Co-occurrence Network Analysis Research Articles

Cultivating crayfish (Procambarus clarkii) significantly enhances the quantity and diversity of soil microorganisms: evidence from the comparison of rice-wheat and rice-crayfish rotation models

Integrated farming of rice (IFA), as a time-honored agricultural model, can effectively increase agricultural productivity and provide ecological benefits. Rice-wheat rotation and rice-crayfish (Procambarus clarkii) rotation are two most widely applied IFA patterns in China. In this study, we compared the differences in soil microbial communities and predicted their functions in these two IFA models by sequencing the 16s rRNA and analyzing the bioinformation. The results showed that crayfish farming effectively increased the abundance and diversity of soil microorganisms. The main differentially abundant phyla between the two groups were Actinobacteriota, Bacteroidota, and Desulfobacterota, while the main differentially abundant genera were Bacteroidetes_vadinHA17, Sphingomonas, and Thiobacillus. The Similarity Percentages (SIMPER) analysis indicated that these species also had the highest contribution to the differences in microbial composition between the two groups. Random forest prediction analysis was employed to identify potential biomarkers to distinguish the two microbial communities. Actinobacteriota, Desulfobacterota, and Spirochaetota were identified as potential biomarker phyla. Streptomyces, Kribbella, and Paludibacter could serve as potential biomarker genera. Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis revealed that the dominant bacterial functions in the rice-wheat rotation model were aerobic chemoheterotrophy and chemoheterotrophy. In contrast, the bacterial functions in the rice-crayfish rotation model were more diverse, primarily including methylotrophy, human pathogens all and methanotrophy. The results of co-occurrence network analysis showed that crayfish farming enhanced the modularity of the soil microbial community, and revealed that the microbial network in rice-wheat soil had fewer nodes and more edges, which implying more internal connections. In conclusion, the wheat planting and crayfish farming drove significant differences in the soil microbial communities of paddy fields, with Actinobacteriota and Desulfobacterota identified as potential biomarkers. Compared to wheat cultivation, the rotation system incorporating crayfish farming enhanced the richness and diversity of soil microbial species and functions, increased the modularity of the microbial community, and promoted the presence of keystone species with connecting roles. Our study would not only clarify the effects of different IFA models on soil microbial communities, and should also provide valuable insights for future adjusting cropping patterns and controlling current soil microbial ecological problems.

Using Klebsiella sp. and Pseudomonas sp. to Study the Mechanism of Improving Maize Seedling Growth Under Saline Stress

The increasing salinization of cultivated soil worldwide has led to a significant reduction in maize production. Using saline–alkaline-tolerant growth-promoting bacteria (PGPR) in the rhizosphere can significantly improve the saline tolerance of maize and ensure the stability of maize yields, which has become a global research hotspot. This study screened salt-tolerant microorganisms Klebsiella sp. (GF2) and Pseudomonas sp. (GF7) from saline soil to clarify the mechanism in improving the saline tolerance of maize. In this study, different application treatments (GF2, GF7, and GF2 + GF7) and no application (CK) were set up to explore the potential ecological relationships between the saline tolerance of maize seedlings, soil characteristics, and microorganisms. The results showed that co-occurrence network and Zi-Pi analysis identified Klebsiella and Pseudomonas as core microbial communities in the rhizosphere soil of maize seedlings grown in saline soil. The deterministic process of microbial assembly mainly controlled the bacterial community, whereas bacteria and fungi were governed by random processes. The application of saline–alkaline-resistant PGPR under saline stress significantly promoted maize seedling growth, increased the activity of soil growth-promoting enzymes, and enhanced total nitrogen, soil organic carbon, and microbial carbon and nitrogen contents. Additionally, it reduced soil salt and alkali ion concentrations [electrical conductivity (EC) and exchangeable Na+]. Among them, GF2 + GF7 treatment had the best effect, indicating that saline–alkaline-tolerant PGPR could directly or indirectly improve the saline tolerance of maize seedlings by improving the rhizosphere soil ecological environment. EC was the determining factor to promote maize seedling growth under saline–alkaline stress (5.56%; p < 0.01). The results provided an important theoretical reference that deciphers the role of soil factors and microecology in enhancing the saline tolerance of maize.

Biodegradation of CAHs and BTEX in groundwater at a multi-polluted pesticide site undergoing natural attenuation: Insights from identifying key bioindicators using machine learning methods based on microbiome data.

Groundwater pollution, particularly in retired pesticide sites, is a significant environmental concern due to the presence of chlorinated aliphatic hydrocarbons (CAHs) and benzene, toluene, ethylbenzene, and xylene (BTEX). These contaminants pose serious risks to ecosystems and human health. Natural attenuation (NA) has emerged as a sustainable solution, with microorganisms playing a crucial role in pollutant biodegradation. However, the interpretation of the diverse microbial communities in relation to complex pollutants is still challenging, and there is limited research in multi-polluted groundwater. Advanced machine learning (ML) algorithms help identify key microbial indicators for different pollution types (CAHs, BTEX plumes, and mixed plumes). The accuracy and Area Under the Curve (AUC) achieved by Support Vector Machines (SVM) were impressive, with values of 0.87 and 0.99, respectively. With the assistance of model explanation methods, we identified key bioindicators for different pollution types which were then analyzed using co-occurrence network analysis to better understand their potential roles in pollution degradation. The identified key genera indicate that oxidation and co-metabolism predominantly drive dechlorination processes within the CAHs group. In the BTEX group, the primary mechanism for BTEX degradation was observed to be anaerobic degradation under sulfate-reducing conditions. However, in the CAHs&BTEX groups, the indicative genera suggested that BTEX degradation occurred under iron-reducing conditions and reductive dechlorination existed. Overall, this study establishes a framework for harnessing the power of ML alongside co-occurrence network analysis based on microbiome data to enhance understanding and provide a robust assessment of the natural attenuation degradation process at multi-polluted sites.

The Microbial Co-infection Interaction Network in Apical Periodontitis with Sinus Tracts

This study aims to characterize the bacterial co-occurrence features and potential interactions associated with the presence of sinus tracts in apical periodontitis in a Chinese population by using 16S rRNA next-generation sequencing (NGS). Thirty-one samples from twenty-six patients were collected from root canals. Following the extraction of the bacterial DNA, the V3-V4 hypervariable regions of the 16S rRNA gene were sequenced. Compositional diversity, prominent taxa and co-occurrence network analysis were compared according to the presence or absence of sinus tracts. The overall microbiota in two groups exhibited distinguished patterns. Actinomyces dominated in samples with sinus tracts while Prevotella was the most abundant in samples without sinus tracts. The major pathogens in sinus tracts exhibited a complex co-occurrence network, in which Pseudomonas formed a distinctive cluster with enriched abundance, and the extensive correlations centered on Desulfovibrio and Pseudoramibacter may suggest novel dependencies. In the network without sinus tracts, the Bacteroidetes and Firmicutes taxa presented close internal associations. The sequencing results confirmed the complexity of the microbiota in AP. The presence of sinus tracts was associated with distinctive infective patterns and complicated microbial co-infection interaction networks. Further investigations should be adopted to elucidate the relationship between the novel interactions and disease progression. Exploring the microbial interactions leads to a better understanding of etiology of apical periodontitis. Utilizing next generation sequencing techniques, our research uncovered the bacterial community structure and observed co-infection networks associated with sinus tracts, providing potential insights for prognosis prediction and targeted therapeutics of persistent inflammation.

Impacts of anthropogenic disturbances on antibiotic resistomes in biological soil crusts on the Qinghai-Tibetan Plateau.

Biological soil crusts (BSCs) are the main landscape on the Qinghai-Tibetan Plateau and an ecological indicator of human disturbance. Information about antibiotic resistomes in BSCs on the Qinghai-Tibetan Plateau can provide baseline for the risk assessment and management of resistomes and yet to be explored. This work investigated the profiles and geographic patterns of antibiotic resistomes in BSCs along the Lhasa River and their response to anthropogenic activities for the first time. Various antibiotic resistance genes (ARGs) were widely distributed in BSCs, but had relatively lower detection frequency and abundance comparing to soils from human disturbed sites. ARGs profiles in BSCs were separated by altitude from 3860 to 3880m, possibly attributing to the difference in anthropogenic activities. Above 3860m, resistomes exhibited lower abundance including total ARGs, aadA, blaSFO and tnpA-04 owing to the rare human activities; at human disturbed sites with altitude <3860m, the detection frequency and relative abundance of tetG02, oprJ, qacEdelta1-01, and ARGs with the mechanism of efflux pump were higher and viewed as potential indicators of human activities. Anthropogenic activities potentially promoted the horizontal gene transfer of ARGs in BSCs at human disturbed sites from co-occurrence network analysis. Our findings provided fundamental information of antibiotic resistomes in BSCs on the Qinghai-Tibetan Plateau, and unraveled possible mechanisms of human disturbance in shaping antibiotic resistomes.

Differential mediation of biogeochemical processes through bioturbation by fiddler and sesarmid mangrove crabs.

Macrobenthic bioturbation is vital to facilitate nutrient turnover in estuarine ecosystems and drives spatial heterogeneity in the sediment matrix. In this study, we compared the sediment physico-chemical properties, microbial community structure and functional genes in vertically-stratified sediment samples from bioturbated (burrows of Parasesarma bidens and Tubuca arcuata) and non-bioturbated area in mangrove ecosystems (the Hanjiang River Estuary, Southern China). The result indicated that bioturbation by P. bidens and T. arcuata had significantly different effects on sediment properties, with the action of P. bidens enhancing nutrient accumulation while T. arcuata promoted N2O emission. Burrow microhabitats harbored distinctive microbial communities although the dominant phylum and genera shared considerable similarity with the control sediment surface with Woeseia dominating in vertical profiles across different habitats. Co-occurrence network analysis revealed that crab bioturbation promoted formation of less complex but more functionally-specialized microbial communities. Crab bioturbation enhanced nutrient metabolism and separated clusters in dendrogram demonstrated the species-specific effect between P. bidens and T. arcuata. Our work verified the significance of bioturbators in regulating biogeochemical processes and highlighted the species-specific bioturbation effect between two dominant mangrove crabs (P. bidens vs. T. arcuata).

In vitro dynamics of rumen microbiota and fermentation profiles with Antler growth of Sika deer.

The rumen microbiota plays a vital role in the nutrient metabolism affecting the growth of velvet antler. However, the fermentation patterns and dynamics of the rumen microbiota across growth stages of velvet antler remain largely unexplored. Here, we employed an in vitro fermentation approach to assess fermentation parameters and microbial composition in the rumen liquid of sika deer during the early growth (EG), metaphase growth (MG), and fast growth (FG) phases . Our findings indicated that the levels of short-chain fatty acids (SCFAs), ammonia nitrogen, and gas production increased over fermentation time in all three groups. The concentrations of total SCFAs, ammonia nitrogen, and gas production, along with the proportions of butyrate, isobutyrate, and isovalerate, were markedly higher in the MG and FG groups compared with the EG group. Principal coordinate analysis highlighted significant variations in microbial communities among the EG, MG, and FG groups during the fermentation process. The abundances of Stomatobaculum and Blautia across the three groups increased over fermentation time, whereas Bacteroides, Lawsonibacter, Sporobacter, Papillibacter, Butyricicoccus, and Succiniclasticum exhibited higher abundances in MG or FG groups than in the EG group after 24 hours of fermentation. Co-occurrence network analysis uncovered positive correlations between butyrate levels and butyrate-producing bacteria (Stomatobaculum, Butyrivibrio) in the MG and FG groups. Additionally, there were positive correlations between proteolytic bacteria (Clostridium and Roseburia) and branched-chain volatile fatty acids in the FG group. These findings shed light on the fermentation patterns and microbial dynamics within the rumen of sika deer during different growth periods of velvet antler.IMPORTANCEVelvet antlers are distinctive and rapidly growing organs that hold significant value in traditional medicine. Through in vitro analysis, our study characterized the dynamics of microbiota and metabolites within the rumen liquid fermentation of sika deer throughout the different antler growth phase. We identified distinct microbial communities at various fermentation time points and observed shifts in fermentation patterns that paralleled antler development. These findings suggest a potentially pivotal role for these microbial dynamics in facilitating the growth process of velvet antlers.

The Role of Internet Public Opinion in Shaping Local Elections: A Case Study of the 2021 Nagoya City Mayoral Election

Internet public opinion builds on the concept of public opinion and refers to the multiple small public spheres represented online. This article analyzes internet public opinion on X (formerly Twitter) during Japan’s 2021 Nagoya mayoral election. This local election has been in the spotlight due to a signature fraud scandal involving the incumbent, despite his eventual victory. Therefore, we selected this unique case study to analyze content and user interactions. To achieve this, we employed morphological analysis, word co-occurrence network analysis, and social network analysis on the collected tweets. The results reveal that, compared to policy pledges, political scandals garnered considerable attention from local citizens and high-profile celebrities. This dynamic influenced public discourse, leading to a bias on X favoring the newcomer over the incumbent. Additionally, this analysis underscored the considerable impact of mass media as critical sources.

Unveiling the conceptual and intellectual map of care bundle research in ICUs: Trends, key issues, and collaborative networks.

Care bundles are evidence-based practices intended to improve patient outcomes and have become a significant focus in intensive care. This study aims to identify research trends, key topics, leading researchers, and significant collaborations in care bundle research within ıntensive care units by mapping the conceptual and intellectual structure of the field. Data were collected from the Web of Science database, covering publications from 2010 to 2024. The search terms included 'bundle*' or 'bundle* care' and 'intensive care unit' or 'critical care'. The analysis used tools like the Biblometrix package in R and VOSviewer, focusing on performance metrics, co-citation analysis, co-occurrence network analysis, and thematic mapping. The annual growth rate of publications on care bundles is 6.26%. The most prolific journals include Critical Care Medicine, the American Journal of Infection Control, and Infection Control and Hospital Epidemiology. Thematic mapping shows research is concentrated on critical areas such as infection control, patient safety, and quality improvement. While some themes, like 'intensive care units' and 'central line-associated bloodstream infection', are well-developed and central, others like 'maternal safety consensus' and 'safety consensus bundle' are highly developed but less central. Emerging themes like 'acute kidney injury' suggest potential areas for future research. This bibliometric analysis offers a comprehensive overview of intensive care unit care bundle research, highlighting a strong focus on critical issues like infection control, patient safety, and care quality improvement. The study provides crucial insights for clinical practice by identifying key research trends and underexplored topics related to intensive care unit care bundles. These findings can guide the development of more effective care protocols, promote multidisciplinary collaboration, and enhance healthcare professional education, ultimately contributing to optimized patient care and high standards in the intensive care unit through improved care bundle implementation.

Deciphering the fungal symphony: unveiling the fungal dynamics during the fermentation of traditional Chinese strong-flavor Daqu

Daqu, a starter culture rich in microorganisms like bacteria and fungi, is central to vinification and liquor brewing, yet fungal contributions are often understudied. In this study, we used Illumina MiSeq sequencing to investigate the succession of fungal community during Chinese strong-flavor liquor fermentation. The results showed that the alpha and beta diversity of fungal community were significantly different during Daqu fermentation. The dominant phyla and genera are Ascomycota and Saccharomycopsis, respectively. Co-occurrence network analysis identified 10 keystone species during Daqu fermentation, displaying that the positive correlations (99.64%) dominated the fungal network. The redundancy analysis showed that moisture has the most significant influence on the Daqu fungal community. Concurrently, a robust association was observed between 10 keystone fungal genera and environmental parameters such as acidity and moisture. These findings not only elucidated the intricate dynamics of the fungal community succession and the interplays among fungi but also pinpointed the primary drivers of the fungal community and its keystone species during the Daqu fermentation process. Ultimately, this research presented novel perspectives for enhancing the quality and precision of liquor production by shedding light on the central role of keystone species in maintaining community stability and their adaptive responses to environmental stimuli.

The dynamics of mental health policy in Iran over the last century

BackgroundMental disorders represent a significant global health concern, accounting for a substantial proportion of disabilities worldwide. Given its significance, it has consistently been a priority for health policy makers. The aim was to provide a comprehensive assessment of mental disorder-related policy events and related interventions in Iran.MethodsA content analysis of the literature and published and unpublished official documents and local media as well as a comprehensive network analysis of the text taken from the main databases of laws and regulations and the official websites of ministries and institutions related to mental health in Iran from 1907 to 2024 were carried out. A co-occurrence network analysis and degree centrality measures were performed on the collected corpus.ResultsA total of 196 documents were identified. Following the removal of duplicate documents and content irrelevant to the topic of mental disorders, 131 documents were extracted. A substantial number of documents pertained to the years 1930–1978, which were concerned primarily with the admission and dispatch of patients to the mental health clinic and psychiatric hospitals and the financial aspects of the care and treatment of patients with mental disorders by the trustee organizations. Following the 1979 revolution, the focus shifted to the expansion of social and insurance support for these patients and their families.ConclusionsThe advancements related to severe mental disorders in Iran highlight the critical importance of public interventions in this field. Nevertheless, over the past century, no discernible pattern or coherence has been identified in this area between responsible agencies and ministries. Future policies related to mental disorders should be based on the principles of increasing community-based care, sustainable financing and economic and social support for mental disorders.

Diversity and Functional Insights into Endophytic Fungi in Halophytes from West Ordos Desert Ecosystems.

Arid desert regions are among the harshest ecological environments on Earth. Halophytes, with their unique physiological characteristics and adaptability, have become the dominant vegetation in these areas. Currently, research on halophytes in this region is relatively limited, particularly concerning studies related to their root endophytic fungi, which have been rarely reported on. Therefore, investigating the diversity and composition of endophytic fungi in halophytes is crucial for maintaining ecological balance in such an arid environment. This study focuses on eight representative angiosperm halophytes from the West Ordos Desert in China (including Nitraria tangutorum, Salsola passerina, Suaeda glauca, Reaumuria trigyna, Reaumuria kaschgarica, Limonium aureum, Apocynum venetum, and Tripolium vulgare), utilizing Illumina MiSeq high-throughput sequencing technology combined with soil physicochemical factor data to analyze the diversity, composition, and ecological functions of their root-associated fungal communities. Ascomycota dominated the fungal composition in most halophytes, particularly among the recretohalophytes, where it accounted for an average of 88.45%, while Basidiomycota was predominant in Suaeda glauca. A Circos analysis of the top 10 most abundant genera revealed Fusarium, Dipodascus, Curvularia, Penicillium, and other dominant genera. Co-occurrence network analysis showed significant differences in fungal networks across halophyte types, with the most complex network observed in excreting halophytes, characterized by the highest number of nodes and connections, indicating tighter fungal symbiotic relationships. In contrast, fungal networks in pseudohalophytes were relatively simple, reflecting lower community cohesiveness. Redundancy analysis (RDA) and Mantel tests demonstrated that soil factors such as organic matter, available sulfur, and urease significantly influenced fungal diversity, richness, and evenness, suggesting that soil physicochemical properties play a critical role in regulating fungal-plant symbiosis. Functional predictions indicated that endophytic fungi play important roles in metabolic pathways such as nucleotide biosynthesis, carbohydrate degradation, and lipid metabolism, which may enhance plant survival in saline-alkaline and arid environments. Furthermore, the high abundance of plant pathogens and saprotrophs in some fungal communities suggests their potential roles in plant defense and organic matter decomposition. The results of this study provide a reference for advancing the development and utilization of halophyte endophytic fungal resources, with applications in desert ecosystem restoration and halophyte cultivation.

Human Milk Archaea Associated with Neonatal Gut Colonization and Its Co-Occurrence with Bacteria.

Archaea have been identified as early colonizers of the human intestine, appearing from the first days of life. It is hypothesized that the origin of many of these archaea is through vertical transmission during breastfeeding. In this study, we aimed to characterize the archaeal composition in samples of mother-neonate pairs to observe the potential vertical transmission. We performed a cross-sectional study characterizing the archaeal diversity of 40 human colostrum-neonatal stool samples by next-generation sequencing of V5-V6 16S rDNA libraries. Intra- and inter-sample analyses were carried out to describe the Archaeal diversity in each sample type. Human colostrum and neonatal stools presented similar core microbiota, mainly composed of the methanogens Methanoculleus and Methanosarcina. Beta diversity and metabolic prediction results suggest homogeneity between sample types. Further, the co-occurrence network analysis showed associations between Archaea and Bacteria, which might be relevant for these organisms' presence in the human milk and neonatal stool ecosystems. According to relative abundance proportions, beta diversity, and co-occurrence analyses, the similarities found imply that there is vertical transmission of archaea through breastfeeding. Nonetheless, differential abundances between the sample types suggest other relevant sources for colonizing archaea to the neonatal gut.

A fragile relationship: Turkey and the European Union moving beyond membership with external differentiated integration

Turkey’s relations with the European Union depend on extensive legal instruments, drivers of interdependence and voluntary compliance to the EU rules. With an Association Agreement dating back to 1963 and accession negotiations opened in 2005, there is a high degree of asymmetric interdependence between Turkey and the EU. This article examines Turkish-EU relations from the angle of external differentiated integration (EDI). Accordingly, this article assesses the feasibility of the current state of Turkey’s fragile relations with the EU as a functional model of external differentiated integration. Turkish EDI provides an innovative framework for keeping Turkey anchored to the European order, for which neither full membership nor a complete break up seems plausible. To assess shades of non-membership for Turkey, the article relies on an extensive keyword-based assessment of EU-Lex documents, trade statistics and a co-occurrence network analysis for the EU’s 2012 and 2022 Progress Reports on Turkey. The findings shed light on the complexities of the EU’s EDI with non-members.

Differential insights into the distribution characteristics of bacterial communities and their response to typical pollutants in the sediment and soil of large drinking water reservoir.

In this study, a large drinking water reservoir (Fengshuba Reservoir) was chosen as a representative case, and the bacterial communities in the sediments and soils of Water-level fluctuating zone (WLFZ) as well as their responses to heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) were systematically investigated. The results indicated that the abundance and diversity of the bacterial community obviously changed with seasonal hydrological variations in sediments, and the absolute abundance and composition of bacteria community differed significantly between the sediment phase and soil phase. Bacteria with the ability to degrade pollutants rapidly proliferate and gain ascendancy in the soil phase, with Burkholderia-Caballeronia-Paraburkholderia (B-C-P) and Bradyrhizobium forming the core of the largest community. Furthermore, Co-occurrence network analysis indicated that a more stable bacterial community composition in the sediment phase. The community assembly pattern of bacteria in sediments exhibit a higher degree of stochasticity than that observed in soils of the WLFZ. Furthermore, the Spearman correlations found that the interaction between physicochemical factors, HMs, and PAHs with bacteria community was stronger in the soils of WLFZ. In total, the structural equation models indicated that PAHs were the main driver in altering the deterministic process of bacterial community in the sediment, while HMs and physicochemical factors had a greater effect on the bacteria community in the WLFZ. This study systematically revealed the differential characteristics of bacterial community and their response to typical pollutants between the sediments and soils of large drinking water reservoir.

Depth weakens effects of long-term fertilization on dissolved organic matter chemodiversity in paddy soils.

Dissolved organic matter (DOM) is pivotal for soil biogeochemical processes, soil fertility, and ecosystem stability. While numerous studies have investigated the impact of fertilization practices on DOM content along soil profiles, variations in DOM chemodiversity and the underlying factors across soil profiles under long-term fertilization regimes remain unclear. Using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and high-throughput sequencing, this study investigated DOM composition characteristics and microbial community compositions across different soil layers (0-20, 20-40, 40-60, and 60-100cm) in paddy soil under different long-term fertilization treatments, including Control (no fertilizer), NPK (mineral NPK fertilizer), NPKHS (NPK fertilizer with half straw return), and NPKS (NPK fertilizer with full straw return). The results revealed that fertilization regimes significantly increased soil TC, TN, and NO3- contents, as well as DOM chemodiversity in the top soil layer, particularly under NPKHS and NPKS treatments. Both the DOM chemodiversity and bacterial diversity decreased with soil depth. However, below 0-20cm, DOM chemodiversity was not significantly affected by fertilization treatments. Co-occurrence network analysis further showed that microbial decomposition primarily drove the changes in DOM composition across soil profile. Overall, our study suggests that long-term NPK fertilization and straw return significantly increased DOM chemodiversity only in the top layer of paddy soil by regulating soil TC, TN, and NO3- contents. Our study provides useful information regarding the vertical molecular composition of DOM and enhances the understanding of DOM chemodiversity along soil profile in rice paddy ecosystems.

Shaping rhizocompartments and phyllosphere microbiomes and antibiotic resistance genes: The influence of different fertilizer regimes and biochar application.

Understanding the impact of different soil amendments on microbial communities and antibiotic resistance genes (ARGs) dissemination is crucial for optimizing agricultural practices and mitigating environmental risks. This study investigated the effects of different fertilizer regimes and biochar on plant-associated bacterial communities and ARGs dissemination. The biochar's structural and chemical characteristics were characterized using scanning electron microscopy (SEM) and Fourier-transform infrared (FTIR) spectroscopy, revealing a porous architecture with diverse functional groups. The presence of ARGs varied significantly across groups, with manure-treated samples exhibiting the greatest diversity and abundance, raising concerns about ARGs dissemination. Soil enzyme activities responded differently to treatments; manure significantly enhanced catalase, acid phosphatase, and urease activities, whereas saccharase was most responsive to chemical fertilizer. These differences are possibly responsible for the distinct microbiome structure associated with the plant's root system. The analysis of bacterial diversity and richness across rhizocompartments and the phyllosphere highlighted that manure-treated rhizospheres and phyllospheres displayed the highest species richness and diversity. Notably, Proteobacteria dominated across most treatments, with distinct shifts in bacterial phyla and genera influenced by manure and biochar applications. The LEfSe analysis identified key indicator genera specific to each group, indicating that both fertilizer type and biochar application significantly shape microbial community composition. Co-occurrence network analysis further demonstrated that manure and biochar treatments created unique microbial networks in the rhizosphere, rhizoplane, phyllosphere, and endosphere, highlighting the role of these amendments in modulating microbial interactions in plant-associated environments. These findings suggest that manure, while enhancing microbial diversity and soil enzyme activities, also increases ARGs, whereas biochar may not contribute to the spread of ARGs and fosters distinct microbial communities, offering valuable insights for sustainable agricultural practices.

Nitrogen-driven shifts in molecular composition of soil dissolved organic matter linked to rare bacterial sub-communities.

The interaction between soil dissolved organic matter (DOM) and bacterial communities is critical for understanding key processes in the global carbon cycle. However, the molecular-level associations between these components remain poorly understood. To address this gap, high-resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was combined with high-throughput sequencing to examine how DOM composition and bacterial sub-community diversity respond to different levels of nitrogen (N) addition (0, 40, and 80kgNha-1yr-1) and to explore the relationships between them. The results demonstrate a significant decline in carbohydrate molecules within DOM under low N conditions. Conversely, the β-diversity and double bond equivalents of DOM molecules increased, indicating greater heterogeneity and stability in DOM composition under this treatment. Rare bacterial sub-communities, as opposed to abundant taxa, were more sensitive to N addition, exhibiting narrower ecological niches and weaker phylogenetic signals. β-Diversity decomposition analysis indicated that compositional differences in abundant taxa were primarily driven by richness differences, whereas those in rare taxa were predominantly influenced by species replacement. Co-occurrence network analysis revealed that DOM molecules were more frequently linked with rare taxa than with abundant taxa. Furthermore, a strong positive relationship was observed between the β-diversity of rare taxa and that of DOM molecules along the N gradient. These findings underscore that rare bacterial sub-communities are the primary drivers of changes in DOM molecular composition under N enrichment, emphasizing their potential role in shaping chemical diversity.

Oral microbiome and nitric oxide biomarkers in older people with mild cognitive impairment and APOE4 genotype.

Apolipoprotein E4 (APOE4) genotype and nitric oxide (NO) deficiency are risk factors for age-associated cognitive decline. The oral microbiome plays a critical role in maintaining NO bioavailability during aging. The aim of this study was to assess interactions between the oral microbiome, NO biomarkers, and cognitive function in 60 participants with mild cognitive impairment (MCI) and 60 healthy controls using weighted gene co-occurrence network analysis and to compare the oral microbiomes between APOE4 carriers and noncarriers in a subgroup of 35 MCI participants. Within the MCI group, a high relative abundance of Neisseria was associated with better indices of cognition relating to executive function (Switching Stroop, rs = 0.33, P = 0.03) and visual attention (Trail Making, rs = -0.30, P = 0.05), and in the healthy group, Neisseria correlated with working memory (Digit Span, rs = 0.26, P = 0.04). High abundances of Haemophilus (rs = 0.38, P = 0.01) and Haemophilus parainfluenzae (rs = 0.32, P = 0.03), that co-occurred with Neisseria correlated with better scores on executive function (Switching Stroop) in the MCI group. There were no differences in oral nitrate (P = 0.48) or nitrite concentrations (P = 0.84) between the MCI and healthy groups. Linear discriminant analysis Effect Size identified Porphyromonas as a predictor for MCI and Prevotella intermedia as a predictor of APOE4-carrier status. The principal findings of this study were that a greater prevalence of oral P. intermedia is linked to elevated genetic risk for dementia (APOE4 genotype) in individuals with MCI prior to dementia diagnosis and that interventions that promote the oral Neisseria-Haemophilus and suppress Prevotella-dominated modules have potential for delaying cognitive decline.

Soil polluted system shapes endophytic fungi communities associated with Arundo donax: a field experiment.

With the expansion of the mining industry, environmental pollution from microelements (MP) and red mud (RM) has become a pressing issue. While bioremediation offers a cost-effective and sustainable solution, plant growth in these polluted environments remains difficult. Arundo donax is one of the few plants capable of surviving in RM-affected soils. To identify endophytic fungi that support A. donax in different contaminated environments and to inform future research combining mycorrhizal techniques with hyperaccumulator plants, we conducted a field experiment. The study compared endophytic fungal communities in A. donax grown in uncontaminated, MP soils contaminated with cadmium (Cd), arsenic (As), and lead (Pb), and RM-contaminated soils. Our findings showed that soil nutrient profiles differed by contamination type, with Cd concentrations in MP soils exceeding national pollution standards (GB 15168-2018) and RM soils characterized by high aluminum (Al), iron (Fe), and alkalinity. There were significant differences in the endophytic fungal community structures across the three soil types (p < 0.001). Co-occurrence network analysis revealed that endophytic fungi in MP soils exhibited competitive niche dynamics, whereas fungi in RM soils tended to share niches. Notably, Pleosporales sp., which accounted for 18% of the relative abundance in RM soils, was identified as a dominant and beneficial endophyte, making it a promising candidate for future bioremediation efforts. This study provides valuable insights into the role of endophytic fungi in phytoremediation and highlights their potential as resources for improving plant-microbe interactions in contaminated environments.