Co-occurrence Network Research Articles

Thiophanate-methyl and its major metabolite carbendazim weaken rhizobacteria-mediated defense responses in cucumbers against Fusarium wilt

AbstractThe effect of fungicides on the plant-rhizosphere microbiome is a subject of ongoing debate, but whether any alteration in the rhizosphere microbiome could affect plant health is an issue that has not been thoroughly investigated. To address this deficiency, we analyzed the rhizosphere microbiome of wilt disease—resistant and disease-susceptible cucumber cultivars to determine whether (and which) plant-associated microorganisms have a role in disease resistance. We further assessed whether the fungicides thiophanate-methyl and carbendazim affect the rhizosphere microbiome, which may contribute to the plant’s immune response. Based on results acquired with both radicle-inoculation and soil-inoculation methods, cultivars Longyuanxiuchun (LYXC) and Shuyan2 (SY2) were identified as being disease resistant, whereas Zhongnong6 (ZN6) and Zhongnong38 (ZN38) were susceptible. The microbiome structure differed substantially between the resistant and susceptible plants, with LYXC and SY2 each having a significantly greater Shannon index than Zhongnong38. These results revealed that the disease-resistant cucumber cultivars recruited more beneficial bacteria, i.e., Bacillus, in their rhizosphere soil; as such, Bacillus was identified as a keystone genus in the microbial co-occurrence network. Thus, the presence of Bacillus may help cucumbers defend against fungal pathogens within the rhizosphere. Bacillus subtilis strain LD15, which was isolated from LYXC rhizosphere soil, could suppress pathogen growth, in vitro, and reduce disease severity in pot assays. Moreover, evidence also confirmed the accumulation of LD1 in the rhizosphere soil of resistant cucumber cultivars. For LYXC, application of thiophanate-methyl or carbendazim altered the microbiome structure, decreased bacterial diversity, and reduced the abundance of Bacillus species. Finally, pot assays verified that fungicide application decreased the proportion of LD15 in rhizosphere soil. From a microbial perspective, thiophanate-methyl and carbendazim may weaken the rhizobacteria-mediated defense response of cucumbers against cucumber Fusarium wilt disease. Our findings reveal a role for the rhizosphere microbiome in protecting plants from pathogens and constitute a reference for assessing the ecotoxicological risk of pesticides to non-target soil microorganisms.

Revealing the characteristics of myxobacterial communities in rhizosphere and non-rhizosphere soils of halophytic plants following wetland degradation using high-throughput sequencing

Myxobacteria represent a distinct group in soil microbial communities, with their predatory capabilities playing a vital role in regulating and stabilizing these communities. However, the characteristics of myxobacterial communities in the soils of Karelinia caspia (KC), a halophytic plant growing in degraded wetlands, remain unclear. In this study, we investigated myxobacterial communities in rhizosphere and non-rhizosphere soils from nine KC’ sampling sites in saline-alkaline land formed after wetland degradation using high-throughput sequencing. A total of 486 myxobacterial ASVs were identified from both rhizosphere and non-rhizosphere soil samples, comprising 2.68% of the total bacterial community. The dominant genera at the genus level were Unclassified_g_bacteriap25 and Haliangium. FAPROTAX functional predictions indicated that myxobacteria in rhizosphere soils performed various ecological functions, such as predation, organic matter decomposition, and cellulose degradation, while in non-rhizosphere soils, they primarily displayed predatory functions. The high proportion of unclassified functions suggests that many aspects of myxobacteria in soil remain unexplored. Correlation analysis showed that electrical conductivity, soil moisture, and total nitrogen significantly affected myxobacterial diversity and abundance. Co-occurrence network analysis revealed multiple associations between myxobacteria and other bacterial groups, highlighting their crucial role in maintaining the dynamic equilibrium of soil bacterial communities. These findings deepen our understanding of the relationship between microbial community dynamics and environmental factors, laying a strong foundation for future research in soil microbial ecology and conservation strategies.

Diversity and interactions of rhizobacteria determine multinutrient traits in tomato host plants under nitrogen and water disturbances

Abstract Coevolution within the plant holobiont extends the capacity of host plants for nutrient acquisition and stress resistance. However, the role of the rhizospheric microbiota in maintaining multinutrient utilization (i.e., multinutrient traits) in the host remains to be elucidated. Multinutrient cycling index (MNC), analogous to the widely used multifunctionality index, provides a straightforward and interpretable measure of the multinutrient traits in host plants. Using tomato as a model plant, we characterized MNC (based on multiple aboveground nutrient contents) in host plants under different nitrogen and water supply regimes and explored the associations between rhizospheric bacterial community assemblages and host-plant multinutrient profiles. Rhizosphere bacterial community diversity, quantitative abundance, predicted function, and key topological features of the co-occurrence network were more sensitive to water supply than to nitrogen supply. A core bacteriome comprising 61 genera, such as Candidatus Koribacter and Streptomyces, persisted across different habitats and served as a key predictor of host-plant nutrient uptake. The MNC index increased with greater diversity and higher core taxon abundance in the rhizobacterial community, while decreasing with higher average degree and graph density of rhizobacterial co-occurrence network. Multinutrient absorption by host plants was primarily regulated by community diversity and rhizobacterial network complexity under the interaction of nitrogen and water. The high biodiversity and complex species interactions of the rhizospheric bacteriome play crucial roles in host-plant performance. This study supports the development of rhizosphere microbiome engineering, facilitating effective manipulation of the microbiome for enhanced plant benefits, which supports sustainable agricultural practices and plant health.

Reducing serious injuries and fatalities in industrial construction-application of machine learning to analyze emotional intelligence and psychosocial factors

Human and organizational factors are recognized as central in incidents; however, there has been little interconnection between individual and organizational psychological variables, such as interpersonal skills. Therefore, this study aims to glean theoretical and empirical insights to reduce severe injuries and fatalities and enhance safety performance. This study classified incidents of an industrial construction organization in Canada based on two attributes of interpersonal skills – emotional intelligence (EI) and psychosocial (PS) factors. A qualitative analysis using NVivo software was employed to classify 1000 incidents from 2018 to 2020 into EI factors. Since PS factors were not observed in the dataset, the analysis was extended to identify PS factors using machine learning techniques as a quantitative approach to analyze 45,603 incidents from 2014 to 2023. The classification was performed using keyword analysis of the incident descriptions. Further, co-occurrence networks were used to investigate patterns and validate the study results. The findings indicate that lack of self-awareness (domain of EI) (56.8%) and improper communication (domain of PS factor) (32.4%) were the most influential causes of incidents substantiated by the co-occurrence networks results. The study’s findings provide insights for decision-makers about the strategies needed to enhance safety performance in the industrial construction industry.

Antibiotics and Pesticides Enhancing the Transfer of Resistomes among Soil-Bayberry-Fruit Fly Food Chain in the Orchard Ecosystem.

While substantial amounts of antibiotics and pesticides are applied to maintain orchard yields, their influence on the dissemination and risk of antibiotic resisitome in the orchard food chain remains poorly understood. In this study, we characterized the bacterial and fungal communities and differentiated both antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the soil, Chinese bayberry (matured and fallen), and fruit fly gut, collected from five geographic locations. Our results showed that fruit fly guts and soils exhibit a higher abundance of ARGs and VFGs compared with bayberry fruits. We identified 112 shared ARGs and 75 shared VFGs, with aminoglycoside and adherence factor genes being among the most abundant. The co-occurrence network revealed some shared microbes, such as Bacillus and Candida, as potential hosts of ARGs, highlighting the vector risks for both above- and below-ground parts of the orchard food chain. Notably, the elevated levels of antibiotics and pesticide residues in orchard soils increase ARGs, mobile genetic elements (MGEs), and VFGs in the soil-bayberry-fruit fly food chain. Our study highlighted that agricultural management, including the overuse of antibiotics and pesticides, could be the key factor in accumulating resistomes in the orchard food chain.

Community composition and co-occurrence of free-living and particle-attached bacteria in the source region of the Ganges and Brahmaputra Rivers.

Bacteria have two trophic lifestyles in aquatic ecosystems, i.e., free-living (FL) and particle-attached (PA), with different but essential ecological roles. However, relevant knowledge is still dearth in the upstream source region of the Himalayan Rivers. Thus, we emphasized a comparative study on community composition, co-occurrence, and geographic distribution of the FL and PA bacteria and the effect of environmental factors in the source region of the Ganges and Brahmaputra Rivers. PA bacteria relative to FL harbored a significantly higher local diversity, richness, and evenness. A significantly higher abundance of Betaproteobacteria, Verrucomicrobiota, and Planctomycetota in PA trophic lifestyle and Gammaproteobacteria and Actinomycetota in FL tropic lifestyle and indicator OTUs belonging to related taxa were observed. The spatial variation of the FL and PA bacterial communities was most significantly impacted by dispersal limitation as a discrete factor. Among the environmental parameters, the total nitrogen (TN) was found to be a significant (P < 0.001) driver of the variation in PA communities. Meanwhile, particulate organic carbon (POC) and TN considerably explained the variation of FL communities. A significant correlation (P < 0.001) of TN with dominant bacterial taxa (Pseudomonadota, Actinomycetota, and Verrucomicrobiota) and FL and PA indicator OTUs associated with these taxa further confirmed nitrogen as the limiting nutrient in the source region of the Ganges and Brahmaputra Rivers. The co-occurrence network topological characteristics showed that the PA network was more stable than the FL network, which was more complicated and unstable. Thus, it can be speculated that FL communities relative to PA are more vulnerable to shifting upon disturbances.

Glacier Retreat Induces Contrasting Shifts in Bacterial Biodiversity Patterns in Glacial Lake Water and Sediment

Glacial lake ecosystems are experiencing rapid changes due to accelerated glacier retreat. As glaciers recede, their influence on downstream habitats diminishes, potentially affecting the biodiversity of glacial lake microbial communities. However, there remains a knowledge gap regarding how bacterial biodiversity patterns in glacial lakes are altered by diminishing glacial influence. Here, we investigated shifts in bacterial communities in paired water and sediment samples collected from seven glacial lakes on the Tibetan Plateau, using a space-for-time substitution approach to understand the consequences of glacier retreat. Our findings reveal that bacterial diversity in lake water increases significantly with a higher glacier index (GI), whereas sediment bacterial diversity exhibits a negative correlation with GI. Both the water and sediment bacterial communities display significant structural shifts along the GI gradient. Notably, reduced glacial influence decreases the complexity of bacterial co-occurrence networks in lake water but enhances the network complexity in sediment. This divergence in diversity and co-occurrence patterns highlights that water and sediment bacterial communities respond differently to changes in glacial influence in these lake ecosystems. This study provides insights into how diminishing glacial influence impacts the bacterial biodiversity in glacial lake water and sediments, revealing contrasting patterns between the two habitats. These findings emphasize the need for comprehensive monitoring to understand the implications of glacier retreat on these fragile ecosystems.

Eucalyptus and Native Broadleaf Mixed Cultures Boost Soil Multifunctionality by Regulating Soil Fertility and Fungal Community Dynamics.

The growing recognition of mixed Eucalyptus and native broadleaf plantations as a means of offsetting the detrimental impacts of pure Eucalyptus plantations on soil fertility and the wider ecological environment is accompanied by a clear and undeniable positive impact on forest ecosystem functions. Nevertheless, the question of how mixed Eucalyptus and native broadleaf plantations enhance soil multifunctionality (SMF) and the mechanisms driving soil fungal communities remains unanswered. In this study, three types of mixed Eucalyptus and native broadleaf plantations were selected and compared with neighboring evergreen broadleaf forests and pure Eucalyptus plantations. SMF was quantified using 20 parameters related to soil nutrient cycling. Partial least squares path modeling (PLS-PM) was employed to identify the key drivers regulating SMF. The findings of this study indicate that mixed Eucalyptus and native broadleaf plantations significantly enhance SMF. Mixed Eucalyptus and native broadleaf plantations led to improvements in soil properties (7.60-52.22%), enzyme activities (10.13-275.51%), and fungal community diversity (1.54-29.5%) to varying degrees compared with pure Eucalyptus plantations. Additionally, the mixed plantations exhibit enhanced connectivity and complexity in fungal co-occurrence networks. The PLS-PM results reveal that soil properties, fungal diversity, and co-occurrence network complexity directly and positively drive changes in SMF. Furthermore, soil properties exert an indirect influence on SMF through their impact on fungal diversity, species composition, and network complexity. The findings of this study highlight the significant role of mixed Eucalyptus and native broadleaf plantations in enhancing SMF through improved soil properties, fungal diversity, and co-occurrence network complexity. This indicates that incorporating native broadleaf species into Eucalyptus plantations can effectively mitigate the negative impacts of monoculture plantations on soil health and ecosystem functionality. In conclusion, our study contributes to the understanding of how mixed plantations influence SMF, offering new insights into the optimization of forest management and ecological restoration strategies in artificial forest ecosystems.

The contribution of seasonal variations and Zostera marina presence to the bacterial community assembly of seagrass bed sediments

BackgroundMicroorganisms play pivotal roles in seagrass ecosystems by facilitating material and elemental cycling as well as energy flux. However, our understanding of how seasonal factors and seagrass presence influence the assembly of bacterial communities in seagrass bed sediments is limited. Employing high-throughput sequencing techniques, this study investigates and characterizes bacterial communities in the rhizosphere of eelgrass (Zostera marina) and the bulk sediments across different seasons. The research elucidates information on the significance of seasonal variations and seagrass presence in impacting the microbial communities associated with Zostera marina.ResultsThe results indicate that seasonal variations have a more significant impact on the bacterial community in seagrass bed sediments than the presence of seagrass. We observed that the assembly of bacterial communities in bulk sediments primarily occurs through stochastic processes. However, the presence of seagrass leading to a transition from stochastic to deterministic processes in bacterial community assembly. This shift further impacts the complexity and stability of the bacterial co-occurrence network. Through LEfSe analysis, different candidate biomarkers were identified in the bacterial communities of rhizosphere sediments in different seasons, indicating that seagrass may possess adaptive capabilities to the environment during different stages of growth and development.ConclusionsSeasonal variations play a significant role in shaping these communities, while seagrass presence influences the assembly processes and stability of the bacterial community. These insights will provide valuable information for the ecological conservation of seagrass beds.

Global Criminology and Criminal Justice Research: A Bibliometric Analysis of Emerging Themes and Gaps

This study examines how organizational factors enhance operational efficiency in criminology and criminal justice through a systematic review of 99 research papers from 2015 to 2024. The primary aim is to identify critical success factors (CSFs) that influence operational effectiveness, distinguishing between internal factors such as personnel development and leadership, and external factors like community expectations and sustainability. Utilizing a systematic literature review and bibliometric analysis of 408 articles, the research maps co-occurrence networks to reveal thematic clusters and gaps in the literature. Findings indicate that strategic organizational practices, including effective leadership and collaboration, are vital for improving efficiency, fostering innovation, and responding to community needs. This research provides valuable insights for practitioners and scholars alike, underscoring the importance of these factors in optimizing operations and serving as a foundation for future studies on their impact within the field of criminology and criminal justice.

Congruence between co-occurrence and trait-based networks is scale-dependent: a case study with flea parasites of small mammalian hosts.

We applied a novel framework based on network theory and a concept of modularity that estimates congruence between trait-based ( = functional) co-occurrence networks, thus allowing the inference of co-occurrence patterns and the determination of the predominant mechanism of community assembly. The aim was to investigate the relationships between species co-occurrence and trait similarity in flea communities at various scales (compound communities: across regions within a biogeographic realm or across sampling sites within a geographic region; component communities: across sampling sites within a geographic region; and infracommunities: within a sampling site). We found that compound communities within biogeographic realms were assembled via environmental or host-associated filtering. In contrast, functional and spatial/host-associated co-occurrence networks, at the scale of regional compound communities, mostly indicated either stochastic processes or the lack of dominance of any deterministic process. Analyses of congruence between functional and either spatial (for component communities) or host-associated (for infracommunities) co-occurrence networks demonstrated that assembly rules in these communities varied among host species. In component communities, stochastic processes prevailed, whereas environmental filtering was indicated in 4 and limiting similarity/competition in 9 of 31 communities. Limiting similarity/competition processes dominated in infracommunities, followed by stochastic mechanisms. We conclude that assembly processes in parasite communities are scale-dependent, with different mechanisms acting at different scales.

Integrated large-scale metagenome assembly and multi-kingdom network analyses identify sex differences in the human nasal microbiome.

Respiratory diseases impose an immense health burden worldwide. Epidemiological studies have revealed extensive disparities in the incidence and severity of respiratory tract infections between men and women. It has been hypothesized that there might also be a nasal microbiome axis contributing to the observed sex disparities. Here, we study the nasal microbiome of healthy young adults in the largest cohort to date with 1593 individuals, using shotgun metagenomic sequencing. We compile the most comprehensive reference catalog for the nasal bacterial community containing 4197 metagenome-assembled genomes and integrate the mycobiome, to provide a valuable resource and a more holistic perspective for the understudied human nasal microbiome. We systematically evaluate sex differences and reveal extensive sex-specific features in both taxonomic and functional levels in the nasal microbiome. Through network analyses, we capture markedly higher ecological stability and antagonistic potentials in the female nasal microbiome compared to the male's. The analysis of the keystone bacteria reveals that the sex-dependent evolutionary characteristics might have contributed to these differences. In summary, we construct the most comprehensive catalog of metagenome-assembled-genomes for the nasal bacterial community to provide a valuable resource for the understudied human nasal microbiome. On top of that, comparative analysis in relative abundance and microbial co-occurrence networks identify extensive sex differences in the respiratory tract community, which may help to further our understanding of the observed sex disparities in the respiratory diseases.

Successive monoculture of Eucalyptus spp. alters the structure and network connectivity, rather than the assembly pattern of rhizosphere and bulk soil bacteria

Eucalyptus as a fast-growing timber tree plays a crucial role in maintaining wood supplication and ecosystem balance worldwide. Nonetheless, the management practices of Eucalyptus plantation in southern China have resulted in productivity decline and soil degradation due to high-intensity successive cultivation. Soil bacteria is a sensitive indicator of soil quality, how does the successive planting of Eucalyptus regulate the soil bacterial community structure for instance the abundance of oligotrophic bacteria, network complexity, and soil bacteria assembly remain ambiguity. To explicate the underlying influencing mechanisms of successive cultivation of Eucalyptus plantations on soil bacterial community structure. Four harvests of Eucalyptus plantations that underwent 0, 1, 2, and 3 times of harvesting were conducted to examine variations in the bacterial community between rhizosphere and bulk soils after successive planting of Eucalyptus. An adjacent evergreen broadleaf forest was employed as control. The present study revealed that successive planting of Eucalyptus increased and reduced the relative abundance of Chloroflexi (oligotrophic bacteria) and Proteobacteria (copiotrophic bacteria), respectively. Continuous planting of Eucalyptus did not modify the assembly pattern of soil bacterial communities, which was governed by stochastic processes. Successive planting of Eucalyptus decreased co-occurrence network complexity, and elevated the proportion of rare microorganisms in the keystone bacterial taxa. Soil particle size composition (clay, silt, sand) indirectly influenced the structure of soil bacterial communities by directly affecting pH, carbon, nutrients, and their stoichiometric ratios. Improving soil physical structure, increasing the input of soil carbon, nitrogen, and other nutrient resources, and maintaining a balanced resource allocation may be effective strategies for ensuring enhanced productivity and sustainable utilization of soil in successive Eucalyptus plantations.

Artificial intelligence in industrial operations management: a bibliometric analysis

Considering the exponential growth of research on Artificial Intelligence (AI) in industrial operations management, this study aims to map the scientific landscape through a bibliometric analysis. The research employed data from the Web of Science, focusing on key terms such as "AI," "industrial operations," and "management." Using VOSviewer, co-occurrence networks and citation analyses were generated to identify research trends and gaps. The results reveal significant contributions from countries like the United States and China, emphasizing AI's role in enhancing efficiency and innovation in industries. The findings provide a foundation for future research and practical implementation strategies in industrial operations.

Revisiting sustainable tourism research: bibliometric insights and future research agenda

ABSTRACT This bibliometric review synthesizes sustainable tourism research over the past three decades, focusing on its alignment with the Sustainable Development Goals (SDGs). Based on 1,383 journal articles from the Web of Science database, the RStudio Bibliometrix package analysed bibliometric performance, thematic maps, and co-occurrence networks. The findings highlight the role of sustainable tourism in advancing different SDGs. Findings also indicate three broader thematic areas for future research, including regenerative tourism ecosystems, responsible tourism behaviours, and right-sizing tourism. Through this review, we propose future research directions to enhance knowledge on sustainable tourism and its contribution to the SDGs, providing a strategic roadmap for researchers and policymakers.

Network Analysis to Visualize Qualitative Results: Example From a Qualitative Content Analysis of The National Child Abuse Hotline.

Data visualization, such as figures created through network analysis, may be one way to present more complete information from qualitative analysis. Segments of qualitatively coded data can be treated as objects in network analysis, thus creating visual representations of the code frequency (i.e., nodes) and the co-occurrence (i.e., edges). By sharing an example of network analysis applied to qualitative data, and then comparing our process with other applications, our goal is to help other researchers reflect on how this approach may support their interpretation and visualization of qualitative data. A total of 265 de-identified transcripts between help-seekers and National Child Abuse Hotline crisis counselors were included in the network analysis. Post-conversation surveys, including help-seekers' perceptions of the conversations, were also included in the analysis. Qualitative content analysis was conducted, which was quantified as the presence or absence of each code within a transcript. Then, we divided the dataset based on help-seekers' perceptions. Individuals who responded that they "Yes/Maybe" felt more hopeful after the conversation were in the "hopeful" dataset, while those who answered "No" were in the "unhopeful" dataset. This information was imported to UCINET to create co-occurrence matrices. Gephi was used to visualize the network. Overall, code co-occurrence networks in hopeful conversations were denser. Furthermore, the average degree was higher in these hopeful conversations, suggesting more codes were consistently present. Codes in hopeful conversations included information, counselor support, and problem-solving. Conversely, non-hopeful conversations focused on information. Overall, network analysis revealed patterns that were not evident through traditional qualitative analysis.

Distribution pattern and assembly mechanism of microbial community to cause biological aging of asphalt materials in forest road domain

The biological aging of asphalt due to microorganism decomposition causes such distresses as loosening and spalling on asphalt pavement in forest region, which deteriorates the durability of asphalt pavement. To study the distribution regularities of microbial communities in forest road domain and reveal the assembly mechanisms of microbial communities, 16S rRNA full-length sequencing was utilized to analyze the collected samples from three forest areas. Results show that when compared with those in roadside slope, the evenness and diversity of microbial community in asphalt pavement are decreased, but the richness of microbial community is significantly increased. Mycolicibacterium is screened for a biomarker in asphalt pavement. Additionally, the increase in the relative abundances of Bacteroidetes and Proteobacteria, which are the dominant bacteria in asphalt pavement, reshapes the co-occurrence network relationship among the microorganisms. The total carbon (TC) plays an important role in regulating the composition of microbial community. The microbial community in roadside slope is dominated by stochastic processes, while the strong interspecies interactions and selection effect of asphalt on microbial community strengthen the role of deterministic processes in remodeling the microbial community structure in asphalt pavement. This study is of great significance for understanding the biological aging mechanism of asphalt pavement.

Biogeographic shifts in the microbial co-occurrence network features of three domains across complex environmental gradients in subtropical coastal waters

BackgroundBacteria, Archaea, and Microeukaryotes comprise taxonomic domains that interact in mediating biogeochemical cycles in coastal waters. Many studies have revealed contrasting biogeographic patterns of community structure and assembly mechanisms in microbial communities from different domains in coastal ecosystems; however, knowledge of specific biogeographic patterns on microbial co-occurrence relationships across complex coastal environmental gradients remains limited. Using a dense sampling scheme at the regional scale, SSU rRNA gene amplicon sequencing, and network analysis, we investigated intra- and inter-domain co-occurrence relationships and network topology-based biogeographic patterns from three microbial domains in coastal waters that show environmental gradients across the inshore-nearshore-offshore continuum in the East China Sea.ResultsOverall, we found the highest complexity and connectivity in the bacterial network, the highest modularity in the archaeal network, and the lowest complexity, connectivity, and modularity in the microeukaryotic network. Although microbial co-occurrence networks from the three domains showed distinct topological features, they exhibited a consistent biogeographic pattern across the inshore-nearshore-offshore continuum. Specifically, the nearshore zones with intermediate levels of terrestrial impacts reflected by multiple environmental factors (including water temperature, salinity, pH, dissolved oxygen, and nutrient-related parameters) had a higher intensity of microbial co-occurrence for all three domains. In contrast, the intensity of microbial co-occurrence was weaker in both the inshore and the offshore zones at the two ends of the environmental gradients. Archaea occupied a central position in the microbial inter-domain co-occurrence network. In particular, members of the Thaumarchaeota Marine Group I (MGI, now placed within the Family Nitrosopumilaceae of the Phylum Thermoproteota) appeared to be the hubs in the biogeographic shift between inter-domain network modules across environmental gradients.ConclusionsOur work offers new insights into microbial biogeography by integrating network features into biogeographic patterns, towards a better understanding of the potential of microbial interactions in shaping biogeographic patterns of coastal marine microbiota.

Microbial inoculants using spent mushroom substrates as carriers improve soil multifunctionality and plant growth by changing soil microbial community structure

Peat is typically used as a carrier for microbial inoculants; however, due to its non-renewable nature alternatives need to be identified as reliable and renewable carriers for mineral-solubilizing inoculants. In pot experiments, solid microbial inoculants were comprised of peat (P), biochar (BC), and spent mushroom substrates (SMS) using Medicago sativa L. as experimental materials, and the purpose of this study is to assess the effect of solid microbial inoculants on soil multifunctionality and plant growth. The results revealed that the SMS microbial inoculant had the greatest positive impact on plant biomass and significantly stimulated soil multifunctionality which is typically managed or assessed based on various soil functions or processes that are crucial for sustaining productivity, in contrast to the peat microbial inoculant, particularly at a supply level of 100 g/pot. There was no significant correlation between soil multifunctionality and bacterial/fungal microbial diversity. However, according to the co-occurrence network of bacteria and fungi, soil multifunctionality was intimately correlated with the biodiversity of the main ecological clusters (modules) of bacteria and fungi, rather than to the entire soil microbial community structure. The keystone species of module hubs and connectors play critical roles in maintaining the stability of ecological clusters of microbial co-occurrence networks and linkages between ecological clusters. Soil pH is a major predictor of changes in plant biomass, and leads to changes therein by affecting the major ecological clusters of bacterial and fungal co-occurrence networks. These results suggested that SMS may serve as a good alternative to peat as a carrier of mineral-solubilizing microorganisms to maintain soil multifunctionality and promote plant growth.

Divergence of rhizosphere microbial communities between females and males of the dioecious Hippophae tibetana at different habitats.

Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, little is known about the difference in rhizosphere microbes in dioecious plants. In this study, we used amplicon sequencing to analyze the differences in rhizosphere microbial diversity and community composition of males and females of dioecious Hippophae tibetana at different habitats, and their key factors in driving the differences were investigated. The results showed that there were differences in the diversity, community composition, and connectivity and complexity of the co-occurrence network of rhizosphere microbes between females and males of the dioecious H. tibetana at different habitats. Zoopagomycota is a unique phylum of rhizosphere fungi in the males of the dioecious H. tibetana, while Dependentiae is a unique phylum of rhizosphere bacteria in the females of the dioecious H. tibetana. Linear discriminant analysis effect size (LEfSe) analysis indicated significant enrichment of species at different levels, suggesting that these species could be potential biomarkers for females and males of H. tibetana. Spearman's analysis showed that the dominant genera of rhizosphere fungi were significantly positively correlated with soil physicochemical properties (total nitrogen and phosphorus; organic matter; available phosphorus, potassium and nitrogen; salt content; water content). PICRUSt and FUNGuild predictive analysis indicated that the function of rhizosphere fungi was different between females and males of the dioecious H. tibetana at different habitats, while metabolites were the dominant functions of rhizosphere bacteria in all samples. These results highlighted the sexual discrimination of rhizosphere microbes on the dioecious plants and provided important knowledge for females and males of the dioecious plant-microbe interaction.IMPORTANCEThis study explores the differences in rhizosphere microbes of dioecious Hippophae tibetana at different habitats and their key factors in driving the differences. Through employing amplicon sequencing techniques, we found that rhizosphere microbial communities and diversity were different between females and males of the dioecious H. tibetana at different habitats, and there notably existed unique phylum and potential biomarkers of rhizosphere microbes between females and males of the dioecious H. tibetana. Rhizosphere fungi were significantly positively correlated with soil physicochemical properties. This study reveals the differences in rhizosphere microbes of dioecious H. tibetana at different habitats and driving factors; it also contributes to our understanding of the dioecious plant-microbe interaction.