Research Articles

Gut mycobiome dysbiosis and its impact on intestinal permeability in attention-deficit/hyperactivity disorder.

Dysbiosis in the gut microbial community might be involved in the pathophysiology of attention-deficit/hyperactivity disorder (ADHD). The fungal component of the gut microbiome, namely the mycobiota, is a hyperdiverse group of multicellular eukaryotes that can influence host intestinal permeability. This study therefore aimed to investigate the impact of fungal mycobiome dysbiosis and intestinal permeability on ADHD. Faecal samples were collected from 35 children with ADHD and from 35 healthy controls. Total DNA was extracted from the faecal samples and the internal transcribed spacer regions were sequenced using high-throughput next-generation sequencing (NGS). The fungal taxonomic classification was analysed using bioinformatics tools and the differentially expressed fungal species between the ADHD and healthy control groups were identified. An in vitro permeability assay (Caco-2 cell layer) was used to evaluate the biological effects of fungal dysbiosis on intestinal epithelial barrier function. The β-diversity (the species diversity between two communities), but not α-diversity (the species diversity within a community), reflected the differences in fungal community composition between ADHD and control groups. At the phylum level, the ADHD group displayed a significantly higher abundance of Ascomycota and a significantly lower abundance of Basidiomycota than the healthy control group. At the genus level, the abundance of Candida (especially Candida albicans) was significantly increased in ADHD patients compared to the healthy controls. In addition, the in vitro cell assay revealed that C. albicans secretions significantly enhanced the permeability of Caco-2 cells. The current study is the first to explore altered gut mycobiome dysbiosis using the NGS platform in ADHD. The findings from this study indicated that dysbiosis of the fungal mycobiome and intestinal permeability might be associated with susceptibility to ADHD.

Role of Fungi in Imparting General Disease Suppressiveness in Soil from Organic Field.

Soil microbial communities are key players responsible for imparting suppressive potential to the soil against soil-borne phytopathogens. Fungi have an immense potential to inhibit soil-borne phytopathogens, but the fungal counterpart has been less explored in this context. We assessed the composition of fungal communities in soil under long-term organic and conventional farmingpractice, and control soil. The disease-suppressive potential of organic field was already established. A comparative analysis of the disease suppressiveness contributed by the fungal component of soil from conventional and organic farms was assessed using dual culture assays. The quantification of biocontrol markers and total fungi was done; the characterization of fungal community was carried out using ITS-based amplicon sequencing. Soil from organic field exhibited higher disease-suppressive potential thanthat from conventional farming, against the pathogens selected for the study. Higher levels of hydrolytic enzymes such as chitinase and cellulase, and siderophore production were observed in soil from the organic field compared to the conventional field. Differences in community composition were observed under conventional and organic farming, with soil from organic field exhibiting specific enrichment of key biocontrol fungal genera. The fungal alpha diversity was lower in soil from the organic field compared to the conventional field. Our results highlight the role of fungi in contributing to general disease-suppressive ability of the soil against phytopathogens. The identification of fungal taxa specifically associated with organic farming can aid in understanding the mechanism of disease suppression under such a practice, and can be exploited to induce general disease suppressiveness in otherwise conducive soil.

Monitoring insect biodiversity and comparison of sampling strategies using metabarcoding: A case study in the Yanshan Mountains, China

Insects are the richest and most diverse group of animals and yet there remains a lack, not only of systematic research into their distribution across some key regions of the planet, but of standardized sampling strategies for their study. The Yanshan Mountains, being the boundary range between the Inner Mongolian Plateau and the North China Plain, present an indispensable piece of the insect biodiversity puzzle: both requiring systematic study and offering opportunities for the development of standardized methodologies. This is the first use of DNA metabarcoding to survey the insect biodiversity of the Yanshan Mountains. The study focuses on differences of community composition among samples collected via different methods and from different habitat types. In total, 74 bulk samples were collected from five habitat types (scrubland, woodland, wetland, farmland and grassland) using three collection methods (sweep netting, Malaise traps and light traps). After DNA extraction, PCR amplification, sequencing and diversity analysis were performed, a total of 7427 Operational Taxonomic Units (OTUs) at ≥97% sequence similarity level were delimited, of which 7083 OTUs were identified as belonging to Insecta. Orthoptera, Diptera, Coleoptera and Hemiptera were found to be the dominant orders according to community composition analysis. Nonmetric multidimensional scaling (NMDS) analysis based on Bray-Curtis distances revealed highly divergent estimates of insect community composition among samples differentiated by the collection method (R = .524802, p = .001), but nonsignificant difference among samples differentiated according to habitat (R = .051102, p = .078). The study therefore appears to indicate that the concurrent use of varied collection methods is essential to the accurate monitoring of insect biodiversity.

Airway microbiota and immune mediator relationships differ in obesity and asthma

Asthma and obesity are both complex conditions characterized by chronic inflammation, and obesity-related severe asthma has been associated with differences in the microbiome. However, whether the airway microbiome and microbiota-immune response relationships differ between obese persons with or without nonsevere asthma is unestablished. We compared the airway microbiome and microbiota-immune mediator relationships between obese and nonobese subjects, with and without mild-moderate asthma. We performed cross-sectional analyses of the airway (induced sputum) microbiome and cytokine profiles from blood and sputum using 16S ribosomal RNA gene and internal transcribed spacer region sequencing to profile bacteria and fungi, and multiplex immunoassays. Analysis tools included QIIME 2, linear discriminant analysis effect size (aka LEfSe), Piphillin, and Sparse inverse covariance estimation for ecological association inference (aka SPIEC-EASI). Obesity, irrespective of asthma status, was associated with significant differences in sputum bacterial community structure and composition (unweighted UniFrac permutational analysis of variance, P= .02), including a higher relative abundance of Prevotella, Gemella, and Streptococcus species. Among subjects with asthma, additional differences in sputum bacterial composition and fungal richness were identified between obese and nonobese individuals. Correlation network analyses demonstrated differences between obese and nonobese asthma in relationships between cytokine mediators, and these together with specific airway bacteria involving blood PAI-1, sputum IL-1β, GM-CSF, IL-8, TNF-α, and several Prevotella species. Obesity itself is associated with an altered sputum microbiome, which further differs in those with mild-moderate asthma. The distinct differences in airway microbiota and immune marker relationships in obese asthma suggest potential involvement of airway microbes that may affect mechanisms or outcomes of obese asthma.

Spatial variation and relationship between soil dissolved organic matter and bacterial community in urban greenspaces

Large-scale investigations of soil dissolved organic matter (DOM) and the relationship between bacterial diversity and DOM with climatic gradients are important to reveal the influence of climatic factors on soil DOM. The objectives of this study were to (1) investigate the distribution pattern of DOM at a large scale, (2) investigate the effects of climate change on DOM components and microbial communities, and (3) investigate the relationship between microbial communities and DOM components. This study involved the collection of 54 urban greenspaces samples from five climate zones in mainland China and utilization of FT-ICR-MS and 16S rRNA sequencing techniques to reveal the relationship between microbial communities and DOM. Our results showed that the DOM in soil was DOM inated by lignins, followed by proteins, unsaturated hydrocarbons and lipids. Structural equation modeling (SEM) indicated that lignins and proteins shared a negative response pattern with mean annual precipitation (MAP), while lipids and tannins showed a positive correlation with MAP. The differences in bacterial community composition among different climatic zones were not significant, and the DOM inant bacteria in the soil were Proteobacteria, followed by Acidobacteria and Actinobacteria. Bacterial diversity was highest in the subtropical monsoon climate, lowest in the tropical monsoon climate. In addition, SEM indicated that there was a significant correlation between the composition and diversity of DOM and the diversity and abundance of bacteria. Our results provided a deeper understanding of the impact of climatic factors on DOM components and the relationship between bacterial diversity and DOM in urban greenspaces.Graphical

The root canal microbiome diversity and function. A whole-metagenome shotgun analysis.

To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome shotgun sequencing. Twenty-two samples from patients with primary root canal infections, and 18 samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analysed with whole-metagenome shotgun sequencing at a depth of 20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray-Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes. Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity p = .001). Community composition was significantly different in primary versus secondary infection (R = .11, p = .005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signalling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, haemolysins, thiol-activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase. Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar.

HPV-related anal cancer is associated with changes in the anorectal microbiome during cancer development.

Squamous cell carcinoma of the anus (SCCA) is a rare gastrointestinal cancer. Factors associated with progression of HPV infection to anal dysplasia and cancer are unclear and screening guidelines and approaches for anal dysplasia are less clear than for cervical dysplasia. One potential contributing factor is the anorectal microbiome. In this study, we aimed to identify differences in anal microbiome composition in the settings of HPV infection, anal dysplasia, and anal cancer in this rare disease. Patients were enrolled in two prospective studies. Patients with anal dysplasia were part of a cross-sectional cohort that enrolled women with high-grade lower genital tract dysplasia. Anorectal tumor swabs were prospectively collected from patients with biopsy-confirmed locally advanced SCCA prior to receiving standard-of-care chemoradiotherapy (CRT). Patients with high-grade lower genital tract dysplasia without anal dysplasia were considered high-risk (HR Normal). 16S V4 rRNA Microbiome sequencing was performed for anal swabs. Alpha and Beta Diversity and composition were compared for HR Normal, anal dysplasia, and anal cancer. 60 patients with high-grade lower genital tract dysplasia were initially enrolled. Seven patients had concurrent anal dysplasia and 44 patients were considered HR Normal. Anorectal swabs from 21 patients with localized SCCA were included, sequenced, and analyzed in the study. Analysis of weighted and unweighted UniFrac distances demonstrated significant differences in microbial community composition between anal cancer and HR normal (p=0.018). LEfSe identified that all three groups exhibited differential enrichment of specific taxa. Peptoniphilus (p=0.028), Fusobacteria (p=0.0295), Porphyromonas (p=0.034), and Prevotella (p=0.029) were enriched in anal cancer specimens when compared to HR normal. Although alpha diversity was similar between HR Normal, dysplasia and cancer patients, composition differed significantly between the three groups. Increased anorectal Peptoniphilus, Fusobacteria, Porphyromonas, and Prevotella abundance were associated with anal cancer. These organisms have been reported in various gastrointestinal cancers with roles in facilitating the proinflammatory microenvironment and neoplasia progression. Future work should investigate a potential role of microbiome analysis in screening for anal dysplasia and investigation into potential mechanisms of how these microbial imbalances influence the immune system and anal carcinogenesis.

Changes in Plant Diversity and Soil Factors under Different Rocky Desertification Degrees in Northern Guangdong, China

Revegetation is an important restoration strategy for the control of rocky desertification. However, few studies have focused on the effects of different rocky desertification degrees (RDDs) on plant diversity and soil fertility in northern Guangdong over long periods of time. In this study, variance analysis, correlation analysis, and canonical correlation analysis (CCA) were used to examine plant diversity, soil physicochemical properties, and their correlations in various rocky desertification areas in northern Guangdong. The results showed that the Pinaceae, Lauraceae, and Fagaceae species were relatively abundant in the rocky desertification areas of northern Guangdong. Additionally, Cinnamomum camphora, Schima superba, Pinus massoniana, Quercus stewardiana, and Acer camphora could be used as indicators for rocky desertification. There were significant differences in plant community compositions and diversity characteristics between the five RDDs, and the vegetation exhibited the trend of initial destruction and then gradual improvement and stabilization. There were significant differences in soil bulk density, mechanical composition, organic matter, total nitrogen, alkaline hydrolysis nitrogen, and available potassium between the different RDDs. Except for pH, the soil chemical characteristics all had clear aggregation effects. Soil organic matter, total nitrogen, total potassium, and alkaline hydrolysis nitrogen all exhibited degradation–improvement cycles. The correlation analysis revealed that there was a significant correlation between soil physicochemical properties and species diversity. The CCA analysis showed that the most important soil factors affecting plant community structures were total phosphorus and available phosphorus. In conclusion, some achievements have been made in the restoration of rocky desertification in northern Guangdong; while the plant community structure improved, some soil nutrients also improved. Vegetation and soil have a strong coupling relationship. In the later stages of recovery, suitable species for rocky desertification could be considered in varying degrees and P and K could be supplemented appropriately. Our study will have implications for the revegetation of rocky desertification.

Differences in gut bacterial community composition between modern and slower-growing broiler breeder lines: Implications of growth selection on microbiome composition.

In the last century broiler chicken lines have undergone an extensive breeding regime aimed primarily at growth and high meat yield. It is not known if breeding has also resulted in a change to the broiler breeder's associated gut microbiota. Here we compared the gut microbiota of 37-week-old commercial Cobb breeding dams with dams from a broiler Legacy line which has not undergone selection since 1986. The dams from both lines were kept together in the same shed under the same management protocol from day of hatch to avoid additional confounders. We chose this age to allow significant bacterial exchange, thus avoiding exposure dependent artifacts and so that we could compare dams at the same developmental state of adulthood and peak laying performance. Significant differences in the composition of the cecum bacterial communities were found. Bacteria of the genus Akkermansia, implicated in mucin degradation and associated with host metabolic health, accounted for 4.98% ± 5.04% of the Cobb cecum community, but were mostly absent from the ceca of the Legacy line dams. Inversely, Legacy dams had higher levels of Clostridiales, Lactobacillales and Aeromonadales. These results show that breeding has resulted in a change in the gut microbiota composition, likely by changing the physiological conditions in the mucosa. It remains unclear if changes in gut microbiota composition are a part of the mechanism affecting growth or are a secondary result of other physiological changes accelerating growth. Therefore, the identification of these changes opens the door to further targeted research.

Bacterial communities in the phyllosphere are distinct from those in root and soil, and sensitive to plant species changes in subtropical tree plantations.

Deciphering the local diversity and community composition of plant-associated microorganisms is crucial to predict their ecological functions in forest ecosystems. The differences in microbial diversity and community composition between the aboveground and belowground tree compartments remain largely unknown. Here we examined bacterial communities in the leaf surface (phyllosphere) and root-associated (root and rhizospheric soil) habitats of 13 tree species. Bacterial richness substantially differed across the three compartments, with the highest value observed in rhizospheric soil. Tree species exerted a significant effect on α-diversity of leaf- and soil- but not root-inhabiting bacteria. Bacterial communities were distinct across habitats and were significantly more divergent in leaf- than in root-associated habitats. Leaf nutrients and soil pH and NH4+-N were the main factors regulating leaf- and root-related community composition, respectively. This study highlights that host selection effects on bacterial community structure were more prominent in aboveground than in belowground habitats. Our findings contribute to a better understanding of the effect of compartments and subtropical tree species on microbial diversity, with crucial implications for sustainable forest plantation management.

Phytoplankton and Microzooplankton Community Structure and Assembly Mechanisms in Northwestern Pacific Ocean Estuaries with Environmental Heterogeneity and Geographic Segregation.

Phytoplankton and microzooplankton are crucial players in marine ecosystems and first responders to environmental changes, but their community structures and how they are shaped by environmental conditions have rarely been studied simultaneously. In this study, we conducted an eDNA metabarcoding sequencing combined with multiple statistical methods to simultaneously analyze the phytoplankton and microzooplankton in Liaohe (LH) and Yalujiang (YLJ) estuaries. The major objective was to examine how plankton community structure and assembly mechanism may differ between two estuaries with similar latitudinal position and climate but geographical segregation and differential level of urbanization (more in LH). Clear differences in diversity and composition of phytoplankton and microzooplankton communities between LH and YLJ estuaries were observed. Richness of phytoplankton was significantly higher in LH than YLJ, while richness of microzooplankton was higher in YLJ. The magnitude of intrahabitat variations in phytoplankton communities was significantly stronger than that of microzooplankton. Some phytoplankton and microzooplankton taxa also showed interhabitat differences in their relative abundances. Phytoplankton showed a stronger geographic distance-decay of similarity than microzooplankton, while significant environmental distance-decay of similarity in microzooplankton was found in the less urbanized YLJ estuary. Community assembly of phytoplankton was, based on the neutral community models, driven primarily by stochastic processes, while deterministic processes contributed more for microzooplankton. Furthermore, we detected wider habitat niche breadths and stronger dispersal abilities in phytoplankton than in microzooplankton. These results suggest that passive dispersal shapes the phytoplankton community whereas environmental selection shapes the microzooplankton community. IMPORTANCE Understanding the underlying mechanisms shaping a metacommunity is useful to management for improving the ecosystem function. The research presented in the manuscript mainly tried to address the effects of habitat geography and environmental conditions on the phytoplankton and microzooplankton communities, and the underlying mechanisms of community assembly in temperate estuaries. In order to achieve this purpose, we developed a metabarcoding sequencing method based on 18S rRNA gene. The phytoplankton and microzooplankton communities from two estuaries with similar latitude and climatic conditions but obvious geographical segregation and significant environmental heterogeneity were investigated. The results of our study could lay a solid foundation for ascertaining phytoplankton and microzooplankton communities in estuaries with obvious environmental heterogeneity and geographic segregation and mechanisms underlying community assembly.

The gut microbiota diversity of five Orthoptera (Insecta, Polyneoptera) insects determined by DNA metabarcoding.

Most orthopteran insects are phytophagous and some are important pests in agriculture and forests. Many intestinal microflora of Orthoptera insects have been reported, primarily from Acridoidea and there have been few reports of other taxa. In this study, we collected 15 individuals representing five species (Ruspolialineosa, Tetrixjaponica, Erianthusversicolor, Gryllotalpaorientalis and Teleogryllusemma) belonging to five orthopteran superfamilies (Tettigonioidea, Tetrigoidea, Eumastacoidea, Gryllotalpoidea and Grylloidea) to characterise and compare the gut microbiota with greater taxonomic width by performing sequencing analysis of the 16S rRNA V4 region in gut material. A total of 606,053 high-quality sequences and 3,105 OTUs were acquired from 15 gut samples representing 24 phyla, 48 classes, 69 orders, 133 families and 219 genera. Firmicutes and bacteria were the most abundant phyla, followed by Bacteroidetes, Cyanobacteria, Actinobacteria and Acidobacteria. At the genus level, Serratia, Citrobacter, Wolbachia, Lactobacillus and Parabacteroides were the most predominant genera in R.lineosa, T.japonica, E.versicolor, G.orientalis and T.emma, respectively. Both Principal Coordinates Analysis (PCoA) and heatmap results revealed significant differences in bacterial community composition across species. Additionally, alpha diversity analysis indicated the bacterial richness was significantly different amongst the five species.

Effects of supplementation of Bacillus amyloliquefaciens on performance, systemic immunity, and intestinal microbiota of weaned pigs experimentally infected with a pathogenic enterotoxigenic E. coli F18.

The objective of this study was to investigate the effects of dietary supplementation of Bacillus (B.) amyloliquefaciens on growth performance, diarrhea, systemic immunity, and intestinal microbiota of weaned pigs experimentally infected with F18 enterotoxigenic Escherichia coli (ETEC). A total of 50 weaned pigs (7.41 ± 1.35 kg BW) were individually housed and randomly allotted to one of the following five treatments: sham control (CON-), sham B. amyloliquefaciens (BAM-), challenged control (CON+), challenged B. amyloliquefaciens (BAM+), and challenged carbadox (AGP+). The experiment lasted 28 days, with 7 days of adaptation and 21 days after the first ETEC inoculation. ETEC challenge reduced (P < 0.05) average daily gain (ADG) of pigs. Compared with CON+, AGP+ enhanced (P < 0.05) ADG, while B. amyloliquefaciens supplementation tended (P < 0.10) to increase ADG in pigs from days 0 to 21 post-inoculation (PI). The ETEC challenge increased (P < 0.05) white blood cell (WBC) count on days 7 and 21 PI, while BAM+ pigs tended (P < 0.10) to have low WBC on day 7 PI and had lower (P < 0.05) WBC on day 21 PI compared with CON+. In comparison to AGP+ fecal microbiota, BAM+ had a lower (P < 0.05) relative abundance of Lachnospiraceae on day 0 and Clostridiaceae on day 21 PI, but a higher (P < 0.05) relative abundance of Enterobacyeriaceae on day 0. In ileal digesta, the Shannon index was higher (P < 0.05) in BAM+ than in AGP+. Bray-Curtis PCoA displayed a difference in bacterial community composition in ileal digesta collected from sham pigs vs. ETEC-infected pigs on day 21 PI. Pigs in BAM+ had a greater (P < 0.05) relative abundance of Firmicutes, but a lower (P < 0.05) relative abundance of Actinomycetota and Bacteroidota in ileal digesta than pigs in AGP+. Ileal digesta from AGP+ had a greater (P < 0.05) abundance of Clostridium sensu stricto 1 but lower (P < 0.05) Bifidobacterium than pigs in BAM+. In conclusion, supplementation of B. amyloliquefaciens tended to increase ADG and had limited effects on the diarrhea of ETEC-infected pigs. However, pigs fed with B. amyloliquefaciens exhibit milder systemic inflammation than controls. B. amyloliquefaciens differently modified the intestinal microbiota of weaned pigs compared with carbadox.

Stand age alters fungal community composition and functional guilds in subalpine Picea asperata plantations

Soil fungi participate in a variety of forest ecological processes and drive the succession of degraded forests. However, how the soil fungal community and functional taxa change with stand age remains unclear in subalpine plantations. We established five vegetation survey plots in four planted Picea asperata forests aged 25, 40, 50 and 75 years and one natural P. asperata forest aged approximately 200 years in a subalpine region and randomly collected rhizosphere and bulk soils of two representative P. asperata individuals in each plot for high-throughput sequencing of fungal communities and determination of soil properties. The fungal community composition in both rhizosphere and bulk soils varied significantly among different stand ages. Fungal operational taxonomic unit (OTU) richness and Shannon diversity in bulk but not rhizosphere soil changed significantly with stand age. Except for the 75-year-old plantation, there was no difference in the fungal community composition between rhizosphere soil and bulk soil. Soil properties, plant production (P. asperata growth indicators) and plant richness jointly determined the fungal community composition, and soil total phosphorous (TP) accounted for the most variation in the fungal community. P. asperata regulated the community composition of fungal functional guilds (i.e., plant pathogens, saprophytes, ectomycorrhizal fungi and endophytes) mainly by changing soil properties rather than plant richness. Interestingly, the community composition of fungi and functional guilds in plantations became increasingly similar to that in the natural forest over time, and the fungal restoration rate (represented by the Bray–Curtis distance between plantations and natural forest) in bulk soil was faster than that in rhizosphere soil. In addition, with increasing stand age, the relative abundance of ectomycorrhizal fungi increased, and the diversity of plant pathogens decreased, both of which were significantly associated with the reduction in soil total phosphorus. These results suggest that stand age is a major factor affecting soil fungal community variation in subalpine P. asperata plantations, which is largely dependent on soil property changes. In particular, soil TP may play a key role in the regulation of different ecological functional fungi.

Biotic interactions contribute more than environmental factors and geographic distance to biogeographic patterns of soil prokaryotic and fungal communities.

Recent studies have shown distinct soil microbial assembly patterns across taxonomic types, habitat types and regions, but little is known about which factors play a dominant role in soil microbial communities. To bridge this gap, we compared the differences in microbial diversity and community composition across two taxonomic types (prokaryotes and fungi), two habitat types (Artemisia and Poaceae) and three geographic regions in the arid ecosystem of northwest China. To determine the main driving factors shaping the prokaryotic and fungal community assembly, we carried out diverse analyses including null model, partial mantel test and variance partitioning analysis etc. The findings suggested that the processes of community assembly were more diverse among taxonomic categories in comparison to habitats or geographical regions. The predominant driving factor of soil microbial community assembly in arid ecosystem was biotic interactions between microorganisms, followed by environmental filtering and dispersal limitation. Network vertex, positive cohesion and negative cohesion showed the most significant correlations with prokaryotic and fungal diversity and community dissimilarity. Salinity was the major environmental variable structuring the prokaryotic community. Although prokaryotic and fungal communities were jointly regulated by the three factors, the effects of biotic interactions and environmental variables (both are deterministic processes) on the community structure of prokaryotes were stronger than that of fungi. The null model revealed that prokaryotic community assembly was more deterministic, whereas fungal community assembly was structured by stochastic processes. Taken together, these findings unravel the predominant drivers governing microbial community assembly across taxonomic types, habitat types and geographic regions and highlight the impacts of biotic interactions on disentangling soil microbial assembly mechanisms.

Niche-mediated bacterial community composition in continental glacier alluvial valleys under cold and arid environments.

Bacteria are an essential component of glacier-fed ecosystems and play a dominant role in driving elemental cycling in the hydrosphere and pedosphere. However, studies of bacterial community composition mechanisms and their potential ecological functions from the alluvial valley of mountain glaciers are extremely scarce under cold and arid environments. Here, we analyzed the effects of major physicochemical parameters related to soil on the bacterial community compositions in an alluvial valley of the Laohugou Glacier No. 12 from the perspective of core, other, and unique taxa and explored their functional composition characteristics. The different characteristics of core, other, and unique taxa highlighted the conservation and difference in bacterial community composition. The bacterial community structure of the glacial alluvial valley was mainly affected by the above sea level, soil organic carbon, and water holding capacity. In addition, the most common and active carbon metabolic pathways and their spatial distribution patterns along the glacial alluvial valley were revealed by FAPTOTAX. Collectively, this study provides new insights into the comprehensive assessment of glacier-fed ecosystems in glacial meltwater ceasing or glacier disappearance.

Persistent decadal differences in plant communities assembled under contrasting climate conditions.

Plant community assembly outcomes can be contingent upon establishment year (year effects) due to variations in the environment. Stochastic events such as interannual variability in climate, particularly in the first year of community assembly, contribute to unpredictable community outcomes over the short term, but less is known about whether year effects produce transient or persistent states on a decadal timescale. To test for short-term (5-year) and persistent (decadal) effects of establishment year climate on community assembly outcomes, we restored prairie in an agricultural field using the same methods in four different years (2010, 2012, 2014, and 2016) that captured a wide range of initial (planting) year climate conditions. Species composition was measured for 5 years in all four restored prairies and for 9 and 11 years in the two oldest restored prairies established under average precipitation and extreme drought conditions. The composition of the four assembled communities showed large and significant differences in the first year of restoration, followed by dynamic change over time along a similar trajectory due to a temporary flush of annual volunteer species. Sown perennial species eventually came to dominate all communities, but communities remained distinct from each other in year five. Precipitation in June and July of the establishment year explained short-term coarse community metrics (i.e., species richness and grass/forb cover), with wet establishment years resulting in a higher cover of grasses and dry establishment years resulting in a higher cover of forbs in restored communities. Short-term differences in community composition, species richness, and grass/forb cover in restorations established under average precipitation and drought conditions persisted for 9-11 years, with low interannual variability in the composition of each prairie over the long term, indicating persistently different states on a decadal timescale. Thus, year effects resulting from stochastic variation in climate can have decadal effects on community assembly outcomes.

Habitats Within the Plant Root Differ in Bacterial Network Topology and Taxonomic Assortativity.

The root microbiome is composed of distinct epiphytic (rhizosphere) and endophytic (endosphere) habitats. Differences in abiotic and biotic factors drive differences in microbial community diversity and composition between these habitats, though how they shape the interactions among community members is unknown. Here, we coupled a large-scale characterization of the rhizosphere and endosphere bacterial communities of 30 plant species across two watering treatments with co-occurrence network analysis to understand how root habitats and soil moisture shape root bacterial network properties. We used a novel bootstrapping procedure and null network modeling to overcome some of the limitations associated with microbial co-occurrence network construction and analysis. Endosphere networks had elevated node betweenness centrality versus the rhizosphere, indicating greater overall connectivity among core bacterial members of the root endosphere. Taxonomic assortativity was higher in the endosphere, whereby positive co-occurrence was more likely between bacteria within the same phylum while negative co-occurrence was more likely between bacterial taxa from different phyla. This taxonomic assortativity could be driven by positive and negative interactions among members of the same or different phylum, respectively, or by similar niche preferences associated with phylum rank among root inhabiting bacteria across plant host species. In contrast to the large differences between root habitats, drought had limited effects on network properties but did result in a higher proportion of shared co-occurrences between rhizosphere and endosphere networks. Our study points to fundamentally different ecological processes shaping bacterial co-occurrence across root habitats. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Life History Traits of Exotic and Native Species Determine Grassland Management Outcomes Following Prescribed Fire

<h3>ABSTRACT</h3> Disturbance regimes, including the historical timing of disturbance, are important components of natural ecosystems and greatly influence ecosystem structure and functioning. Consequently, disturbance timing can be an important component of biodiversity management. We evaluated the effect of prescribed fires ignited during the warm and cool seasons (summer and spring, respectively) on the plant community of a calcareous grassland in northern Mississippi (USA). We found that fire season influenced plant community composition by having differential impacts on species with different life history traits. Differences among species were primarily driven by the dichotomy between cool-season (C₃) and warm-season (C₄) plants, independent of species native status. Spring burns reduced the cover of cool-season C₃ graminoids, but had the opposite effect on C₄ graminoids, which likely benefited from increases in resource availability due to the reduction of C₃ species. However, summer burns decreased the abundance of C₄ graminoids, as summer burns were ignited during the active growing and reproductive period for the C₄ species. We found the same patterns for the number of inflorescences of the most abundant C₃ and C₄ graminoids. Summer burns also increased overall species diversity and the abundance of native C₃ graminoids, forbs, and vines, resulting in significant differences in plant community composition between spring- and summer-burned areas. Programs that aim to restore native grassland communities in the short-term using prescribed fire should consider the life history traits of target plants (including invasive species) to determine the best time for prescribed fire implementation.

Invading the Greek Seas: Spatiotemporal Patterns of Marine Impactful Alien and Cryptogenic Species

The Greek Seas are greatly exposed to the proliferation of marine alien species. At least 242 alien species have been reported within Greek territorial waters, three-quarters of which are considered established, while their rate of introduction is increasing. Some of these species exhibit high invasiveness, imposing severe impacts on native ecosystems and ecosystem services. The spatiotemporal proliferation of these species outside their natural boundaries depends on several parameters, including their biological characteristics, native distribution range, introduction pathway, and time of initial introduction. Knowing the current and potential alien species distribution is essential for the implementation of effective management actions. To investigate the distribution of impactful cryptogenic and alien species (ICAS) in the Greek Seas, we combined all records available until the end of 2020 from eight types of data sources: (1) scientific literature, (2) grey literature, (3) offline databases, (4) online scientific databases, (5) personal observations of independent researchers, (6) communications with divers and diving centers, (7) in situ underwater sampling, and (8) social networks. The results of 5478 georeferenced records refer to 60 marine ICAS belonging to 16 taxonomic groups. The number of records and the overall number of ICAS present an increasing trend from the northern to the southern parts of our study area, and there is a clear distinction in community composition between the northern and southern subregions. This latitudinal gradient is mainly due to the large number of thermophilous Lessepsian species of West Indo-Pacific origin, which reach the southern parts of the study area through unaided dispersal. On the other hand, transport stowaways appear to be more prevalent in areas located near large ports, which show significant differences in ICAS numbers and community composition compared to sites located far from ports. Most records (&gt;40% of the total) were associated with rocky reefs, partly reflecting the preference of divers for this habitat type but also the presence of conspicuous, reef-associated impactful fish. The number of published records, as well as the number of reported ICAS, shows a dramatic increase with time, highlighting the urgent need for immediate proactive management actions and scientifically informed control measures.