Analysis of Microbial Community Structure and Dynamic Changes during the Domestication Process of Embedded Particles

Metabolic exploration of glycogen accumulating organisms' sludge with Candidatus Contendobacter in enhanced biological phosphorus removal.

The microbiota associated with Cannabis sativa L. plays a crucial role in plant growth and health, although the mechanisms by which it is modulated in response to different types of stress during cultivation remains under investigation. In this study, the bacterial microbiota of both rhizospheric and bulk soil associated with a therapeutic C. sativa variety was characterized across three stages of the cultivation cycle (early vegetative, late vegetative, and late flowering), comparing healthy plants and those under stress induced by Tetranychus urticae. In addition to microbial profiling, plant physiological parameters were assessed, along with the analysis of cannabinoid and terpene profiles in floral tissues. Analyses of alpha diversity, community structure, discriminant taxa (LEfSe), and functional predictions (PICRUSt2) were performed using 16S rRNA gene sequencing data. The results revealed stress-associated shifts in the rhizospheric bacterial community, characterized by changes in the dominance of several genera across plant developmental stages, including a reduced representation of taxa commonly associated with plant growth promotion. Functional predictions further indicated that in control conditions the rhizosphere community exhibited higher metabolic activity, enriched in pathways related to replication, transcription and protein synthesis, whereas under stress, functions shifted toward resource recycling and metabolic flexibility. These findings suggest that biotic stress triggers a functional and structural reorganization of the soil bacterial microbiota, favoring more resilient yet less beneficial communities for plant development.This study provides novel evidence of the interaction between insect, plant, and microbiota, with both agronomic and biotechnological implications.

Hurricanes are major natural disturbances that significantly influence tropical ecosystems. While most research focuses on large-bodied organisms, understanding the impact of hurricanes on small-bodied biota, such as meiofauna, is crucial, especially as climate change models predict more frequent and intense storms. Puerto Rico offers a unique setting to study these effects, as hurricanes and tropical storms are frequent. This research examined the short- (Post-Hurricane A) and medium-term (Post-Hurricane B) impacts of Hurricanes Irma and María (September 2017) on stream meiofaunal communities in a tropical stream in the Luquillo Experimental Forest. Twelve samples were collected monthly from pools across two stream reaches for eight months before and after the hurricanes. Environmental variables, such as discharge, sediment composition, and biotic data, were recorded. Meiofauna were identified to the lowest possible taxonomic level and categorized by phyla and feeding groups. Results showed a significant increase in both richness and abundance of meiofauna following the hurricanes. Richness and abundance peaked during Post-Hurricane A and declined slightly during Post-Hurricane B. This trend was linked to an increase in coarse particulate organic matter, potentially the result of defoliation and debris from hurricane damage of riparian forest. Community structure analyses revealed significant differences between pre- and post-hurricane periods. Variables such as stream discharge, macroinvertebrate presence, sediment size, and shrimp abundance were all influenced by hurricane impacts and correlated with changes in meiofaunal communities. During Post-Hurricane A, models explaining meiofaunal variation involved variables associated with ecosystem disturbance. In contrast, Post-Hurricane B models were simpler, suggesting a level of ecological stabilization. These findings suggest that hurricanes influence meiofaunal communities, but that these organisms are likely benefiting from hurricane disturbance. Given expected increases in hurricane activity due to climate change, hurricanes may play a long-term role in shaping the structure and function of tropical stream communities, in particular for small-body size organisms.

Background and Aims: Mangrove forests are very important in ensuring the ecological balance of the coastal areas, but the sustainability of these forests is being affected by abrasion, pollution, and natural regeneration to the point where it is becoming rare. This was research conducted to determine the present ecological state of the Baros mangrove ecosystem through analysis of the vegetation community structure in terms of ecological indices. Study Design: An observational ecological study focusing on vegetation community structure analysis. Place and Duration of Study: The research was conducted in June 2025 at the Mangrove Baros ecosystem in Bantul Regency, Yogyakarta Special Region. Methodology: Data on vegetation were obtained by use of the quadrat transect method on three observation stations which represented the tree, sapling and seedling strata. The species were identified, the number of each species counted, and structural measurements made. The Shannon-Wiener diversity, Simpson’s dominance, evenness, and species richness indices were used to assess community structure. Results: Mangrove diversity ranged from low to moderate across stations and strata. The community was strongly dominated by Rhizophora apiculata and Avicennia marina, resulting in uneven species distribution and low richness. Regeneration was limited, with seedlings recorded at only one station. These patterns indicate a simplified vegetation structure and reduced ecological resilience, likely associated with environmental pressures such as waste accumulation and coastal abrasion. Conclusion: The Baros mangrove ecosystem is experiencing ecological stress and constrained natural recovery. Management strategies should prioritize multi-species rehabilitation and ecosystem-based conservation to enhance biodiversity and long-term stability.

Environmental DNA (eDNA) serves as the material foundation for biodiversity research. As a revolutionary biomonitoring tool, eDNA technology offers significant advantages such as being non-invasive, efficient, and cost-effective. Understanding the eDNA research landscape in China is important for global scholars, both for tracking progress in this field and for observing how an advanced biodiversity monitoring technology is systematically validated and applied in a major biodiversity-rich country. This study employs the CiteSpace bibliometric analysis tool, based on 304 publications from the CNKI database, to systematically map the research landscape in this field. The results indicate a consistent upward trend in the number of publications within China’s eDNA research domain, which has evolved through three stages. The field involves numerous researchers, with the top three prolific authors being Xiao-wei Zhang, Jiang-hua Yang, and Zhi Chen. Some research institutions have formed clusters, but a close cross-institutional collaborative network has yet to be established. Chinese eDNA research is oriented toward technological application and addressing ecological issues, with current hotspots focusing on applying eDNA technology to biodiversity studies through biomonitoring, biomass assessment, and biological community structure analysis, targeting phytoplankton, benthic animals, fish, and environmental microorganisms, among others. However, it also faces common global challenges. This study provides a reference for environmental DNA-related research and contributes Chinese experience and insights to global biodiversity monitoring.

ABSTRACT Connectivity is a multifaceted concept that has important implications for the management and conservation of marine and freshwater fishes. We developed a conceptual framework that encompasses multiple, interrelated categories of connectedness, including landscape (e.g., structural, functional) connectivity and ecological (e.g., trophic, genetic, demographic) connectivity, that together shape the flow of organisms, energy and information across ecosystems. We also synthesised six key methods that can be used to study connectivity of fishes: (1) telemetry, including satellite, acoustic, radio and passive integrated transponders (PIT), (2) mark‐recapture, (3) environmental tracers, including stable isotopes and otolith‐microchemistry, (4) genetics, (5) community structure analysis and (6) emerging technologies and tools (e.g., remote sensing and artificial intelligence). For each method, we describe the categories of connectivity it can assess and provide real‐world examples where they have been effectively used. We also identify limitations of each method. This article highlights the diverse and evolving toolbox of methods used to assess fish connectivity, underscoring the need for continued collaboration, innovation and integration of new approaches to refine our understanding and address remaining challenges in this critical area of aquatic ecology and fisheries management.

Reef fish communities are widely used as sensitive bioindicators of coral reef ecosystem condition and provide an ecological basis for area- based conservation planning, including Other Effective Area-based Conservation Measures, yet site-specific ecological evidence supporting OECM screening remains limited in many eastern Indonesian reef systems. This study assessed reef fish community structure at nine stations in the Kilwaru-Kiltay waters, East Seram, using a standardized Underwater Visual Census conducted in May-June 2023, with species-level identification based on direct underwater observations and standard identification guides. Community structure was evaluated using abundance metrics, ecological indices, and Principal Component Analysis at family and species levels. A total of 115 reef fish species were recorded, showing high species richness and pronounced spatial variation among stations. Pomacentridae consistently dominated most sites, while diversity, evenness, and dominance indices revealed clear site-specific differences in internal community organization rather than uniform ecological conditions. Multivariate ordination further highlighted distinct spatial differentiation in assemblage composition and functional group structure across stations. These results demonstrate that reef fish community structure provides a robust, site- specific ecological indicator for screening potential OECM areas and supports spatially informed conservation planning beyond formally protected areas in eastern Indonesia.

Recent investigations of coral symbiotic microorganisms have largely centered on their ecological functions, while systematic analyses of the community composition, diversity, and functional potential of bacteria associated with different coral species remain limited. This study presents the first systematic analysis of the distinct community structures and highly conserved core functions of symbiotic bacteria in four species of stony corals Favites abdita (Fa), Favia speciosa (Fs), Montipora digitata (Md), and Porites solida (Ps) from the South China Sea by high-throughput sequencing. The results identified 23 phyla and 250 genera of bacterial taxa, revealing considerable taxonomic richness in these coral-associated bacterial communities. Significant differences (p < 0.05) in bacterial community composition were observed among four coral species. Proteobacteria was the absolutely dominant phylum in Fa, Fs, and Ps, whereas Md was dominated by the phylum Firmicutes. At the genus level, the core microbial communities of the four coral species were similar in composition but exhibited marked differences in abundance. Md showed the highest species richness and diversity, and Fs the lowest. Among them, the Fa, Fs, and Ps groups were dominated by Ruegeria, while the Md group was characterized by a high abundance of Paramaledivibacter, which was significantly more abundant than in other groups. Functional prediction indicated that the relative abundances of core functional categories, such as amino acid transport and metabolism and energy production and conversion, were highly consistent across the four coral species, reflecting functional conservation within these communities. These findings enrich the basic data on the diversity and function of Coral symbiotic microorganisms in the South China Sea, revealing the connection between coral community variability and the conservation of core functions.

Enhancing the low-carbon performance for municipal wastewater treatment through high-rate activated sludge-three-stage constructed wetland system: Water quality, energy recovery and carbon emissions reduction.

The mangrove ecosystem in Teluk Bogam Village plays an essential role in maintaining the balance of the coastal environment. Variations in the utilization of mangrove areas have the potential to cause differences in water quality conditions. To date, no study has specifically examined the macrozoobenthic community structure in Teluk Bogam Village. This study aims to analyze the macrozoobenthic community structure within the mangrove ecosystem of Teluk Bogam Village, Central Kalimantan. Sampling of macrozoobenthos and water quality observations were conducted in March, June, and September 2024, as well as in January 2025, at three observation stations. Data analyses included assessments of macrozoobenthic community structure and Principal Component Analysis (PCA). Macrozoobenthos in the study area consisted of the classes Gastropoda, Bivalvia, and Polychaeta, with the genus Cerithium being the most dominant. The community structure was categorized as stable, characterized by moderate diversity (H'=2.04-2.06), high evenness (E= 0.92-0.97), and low dominance (D = 0.13-0.14). The PCA results indicated that macrozoobenthic density exhibited a strong association with water quality parameters, particularly turbidity and total suspended solids (TSS).

Industrial, agricultural and construction development has brought improvements in living conditions, but have also increased the amount of pollution in the environment. Atmospheric precipitation collects pollutants from urban surfaces, which then end up in stormwater systems, contaminating surface waters. These pollutants are also linked to the similar effects of agriculture, as biogenic pollutants originate from over-fertilized crops. Contaminated surface water forces flora and fauna to adapt to new conditions, and affecting the structure and extent of ecosystems. Monitoring the environment with bio-indication methods is important because it enables identification of the areas in need of protection, in an inexpensive and environmentally harmless way. The aim of this study was to evaluate the possibility of using biocenotic indices to assess the impact of a stormwater system on the aquatic environment. Bio-indicative studies were conducted on periphyton sampled at 4 points on the Bystrzyca River in Lublin, eastern Poland, under the influence of stormwater discharge and 1 reference point localized before the stormwater system outflow. The quantitative data concerning the number of chosen algae species was analyzed using indices for the examination of community structure. Considered the indices, i.e. taxonomic richness, Shannon, MacArthur, Menhinick and McIntosh were calculated, evaluated, and shown in various types of graphs showing the fluctuation of indices at measurement points. The use of bioindication and classic biocenotic indices allowed for the description, analysis of changes in the periphyton biocenosis under the influence of point source stormwater discharges, and linking measurements from tested samples with environmental conditions and biodiversity in the analyzed study sites and periods.

As an organic soil amendment, biochar plays a significant role in ameliorating soil acidification and promoting microbial activity. Through field experiments, the impact of biochar on the composition and functions of bacterial communities in acidic purple soil were evaluated. Four treatments were established： no fertilizer （CK）, conventional fertilization （F）, chemical fertilizer combined with organic fertilizer （OF）, and chemical fertilizer combined with biochar （BF）. Using indoor analysis and Illumina MiSeq high-throughput sequencing technology, we analyzed the changes in soil physicochemical properties, bacterial community diversity, community composition, bacterial network, and functional predictions under different treatments over time. The results indicated that biochar treatment significantly increased soil pH and the content of available nutrients （such as alkali-hydrolyzable nitrogen, available phosphorus, and readily available potassium） and significantly enhanced the α and β diversity of bacterial communities, particularly in the second year （P &lt; 0.05）. After two years of biochar and organic fertilizer application, the complexity and stability of the soil microbial network were significantly reduced, promoting microbial synergism. Functional predictions showed that the BF treatment significantly improved key bacterial functions such as organic matter degradation, energy production and conversion, and amino acid transport and metabolism, but these functional activities significantly weakened in the second year. Additionally, the application of biochar significantly increased the relative abundance of Paeniglutamicibacter and Rhodococcus, which play key roles in organic matter degradation and energy production. Overall, biochar not only improved soil physicochemical properties but also enhanced bacterial community functions and diversity, thereby improving soil health and ecosystem functions. However, its long-term effects require continuous attention and maintenance, providing scientific evidence for achieving sustainable agricultural development.

Enhancement mechanism of iron autotrophic denitrification system based on resource utilization of waste membranes.

ABSTRACTThe distinctive flavor of stinky tofu arises from intricate microbial metabolic networks during traditional fermentation, yet the genetic mechanisms linking microbial community structure to flavor formation remain incompletely resolved. This study employed metagenomic sequencing (Illumina NovaSeq 6000, Q30 > 92%) to generate 7.32 Gb of high‐quality data, integrated with functional annotations from KEGG, eggNOG, and CAZy databases, to systematically dissect core microbial taxa and metabolic genes driving flavor biosynthesis. Dominant genera included Pseudomonas (relative abundance: 74.3%), Acinetobacter (14.4%), and Enterobacter (5%), with Pseudomonas putida (12.5%) and Pseudomonas fluorescens (3.2%) orchestrating carbohydrate metabolism (68.22% KEGG pathways) and amino acid degradation via glycoside hydrolases (GHs, 73% of CAZy‐annotated enzymes) and dehydrogenases (e.g., 125 lactate dehydrogenase genes). Key flavor compounds, such as diacetyl (379 α‐acetolactate synthase genes) and 3‐methylbutanoic acid, were synthesized through synergistic pathways. Additionally, Lactococcus and Kluyvera contributed to ester and short‐chain fatty acid production via α‐keto acid dehydrogenase complexes (55 genes). A total of 410,231 non‐redundant genes were identified, annotated to 4690 microbial species, establishing a multi‐layered microbial‐gene‐metabolite regulatory network. This work elucidates the molecular basis of stinky tofu flavor formation and provides a framework for optimizing traditional fermentation processes through targeted microbial engineering.

Phyllosphere microorganisms play a vital role in supporting host plant health and adaptability. Although previous research on the effects of host performance and their phylogenetic associations on phyllosphere microbial communities has predominantly focused on tropical, subtropical, and temperate forestry ecosystems, the responses of these microbial communities to plant phylogeny and functional traits in temperate desert environments remains poorly understood. In this study, we conducted a quantitative analysis of bacterial and fungal community structures in the phyllosphere of 39 plant species from the Gurbantunggut Desert, a typical temperate desert in Central Asia. Variation partitioning analysis revealed that plant phylogeny, leaf physicochemical properties, and leaf morphological characteristics collectively explained the variation in phyllosphere microbial communities. Specifically, these factors accounted for 19.26%, 14.53%, and 2.32% of the variance in bacterial communities, and 11.55%, 8.36%, and 2.19% of the variance in fungal communities, respectively. A significant hierarchical pattern emerged: plant phylogeny > leaf physicochemical properties > leaf morphological characteristics, highlighting the dominant role of plant filtering effects in community assembly. Linear mixed-effects model analysis further confirmed the significant influence of multiple plant attributes, including phylogeny and functional traits, on microbial community structure. Plant–microbe interaction analysis revealed distinct host preferences of microbial taxa across different plant taxonomic levels. Co-evolutionary analysis also indicated a significant phylogenetic association between host plants and their phyllosphere amplicon sequence variants (ASVs). Overall, our findings demonstrate that plant attributes, particularly plant phylogeny and functional traits, are key factors driving the assembly of phyllosphere microbial communities in deserts. This study provides new insights into species coexistence mechanisms in fragile habitats and enhances our understanding of plant–microbe interactions in global desert ecosystem.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00248-025-02635-9.

In agricultural lands, cadmium (Cd) and lead (Pb) co-contamination poses a significant threat to soil health and crop safety. This study evaluates the ryegrass-maize intercropping system as a sustainable approach to mitigate these environmental challenges. A 120-day pot experiment was conducted, revealing that the intercropping system significantly reduced soil Cd and Pb, achieving residual levels below national risk thresholds. Maize grains were confirmed safe, while ryegrass acted as an efficient bioaccumulator. The system enhanced soil ecosystem services, evidenced by a significant increase in key soil enzyme activities and nutrient cycling indicators. Specifically, the intercropping system boosted the activities of catalase, alkaline protease, and urease, which are crucial for redox regulation and nitrogen cycling. Notably, the activity of alkaline protease, responsible for organic nitrogen decomposition, increased by approximately 18.5 times in the intercropping group. Furthermore, the system increased soil organic matter by 5.89%, a core indicator of soil fertility and carbon sequestration, a key supporting service. Habitat sustainability was substantiated through the analysis of microbial community structure and diversity. Although Cd-Pb contamination initially reduced microbial diversity, the intercropping system (C2) mitigated this decline more effectively than monoculture (C1). More importantly, the intercropping system enriched metal-tolerant and functionally critical microbial taxa, such as Actinobacteriota, whose relative abundance reached 43.99% in the C2 group after the experiment. Despite observed phosphorus depletion, which suggests the need for targeted fertilization, the findings support ryegrass-maize intercropping as a viable, nature-based solution for soil remediation. This scalable strategy not only addresses contamination but also supports sustainable land management, contributing to the resilience and restoration of degraded farmlands.

Liquid inoculum is widely adopted in the mushroom industry, yet preparing Tremella fuciformis liquid inoculum remains challenging due to its complex microbial community and dimorphic growth. This study aimed to establish a reliable protocol for T. fuciformis liquid inoculum and assess its practical application. Initially, liquefied spawn was produced by liquefying solid spawn. The application of standard liquefied spawn increased fruiting body yield by 8.2% (502.4 g/kg dry substrate) compared to solid spawn, but exhibited substantial batch-to-batch variation due to unstable microbial communities and low Tremellomycetes abundance. To address these limitations, liquid spawn was developed via pre-culture of pure T. fuciformis and Annulohypoxylon stygium mycelia. Cultivation tests demonstrated significantly enhanced performance with 608.2 g of fruiting bodies, which represented 11.1% improvement compared to solid spawn. Moreover, consistent yields could be observed across multiple batches. This stability was attributed to stable microbial community structure and the dominance of Tremellomycetes (abundance > 50%) in the fungal community. These results confirm the cultivation performance of T. fuciformis liquid spawn, highlighting its potential as an effective alternative to solid spawn for T. fuciformis industrial production.

This article presents a comprehensive study of the socio-economic structure and development potential of territorial communities in Eastern Podillia, in the context of the decentralization reform in Ukraine. The relevance of the topic stems from the need for an in-depth analysis of community structures as basic local self-government units, considering their resource capacity, institutional strength, and spatial characteristics, which directly affect regional policy and management effectiveness. The main goal of the study is to perform a socio-economic analysis of the territorial communities in Eastern Podillia, taking into account their structural differentiation and development dynamics. The object of the research is the territorial communities as spatial-administrative entities, while the subject is their structure, development level, and internal potential. The geographical scope includes the southern part of Khmelnytskyi region, the central and northern parts of Vinnytsia region, and part of Cherkasy region. The article applies a range of methods, including index, cluster, and correlation-regression analysis, expert evaluation, and GIS-based visualization approaches. Based on the calculated indicators, the communities were classified into three development levels: high, medium, and low. Specific examples of communities with different development statuses are given, such as Zhmerynka, Kalynivka, and Severynivka. The study identifies key factors that shape the development potential of communities: financial capacity, local economic structure, human capital, infrastructure, and governance quality. The findings reveal regional development disparities and serve as a basis for practical recommendations in strategic community planning based on development potential. The scientific novelty of the work lies in the integrated analytical approach to studying communities of Eastern Podillia, combining quantitative indicators with spatial characteristics. The practical value is in the applicability of results for local governments, regional authorities, and developers of territorial development strategies.

Abstract Subalpine coniferous forest ecosystems are sensitive to climate change. However, the community formation mechanisms of subalpine coniferous forests in northeastern Asia remain poorly understood. In this study, we assessed the factors controlling the phylogenetic community structure in different strata (whole strata, upperstory, and understory) of Abies nephrolepis and Abies koreana forests in the subalpine zone in South Korea. Piecewise structural equation modeling (pSEM) was performed based on terrain, climate, taxonomic diversity, stand structure characteristics, and disturbance factors. The controlling factors presented different responses for each species depending on the stratum and phylogenetic community structure indices (net relatedness index and nearest taxon index). A. nephrolepis showed a unique community formation mechanism and formed climate refugia through high rock exposure, whereas A. koreana showed niche conservation at high elevations and a community overdispersion trend when forest gaps appeared due to overstory vegetation loss. The Mantel test and partial Mantel test were performed to examine the impact of turnover and nestedness on phylogenetic β‐diversity, as well as to establish their correlations with climatic, geographic, and environmental distance. Turnover was a major contributing factor to β‐diversity and strongly correlated with environmental distance. Further, geographical and climatic distance presented differential contributions to each species depending on the community characteristics. Integrated analyses of phylogenetic community structure and β‐diversity provided detailed insights into the mechanisms underlying community formation and biodiversity patterns. This reveals that biodiversity patterns are driven by interactions between community structure and inter‐community characteristics, with internal structure as a key mechanism influencing β‐diversity.