The development of fungicides is time-consuming and costly.Introducing a fungicide-likeness assessment strategy at the early screening stage can help reduce development risks and improve the success rate.However,exist...The development of fungicides is time-consuming and costly.Introducing a fungicide-likeness assessment strategy at the early screening stage can help reduce development risks and improve the success rate.However,existing assessment methods are often plagued by low accuracy and poor generalization,while fragment-based design strategies commonly fail to account for synergistic effects between structural units.Therefore,based on a small-scale sample set,this study developed a more efficient global predictive model for fungicidal activity—-named APPf—by integrating multi-scale feature screening methods and machine learning algorithms,which also accounts for synergistic effects among different structural fragments.We utilized three independent external test sets for model validation:External Test Set 1 for general validation,External Test Set 2 for comparison with existing models,and External Test Set 3 for disease-specific fungicide evaluation.On External Test Set 1,the APPf model achieved a precision of 0.6454,a recall of 0.8535,and an F1 score of 0.7350,demonstrating its robust predictive performance.It also exhibited strong enrichment capability for positive samples in External Test Set 2.For External Test Set 3,APPf achieved a prediction accuracy exceeding 80%for each disease,suggesting its promising potential in practical fungicide development.Furthermore,we quantified the contribution of molecular descriptors to the model predictions using SHAP value analysis and identified nHdNH and NssssNp as strong indicative features for predicting fungicidal activity,thereby enhancing the interpretability of the model.APPf has been deployed on a public web server(http://pesticides.cau.edu.cn/APPf),providing a user-friendly online prediction service to support the discovery of novel fungicides.Meanwhile,we employed a molecular fragmentation strategy to analyze the co-occurrence relationships between fragments in fungicides and constructed a network map of fragment co-occurrence associated with fungicidal activity.This study provides both an active fragment library and a global fungicide-likeness assessment tool for AI-based de novo molecular generation aimed at discovering novel fungicidal leads,which is expected to enhance the efficiency of developing new fungicides.展开更多
Land use influences soil biota community composition and diversity,and then belowground ecosystem processes and functions.To characterize the effect of land use on soil biota,soil nematode communities in crop land,for...Land use influences soil biota community composition and diversity,and then belowground ecosystem processes and functions.To characterize the effect of land use on soil biota,soil nematode communities in crop land,forest land and fallow land were investigated in six regions of northern China.Generic richness,diversity,abundance and biomass of soil nematodes was the lowest in crop land.The richness and diversity of soil nematodes were 28.8and 15.1%higher in fallow land than in crop land,respectively.No significant differences in soil nematode indices were found between forest land and fallow land,but their network keystone genera composition was different.Among the keystone genera,50%of forest land genera were omnivores-predators and 36%of fallow land genera were bacterivores.The proportion of fungivores in forest land was 20.8%lower than in fallow land.The network complexity and the stability were lower in crop land than forest land and fallow land.Soil pH,NH_(4)^(+)-N and NO_(3)^(–)-N were the major factors influencing the soil nematode community in crop land while soil organic carbon and moisture were the major factors in forest land.Soil nematode communities in crop land influenced by artificial management practices were more dependent on the soil environment than communities in forest land and fallow land.Land use induced soil environment variation and altered network relationships by influencing trophic group proportions among keystone nematode genera.展开更多
Objective:This study investigated trends in the study of phytochemical treatment of post-traumatic stress disorder(PTSD).Methods:The Web of Science database(2007-2022)was searched using the search terms“phytochemical...Objective:This study investigated trends in the study of phytochemical treatment of post-traumatic stress disorder(PTSD).Methods:The Web of Science database(2007-2022)was searched using the search terms“phytochemicals”and“PTSD,”and relevant literature was compiled.Network clustering co-occurrence analysis and qualitative narrative review were conducted.Results:Three hundred and one articles were included in the analysis of published research,which has surged since 2015 with nearly half of all relevant articles coming from North America.The category is dominated by neuroscience and neurology,with two journals,Addictive Behaviors and Drug and Alcohol Dependence,publishing the greatest number of papers on these topics.Most studies focused on psychedelic intervention for PTSD.Three timelines show an“ebb and flow”phenomenon between“substance use/marijuana abuse”and“psychedelic medicine/medicinal cannabis.”Other phytochemicals account for a small proportion of the research and focus on topics like neurosteroid turnover,serotonin levels,and brain-derived neurotrophic factor expression.Conclusion:Research on phytochemicals and PTSD is unevenly distributed across countries/regions,disciplines,and journals.Since 2015,the research paradigm shifted to constitute the mainstream of psychedelic research thus far,leading to the exploration of botanical active ingredients and molecular mechanisms.Other studies focus on anti-oxidative stress and anti-inflammation.展开更多
The elevational distributions of bacterial communities in natural mountain forests,especially along large elevational gradients,have been studied for many years.However,the distributional patterns that underlie variat...The elevational distributions of bacterial communities in natural mountain forests,especially along large elevational gradients,have been studied for many years.However,the distributional patterns that underlie variations in soil bacterial communities along small-scale elevational gradients in urban ecosystems are not yet well understood.Using Illumina MiSeq DNA sequencing,we surveyed soil bacterial communities at three elevations on Zijin Mountain in Nanjing City:the hilltop(300 m a.s.l.),the hillside(150 m a.s.l.),and the foot of the hill(0 m a.s.l.).The results showed that edaphic properties differed significantly with elevation.Bacterial community composition,rather than alpha diversity,strongly differed among the three elevations(Adonis:R2=0.12,P<0.01).Adonis and DistLM analyses demonstrated that bacterial community composition was highly correlated with soil pH,elevation,total nitrogen(TN),and dissolved organic carbon(DOC).The degree scores,betweenness centralities,and composition of keystone species were distinct among the elevations.These results demonstrate strong elevational partitioning in the distributions of soil bacterial communities along the gradient on Zijin Mountain.Soil pH and elevation together drove the smallscale elevational distribution of soil bacterial communities.This study broadens our understanding of distribution patterns and biotic co-occurrence associations of soil bacterial communities from large elevational gradients to short elevational gradients.展开更多
We identified a sporocarp as Agrocybe dura growing next to a living corn using PacBio sequencing.The mycoparasitism of Trichoderma spp.on A.dura were revealed by the co-occurrence network analysis.For long-read HTS da...We identified a sporocarp as Agrocybe dura growing next to a living corn using PacBio sequencing.The mycoparasitism of Trichoderma spp.on A.dura were revealed by the co-occurrence network analysis.For long-read HTS data,we updated a bioinformatic pipeline to enhance fungal taxonomic resolution.In forests,fungal sporocarps house the diverse fungicolous fungi;however,the relationships of sporocarps and associated fungal communities are rarely explored in agroecosystems.In a corn field near Gongzhuling City,Jilin Province,China,we found an epigeous sporocarp with agaricoid morphology that could grow next to the living corn plants.Using PacBio metabarcoding combined with an updated bioinformatic pipeline,we surveyed the fungal community profile along its cap,rhizomorph and hyphosphere soil at a much-improved taxonomic resolution.We identified the sporocarp,at a high probability,as Agrocybe dura,and this mushroom was significantly negatively correlated with Trichoderma hamatum and T.harzianum in the co-occurrence network.Fungal diversity in hyphosphere habitat was significantly higher than that in cap and rhizomorph habitats.Consistent with the pattern in fungal diversity,the node number,edge number,network diameter and average degree were significantly higher in hyphosphere habitat than other habitats.However,both the negative and positive cohesion were significantly higher in rhizomorph habitat than other habitats.Moreover,the z-c plot identified A.dura as the only network hub,linking multiple fungal species.The results give us a glimpse of the ecological relevance of saprobic mushrooms across the extensive northeastern black soil region of China.Our findings will aid in the assessment and forecasting of fungal diversity hotspots and their relationships with soil fertility in the‘Golden Corn Belt’of northeast China.展开更多
Understanding the fundamental drivers of large-scale species co-occurrence is a critical issue in ecology and conservation research. Here, we assessed foraging guilds, habitat type and disturbances as drivers of bird ...Understanding the fundamental drivers of large-scale species co-occurrence is a critical issue in ecology and conservation research. Here, we assessed foraging guilds, habitat type and disturbances as drivers of bird species co-occurrence in Ghana's Central Region over six months. Birds were sampled in 120 points across six different habitat types (farmland, forest reserve, urban area, coastal savannah, wetland, and mangrove), using the point-centred count technique. In total, 4060 individuals belonging to 216 species were recorded across all six habitat types. We found that co-occurring species were more similar in their foraging behaviour and habitat association. About 60% of the birds were found to co-occur randomly, 15% co-occurred negatively, and 25% co-occurred positively. Carnivores like the Black Heron (Egretta ardesiaca) and Spur-winged Lapwing (Vanellus spinosus) randomly co-occurred with other guild groups and were dominant in the mangroves and wetlands. Frugivores from forest reserves had only a 25% chance of randomly co-occurring with other birds and about a 60% chance of positively co-occurring with other birds. Our findings suggest that foraging guilds and habitat type are major factors driving bird co-occurrence and community assemblages in this West African suburban region.展开更多
Classifying the texture of granules in 2D images has aroused manifold research atten-tion for its technical challenges in image processing areas.This letter presents an aggregate texture identification approach by joi...Classifying the texture of granules in 2D images has aroused manifold research atten-tion for its technical challenges in image processing areas.This letter presents an aggregate texture identification approach by jointly using Gray Level Co-occurrence Probability(GLCP) and BP neural network techniques.First, up to 8 GLCP-associated texture feature parameters are defined and computed, and these consequent parameters next serve as the inputs feeding to the BP neural network to calculate the similarity to any of given aggregate texture type.A finite number of aggregate images of 3 kinds, with each containing specific type of mineral particles, are put to the identification test, experimentally proving the feasibility and robustness of the proposed method.展开更多
Background Bacteria,Archaea,and Microeukaryotes comprise taxonomic domains that interact in mediating biogeochemical cycles in coastal waters.Many studies have revealed contrasting biogeographic patterns of community ...Background Bacteria,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 diferent domains in coastal ecosystems;however,knowledge of specifc 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-ofshore continuum in the East China Sea.Results Overall,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-ofshore continuum.Specifcally,the nearshore zones with intermediate levels of terrestrial impacts refected 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 ofshore 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.Conclusions Our work ofers 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.展开更多
Impact statement Habitat loss has been a primary threat to biodiversity.However,species do not function in isolation but often associate with each other and form complex networks.Thus,revealing how the network complex...Impact statement Habitat loss has been a primary threat to biodiversity.However,species do not function in isolation but often associate with each other and form complex networks.Thus,revealing how the network complexity and stability scale with habitat area will give us more insights into the effects of habitat loss on ecosystems.In this study,we explored the relationships between the island area and the network complexity and stability of soil microbes.We found that the complexity and stability of soil microbial co‐occurrence networks scale positively with island area,indicating that habitat loss will potentially simplify and destabilize soil microbial networks.展开更多
Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems.Although their diversity and composition have been widely investigated in aquaculture systems,the co-...Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems.Although their diversity and composition have been widely investigated in aquaculture systems,the co-occurrence bipartite network between microeukaryotes and bacteria remains poorly understood.This study used the bipartite network analysis of high-throughput sequencing datasets to detect the co-occurrence relationships between microeukaryotes and bacteria in water and sediment from coastal aquaculture ponds.Chlorophyta and fungi were dominant phyla in the microeukaryotic–bacterial bipartite networks in water and sediment,respectively.Chlorophyta also had overrepresented links with bacteria in water.Most microeukaryotes and bacteria were classified as generalists,and tended to have symmetric positive and negative links with bacteria in both water and sediment.However,some microeukaryotes with high density of links showed asymmetric links with bacteria in water.Modularity detection in the bipartite network indicated that four microeukaryotes and twelve uncultured bacteria might be potential keystone taxa among the module connections.Moreover,the microeukaryotic–bacterial bipartite network in sediment harbored significantly more nestedness than that in water.The loss of microeukaryotes and generalists will more likely lead to the collapse of positive co-occurrence relationships between microeukaryotes and bacteria in both water and sediment.This study unveils the topology,dominant taxa,keystone species,and robustness in the microeukaryotic–bacterial bipartite networks in coastal aquaculture ecosystems.These species herein can be applied for further management of ecological services,and such knowledge may also be very useful for the regulation of other eutrophic ecosystems.展开更多
BACKGROUND Non-suicidal self-injury(NSSI)is common among adolescents with depressive disorders and poses a major public health challenge.Rumination,a key cognitive feature of depression,includes different subtypes tha...BACKGROUND Non-suicidal self-injury(NSSI)is common among adolescents with depressive disorders and poses a major public health challenge.Rumination,a key cognitive feature of depression,includes different subtypes that may relate to NSSI through distinct psychological mechanisms.However,how these subtypes interact with specific NSSI behaviors remains unclear.AIM To examine associations between rumination subtypes and specific NSSI behaviors in adolescents.METHODS We conducted a cross-sectional study with 305 hospitalized adolescents diagnosed with depressive disorders.The subjects ranged from 12-18 years in age.Rumi-nation subtypes were assessed using the Ruminative Response Scale,and 12 NSSI behaviors were evaluated using a validated questionnaire.Network analysis was applied to explore symptom-level associations and identify central symptoms.RESULTS The network analysis revealed close connections between rumination subtypes and NSSI behaviors.Brooding was linked to behaviors such as hitting objects and burning.Scratching emerged as the most influential NSSI symptom.Symptomfocused rumination served as a key bridge connecting rumination and NSSI.CONCLUSION Symptom-focused rumination and scratching were identified as potential intervention targets.These findings highlight the psychological significance of specific cognitive-behavioral links in adolescent depression and suggest directions for tailored prevention and treatment.However,the cross-sectional,single-site design limits causal inference and generalizability.Future longitudinal and multi-center studies are needed to confirm causal pathways and verify the generalizability of the findings to broader adolescent populations.展开更多
Background:Wenqing Yin(WQY)is a classic prescription used to treat skin diseases like atopic dermatitis(AD)in China,and the aim of this study is to investigate the therapeutic effects and molecular mechanisms of WQY o...Background:Wenqing Yin(WQY)is a classic prescription used to treat skin diseases like atopic dermatitis(AD)in China,and the aim of this study is to investigate the therapeutic effects and molecular mechanisms of WQY on AD.Methods:The DNFB-induced mouse models of AD were established to investigate the therapeutic effects of WQY on AD.The symptoms of AD in the ears and backs of the mice were assessed,while inflammatory factors in the ear were quantified using quantitative real-time-polymerase chain reaction(qRT-PCR),and the percentages of CD4^(+)and CD8^(+)cells in the spleen were analyzed through flow cytometry.The compounds in WQY were identified using ultra-performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS)analysis and the key targets and pathways of WQY to treat AD were predicted by network pharmacology.Subsequently,the key genes were tested and verified by qRT-PCR,and the potential active components and target proteins were verified by molecular docking.Results:WQY relieved the AD symptoms and histopathological injuries in the ear and back skin of mice with AD.Meanwhile,WQY significantly reduced the levels of inflammatory factors IL-6 and IL-1βin ear tissue,as well as the ratio of CD4^(+)/CD8^(+)cells in spleen.Additionally,a total of 142 compounds were identified from the water extract of WQY by UPLC-Orbitrap-MS/MS.39 key targets related to AD were screened out by network pharmacology methods.The KEGG analysis indicated that the effects of WQY were primarily mediated through pathways associated with Toll-like receptor signaling and T cell receptor signaling.Moreover,the results of qRT-PCR demonstrated that WQY significantly reduced the mRNA expressions of IL-4,IL-10,GATA3 and FOXP3,and molecular docking simulation verified that the active components of WQY had excellent binding abilities with IL-4,IL-10,GATA3 and FOXP3 proteins.Conclusion:The present study demonstrated that WQY effectively relieved AD symptoms in mice,decreased the inflammatory factors levels,regulated the balance of CD4^(+)and CD8^(+)cells,and the mechanism may be associated with the suppression of Th2 and Treg cell immune responses.展开更多
This paper investigates the reliability of internal marine combustion engines using an integrated approach that combines Fault Tree Analysis(FTA)and Bayesian Networks(BN).FTA provides a structured,top-down method for ...This paper investigates the reliability of internal marine combustion engines using an integrated approach that combines Fault Tree Analysis(FTA)and Bayesian Networks(BN).FTA provides a structured,top-down method for identifying critical failure modes and their root causes,while BN introduces flexibility in probabilistic reasoning,enabling dynamic updates based on new evidence.This dual methodology overcomes the limitations of static FTA models,offering a comprehensive framework for system reliability analysis.Critical failures,including External Leakage(ELU),Failure to Start(FTS),and Overheating(OHE),were identified as key risks.By incorporating redundancy into high-risk components such as pumps and batteries,the likelihood of these failures was significantly reduced.For instance,redundant pumps reduced the probability of ELU by 31.88%,while additional batteries decreased the occurrence of FTS by 36.45%.The results underscore the practical benefits of combining FTA and BN for enhancing system reliability,particularly in maritime applications where operational safety and efficiency are critical.This research provides valuable insights for maintenance planning and highlights the importance of redundancy in critical systems,especially as the industry transitions toward more autonomous vessels.展开更多
This study investigates the feasibility of applying complex networks to fine-grained language classification and of employing word co-occurrence networks based on parallel texts as a substitute for syntactic dependenc...This study investigates the feasibility of applying complex networks to fine-grained language classification and of employing word co-occurrence networks based on parallel texts as a substitute for syntactic dependency networks in complex-network-based language classification.14 word co-occurrence networks were constructed based on parallel texts of 12 Slavic languages and 2 non-Slavic languages,respectively.With appropriate combinations of major parameters of these networks,cluster analysis was able to distinguish the Slavic languages from the non-Slavic and correctly group the Slavic languages into their respective sub-branches.Moreover,the clustering could also capture the genetic relationships of some of these Slavic languages within their sub-branches.The results have shown that word co-occurrence networks based on parallel texts are applicable to fine-grained language classification and they constitute a more convenient substitute for syntactic dependency networks in complex-network-based language classification.展开更多
Interactions between dissolved organic matter(DOM)and bacteria are central in the biogeochemical cycles of aquatic ecosystems;however,the relative importance of biodegradable dissolved organic carbon(BDOC)compared wit...Interactions between dissolved organic matter(DOM)and bacteria are central in the biogeochemical cycles of aquatic ecosystems;however,the relative importance of biodegradable dissolved organic carbon(BDOC)compared with other environmental variables in structuring the bacterial communities needs further investigation.Here,we investigated bacterial communities,chromophoric DOM(CDOM)characteristics and physico-chemical parameters as well as examined BDOC via bioassay incubations in large eutrophic Lake Taihu,China,to explore the importance of BDOC for shaping bacterial community structures and co-occurrence patterns.We found that the proportion of BDOC(%BDOC)correlated significantly and positively with the DOC concentration and the index of the contribution of recent produced autochthonous CDOM(BIX).%BDOC,further correlated positively with the relative abundance of the tryptophan-like component and negatively with CDOM aromaticity,indicating that autochthonous production of protein-like CDOM was an important source of BDOC.The richness of the bacterial communities correlated negatively with%BDOC,indicating an enhanced number of species in the refractory DOC environments.%BDOC was identified as a significant stronger factor than DOC in shaping bacterial community composition and the co-occurrence network,suggesting that substrate biodegradability is more significant than DOC quantity determining the bacterial communities in a eutrophic lake.Environmental factors explained a larger proportion of the variation in the conditionally rare and abundant subcommunity than for the abundant and the rare bacterial subcommunities.Our findings emphasize the importance of considering bacteria with different abundance patterns and DOC biodegradability when studying the interactions between DOM and bacteria in eutrophic lakes.展开更多
Denitrifying bacteria in epiphytic biofilms play a crucial role in nitrogen cycle in aquatic habitats.However,little is known about the connection between algae and denitrifying bacteria and their assembly processes i...Denitrifying bacteria in epiphytic biofilms play a crucial role in nitrogen cycle in aquatic habitats.However,little is known about the connection between algae and denitrifying bacteria and their assembly processes in epiphytic biofilms.Epiphytic biofilms were collected from submerged macrophytes(Patamogeton lucens and Najas marina L.)in the Caohai Lake,Guizhou,SW China,from July to November 2020 to:(1)investigate the impact of abiotic and biotic variables on denitrifying bacterial communities;(2)investigate the temporal variation of the algae-denitrifying bacteria co-occurrence networks;and(3)determine the contribution of deterministic and stochastic processes to the formation of denitrifying bacterial communities.Abiotic and biotic factors influenced the variation in the denitrifying bacterial community,as shown in the Mantel test.The co-occurrence network analysis unveiled intricate interactions among algae to denitrifying bacteria.Denitrifying bacterial community co-occurrence network complexity(larger average degrees representing stronger network complexity)increased continuously from July to September and decreased in October before increasing in November.The co-occurrence network complexity of the algae and nirS-encoding denitrifying bacteria tended to increase from July to November.The co-occurrence network complexity of the algal and denitrifying bacterial communities was modified by ammonia nitrogen(NH_(4)^(+)-N)and total phosphorus(TP),pH,and water temperature(WT),according to the ordinary least-squares(OLS)model.The modified stochasticity ratio(MST)results reveal that deterministic selection dominated the assembly of denitrifying bacterial communities.The influence of environmental variables to denitrifying bacterial communities,as well as characteristics of algal-bacterial co-occurrence networks and the assembly process of denitrifying bacterial communities,were discovered in epiphytic biofilms in this study.The findings could aid in the appropriate understanding and use of epiphytic biofilms denitrification function,as well as the enhancement of water quality.展开更多
Climate change and human activity have led to the degradation of desert wetlands.Free-living diazotrophs are vital for soil nitrogen input.However,a comprehensive understanding of how soil free-living diazotrophic com...Climate change and human activity have led to the degradation of desert wetlands.Free-living diazotrophs are vital for soil nitrogen input.However,a comprehensive understanding of how soil free-living diazotrophic communities and their co-occurrence patterns respond to desert wetland degradation is lacking.Here,quantitative polymerase chain reaction(qPCR),amplicon sequencing targeting nitrogenase gene(nifH),and network analysis were used to investigate the abundance,diversity,community composition,and co-occurrence patterns of soil free-living diazotrophs along the wetland degradation gradient,i.e.,non-degraded(ND),lightly degraded(LD),moderately degraded(MD),and severely degraded(SD),in the southeastern Mu Us Desert,northern China.The abundance and Shannon,Simpson,Chao 1,and ACE indexes decreased(P<0.05)by 14.6%,20.7%,2.1%,46.5%,and 45.0%,respectively,in SD wetland,whereas no significant difference(P>0.05)was observed between ND and LD wetlands.The relative abundance of Proteobacteria generally decreased(by 53.5%–19.7%)across the different degradation levels,while the relative abundance of Cyanobacteria increased(by 6.2%–40.1%)from ND to MD levels.The abundance,diversity,and community composition of diazotrophs were most strongly related to soil organic carbon,followed by total nitrogen,moisture,and pH.The least number of network nodes and edges and the lowest density were observed for MD and SD wetlands,indicating that the complexity of free-living diazotrophic networks was reduced by continued degeneration.Overall,severe desert wetland degradation affected the abundance,diversity,and network complexity of soil free-living diazotrophs more negatively than light degradation.This degradation promoted the growth of autotrophic diazotrophs and inhibited the growth of heterotrophic diazotrophs.These changes were mostly related to the loss of soil organic carbon.展开更多
The co-occurrence of bacteria and microeukaryote species is a ubiquitous ecological phenomenon,but there is limited cross-domain research in aquatic environments.We conducted a network statistical analysis and visuali...The co-occurrence of bacteria and microeukaryote species is a ubiquitous ecological phenomenon,but there is limited cross-domain research in aquatic environments.We conducted a network statistical analysis and visualization of microbial cross-domain co-occurrence patterns based on DNA sampling of a typical subtropical bay during four seasons,using high-throughput sequencing of both 18S rRNA and 16S rRNA genes.First,we found obvious relationships between network stability and network complexity indices.For example,increased cooperation and modularity were found to weaken the stability of cross-domain networks.Secondly,we found that bacterial operational taxonomic units(OTUs)were the most important contributors to network complexity and stability as they occupied more nodes,constituted more keystone OTUs,built more connections,more importantly,ignoring bacteria led to greater variation in network robustness.Gammaproteobacteria,Alphaproteobacteria,Bacteroidetes,and Actinobacteria were the most ecologically important groups.Finally,we found that the environmental drivers most associated with cross-domain networks varied across seasons(in detail,the network in January was primarily constrained by temperature and salinity,the network in April was primarily constrained by depth and temperature,the network in July was mainly affected by depth,temperature,and salinity,depth was the most important factor affecting the network in October)and that environmental influence was stronger on bacteria than on microeukaryotes.展开更多
The Western Subarctic Gyre(WSG)is one of the two gyre-systems in the subarctic North Pacific known for high nutrient and low-chlorophyll waters.However,the bacterioplankton in marine water of this area,either in terms...The Western Subarctic Gyre(WSG)is one of the two gyre-systems in the subarctic North Pacific known for high nutrient and low-chlorophyll waters.However,the bacterioplankton in marine water of this area,either in terms of the taxonomic composition or functional structure,remains relatively unexplored.A total of 22 sampling sites from two water layers(surface water,SW and 50-m layer water,FW)were collected in this area.The physiochemical parameters of waters,Synechococcus,and bacterial density,as well as the bacterioplankton community composition and distribution pattern,were analyzed.The nutrient concentrations of DIN,DIP,and DSi,Chl-a concentration,and the average abundance of heterobacteria in FW were higher than those in SW.However,temperature and the average abundance of Synechococcus and pico-eukaryotes were higher in SW.A total of 3269 OTUs were assigned,and 2123OTUs were commonly shared;moreover,similar alpha diversity patterns were observed in both SW and FW.The bacterioplankton community showed significantly obvious correlation with salinity,DIP,DIN,and Chl a in both SW and FW.Proteobacteria,Cyanobacteria,Bacteroidota,Actinobacteriota,and Firmicutes were the main phyla while Synechococcus_CC9902,Psychrobacter,and Sulfitobacter were the dominant genera in each sampling site.Most correlations that happened between the OTUs in the cooccurrence network were positive and inter-module.Higher edges and graph density were found in SW,indicating that more correlations occurred,and the community was more complex in SW.This study provided novel knowledge on the bacterioplankton community structure and the correlation characteristics in WSG.展开更多
基金the National Key R&D Program of China(No.2022YFD1700200).
文摘The development of fungicides is time-consuming and costly.Introducing a fungicide-likeness assessment strategy at the early screening stage can help reduce development risks and improve the success rate.However,existing assessment methods are often plagued by low accuracy and poor generalization,while fragment-based design strategies commonly fail to account for synergistic effects between structural units.Therefore,based on a small-scale sample set,this study developed a more efficient global predictive model for fungicidal activity—-named APPf—by integrating multi-scale feature screening methods and machine learning algorithms,which also accounts for synergistic effects among different structural fragments.We utilized three independent external test sets for model validation:External Test Set 1 for general validation,External Test Set 2 for comparison with existing models,and External Test Set 3 for disease-specific fungicide evaluation.On External Test Set 1,the APPf model achieved a precision of 0.6454,a recall of 0.8535,and an F1 score of 0.7350,demonstrating its robust predictive performance.It also exhibited strong enrichment capability for positive samples in External Test Set 2.For External Test Set 3,APPf achieved a prediction accuracy exceeding 80%for each disease,suggesting its promising potential in practical fungicide development.Furthermore,we quantified the contribution of molecular descriptors to the model predictions using SHAP value analysis and identified nHdNH and NssssNp as strong indicative features for predicting fungicidal activity,thereby enhancing the interpretability of the model.APPf has been deployed on a public web server(http://pesticides.cau.edu.cn/APPf),providing a user-friendly online prediction service to support the discovery of novel fungicides.Meanwhile,we employed a molecular fragmentation strategy to analyze the co-occurrence relationships between fragments in fungicides and constructed a network map of fragment co-occurrence associated with fungicidal activity.This study provides both an active fragment library and a global fungicide-likeness assessment tool for AI-based de novo molecular generation aimed at discovering novel fungicidal leads,which is expected to enhance the efficiency of developing new fungicides.
基金supported by the National Natural Science Foundation of China(U22A20501)the National Key Research and Development Plan of China(2022YFD1500601)+4 种基金the National Science and Technology Fundamental Resources Investigation Program of China(2018FY100304)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA28090200)the Liaoning Province Applied Basic Research Plan Program,China(2022JH2/101300184)the Shenyang Science and Technology Plan Program,China(21-109-305)the Liaoning Outstanding Innovation Team,China(XLYC2008015)。
文摘Land use influences soil biota community composition and diversity,and then belowground ecosystem processes and functions.To characterize the effect of land use on soil biota,soil nematode communities in crop land,forest land and fallow land were investigated in six regions of northern China.Generic richness,diversity,abundance and biomass of soil nematodes was the lowest in crop land.The richness and diversity of soil nematodes were 28.8and 15.1%higher in fallow land than in crop land,respectively.No significant differences in soil nematode indices were found between forest land and fallow land,but their network keystone genera composition was different.Among the keystone genera,50%of forest land genera were omnivores-predators and 36%of fallow land genera were bacterivores.The proportion of fungivores in forest land was 20.8%lower than in fallow land.The network complexity and the stability were lower in crop land than forest land and fallow land.Soil pH,NH_(4)^(+)-N and NO_(3)^(–)-N were the major factors influencing the soil nematode community in crop land while soil organic carbon and moisture were the major factors in forest land.Soil nematode communities in crop land influenced by artificial management practices were more dependent on the soil environment than communities in forest land and fallow land.Land use induced soil environment variation and altered network relationships by influencing trophic group proportions among keystone nematode genera.
基金the National Natural Science Foundation of China(No.81573150)Military Key Discipline Construction Projects of China(No.HL21JD1206).
文摘Objective:This study investigated trends in the study of phytochemical treatment of post-traumatic stress disorder(PTSD).Methods:The Web of Science database(2007-2022)was searched using the search terms“phytochemicals”and“PTSD,”and relevant literature was compiled.Network clustering co-occurrence analysis and qualitative narrative review were conducted.Results:Three hundred and one articles were included in the analysis of published research,which has surged since 2015 with nearly half of all relevant articles coming from North America.The category is dominated by neuroscience and neurology,with two journals,Addictive Behaviors and Drug and Alcohol Dependence,publishing the greatest number of papers on these topics.Most studies focused on psychedelic intervention for PTSD.Three timelines show an“ebb and flow”phenomenon between“substance use/marijuana abuse”and“psychedelic medicine/medicinal cannabis.”Other phytochemicals account for a small proportion of the research and focus on topics like neurosteroid turnover,serotonin levels,and brain-derived neurotrophic factor expression.Conclusion:Research on phytochemicals and PTSD is unevenly distributed across countries/regions,disciplines,and journals.Since 2015,the research paradigm shifted to constitute the mainstream of psychedelic research thus far,leading to the exploration of botanical active ingredients and molecular mechanisms.Other studies focus on anti-oxidative stress and anti-inflammation.
基金the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB15010101)the National Natural Science Foundation of China(41907039)the China Biodiversity Observation Networks(Sino BON).
文摘The elevational distributions of bacterial communities in natural mountain forests,especially along large elevational gradients,have been studied for many years.However,the distributional patterns that underlie variations in soil bacterial communities along small-scale elevational gradients in urban ecosystems are not yet well understood.Using Illumina MiSeq DNA sequencing,we surveyed soil bacterial communities at three elevations on Zijin Mountain in Nanjing City:the hilltop(300 m a.s.l.),the hillside(150 m a.s.l.),and the foot of the hill(0 m a.s.l.).The results showed that edaphic properties differed significantly with elevation.Bacterial community composition,rather than alpha diversity,strongly differed among the three elevations(Adonis:R2=0.12,P<0.01).Adonis and DistLM analyses demonstrated that bacterial community composition was highly correlated with soil pH,elevation,total nitrogen(TN),and dissolved organic carbon(DOC).The degree scores,betweenness centralities,and composition of keystone species were distinct among the elevations.These results demonstrate strong elevational partitioning in the distributions of soil bacterial communities along the gradient on Zijin Mountain.Soil pH and elevation together drove the smallscale elevational distribution of soil bacterial communities.This study broadens our understanding of distribution patterns and biotic co-occurrence associations of soil bacterial communities from large elevational gradients to short elevational gradients.
基金supported by the National Program on Key Basic Research Project(Grant No.2022YFD1500202)the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDA28020202)the National Natural Science Foundation of China(Grant No.42277308).
文摘We identified a sporocarp as Agrocybe dura growing next to a living corn using PacBio sequencing.The mycoparasitism of Trichoderma spp.on A.dura were revealed by the co-occurrence network analysis.For long-read HTS data,we updated a bioinformatic pipeline to enhance fungal taxonomic resolution.In forests,fungal sporocarps house the diverse fungicolous fungi;however,the relationships of sporocarps and associated fungal communities are rarely explored in agroecosystems.In a corn field near Gongzhuling City,Jilin Province,China,we found an epigeous sporocarp with agaricoid morphology that could grow next to the living corn plants.Using PacBio metabarcoding combined with an updated bioinformatic pipeline,we surveyed the fungal community profile along its cap,rhizomorph and hyphosphere soil at a much-improved taxonomic resolution.We identified the sporocarp,at a high probability,as Agrocybe dura,and this mushroom was significantly negatively correlated with Trichoderma hamatum and T.harzianum in the co-occurrence network.Fungal diversity in hyphosphere habitat was significantly higher than that in cap and rhizomorph habitats.Consistent with the pattern in fungal diversity,the node number,edge number,network diameter and average degree were significantly higher in hyphosphere habitat than other habitats.However,both the negative and positive cohesion were significantly higher in rhizomorph habitat than other habitats.Moreover,the z-c plot identified A.dura as the only network hub,linking multiple fungal species.The results give us a glimpse of the ecological relevance of saprobic mushrooms across the extensive northeastern black soil region of China.Our findings will aid in the assessment and forecasting of fungal diversity hotspots and their relationships with soil fertility in the‘Golden Corn Belt’of northeast China.
文摘Understanding the fundamental drivers of large-scale species co-occurrence is a critical issue in ecology and conservation research. Here, we assessed foraging guilds, habitat type and disturbances as drivers of bird species co-occurrence in Ghana's Central Region over six months. Birds were sampled in 120 points across six different habitat types (farmland, forest reserve, urban area, coastal savannah, wetland, and mangrove), using the point-centred count technique. In total, 4060 individuals belonging to 216 species were recorded across all six habitat types. We found that co-occurring species were more similar in their foraging behaviour and habitat association. About 60% of the birds were found to co-occur randomly, 15% co-occurred negatively, and 25% co-occurred positively. Carnivores like the Black Heron (Egretta ardesiaca) and Spur-winged Lapwing (Vanellus spinosus) randomly co-occurred with other guild groups and were dominant in the mangroves and wetlands. Frugivores from forest reserves had only a 25% chance of randomly co-occurring with other birds and about a 60% chance of positively co-occurring with other birds. Our findings suggest that foraging guilds and habitat type are major factors driving bird co-occurrence and community assemblages in this West African suburban region.
基金Funded by Ningbo Natural Science Foundation (No.2006A610016)
文摘Classifying the texture of granules in 2D images has aroused manifold research atten-tion for its technical challenges in image processing areas.This letter presents an aggregate texture identification approach by jointly using Gray Level Co-occurrence Probability(GLCP) and BP neural network techniques.First, up to 8 GLCP-associated texture feature parameters are defined and computed, and these consequent parameters next serve as the inputs feeding to the BP neural network to calculate the similarity to any of given aggregate texture type.A finite number of aggregate images of 3 kinds, with each containing specific type of mineral particles, are put to the identification test, experimentally proving the feasibility and robustness of the proposed method.
基金supported by the National Natural Science Foundation of China(41977192)Zhejiang Provincial Natural Science Foundation of China(LY21D060004)+2 种基金Natural Science Foundation of Ningbo(2021J060 and 2019A610449)Fundamental Research Funds for the Provincial Universities of Zhejiang(SJLY2022001)K.C.Wong Magna Fund in Ningbo University
文摘Background Bacteria,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 diferent domains in coastal ecosystems;however,knowledge of specifc 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-ofshore continuum in the East China Sea.Results Overall,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-ofshore continuum.Specifcally,the nearshore zones with intermediate levels of terrestrial impacts refected 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 ofshore 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.Conclusions Our work ofers 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.
基金This research was supported by the National Natural Science Foundation of China(31971553,32222051,and 31361123001)the National Science Foundation of the United States of America(DEB-1342754 and DEB-1856318)+1 种基金the Shanghai Rising-Star ProgramP.W.was supported by the research fund of the post-doctor who came to Shenzhen(szbo202306).
文摘Impact statement Habitat loss has been a primary threat to biodiversity.However,species do not function in isolation but often associate with each other and form complex networks.Thus,revealing how the network complexity and stability scale with habitat area will give us more insights into the effects of habitat loss on ecosystems.In this study,we explored the relationships between the island area and the network complexity and stability of soil microbes.We found that the complexity and stability of soil microbial co‐occurrence networks scale positively with island area,indicating that habitat loss will potentially simplify and destabilize soil microbial networks.
基金This study was supported by the Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(SML2021SP203,313022004)the National Natural Science Foundation of China(32102821,92051120)+4 种基金the Yongjiang Talent Introduction Programme,the Natural Science Foundation of Ningbo(2022J050)the Zhejiang Major Program of Science and Technology(2021C02069-5-4)the Key Research and Development Program of Zhejiang Province(2019C02054)the Key Research and Development Program of Ningbo(2022Z172)China Agriculture Research System of MOF and MARA.
文摘Microeukaryotes and bacteria are key drivers of primary productivity and nutrient cycling in aquaculture ecosystems.Although their diversity and composition have been widely investigated in aquaculture systems,the co-occurrence bipartite network between microeukaryotes and bacteria remains poorly understood.This study used the bipartite network analysis of high-throughput sequencing datasets to detect the co-occurrence relationships between microeukaryotes and bacteria in water and sediment from coastal aquaculture ponds.Chlorophyta and fungi were dominant phyla in the microeukaryotic–bacterial bipartite networks in water and sediment,respectively.Chlorophyta also had overrepresented links with bacteria in water.Most microeukaryotes and bacteria were classified as generalists,and tended to have symmetric positive and negative links with bacteria in both water and sediment.However,some microeukaryotes with high density of links showed asymmetric links with bacteria in water.Modularity detection in the bipartite network indicated that four microeukaryotes and twelve uncultured bacteria might be potential keystone taxa among the module connections.Moreover,the microeukaryotic–bacterial bipartite network in sediment harbored significantly more nestedness than that in water.The loss of microeukaryotes and generalists will more likely lead to the collapse of positive co-occurrence relationships between microeukaryotes and bacteria in both water and sediment.This study unveils the topology,dominant taxa,keystone species,and robustness in the microeukaryotic–bacterial bipartite networks in coastal aquaculture ecosystems.These species herein can be applied for further management of ecological services,and such knowledge may also be very useful for the regulation of other eutrophic ecosystems.
基金Supported by Key Research and Development Program of Shaanxi Province,China,No.2024SF-YBXM-078.
文摘BACKGROUND Non-suicidal self-injury(NSSI)is common among adolescents with depressive disorders and poses a major public health challenge.Rumination,a key cognitive feature of depression,includes different subtypes that may relate to NSSI through distinct psychological mechanisms.However,how these subtypes interact with specific NSSI behaviors remains unclear.AIM To examine associations between rumination subtypes and specific NSSI behaviors in adolescents.METHODS We conducted a cross-sectional study with 305 hospitalized adolescents diagnosed with depressive disorders.The subjects ranged from 12-18 years in age.Rumi-nation subtypes were assessed using the Ruminative Response Scale,and 12 NSSI behaviors were evaluated using a validated questionnaire.Network analysis was applied to explore symptom-level associations and identify central symptoms.RESULTS The network analysis revealed close connections between rumination subtypes and NSSI behaviors.Brooding was linked to behaviors such as hitting objects and burning.Scratching emerged as the most influential NSSI symptom.Symptomfocused rumination served as a key bridge connecting rumination and NSSI.CONCLUSION Symptom-focused rumination and scratching were identified as potential intervention targets.These findings highlight the psychological significance of specific cognitive-behavioral links in adolescent depression and suggest directions for tailored prevention and treatment.However,the cross-sectional,single-site design limits causal inference and generalizability.Future longitudinal and multi-center studies are needed to confirm causal pathways and verify the generalizability of the findings to broader adolescent populations.
基金supported by grants from the National Natural Science Foundation of China(82004252)the Project of Administration of Traditional Chinese Medicine of Guangdong Province(202405112017596500)the Basic and Applied Basic Research Foundation of Guangzhou Municipal Science and Technology Bureau(202102020533).
文摘Background:Wenqing Yin(WQY)is a classic prescription used to treat skin diseases like atopic dermatitis(AD)in China,and the aim of this study is to investigate the therapeutic effects and molecular mechanisms of WQY on AD.Methods:The DNFB-induced mouse models of AD were established to investigate the therapeutic effects of WQY on AD.The symptoms of AD in the ears and backs of the mice were assessed,while inflammatory factors in the ear were quantified using quantitative real-time-polymerase chain reaction(qRT-PCR),and the percentages of CD4^(+)and CD8^(+)cells in the spleen were analyzed through flow cytometry.The compounds in WQY were identified using ultra-performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS)analysis and the key targets and pathways of WQY to treat AD were predicted by network pharmacology.Subsequently,the key genes were tested and verified by qRT-PCR,and the potential active components and target proteins were verified by molecular docking.Results:WQY relieved the AD symptoms and histopathological injuries in the ear and back skin of mice with AD.Meanwhile,WQY significantly reduced the levels of inflammatory factors IL-6 and IL-1βin ear tissue,as well as the ratio of CD4^(+)/CD8^(+)cells in spleen.Additionally,a total of 142 compounds were identified from the water extract of WQY by UPLC-Orbitrap-MS/MS.39 key targets related to AD were screened out by network pharmacology methods.The KEGG analysis indicated that the effects of WQY were primarily mediated through pathways associated with Toll-like receptor signaling and T cell receptor signaling.Moreover,the results of qRT-PCR demonstrated that WQY significantly reduced the mRNA expressions of IL-4,IL-10,GATA3 and FOXP3,and molecular docking simulation verified that the active components of WQY had excellent binding abilities with IL-4,IL-10,GATA3 and FOXP3 proteins.Conclusion:The present study demonstrated that WQY effectively relieved AD symptoms in mice,decreased the inflammatory factors levels,regulated the balance of CD4^(+)and CD8^(+)cells,and the mechanism may be associated with the suppression of Th2 and Treg cell immune responses.
基金supported by Istanbul Technical University(Project No.45698)supported through the“Young Researchers’Career Development Project-training of doctoral students”of the Croatian Science Foundation.
文摘This paper investigates the reliability of internal marine combustion engines using an integrated approach that combines Fault Tree Analysis(FTA)and Bayesian Networks(BN).FTA provides a structured,top-down method for identifying critical failure modes and their root causes,while BN introduces flexibility in probabilistic reasoning,enabling dynamic updates based on new evidence.This dual methodology overcomes the limitations of static FTA models,offering a comprehensive framework for system reliability analysis.Critical failures,including External Leakage(ELU),Failure to Start(FTS),and Overheating(OHE),were identified as key risks.By incorporating redundancy into high-risk components such as pumps and batteries,the likelihood of these failures was significantly reduced.For instance,redundant pumps reduced the probability of ELU by 31.88%,while additional batteries decreased the occurrence of FTS by 36.45%.The results underscore the practical benefits of combining FTA and BN for enhancing system reliability,particularly in maritime applications where operational safety and efficiency are critical.This research provides valuable insights for maintenance planning and highlights the importance of redundancy in critical systems,especially as the industry transitions toward more autonomous vessels.
基金supported by the National Social Science Foundation of China (09BYY024 and 11&ZD188)
文摘This study investigates the feasibility of applying complex networks to fine-grained language classification and of employing word co-occurrence networks based on parallel texts as a substitute for syntactic dependency networks in complex-network-based language classification.14 word co-occurrence networks were constructed based on parallel texts of 12 Slavic languages and 2 non-Slavic languages,respectively.With appropriate combinations of major parameters of these networks,cluster analysis was able to distinguish the Slavic languages from the non-Slavic and correctly group the Slavic languages into their respective sub-branches.Moreover,the clustering could also capture the genetic relationships of some of these Slavic languages within their sub-branches.The results have shown that word co-occurrence networks based on parallel texts are applicable to fine-grained language classification and they constitute a more convenient substitute for syntactic dependency networks in complex-network-based language classification.
基金supported by the National Natural Science Foundation of China (Nos.41930760, 41807362, and 41977322)the Provincial Natural Science Foundation of Jiangsu in China (No.BK20181104)+2 种基金the Key Research Program of Frontier Sciences, Chinese Academy of Sciences (No.QYZDB-SSWDQC016)supported by WATEC (Centre for Water Technology, AU)the TüBITAK outstanding scientists program 2232 (project 118C250)。
文摘Interactions between dissolved organic matter(DOM)and bacteria are central in the biogeochemical cycles of aquatic ecosystems;however,the relative importance of biodegradable dissolved organic carbon(BDOC)compared with other environmental variables in structuring the bacterial communities needs further investigation.Here,we investigated bacterial communities,chromophoric DOM(CDOM)characteristics and physico-chemical parameters as well as examined BDOC via bioassay incubations in large eutrophic Lake Taihu,China,to explore the importance of BDOC for shaping bacterial community structures and co-occurrence patterns.We found that the proportion of BDOC(%BDOC)correlated significantly and positively with the DOC concentration and the index of the contribution of recent produced autochthonous CDOM(BIX).%BDOC,further correlated positively with the relative abundance of the tryptophan-like component and negatively with CDOM aromaticity,indicating that autochthonous production of protein-like CDOM was an important source of BDOC.The richness of the bacterial communities correlated negatively with%BDOC,indicating an enhanced number of species in the refractory DOC environments.%BDOC was identified as a significant stronger factor than DOC in shaping bacterial community composition and the co-occurrence network,suggesting that substrate biodegradability is more significant than DOC quantity determining the bacterial communities in a eutrophic lake.Environmental factors explained a larger proportion of the variation in the conditionally rare and abundant subcommunity than for the abundant and the rare bacterial subcommunities.Our findings emphasize the importance of considering bacteria with different abundance patterns and DOC biodegradability when studying the interactions between DOM and bacteria in eutrophic lakes.
基金Supported by the National Natural Science Foundation of China(No.41867056)the Guizhou Provincial Key Technology R&D Program(Nos.2021470,2023216)。
文摘Denitrifying bacteria in epiphytic biofilms play a crucial role in nitrogen cycle in aquatic habitats.However,little is known about the connection between algae and denitrifying bacteria and their assembly processes in epiphytic biofilms.Epiphytic biofilms were collected from submerged macrophytes(Patamogeton lucens and Najas marina L.)in the Caohai Lake,Guizhou,SW China,from July to November 2020 to:(1)investigate the impact of abiotic and biotic variables on denitrifying bacterial communities;(2)investigate the temporal variation of the algae-denitrifying bacteria co-occurrence networks;and(3)determine the contribution of deterministic and stochastic processes to the formation of denitrifying bacterial communities.Abiotic and biotic factors influenced the variation in the denitrifying bacterial community,as shown in the Mantel test.The co-occurrence network analysis unveiled intricate interactions among algae to denitrifying bacteria.Denitrifying bacterial community co-occurrence network complexity(larger average degrees representing stronger network complexity)increased continuously from July to September and decreased in October before increasing in November.The co-occurrence network complexity of the algae and nirS-encoding denitrifying bacteria tended to increase from July to November.The co-occurrence network complexity of the algal and denitrifying bacterial communities was modified by ammonia nitrogen(NH_(4)^(+)-N)and total phosphorus(TP),pH,and water temperature(WT),according to the ordinary least-squares(OLS)model.The modified stochasticity ratio(MST)results reveal that deterministic selection dominated the assembly of denitrifying bacterial communities.The influence of environmental variables to denitrifying bacterial communities,as well as characteristics of algal-bacterial co-occurrence networks and the assembly process of denitrifying bacterial communities,were discovered in epiphytic biofilms in this study.The findings could aid in the appropriate understanding and use of epiphytic biofilms denitrification function,as well as the enhancement of water quality.
基金supported by the National Natural Science Foundation of China(No.41471437)the National Key R&D Program of China(Nos.2016YFA0600801,2017YFC0504504)the West Light Foundation of the Chinese Academy of Sciences(No.XAB2016A04).
文摘Climate change and human activity have led to the degradation of desert wetlands.Free-living diazotrophs are vital for soil nitrogen input.However,a comprehensive understanding of how soil free-living diazotrophic communities and their co-occurrence patterns respond to desert wetland degradation is lacking.Here,quantitative polymerase chain reaction(qPCR),amplicon sequencing targeting nitrogenase gene(nifH),and network analysis were used to investigate the abundance,diversity,community composition,and co-occurrence patterns of soil free-living diazotrophs along the wetland degradation gradient,i.e.,non-degraded(ND),lightly degraded(LD),moderately degraded(MD),and severely degraded(SD),in the southeastern Mu Us Desert,northern China.The abundance and Shannon,Simpson,Chao 1,and ACE indexes decreased(P<0.05)by 14.6%,20.7%,2.1%,46.5%,and 45.0%,respectively,in SD wetland,whereas no significant difference(P>0.05)was observed between ND and LD wetlands.The relative abundance of Proteobacteria generally decreased(by 53.5%–19.7%)across the different degradation levels,while the relative abundance of Cyanobacteria increased(by 6.2%–40.1%)from ND to MD levels.The abundance,diversity,and community composition of diazotrophs were most strongly related to soil organic carbon,followed by total nitrogen,moisture,and pH.The least number of network nodes and edges and the lowest density were observed for MD and SD wetlands,indicating that the complexity of free-living diazotrophic networks was reduced by continued degeneration.Overall,severe desert wetland degradation affected the abundance,diversity,and network complexity of soil free-living diazotrophs more negatively than light degradation.This degradation promoted the growth of autotrophic diazotrophs and inhibited the growth of heterotrophic diazotrophs.These changes were mostly related to the loss of soil organic carbon.
基金Supported by the National Natural Science Foundation of China(Nos.42141003,42176147)the National Key Research and Development Program of China(No.2022YFF0802204)the Natural Science Foundation of Fujian Province of China(No.2021J01025)。
文摘The co-occurrence of bacteria and microeukaryote species is a ubiquitous ecological phenomenon,but there is limited cross-domain research in aquatic environments.We conducted a network statistical analysis and visualization of microbial cross-domain co-occurrence patterns based on DNA sampling of a typical subtropical bay during four seasons,using high-throughput sequencing of both 18S rRNA and 16S rRNA genes.First,we found obvious relationships between network stability and network complexity indices.For example,increased cooperation and modularity were found to weaken the stability of cross-domain networks.Secondly,we found that bacterial operational taxonomic units(OTUs)were the most important contributors to network complexity and stability as they occupied more nodes,constituted more keystone OTUs,built more connections,more importantly,ignoring bacteria led to greater variation in network robustness.Gammaproteobacteria,Alphaproteobacteria,Bacteroidetes,and Actinobacteria were the most ecologically important groups.Finally,we found that the environmental drivers most associated with cross-domain networks varied across seasons(in detail,the network in January was primarily constrained by temperature and salinity,the network in April was primarily constrained by depth and temperature,the network in July was mainly affected by depth,temperature,and salinity,depth was the most important factor affecting the network in October)and that environmental influence was stronger on bacteria than on microeukaryotes.
基金Supported by the National Key Research and Development Program of China(No.2019YFD0901401)the Natural Science Foundation of Shandong Province(No.ZR202102280248)+1 种基金the National Natural Science Foundation of China(No.81900630)the Outstanding Youth Project of Yunnan Provincial Department of Science and Technology(No.2019F1019)。
文摘The Western Subarctic Gyre(WSG)is one of the two gyre-systems in the subarctic North Pacific known for high nutrient and low-chlorophyll waters.However,the bacterioplankton in marine water of this area,either in terms of the taxonomic composition or functional structure,remains relatively unexplored.A total of 22 sampling sites from two water layers(surface water,SW and 50-m layer water,FW)were collected in this area.The physiochemical parameters of waters,Synechococcus,and bacterial density,as well as the bacterioplankton community composition and distribution pattern,were analyzed.The nutrient concentrations of DIN,DIP,and DSi,Chl-a concentration,and the average abundance of heterobacteria in FW were higher than those in SW.However,temperature and the average abundance of Synechococcus and pico-eukaryotes were higher in SW.A total of 3269 OTUs were assigned,and 2123OTUs were commonly shared;moreover,similar alpha diversity patterns were observed in both SW and FW.The bacterioplankton community showed significantly obvious correlation with salinity,DIP,DIN,and Chl a in both SW and FW.Proteobacteria,Cyanobacteria,Bacteroidota,Actinobacteriota,and Firmicutes were the main phyla while Synechococcus_CC9902,Psychrobacter,and Sulfitobacter were the dominant genera in each sampling site.Most correlations that happened between the OTUs in the cooccurrence network were positive and inter-module.Higher edges and graph density were found in SW,indicating that more correlations occurred,and the community was more complex in SW.This study provided novel knowledge on the bacterioplankton community structure and the correlation characteristics in WSG.
