Non-metric Multidimensional Scaling Analysis Research Articles

Stable Diversity but Distinct Metabolic Activity of Microbiome of Roots from Adult and Young Chinese Fir Trees

The tree-associated microbiome is vital for both individual trees and the forest ecosystem. The microbiome is dynamic; however, it is influenced by the developmental stages and environmental stresses experienced by host trees. Chinese fir (Cunninghamia lanceolata) is an economically important tree species in the subtropical regions of China. This study investigated the diversity of microbial communities, including bacteria and fungi, in the roots and bulk soil of young (2 years old) and old (46 years old) Chinese fir. It specifically examined the functional characteristics of these microbial communities. Through a non-metric multidimensional scaling (NMDS) analysis, we examined differences in microbial community structures among root and soil samples of Chinese fir. Evaluations using α-diversity metrics (Chao1, Shannon, Pielou, etc.) confirmed significant differences in diversity and structure between soil and root samples but high similarity between young and old tree samples. A network analysis identified key bacterial and fungal genera, such as Burkholderia and Russula, which play pivotal roles in the microbiome structure. We also demonstrated significant variations in microbial metabolic functions, such as dioxin and benzoic acid degradation metabolic pathways, which might relate to stress alleviation for tree fitness. Additionally, for the detection of endophytic microorganisms in Chinese fir seeds, only small amounts (less than 10%) of fungal endophytes and bare bacterial endophytes were identified. In summary, this study revealed that the stable structure of the rhizosphere microbiome was established in the early stage of tree life in Chinese fir, which mostly originated from surrounding soil rather than seed endophytes. The associated microbial metabolic activity naturally decreased with tree aging, implicating the tree microbial dynamics and the need for the addition of an actively functional synthetic community for tree fitness.

Diversity of Ectomycorrhizal Fungal Communities Associated with Tuber koreanum in Korea

Ectomycorrhizal fungi (EMF) are crucial for the formation of Tuber fruiting bodies, including the newly discovered T. koreanum, in Korea. This study explores the diversity and distribution of EMF communities associated with T. koreanum across various regions in Korea and assesses the effects of soil physicochemical properties on these communities. Soil analysis indicated that T. koreanum habitats have a lower pH compared to T. melanosporum habitats documented in other studies, with sandy loam texture being optimal for fruiting body development. Nonmetric multidimensional scaling analysis revealed significant positive correlations between the relative abundances of certain EMF genera and exchangeable potassium and calcium. These findings offer valuable insights into the ecological requirements of T. koreanum and support future conservation and cultivation strategies for truffle species in Korea.

Heavy metal bioaccumulation based on seasonal monsoon impact in benthic macroinvertebrates of Korean streams.

This study investigates the influence of seasonal monsoon flooding on heavy metal contamination and bioaccumulation in benthic macroinvertebrate communities within a stream ecosystem. We analyzed sediment and benthic macroinvertebrate samples for eight heavy metals [zinc (Zn), chromium (Cr), nickel (Ni), lead (Pb), copper (Cu), arsenic (As), cadmium (Cd), and mercury (Hg)] ) before (BF) and after (AF) a major flooding event. Significant spatial and temporal variations in heavy metal concentrations were observed, with generally higher levels detected after the flood. Chironomidae consistently exhibited high bioaccumulation factors (BAFs) for several metals, highlighting their role as bioindicators. Notably, elevated Cu accumulation was observed in multiple species, including Radix auricularia (R. auricularia), Cipangopaludina chinensis malleata (C. c. malleata), and Palaemon spp. Non-metric multidimensional scaling (NMDS) analysis revealed shifting correlations between environmental variables and bioaccumulation patterns before and after flooding. Pre-flood, total nitrogen (TN) showed a strong positive correlation with Hg bioaccumulation, while post-flood, large sand content emerged as a more influential factor for Zn, Cr, Ni, and Pb bioaccumulation. Our findings emphasize the complex interplay between seasonal flooding, environmental factors, and heavy metal dynamics, with potential implications for ecological risk assessment and water quality management.

Iron-bound organic carbon declined after estuarine wetland reclamation into paddy fields

Iron-bound organic carbon (Fe-OC) is a main pathway for the long-term maintenance of soil organic carbon (SOC), but research on its mechanism is still relatively weak. We investigated the coupling relationships among iron (Fe), carbon (C) and Fe-reducing bacteria (FeRB) in the soil of a reclaimed paddy field in comparison with natural Phragmites australis wetland in the Minjiang River estuary in southeastern China. The results showed that conversion of P. australis wetland to paddy cultivation changed the soil redox process. After reclamation, soil Fe(II), Fe(III), HCl-Fet, free iron oxide (Fed) and amorphous iron (Feo) contents and Fe(III)/Fe(II) decreased significantly (p < 0.05), while the content of complexed iron (Fep) increased. Nonmetric multidimensional scaling analysis (NMDS) demonstrated variability in FeRB across soil types (r = 0.900, p = 0.001). The lower Fe-OC concentration in soil after wetland reclamation may be the result of Fe reduction by dissimilatory FeRB (e.g., Bacillus, Anaeromyxobacter). On average, both Fe-OC and SOC contents decreased significantly (p < 0.05), while the contribution of Fe-OC to total SOC (fFe-OC) increased significantly (p < 0.05), after conversion to paddy cultivation. Structural equation modeling (SEM) showed that SOC, dissolved organic C, and Fe-OC were affected by FeRB and the speciation of Fe. In addition, Fe (III) concentration affected SOC concentration (r = 0.60, p < 0.05) and DOC concentration (r = 0.58, p < 0.05), and Fed affected DOC concentration (r = 0.69, p < 0.05). We conclude that after rice field reclamation in estuarine wetlands, Fe-reducing bacteria can mediate iron-bonded organic C decoupling, affecting SOC stabilization.

Gut microbiota alterations and associations with nutrients in children with celiac disease.

Celiac disease is a chronic inflammatory condition that is not well understood in relation to the microbiome. Our objective was to demonstrate changes in the microbiota and the relationships between nutrients in children with celiac disease (CD) who followed a gluten-free diet (GFD). A group of 11 children who were recently diagnosed with CD, ranging in age from 3 to 12, were monitored for a period of 6 months. GFD is designed based on the individual's specific energy and nutrient needs, with strict control over dietary adherence. Food consumption, blood, and fecal samples were taken. Fecal samples were put through 16s rRNA sequencing. Microbial modifications were demonstrated using alpha diversity, beta diversity, nonmetric multidimensional scaling analysis (NDMS), t-test, and metastats. Mean age was 6.4 ± 2.66 years and 54.5% were male participants. Serological parameters were negative after 6 months. Both unweighted (p = .019) and weighted (p = .021) Unifrac distances were higher before GFD, and differences were reliable according to NDMS analysis (stress = 0.189). The abundance of Bacteroides ovatus was increased (p = .014), whereas unidentified Lachnospiraceae, Paeniclostridium, Paraclostridium Peptostreptococcus, and Dielma were decreased after GFD (p < .001). Associations between nutrients and several genera and species were identified. The presence of genus Bifidobacterium and Bifidobacterium adolescentis was inversely associated with fat intake after GFD (p < .01). Microbiota changes became evident over a period of 6 months. The presence or absence of small bacteria may play a role in the development of CD. Modifying the children's dietary intake can potentially influence the microbial composition.

Plant Species Diversity and Composition Differ Significantly Between the Boundaries of Kettle Holes and Field Borders.

The boundaries around habitat islands in agricultural fields are rather unexamined, although they may be an important part of agroecosystems in some regions. In this study, we surveyed field boundaries in northeastern Brandenburg both at outer field borders and around kettle holes, which are typical habitat islands in the region. We examined, described, and compared the plant species diversity and composition at both the inner and outer field boundaries in the arable fields (crop edge) as well as in permanent vegetation (field margins). Diversity was assessed and compared with Hill diversity values, using the iNext framework. Non-metric multidimensional scaling and permutational analysis of variance were used to compare species composition at different field boundaries and to search for variables that drive species composition at the local scale. The results revealed that both species diversity and composition differed significantly between the inner and outer boundary along the crop edges and at the field margins. Local site conditions, namely a moisture gradient, influenced the species composition of the field margins, resulting in differences between the inner and outer field margins. Mitigated through crop growth and cover, the moisture gradient influenced also the species composition of the inner and outer crop edges, despite the management practices on the fields were the same.

Diversity Patterns of Bacteria in the Root Zone of Davidia involucrata Along an Altitudinal Gradient

Davidia involucrata has an ancient origin, representing a remnant from the paleotropical flora that thrived during the Tertiary period. Altitudinal gradient acts as a natural testing ground for studying climate change, and research on the distribution patterns of microorganisms along altitudinal gradients is crucial in understanding the adaptability of D. involucrata to climate change. In our study, we examined sample sites ranging from 1600 to 2200 m in elevation, which are part of the primary habitat zone for Davidia involucrata within the Xuebaoding National Nature Reserve. In 2021, field surveys were conducted across four altitudinal gradients (1600 m, 1800 m, 2000 m and 2200 m) of the D. involucrata distribution in the nature reserve. The sampling plots were set in each altitudinal gradient, and three representative and healthy mature trees were selected as sample trees for each plot. Rhizosphere soils were used to test the soil stoichiometry characteristics and root zone microbial communities. Our findings indicated pronounced differences in soil total carbon (TC) and total phosphorus (TP) content and C:P and N:P ratios between the four altitude sites (p &lt; 0.05). Analysis of the bacterial communities revealed higher richness (PD and Chao1 indexes) at ASL2000 and ASL2200 (high altitude) compared to ASL1600 and ASL2000 (low altitude) (p &lt; 0.05). Non-metric multidimensional scaling analysis demonstrated a distinct clustering of bacterial communities between the high and low altitudes (p &lt; 0.01). At the phylum level, Proteobacteria and Acidobacteria were predominant at high altitudes, while Actinobacteria and Chloroflexi dominated at low altitudes. The core microbiome, shared among all altitudes, comprised 377 genes. The analysis of differential abundance revealed notable disparities in the prevalence of certain bacterial genera with altitude, with Arthrobacter and Acidothermus experiencing the most pronounced shifts (p &lt; 0.05). This confirmed that environmental factors significantly influenced bacterial community structure and abundance. Spearman’s rank correlations revealed that both Chao1 and PD indices were positively correlated with elevation, TC, and TN, with Chao1 showing stronger relationships. Both indices were negatively correlated with MAT, while only Chao1 exhibited a significant negative correlation with pH. Linear regression analysis further confirmed the significant associations between Chao1 index and elevation, TN, MAT, and pH. Furthermore, redundancy analysis demonstrated that altitude (ASL) and TN were the primary factors shaping soil bacterial community composition, explaining 21.32% and 30.70% of the variance, respectively. Altitude significantly influenced microbial community structure (p = 0.003). Distinct microbial taxa showed specific associations with environmental gradients, suggesting niche specialization in response to soil conditions. These findings suggest that altitude influences soil nutrient characteristics and microbial community composition in the D. involucrata habitat, offering insights into the ecological factors affecting this endangered species.

Deciphering stratified structure and microbiota assembly of biofilms from a pyrite-based biofilter driven by mixotrophic denitrification

The precise structure and assembly process of pyrite-based biofilms remain poorly understood. The polysaccharides (PN), proteins (PS), and extracellular DNA were enriched in the soluble extracellular polymeric substance (EPS), loosely bound EPS, and tightly bound EPS, respectively, indicating a significant stratified structure of biofilms. The tryptophan facilitated mixotrophic metabolic processes. Both dominant (>1%) and rare species (<0.01 %) harbored core bacteria, including sulfur autotrophic bacteria, sulfate-reducing bacteria, and heterotrophic bacteria. Furthermore, partial least-squares path modeling quantified the contributions of total phosphorus (TP) (λ = 0.32), dissolved organic matter (DOC) (λ = 0.29), and NH4+–N (λ = 0.26) to variations in the microbial community. Nonmetric multidimensional scaling analysis revealed three distinct stages in biofilm development: colonization (0–36 d), succession (36–149 d), and maturation/old (149–215 d). Furthermore, neutral community model indicated that stochastic processes drove the colonization and maturation/old stages, while deterministic processes dominated the succession stage. This study offered valuable insights into the regulation of pyrite-based engineered ecosystems.

Environmental DNA reveals spatial and temporal variation in fish communities before the 10-year fishing ban in the Poyang Lake Basin

Poyang Lake is the largest freshwater lake in China, and its unique ecosystem is an important biodiversity reservoir. Fish play an important role in the aquatic ecosystem of Poyang Lake. Accurate assessment of fish species diversity and community composition is essential for studies of fish ecology and conservation management. In this study, environmental DNA metabarcoding was used to analyze fish diversity and community structure in different habitats and seasons in the Poyang Lake Basin. A total of 52 fish species were identified, and limnicolous fish were the most abundant; most fish were omnivorous and small. The fish diversity index was highest in the spring and in the main lake area of Poyang Lake. Cluster analysis and non-metric multidimensional scaling analysis revealed significant differences in fish community structure among habitats. Water temperature and pH were the main environmental factors affecting fish community structure in the Poyang Lake Basin. Non-invasive environmental DNA monitoring methods could provide an important auxiliary method for monitoring fishery resources during the 10-year fishing ban period. This study provides basic information on the fish resources in the Poyang Lake Basin and has implications for fishery management and the development of ecological protection policies.

Impacts of an intensive traditional mariculture model on offshore environments as evidenced by dissolved organic matter and bacterial communities

Mariculture is a key protein source and economic driver but traditional methods pollute coastal waters, hindering sustainable development. Current research on the ecological impacts of mariculture mainly focuses on specific pollutants and lacks an assessment of the biogeochemical impacts of mariculture discharge. This study examined Xiangshan Bay, a representative intensive mariculture area in China, to explore the impact of mariculture tailwater discharge on water quality, focusing on dissolved organic matter (DOM) and bacterial communities. Based on the fluorescence excitation-emission matrix combined with parallel factor analysis, a characteristic fluorescence component C4 was identified in mariculture tailwater (intensity of 40 ± 4 %, n = 8), while higher C4 components (47 ± 3 %, n = 15) were found throughout the bay. Humic-like components from riverine input (C1 + C2: 32 ± 3 %, n = 15) and protein-like components from domestic sewage (C5: 2 ± 1 %, n = 15) were significantly lower in the seawater samples, indicating the strong influence of mariculture tailwater on the entire DOM structure of the bay. The bacterial community structure showed a response consistent with DOM, as revealed by nonmetric multidimensional scaling analysis. This showed that bacterial communities in mariculture tailwater and bay water samples clustered together, independent of riverine input. The SourceTracker model indicated that mariculture tailwater (91 ± 5 %) predominantly contributed to the bacterial community, with minimal contributions from riverine input (< 5 %). Co-occurrence network analysis further showed that under long-term high-intensity mariculture discharge, the C4 component became the core DOM and was closely associated with the bacterial community. The results here demonstrate the profound impact of traditional mariculture on coastal water quality and show that riverine input is not the primary pollution source in this region, providing clear directions for coastal environmental restoration efforts.

Quantitative analysis of the morphological variation within the tiger beetle Calomera littoralis (Fabricius, 1787) (Coleoptera: Cicindelidae) in Mongolia.

For the past couple of centuries, much of tiger beetle taxonomic work has been focused on explaining intraspecific variation. In the Northern Hemisphere, over a thousand subspecies have been described and many have since been relegated to synonymy. Generally, the phenotypic-based subspecies circumscription has been purely descriptive. More quantitative and integrative analyses of the color and pattern variation in tiger beetles would be valuable. The geographically wide-ranging species, Calomera littoralis (Fabricius, 1987) contains 11 currently recognized subspecies, including two described from Mongolia that have been of questionable status due to the paucity of material available when they were described. Here, we assess the distribution of phenotypic variation within C. l. peipingensis (Mandl, 1934) and C. l. mongolensis (Mandl, 1981) to determine whether it best fits a pattern of two subspecies with a contact zone or a gradual cline, based on 494 specimens from 34 populations. Non-metric multidimensional scaling analyses and modeling of the fit between longitude and black dorsal phenotypes both indicate that the variation is best explained by a gradual cline of phenotype along an east-west gradient, not the presence of separate subspecies. As a result, we synonymize C. littoralis mongolensis, syn, nov. with C. littoralis peipingensis.

Facies variability and depositional cyclicity in central Northern Switzerland: insights from new Opalinus Clay drill cores

The Opalinus Clay, a silty to sandy claystone formation, Early to Middle Jurassic (Toarcian and Aalenian) in age, has been selected as the host rock for deep subsurface disposal of radioactive waste in Switzerland. Over the past thirty years, numerous geotechnical, mineralogical, and sedimentological studies have been conducted on the Opalinus Clay within the framework of the Nagra (National Cooperative for the Disposal of Radioactive Waste) deep drilling campaigns and the Mont Terri Project, an international research program dedicated to the study of claystone. The present study aims to unravel the variability of the lateral and vertical facies of the Opalinus Clay in central Northern Switzerland and to place this variability in a regional and basinal context. Analyses of new cores drilled in central Northern Switzerland, including petrographic, mineralogical (X-ray diffraction, multi-mineral interpretation), geochemical (X-ray fluorescence), statistical (non-metric multidimensional scaling analysis), and bedding dip and azimuth data, shed new light on the depositional facies and the spatial and temporal variability of the Opalinus Clay. Petrographic descriptions encompass nine new drill cores using a revised subfacies/facies classification scheme based on texture (colour, grain size, bedding) and composition (mineralogy). Particularly, one new subfacies (SF6) is described and interpreted as mass-wasting deposits. The drill cores are correlated laterally using specific marker horizons. This correlation is achieved by combining thorough facies investigations with lithostratigraphy, biostratigraphy, and chemostratigraphy. Six to seven small coarsening-upward cycles and two long-term coarsening-upward sequences can be interpreted as regressive trends. The observed trends are influenced by the interplay between sediment supply, eustatic sea level change, synsedimentary subsidence, but also the palaeogeographic configuration in an epicontinental sea, provenance and delivery of sediments, current dynamics and climate change. Finally, combined results show that the current dynamics in the Opalinus Clay has been underestimated until now and new depositional models, including the occurrence of drift deposits, are discussed.

Responses of soil fungal community composition and function to wetland degradation in the Songnen Plain, northeastern China.

Wetlands are ecosystems that have a significant impact on ecological services and are essential for the environment. With the impacts of rapid population growth, wetland reclamation, urbanization, and land use change, wetlands have undergo severe degradation or loss. However, the response of soil fungal communities to wetland degradation remains unknown. It is crucial to comprehend how the diversity and population dynamics of soil fungi respond to varying levels of degradation and ecological progression in the wetlands of the Songnen Plain. In this study, high- throughput sequencing technology to analyze the variety and abundance of soil fungi in the undegraded (UD), light degraded (LD), moderate degraded (MD), and severe degraded (SD) conditions in the Halahai Nature Reserve of Songnen Plain. This study also explored how these fungi are related to the soil's physicochemical properties in wetlands at various degradation levels. The findings indicated that Basidiomycota and Ascomycota were the primary phyla in the Songnen Plain, with Ascomycota increasing and Basidiomycota decreasing as wetland degradation progressed. Significant differences were observed in soil organic carbon (SOC), total nitrogen (TN),and soil total potassium (TK) among the succession degradation stages. With the deterioration of the wetland, there was a pattern of the Shannon and Chao1 indices increasing and then decreasing. Non-metric Multidimensional Scaling (NMDS) analysis indicated that the fungal community structures of UD and LD were quite similar, whereas MD and SD exhibited more distinct differences in their fungal community compositions. Redundancy analysis (RDA) results indicated that Soil Water content (SWC) and total nitrogen (TN) were the primary environmental factors influencing the dominant fungal phylum. According to the FUNGuild prediction, Ectomycorrhizal and plant pathogens gradually declining with wetland degradation. In general, our findings can offer theoretical support develop effective solutions for the preservation and rehabilitation of damaged wetlands.

Characterization of the Ecological Niche and Interspecific Connectivity of Plankton in Baiyangdian Lake by Combining Ecological Networks

To understand the structure of the plankton community and the ecological niche characteristics of their dominant species, sampling surveys of plankton were conducted in Baiyangdian Lake in the spring （March）, summer （July）, and autumn （September） of 2022. The changes in the plankton community during the three seasons were analyzed by constructing ecological network diagrams, non-metric multidimensional scaling analysis （NMDS）, and the ecological niche width. The niche overlap of zooplankton dominant species was evaluated by the improved Levins' formula and Petraitis' index. The interspecific connectivity of dominant species was judged using the chi-square test and interspecies connectivity coefficients. The results showed that the niche width of plankton in the whole area was low. Zooplankton was dominated by rotifers, and phytoplankton was dominated by diatoms, cyanobacteria, and green algae. There were significant seasonal changes in the community structures of plankton. Compared with that in summer and autumn, there were fewer species of plankton in spring and lower interspecies connectivity. The overlap of dominant species of zooplankton was high in summer, and the interspecific competition was intensified, whereas the interspecific overlap of phytoplankton was at a low level in all three seasons. There was a significant positive correlation （W &gt; χ20.05） between phytoplankton in summer and autumn, and the community structure was stable. The interdomain ecological network of zooplankton and phytoplankton showed a high negative correlation ratio in autumn, especially between copepods and cladoceras of zooplankton and chlorophyta and cyanophyta of phytoplankton. The plankton species in Baiyangdian Lake were abundant, with obvious seasonal differences. The dominant species were mainly a narrow ecological niche. The plankton community was generally in a stable state, and there was a strong predation relationship between copepods and cladoceras and green algae and cyanobacteria.

Nanopore sequencing provides snapshots of the genetic variation within salmonid alphavirus-3 (SAV3) during an ongoing infection in Atlantic salmon (Salmo salar) and brown trout (Salmo trutta)

Frequent RNA virus mutations raise concerns about evolving virulent variants. The purpose of this study was to investigate genetic variation in salmonid alphavirus-3 (SAV3) over the course of an experimental infection in Atlantic salmon and brown trout. Atlantic salmon and brown trout parr were infected using a cohabitation challenge, and heart samples were collected for analysis of the SAV3 genome at 2-, 4- and 8-weeks post-challenge. PCR was used to amplify eight overlapping amplicons covering 98.8% of the SAV3 genome. The amplicons were subsequently sequenced using the Nanopore platform. Nanopore sequencing identified a multitude of single nucleotide variants (SNVs) and deletions. The variation was widespread across the SAV3 genome in samples from both species. Mostly, specific SNVs were observed in single fish at some sampling time points, but two relatively frequent (i.e., major) SNVs were observed in two out of four fish within the same experimental group. Two other, less frequent (i.e., minor) SNVs only showed an increase in frequency in brown trout. Nanopore reads were de novo clustered using a 99% sequence identity threshold. For each amplicon, a number of variant clusters were observed that were defined by relatively large deletions. Nonmetric multidimensional scaling analysis integrating the cluster data for eight amplicons indicated that late in infection, SAV3 genomes isolated from brown trout had greater variation than those from Atlantic salmon. The sequencing methods and bioinformatics pipeline presented in this study provide an approach to investigate the composition of genetic diversity during viral infections.

Macrogenome-based study on the mechanism of Bacillus velezensis SX13 in regulating rhizophere environment and cucumber growth under different cultivation environments

Microbial activities are the dynamic core of nutrient cycling in organic substrates, and the exploitation of plant growth-promoting rhizobacteria strains contributes to sustainable agricultural development. This study aimed to investigate the effect and mechanism of Bacillus velezensis SX13 in nutrient cycling and plant promotion under different substrate supply conditions. The effects of reduced substrate amount (sCK) and inoculation of SX13 strain under both substrate supply conditions (Bv and sBv) on rhizosphere microenvironment and plant growth were investigated using conventional substrate amount (CK) as a control. Results showed no significant difference in the α-diversity indexes (Chao1 and Shannon) of the rhizospheric microbial community among the four treatments. However, nonmetric multidimensional scaling analysis and principal coordinate analysis revealed that compared with CK treatment, the inoculation of SX13 strain and reduced substrate supply reshaped the β-diversity structure of microbial communities. Furthermore, inoculation with B. velezensis SX13 under both substrate supply conditions increased the abundance of Proteobacteria (1.64%–2.46 %), Acidobacteria (14.09%–43.07 %), and Firmicutes (179.29%–861.29 %). The results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the metabolic pathway with the highest abundance of enriched genes was also the pathway with the most enriched differential genes caused by reducing substrate supply or inoculation of B. velezensis SX13. The rhizosphere inoculation of B. velezensis SX13 significantly up-regulated the top genes related to carbohydrate esterases, carbohydrate binding modules, glycoside hydrolases, glycoside transferases, and polysaccharide lyases. As a result, the activities of carbon and nitrogen cycle-related enzymes such as cellobiohydrolase, β-glucosidase, urease, l-leucine amino peptidase, and β-1 4-N-acetylglucosaminidase were increased, which in turn accelerated nutrient cycling. B. velezensis SX13 and its mediated improvement of the rhizospheric microenvironment resulted in the up-regulation of root CsNRT family genes (such as CsNRT1.1, CsNRT1.4a, CsNRT1.4b, CsNRT1.5a, CsNRT1.5b, CsNRT1.5c, and CsNRT1.8), which accelerated nitrogen uptake, accumulation, and utilization efficiency and ultimately improved the yield and quality of cucumber. The effect of SX13 strain was more stable and efficient under conventional substrate supply conditions than under reduced substrate supply conditions.

Estimating taxonomic and functional structure along a tropical estuary: linking metabolic traits and aspects of ecosystem functioning.

Microbial life forms are among the most ubiquitous on Earth, yet many remain understudied in Caribbean estuaries. We report on the prokaryote community composition of the Urabá Estuary in the Colombian Caribbean using 16S rRNA gene-transcript sequencing. We also assessed potential functional diversity through 38 metabolic traits inferred from 16S rRNA gene data. Water samples were collected from six sampling stations at two depths with contrasting light-penetration conditions along an approximately 100 km transect in the Gulf of Urabá in December 2019. Non-metric multidimensional scaling analysis grouped the samples into two distinct clusters along the transect and between depths. The primary variables influencing the prokaryote community composition were the sampling station, depth, salinity, and dissolved oxygen levels. Twenty percent of genera (i.e., 58 out 285) account for 95% of the differences between groups along the transect and among depths. All of the 38 metabolic traits studied showed some significant relationship with the tested environmental variables, especially salinity and except with temperature. Another non-metric multidimensional scaling analysis, based on community-weighted mean of traits, also grouped the samples in two clusters along the transect and over depth. Biodiversity facets, such as richness, evenness, and redundancy, indicated that environmental variations-stemming from river discharges-introduce an imbalance in functional diversity between surface prokaryote communities closer to the estuary's head and bottom communities closer to the ocean. Our research broadens the use of 16S rRNA gene transcripts beyond mere taxonomic assignments, furthering the field of trait-based prokaryote community ecology in transitional aquatic ecosystems.IMPORTANCEThe resilience of a dynamic ecosystem is directly tied to the ability of its microbes to navigate environmental gradients. This study delves into the changes in prokaryote community composition and functional diversity within the Urabá Estuary (Colombian Caribbean) for the first time. We integrate data from 16S rRNA gene transcripts (taxonomic and functional) with environmental variability to gain an understanding of this under-researched ecosystem using a multi-faceted macroecological framework. We found that significant shifts in prokaryote composition and in primary changes in functional diversity were influenced by physical-chemical fluctuations across the estuary's environmental gradient. Furthermore, we identified a potential disparity in functional diversity. Near-surface communities closer to the estuary's head exhibited differences compared to deeper communities situated farther away. Our research serves as a roadmap for posing new inquiries about the potential functional diversity of prokaryote communities in highly dynamic ecosystems, pushing forward the domain of multi-trait-based prokaryote community ecology.

Linear Morphometry of Male Genitalia Distinguishes the Ant Genera Monomorium and Syllophopsis (Hymenoptera: Formicidae) in Madagascar.

Morphometric analyses of male genitalia are routinely used to distinguish genera and species in beetles, butterflies, and flies, but are rarely used in ants, where most morphometric analyses focus on the external morphology of the worker caste. In this work, we performed linear morphometric analysis of the male genitalia to distinguish Monomorium and Syllophopsis in Madagascar. For 80 specimens, we measured 10 morphometric characters, especially on the paramere, volsella, and penisvalvae. Three datasets were made from linear measurements: mean (raw data), the ratios of characters (ratio data), and the Removal of Allometric Variance (RAV data). The following quantitative methods were applied to these datasets: hierarchical clustering (Ward's method), unconstrained ordination methods including Principal Component Analysis (PCA), Non-Metric Multidimensional Scaling analyses (NMDS), Linear Discriminant Analysis (LDA), and Conditional Inference Trees (CITs). The results from statistical analysis show that the ratios proved to be the most effective approach for genus-level differentiation. However, the RAV method exhibited overlap between the genera. Meanwhile, the raw data facilitated more nuanced distinctions at the species level compared with the ratios and RAV approaches. The CITs revealed that the ratios of denticle length of the valviceps (SeL) to the paramere height (PaH) effectively distinguished between genera and identified key variables for species-level differentiation. Overall, this study shows that linear morphometric analysis of male genitalia is a useful data source for taxonomic delimitation.

Comparison of freshwater diatom assemblage between old-growth broad-leaved and planted coniferous forest basins in temperate region, Japan

Various forest types are distributed in headwater streams. However, differences in diatom assemblages among forest types in Japan have not been thoroughly investigated. The objective of this study was to determine differences in diatom assemblages in the most common forest types in Japanese headwater streams, old-growth broadleaf forest (OBF) and planted coniferous forest (PCF) types, and to identify diatom species that tend to grow in either the OBF or PCF forest types. Diatom abundance differed between the forest types, but the numbers of species, genera and families did not. Nonmetric multidimensional scaling analysis revealed the differences in diatom assemblages in OBF and PCF types and this difference was brought by particularly of some genera such as Gomphonema, Planothidium and Navicula. Differences in diatom assemblages between the two forest types were considered to be a reflection of the different environmental conditions such as light condition and alkalinity, created by the different forest types.

Understanding the influence of environmental factors on forest composition along the vertical gradient of Northwestern Himalaya

Temperate and alpine ecosystems are considered the most sensitive and vulnerable region towards climate change in the Indian Himalayan region. The current study investigates forest composition in relation to environmental and edaphic factors, which is critical for determining plant community patterns. The impact of climatic and soil properties was studied to better understand species diversity and composition over an elevational gradient (2500–4800 m) in Beas Valley, Northwestern Himalaya. A total of 181 species from 15 community types, representing 122 genera and 53 families (9 Trees, 13 shrubs, and 142 herbs) were recorded from the valley. Non-metric multidimensional scaling (NMDS) analysis revealed significant compositional dissimilarity (PseudoF = 10.16, R2 = 0.48, p < 0.001) among vegetation types. Structural equation modeling (SEM) results indicated that tree species diversity was significantly influenced by solar radiation (β=0.17, p = 0.001) and winter temperature (β=41.95, p = 0.017). It was observed that solar radiation and winter temperature shape the community types in high elevation temperate regions. In contrast, precipitation, solar radiation along with summer temperature determine the composition of sub-alpine communities, whereas solar radiation, winter temperature and soil pH determine the composition of alpine communities. This indicated that multiple environmental factors are responsible for this diversity. The research findings shed light on crucial factors influencing high elevation plant diversity, emphasizing the significance of understanding environmental correlations for effective conservation. This is pioneer study, which will act as a reference for future studies in Beas valley. This scientific foundation allows for prioritized conservation efforts, focusing on areas with specific environmental conditions influencing forest composition and plant diversity, ultimately contributing to better management and preservation of high elevation plant communities.