Analysis Of Co-occurrence Networks Research Articles

Global trends in publications regarding macrophages-related diabetic foot ulcers in the last two decades.

Diabetic foot ulcers (DFUs) are one of the most severe and popular complications of diabetes. The persistent non-healing of DFUs is the leading cause of ampu-tation, which causes significant mental and financial stress to patients and their families. Macrophages are critical cells in wound healing and perform essential roles in all phases of wound healing. However, no studies have been carried out to systematically illustrate this area from a scientometric point of view. Although there have been some bibliometric studies on diabetes, reports focusing on the investigation of macrophages in DFUs are lacking. To perform a bibliometric analysis to systematically assess the current state of research on macrophage-related DFUs. The publications of macrophage-related DFUs from January 1, 2004, to December 31, 2023, were retrieved from the Web of Science Core Collection on January 9, 2024. Four different analytical tools: VOSviewer (v1.6.19), CiteSpace (v6.2.R4), HistCite (v12.03.07), and Excel 2021 were used for the scientometric research. A total of 330 articles on macrophage-related DFUs were retrieved. The most published countries, institutions, journals, and authors in this field were China, Shanghai Jiao Tong University of China, Wound Repair and Regeneration, and Aristidis Veves. Through the analysis of keyword co-occurrence networks, historical direct citation networks, thematic maps, and trend topics maps, we synthesized the prevailing research hotspots and emerging trends in this field. Our bibliometric analysis provides a comprehensive overview of macrophage-related DFUs research and insights into promising upcoming research.

Biogeographical distribution and community assembly of Myxococcota in mangrove sediments

BackgroundMyxococcota, characterized by their distinct social lifestyles, are widely distributed micro-predators in global sediments. They can feed on a wide range of bacterial, archaeal, and fungal prey. Myxococcota are capable of producing diverse secondary metabolites, playing key roles in microbial food webs, and regulating the microbial community structures in different ecosystems. However, Myxococcota are rarely pure cultured due to the challenging and stringent culturing conditions. Their natural distribution, niche differentiation, and predator–prey relationships in a specific habitat are poorly understood.ResultsIn this study, we conducted a comprehensive analysis of the 16S rRNA gene sequence data from public databases and our collection. We compared the abundance, diversity, and distribution patterns of Myxococcota in various habitats, with a specific focus on mangroves. We found that Myxococcota accounted for 1.45% of the total prokaryotes in global sediments based on the abundance of 16S rRNA genes. Myxococcota are abundant and diverse in mangrove sediments. They tend to be more generalistic in mangroves than in other habitats due to their wide niche breadth. Besides, the deterministic processes (variable selection) influenced the assembly of mangrove Myxococcota communities significantly more than stochastic processes. Further, we determined that environmental factors explained a greater amount of total community variation in mangrove Myxococcota than geographical variables (latitude and sediment depth). In the end, through the analysis of microbial co-occurrence networks, Myxococcota emerges as a key component and functions as a connector in the mangrove microbial community.ConclusionsOur study enhances comprehension of mangrove Myxococcota's biogeography, assembly patterns, driving factors, and co-occurrence relationships, as well as highlights their unique niche and ecological importance in mangrove sediments.

The Potential of Co-Fermentation of Whole-Plant Cassava with Piper sarmentosum: A Comprehensive Study of Fermentation Quality, Antioxidant Activity, Bacterial Community Structure, and Microbial Ecological Networks in Novel Foods.

The objective of this study was to explore the preservation of food products through the co-fermentation of whole-plant cassava and Piper sarmentosum (PS) without additives. We assessed fermentation quality, antioxidant activity, bacterial community structure, function profile, and microbial ecological network features. Our results demonstrate that co-fermentation of whole-plant cassava with 10% PS significantly improves food quality. The co-fermented samples exhibited enhanced lactic acid concentrations and increased antioxidant activity, with reduced pH values and concentrations of acetic acid, butyric acid, and ammonia-N(NH3-N) compared to whole-plant cassava fermented alone. In addition, PS addition also optimized microbial community structure by elevating the total abundance of lactic acid bacteria and influenced bacterial predicted functions. Furthermore, our analysis of co-occurrence networks reveals that co-fermentation impacts microbial network features, including module numbers and bacterial relative abundances, leading to altered complexity and stability of the networks. Moreover, out study also highlights the impact of ferment undesirable bacteria like Pseudomonas aeruginosa and unclassified_Muribaculaceae playing crucial roles in microbial network complexity and stability. These findings provide valuable insights into the anaerobic fermentation process and offers strategies for regulating food fermentation quality.

Reshaping the root endophytic microbiota in plants to combat mercury-induced stress

Emerging evidence suggests that plants experiencing abiotic stress actively seek help from soil microbes. However, the empirical evidence supporting this strategy is limited, especially in response to heavy metal stress. We used integrated microbial community profiling and culture-based methods to investigate the interaction between mercury (Hg) stress, the entophytic root microbiome, and maize seedlings. The results of the pot experiment showed that soil Hg (20 mg/kg) strongly inhibited maize growth, indicating its strong phytotoxicity. Furthermore, Hg stress significantly altered the structure of the bacterial and fungal communities and enriched the potentially pathogenic Fusarium sp., suggesting that soil Hg stress may enhance the bio-stress induced by Fusarium species in maize. Additionally, soil Hg also led to the enrichment of beneficial bacterial members of Streptomyces, Lysobacter, and Sphingomonas (defined as differential species), which were also identified as keystone species in the Hg treatment by the analysis of co-occurrence networks. Therefore, it can be postulated that the members of Streptomyces, Lysobacter, and Sphingomonas function as stress-alleviating microbes. We successfully isolated the representatives of these stress-alleviating microbes. As expected, these strains mitigated the detrimental effects of Hg stess for the maize seedlings, suggesting that plants recruit the stress-alleviated microbiota to combat Hg stress. This study provides insights into the potential of manipulating the root microbiome to enhance plant growth in polluted environments.

Co-Ensiling Whole-Plant Cassava with Corn Stalk for Excellent Silage Production: Fermentation Characteristics, Bacterial Community, Function Profile, and Microbial Ecological Network Features

The objective of this study was to explore excellent silage production through co-ensiling whole-plant cassava and corn stalk, and different ratios of whole-plant cassava (0%, 10%, 20%, 30%, 40%, and 50%, fresh-matter basis) co-ensiled with corn stalk were analyzed based on the silage bacterial community, function profile, and microbial ecological network features. The results demonstrated that co-ensiling 30% whole-plant cassava with 70% corn stalk could be considered an efficient mode of production. The mixed silage showed great quality, as reflected by the reduced pH value and concentrations of acetic acid, butyric acid, and ammonia nitrogen and the enhanced lactic acid concentration, V-score, and nutritional value compared with corn stalk ensiled alone. Meanwhile, co-ensiling restricted the undesirable bacterial Acetobacter fabarum of corn stalk and Pseudomonas aeruginosa of whole-plant cassava and raised the abundance of lactic acid bacteria (LAB) such as Levilactobacillus brevis, Lactiplantibacillus plantarum, Lactobacillus harbinensis, etc. Besides that, the predicted functions of the bacterial community showed large differences in mixed silage compared with whole-plant cassava or corn stalk ensiled alone. Moreover, the analysis of co-occurrence networks showed that mixed silage affected microbial network features, module numbers, and bacterial relative abundances and weakened the complexity and stability of the networks compared with whole-plant cassava single silage. Furthermore, silage microbial community composition had a huge impact on the network properties, and undesirable Pseudomonas aeruginosa played a crucial role in the complexity and stability. Overall, this study revealed the characteristics of whole-plant cassava with corn stalk mixed-silage microbial communities and co-occurrence network modules, complexity, and stability and partly clarified the microbial mechanism of co-ensiling for producing high-quality silage. The findings of this study have important implications for deeply understanding the ensiling process and precisely regulating silage fermentation quality.

Ralstonia solanacearum differentially modulates soil physicochemical properties and rhizospheric bacteriome of resistant and susceptible tobacco cultivars

Ralstonia solanacearum is a devastating soilborne pathogen which poses significant yield and economic losses to tobacco production globally. The impact of R. solanacearum on rhizosphere bacteriome and soil physicochemical characteristics in resistant and susceptible tobacco cultivars is poorly understood. This study aims to determine the effect of R. solanacearum on soil physicochemical parameters and rhizosphere bacteriome of resistant (K326) and susceptible (Hongda) tobacco cultivars at various growth stages. Results demonstrated that the contents of available potassium and phosphorus, as well as soil pH were significantly increased in K326 soils (CK and T2) compared with Hongda (T1) after 21, 42, and 63 days post-inoculation (dpi) of R. solanacearum except for available nitrogen which showed an opposite trend. The qPCR results showed a significant decrease in R. solanacearum population in rhizosphere of K326 (T2) compared to the Hongda (T1) at 21 and 63 dpi than that after 42 dpi. The rhizosphere bacteriome analysis through 16S rRNA amplicon sequencing revealed that rhizosphere bacterial community composition was significantly different between two tobacco cultivars (Hongda and K326) and this effect was more prominent after 63 dpi (93 days after post-transplantation), suggesting that each cultivar recruits a unique set of bacterial communities. There was no obvious difference observed in the rhizosphere bacteriome of CK (K326) and T2 (K326), which might be attributed to the same genetic makeup and inherent resistance of K326 to bacterial wilt infection. Analysis of co-occurrence networks revealed that the microbial network in T1 (Hongda) was more complex than those in T2 (K326) and CK (K326), while the networks in CK and T2 were almost identical. The present research highlights the time-course relationship between environmental factors and rhizosphere bacteriome of tobacco cultivars showing different levels of resistance against R. solanacearum. Conclusively, studying the plant-soil-microbe interaction system in susceptible and resistant tobacco cultivars may enable us to develop effective integrated disease control plans for the healthy production of tobacco crops.

Effects of molybdenum supply on microbial diversity and mineral nutrient availability in the rhizosphere soil of broad bean (Vicia Faba L.)

Molybdenum application holds the potential to enhance agricultural productivity. However, the precise impact on soil microbial diversity and mineral nutrient availability remains uncertain. In this study, we collected rhizosphere soil samples from different growth stages of broad beans. By analyzing mineral element contents, soil phosphorus and zinc fractions, as well as fungal and bacterial diversity, we observed that Mo application resulted in a reduction of soil Citrate‒P and HCl‒P content. This reduction led to an increase in available P content at different stages. Moreover, Mo application elevated root P concentration, but concurrently impeded the translocation of P to the shoots. Mo application also decreased the soil Exc‒Zn (exchangeable Zn) content while increasing the Res‒Zn (residual Zn) content, ultimately causing a decrease in available Zn content at different stages. Consequently, the Zn concentration within broad beans correspondingly decreased. Mo application fostered an augmentation in fungal richness and Shannon indices at the branching and podding stages. The analysis of microbial co-occurrence networks indicated that Mo application bolstered positive connectivity among fungal taxa. Remarkably, Mo significantly increased the abundance of Chaetomium, Leucosporidium, and Thielavia fungi. Spearman correlation analysis demonstrated a significant positive correlation between fungal diversity and soil available P content, as well as a notable negative correlation with soil available Zn content. These findings suggest that Mo application may modify the availability of soil P and Zn by influencing fungal diversity in the rhizosphere of crop soil, ultimately impacting nutrient accumulation within the grains.

Soil rare microorganisms mediated the plant cadmium uptake: The central role of protists

Plants and microorganisms symbiotically mediate and/or catalyse the turnover of elements in rhizosphere soils, thus directly influencing the effectiveness of phytoremediation in addressing heavy metal contamination. Soil rare microbial communities are diverse but not well understood in terms of their importance for phytoremediation. In this study, we simulated the loss of rare microorganisms through dilution-to-extinction approach, and investigated the effects on integrated rhizosphere microbiome with soil microcosm experiments, including bacteria, fungi, protists, and microfauna. Additionally, we explored the implications for ryegrass (Lolium multiflorum Lam.) growth and its uptake of Cd (cadmium). Compared with the undiluted group, ryegrass exhibited a significant decrease in Cd uptake ranging from 52.34 % to 73.71 % in the rare species-loss soils, indicating a lack of functional redundancy in rhizosphere soil microbial community following rare species loss. Interestingly, these soils displayed a remarkable 1.79-fold increase in plant biomass and a 41.02 % increase in plant height. By sequencing the 16S, 18S, and ITS rRNA gene amplicons of rhizosphere microbes, we found that soil rare species loss decreased the rhizosphere microbial α-diversity, changed the community structures, and shifted the functional potential. Protists were particularly affected. Through the analysis of species co-occurrence networks, along with the partial least squares path modeling, we found that the diversity of protists and bacteria and the co-occurring network connectivity of protists and fungi contributed most to plant Cd uptake and growth. These results highlighted the potential significance of rare microorganisms, particularly protists, in phytoextraction of Cd-contaminated soils, owing to their central role in the microbial food web.

Visualization and Analysis of the Data Mining Domain of Scientific Medical Publications in the Web of Science Database Using Co-word Analysis

Background: The present study aims at visualizing and analyzing the scientific productions of data mining in medical sciences in the Web of Science (WoS) database to identify knowledge structure in this field. Methods: The present study was carried out using co-word analysis, which is a scientometrics method. Also, the analysis of the WoS approach was used for the visualization and analysis of word co-occurrence networks in the data mining domain. The research population consisted of 14,430 records related to data mining published in WoS from 2008 to 2016. The data were analyzed after retrieval using VoSviewer scientometric software. Results: The research findings showed that the average annual growth rate of scientific productions in the data mining field had an upward trend and reached its peak in 2016. The findings also showed that the USA was the most productive country, with 8123 degrees, claiming the first rank by 27.4% of the total scientific production, and Iran was in the 13th rank with 678 degrees. Among universities and institutions, the Chinese Academy of Sciences (692 degrees), the University of California (621 degrees), and the National Center for Scientific Research (CNSR) (514 degrees) were ranked first to third globally. Among Iranian institutions and universities, Islamic Azad University (IAU), Tehran University, and Iran University of Technological Sciences were ranked 41st, 94th, and 200th in the world with 140, 105, and 66 degrees, respectively. The results of the current research also showed that the field of data mining was formed based on four vocabulary clusters with 108, 82, 73, and 42 words, respectively. Conclusions: The recognition of Iran as a successful country in the field of data mining should encourage researchers from other countries to communicate with Iranian scientists.

Different responses of the rhizosphere microbiome to Verticillium dahliae infection in two cotton cultivars.

Verticillium wilt is a disastrous disease caused by Verticillium dahliae that severely damages the production of cotton in China. Even under homogeneous conditions, the same cotton cultivar facing V. dahliae tends to either stay healthy or become seriously ill and die. This binary outcome may be related to the interactions between microbiome assembly and plant health. Understanding how the rhizosphere microbiome responds to V. dahliae infection is vital to controlling Verticillium wilt through the manipulation of the microbiome. In this study, we evaluated the healthy and diseased rhizosphere microbiome of two upland cotton cultivars that are resistant to V. dahliae, Zhong 2 (resistant) and Xin 36 (susceptible), using 16S rRNA and ITS high-throughput sequencing. The results showed that the healthy rhizosphere of both resistant cultivar and susceptible cultivar had more unique bacterial ASVs than the diseased rhizosphere, whereas fewer unique fungal ASVs were found in the healthy rhizosphere of resistant cultivar. There were no significant differences in alpha diversity and beta diversity between the resistant cultivar and susceptible cultivar. In both resistant cultivar and susceptible cultivar, bacterial genera such as Pseudomonas and Acidobacteria bacterium LP6, and fungal genera such as Cephalotrichum and Mortierella were both highly enriched in the diseased rhizosphere, and Pseudomonas abundance in diseased rhizospheres was significantly higher than that in the healthy rhizosphere regardless of the cultivar type. However, cultivar and V. dahliae infection can cause composition changes in the rhizosphere bacterial and fungal communities, especially in the relative abundances of core microbiome members, which varied significantly, with different responses in the two cotton cultivars. Analysis of co-occurrence networks showed that resistant cultivar has a more complex network relationship than susceptible cultivar in the bacterial communities, and V. dahliae has a significant impact on the bacterial community structure. These findings will further broaden the understanding of plant-rhizosphere microbiome interactions and provide an integrative perspective on the cotton rhizosphere microbiome, which is beneficial to cotton health and production.

Enhanced bioremediation of triclocarban-contaminated soil by Rhodococcus rhodochrous BX2 and Pseudomonas sp. LY-1 immobilized on biochar and microbial community response.

Triclocarban (TCC), an emerging organic contaminant (EOC), has become a severe threat to soil microbial communities and ecological security. Here, the TCC-degrading strain Rhodococcus rhodochrous BX2 and DCA-degrading strain Pseudomonas sp. LY-1 (together referred to as TC1) were immobilized on biochar to remove TCC and its intermediates in TCC-contaminated soil. High-throughput sequencing was used to investigate the microbial community structure in TCC-contaminated soil. Analysis of co-occurrence networks was used to explore the mutual relationships among soil microbiome members. The results showed that the immobilized TC1 significantly increased the removal efficiency of TCC from 84.7 to 92.7% compared to CK (no TC1 cells on biochar) in 10 mg/L TCC liquid medium. The utilization of immobilized TC1 also significantly accelerated the removal of TCC from contaminated soil. Microbial community analysis revealed the crucial microorganisms and their functional enzymes participating in TCC degradation in soil. Moreover, the internal labor division patterns and connections of TCC-degrading microbes, with a focus on strains BX2 and LY-1, were unraveled by co-occurrence networks analysis. This work provides a promising strategy to facilitate the bioremediation of TCC in soil, which has potential application value for sustainable biobased economies.

RNA outperforms DNA-based metabarcoding in assessing the diversity and response of microeukaryotes to environmental variables in the Arctic Ocean

The Arctic Ocean (AO) has a harsh environment characterized by low temperatures, extensive ice coverage, and periodic freezing and melting of sea ice, which has provided diverse habitats for microorganisms. Prior studies primarily focused on microeukaryote communities in the upper water or sea ice based on environmental DNA, leaving the composition of active microeukaryotes in the diverse AO environments largely unknown. This study provided a vertical assessment of microeukaryote communities in the AO from snow and ice to sea water at a depth of 1670 m using high-throughput sequencing of co-extracted DNA and RNA. RNA extracts depicted microeukaryote community structure and intergroup correlations more accurately and responded more sensitively to environmental conditions than those derived from DNA. Using RNA:DNA ratios as a proxy for relative activity of major taxonomic groups, the metabolic activities of major microeukaryote groups were determined along depth. Analysis of co-occurrence networks showed that parasitism between Syndiniales and dinoflagellates/ciliates in the deep ocean may be significant. This study increased our knowledge of the diversity of active microeukaryote communities and highlighted the importance of using RNA-based sequencing over DNA-based sequencing to examine the relationship between microeukaryote assemblages and the responses of microeukaryotes to environmental variables in the AO.

BIOMEDICAL CONVERGENCE FACILITATED BY THE EMERGENCE OF TECHNOLOGICAL AND INFORMATIC CAPABILITIES

We leverage the knowledge network representation of the Medical Subject Heading (MeSH) ontology to infer conceptual distances between roughly 30,000 distinct MeSH keywords — each being prescribed to particular knowledge domains — in order to quantify the origins of cross-domain biomedical convergence. Analysis of MeSH co-occurrence networks based upon 21.6 million research articles indexed by PubMed identifies three robust knowledge clusters: micro-level biological entities and structures; meso-level representations of systems, and diseases and diagnostics; and emergent macro-level biological and social phenomena. Analysis of cross-cluster dynamics shows how these domains integrated from the 1990s onward via technological and informatic capabilities — captured by MeSH belonging to the “Technology, Industry, and Agriculture” (J) and “Information Science” (L) branches — representing highly controllable, scalable and permutable research processes and invaluable imaging techniques for illuminating fundamental yet transformative structure–function–behavior questions. Our results indicate that 8.2% of biomedical research from 2000 to 2018 include MeSH terms from both the J and L MeSH branches, representing a 291% increase from 1980s levels. Article-level MeSH analysis further identifies the increasing prominence of cross-domain integration, and confirms a positive relationship between team size and topical diversity. Journal-level analysis reveals variable trends in topical diversity, suggesting that demand and appreciation for convergence science vary by scholarly community. Altogether, we develop a knowledge network framework that identifies the critical role of techno-informatic inputs as convergence bridges — or catalyzers of integration across distinct knowledge domains — as highlighted by the 1990s genomics revolution, and onward in contemporary brain, behavior and health science initiatives.

Soil microbial trait-based strategies drive the storage and stability of the soil carbon pool in Robinia pseudoacacia plantations

Soil microorganisms play an essential role in soil carbon sequestration and stability in forest ecosystems. However, how trade-offs in distinct microbial traits affect soil carbon storage and stability remains largely unknown, especially for forest soils that stock significant amounts of organic carbon. Here, we assessed the influences of the chronosequence of Robinia pseudoacacia (8, 18, and 30 years) on soil organic carbon (SOC) fractions and further explored the specific roles of microbial taxa in regulating soil carbon sequestration on the Loess Plateau via high-throughput sequencing techniques and analysis of co-occurrence networks and assembly processes. The results showed that the concentrations of soil easily oxidizable carbon (EOC), recalcitrant organic carbon (ROC), and SOC storage increased with stand age. However, the dissolved organic carbon (DOC) and microbial biomass carbon (MBC) concentrations increased from 8 years to 18 years and then decreased after 30 years. Stand age significantly affected the soil bacterial and fungal structures and diversity. Stochastic processes, especially dispersal limitation, were the main assembly processes affecting the bacterial and fungal communities. Soil pH, DOC and the N:P ratio drove bacterial assembly. However, fungal assembly was not affected by soil properties. Moreover, network analysis showed that three major bacterial modules and one major fungal module (Bac_Mod 1, 3, 4 and Fun_Mod 2) showed strong relationships with soil carbon storage and were considered soil carbon pool-associated modules. These modules based on the co-occurrence network analysis were composed of microbial taxa with different taxonomic and functional traits. Both random forest and correlation analyses indicated that increases or decreases in these modules were strongly correlated to variations in SOC fractions. These results demonstrated that with R. pseudoacacia plantation development, the recalcitrant-related module attributed to SOC became more stable.

Resistance-distance betweenness: Definition, properties, and application in complex linguistic networks

Betweenness centrality measures how a node lies on the paths between other nodes. We propose the so-called resistance-distance betweenness (RDB) which takes a new viewpoint on scoring paths and contribution of each node in the paths. This new betweenness is developed based on the two facts: (1) the resistance distance characterizes the aggregate distance between two nodes in the context of electrical networks; (2) the resistance distance has an edge-wise decomposition form. Thus, the RDB of a node is defined as the sum of resistance distance components associated with the node’s incident edges, which measures how a node lies on the “aggregated path” between other nodes. The basic properties of RDB and its relation and difference from current-flow betweenness (CFB) are investigated. Then, we apply the RDB to the study of an open question in linguistic networks, i.e., to check whether the Yuan poems written by Han and non-Han poets are similar. We also compare the performance of RDB with CFB. The betweenness analysis of the character co-occurrence networks of Han’s and non-Han’s poems provides a fresh and quantitative perspective to support that Han’s and non-Han’s poems are similar in general.

Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects.

In recent years, several studies have evidenced the importance of the microbiome to host physiology as metabolism regulator, along with its potential role in triggering various diseases. In this study, we analyzed the gut microbiota in hypercholesterolemic (cases) and normocholesterolemic (controls) individuals to identify characteristic microbial signature for each condition. Stool samples were obtained from 57 adult volunteers (27 hypercholesterolemic and 30 controls). The taxonomic profiling of microbial communities was performed using high-throughput sequencing of 16S rRNA V3-V4 amplicons, followed by data analysis using Quantitative Insights Into Microbial Ecology 2 (QIIME2) and linear discriminant analysis (LDA) effect size (LEfSe). Significant differences were observed in weight, height, body mass index (BMI) and serum levels of triglycerides, total cholesterol and low-density lipoprotein cholesterol (LDL-C) between the groups (p<0.05). LEfSe showed differentially abundant prokaryotic taxa (α=0.05, LDA score > 2.0) in the group of hypercholesterolemic individuals (Methanosphaera, Rothia, Chromatiales, Clostridiales, Bacillaceae and Coriobacteriaceae) and controls (Faecalibacterium, Victivallis and Selenomonas) at various taxonomic levels. In addition, through the application of Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2), the predominance of pathways related to biosynthesis in hypercholesterolemic patients was established, compared to controls in which degradation pathways were predominant. Finally, in the analysis of co-occurrence networks, it was possible to identify associations between the microorganisms present in both studied groups. Our results point out to unique microbial signatures, which likely play a role on the cholesterol metabolism in the studied population.

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure

Sugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane—whose role in its health and growth is crucial—remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3–V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments—especially in fungi—and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.

Combination of biochar and AMF promotes phosphorus utilization by stimulating rhizosphere microbial co-occurrence networks and lipid metabolites of Phragmites

Agricultural biochar and arbuscular mycorrhizal fungi were used to promote the growth of Phragmites in the structural damaged and nutritional imbalanced littoral zone soils. Wheat straw biochar played a significant role in improving soil porosity and supplementing available phosphorus to 79.20 ± 3.20 mg/kg, compared with CK at 17.50 ± 0.88 mg/kg. The addition of Diversispora versiformis improved the plant net photosynthetic rate reaching up to 25.66 ± 0.65 μmol·m−2·s−1, which was 36.60 % higher than CK. The combination of biochar and fungi contributed to the whole plant dry weight biomass of 32.30 % and 234.00 % higher than the single biochar or AMF amendment groups, respectively. Meanwhile, the analysis of microbial co-occurrence networks showed the most relevant networks node species were mainly Talaromyces, Chaetomiacea and Gemmatimonadetes etc. Root lipid metabolite of Glycerophospholines further proved that phosphorus utilization was also enhanced endogenously in the rhizosphere soil. These results indicate that the combination of biochar and arbuscular mycorrhizal fungi play synergic role in enhancing phosphorus utilization endogenously and exogenously.

Microbial co-occurrence networks driven by low-abundance microbial taxa during composting dominate lignocellulose degradation

Lignocellulose, which contains cellulose, hemicellulose and lignin, is one of the most important factors determining the rate and quality of compost decomposition, and the microbial community composition affects the rate of lignocellulose decomposition. Interactions between microbial taxa contribute significantly to ecosystem energy flow and material cycling. However, it is not clear how interactions between microbial taxa affect the degradation of lignocellulose during the composting process. For this reason we carried out aerobic co-composting experiments with maize straw and cattle manure to explore the contribution of microbial community diversity and the interaction between taxa to lignocellulosic degradation. The results showed that moisture and temperature had the greatest effect on microbial communities during composting and that lignocellulose degradation was dominated by microbial co-occurrence networks rather than microbial community diversity. Overall co-occurrence network and bacterial–fungal interactions explained 23.9–84.1 % of lignocellulosic degradation, whereas microbial diversity only accounted for 24.6–31.5 %. Interestingly, keystone taxa analysis of the microbial co-occurrence networks revealed that low-abundance taxa influenced microbial interactions driving lignocellulose degradation. Our results provide a new perspective for understanding lignocellulose degradation during composting, offering insights into important microbial interaction mechanisms for improving compost quality and efficiency.

Current Status and Trends in Research on Caries Diagnosis: A Bibliometric Analysis.

There are a wide variety of devices for the detection and diagnosis of caries from the initial stages. The purpose of this study was to perform a bibliometric study on research regarding caries diagnosis by identifying the contributing researchers, organizations, countries or regions, journals, and to provide an analysis of keyword co-occurrence and co-authorship networks. An advanced search was performed in Web of Science (WOS) Core Collection database, using the terms “caries diagno*” and “caries detect*” in the “topic” field, from 2013 to 2021. Bibliometric parameters were extracted using WOS’s analyze results tools and VOSviewer software. A total of 816 documents were identified. Most of them, (61.3%) are included in “Dentistry Oral Surgery & Medicine” category within WOS. The largest scientific production on the subject is observed between 2018 and 2021, with a total of 344 records. The most productive author is Mendes FM, followed by Braga MM. The journal with the most articles published on caries diagnosis is Caries Research, with 55 articles (6.74%). The terms with the highest co-occurrence refer to the validity of diagnostic methods, tools or principles used in diagnosis or general aspects related to caries detection and diagnosis.