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
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
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
Popular fermented golden pomfret(Trachinotus ovatus)is prepared via spontaneous fermentation;however,the mechanisms underlying the regulation of its flavor development remain unclear.This study shows the roles of the ...Popular fermented golden pomfret(Trachinotus ovatus)is prepared via spontaneous fermentation;however,the mechanisms underlying the regulation of its flavor development remain unclear.This study shows the roles of the complex microbiota and the dynamic changes in microbial community and flavor compounds during fish fermentation.Single-molecule real-time sequencing and molecular networking analysis revealed the correlations among different microbial genera and the relationships between microbial taxa and volatile compounds.Mechanisms underlying flavor development were also elucidated via KEGG based functional annotations.Clostridium,Shewanella,and Staphylococcus were the dominant microbial genera.Forty-nine volatile compounds were detected in the fermented fish samples,with thirteen identified as characteristic volatile compounds(ROAV>1).Volatile profiles resulted from the interactions among the microorganisms and derived enzymes,with the main metabolic pathways being amino acid biosynthesis/metabolism,carbon metabolism,and glycolysis/gluconeogenesis.This study demonstrated the approaches for distinguishing key microbiota associated with volatile compounds and monitoring the industrial production of high-quality fermented fish products.展开更多
Atmospheric nitrogen(N)deposition is predicted to increase,especially in the subtropics.However,the responses of soil microorganisms to long-term N addition at the molecular level in N-rich subtropical forests have no...Atmospheric nitrogen(N)deposition is predicted to increase,especially in the subtropics.However,the responses of soil microorganisms to long-term N addition at the molecular level in N-rich subtropical forests have not been clarified.A long-term nutrient addition experiment was conducted in a subtropical evergreen old-growth forest in China.The four treatments were:control,low N(50 kg N ha^(-1)a^(-1)),high N(100 kg N ha^(-1)a^(-1)),and combined N and phosphorus(P)(100 kg N ha^(-1)a^(-1)+50 kg P ha^(-1)a^(-1)).Metagenomic sequencing characterized diversity and composition of soil microbial communities and used to construct bacterial/fungal co-occurrence networks.Nutrient-treated soils were more acidic and had higher levels of dissolved organic carbon than controls.There were no significant differences in microbial diversity and community composition across treatments.The addition of nutrients increased the abundance of copiotrophic bacteria and potentially beneficial microorganisms(e.g.,Gemmatimonadetes,Chaetomium,and Aureobasidium).Low N addition increased microbiome network connectivity.Three rare fungi were identified as module hubs under nutrient addition,indicating that low abundance fungi were more sensitive to increased nutrients.The results indicate that the overall composition of microbial communities was stable but not static to long-term N addition.Our findings provide new insights that can aid predictions of the response of soil microbial communities to long-term N addition.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 microbial communities colonized on microplastics(MPs)have attracted widespread attention.However,few studies focused on the MPs impacts on mangrove ecosystems,particularly on bacterial communities.We investigated ...The microbial communities colonized on microplastics(MPs)have attracted widespread attention.However,few studies focused on the MPs impacts on mangrove ecosystems,particularly on bacterial communities.We investigated the MPs pollution in mangrove of Zhujiang(Pearl)River estuary(ZRE).To study the potential risk posed by MPs to the mangrove ecosystems,the differences in bacterial communities,functions,and complexity between MPs and sediment samples were reported for the first time.Microplastics(2991±1586 items/kg dry weight(dw))in sediment were mainly fibers and polyethylene,mostly transparent,and in size less than 0.5 mm.Bacterial communities and functions significantly differed from MPs in mangrove sediment.Compared with sediment,MPs significantly enriched members of Proteobacteria,Bacteroidetes,and Actinobacteria,as well as the bacteria associated with plastic-degrading and human diseases on their surface,suggesting that microbial communities on MPs may promote MPs degradation and the spread of diseases,posing potential risk to mangrove ecosystems and human health.Although bacteria on MPs exhibited a lower diversity,the co-occurrence network analysis indicated that network of bacteria colonized on MPs was bigger and more complex than those of mangrove sediment,illustrating that MPs can act as a distinct habitat in this special ecosystem.This study provides a new perspective for increasing our understanding of microplastic pollution in mangrove ecosystems.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
Soil fungi in forest ecosystems have great potential to enhance host plant growth and systemic ecological functions and services.Reforestation at Saihanba Mechanized Forest Farm,the world's largest artificial plan...Soil fungi in forest ecosystems have great potential to enhance host plant growth and systemic ecological functions and services.Reforestation at Saihanba Mechanized Forest Farm,the world's largest artificial plantation,has been integral to global forest ecosystem preservation since the 1950s.To better assess the ecological effects of soil microbiology after afforestation,fungal diversity and community structure(using Illumina sequencing)from forests dominated by Larix gmelinii var.principis-rupprechtii,Pinus sylvestris var.mongolica and Picea asperata,and from grassland were surveyed.In total,4,540 operational taxonomic units(OTUs)were identified,with Mortierella and Solicoccozyma being the dominant genera of grassland soil and Inocybe,Cortinarius,Piloderma,Tomentella,Sebacina,Hygrophorus and Saitozyma dominating the plantation soil.Principle coordinate analysis(PCoA)and co-occurrence networks revealed differences in fungal structure after afforestation.Significantly,more symbiotroph guilds were dominated by ectomycorrhizal fungi in plantations under the prediction of FUNGuild.The community composition and diversity of soil fungi were significantly influenced by pH via redundancy analysis(RDA)and the Mantel test(p<0.01).This finding emphasizes that soil pH has a strong effect on the transition of fungal communities and functional taxa from grassland to plantation,providing a novel indicator for forest restoration.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
Synechococcus is one of the most abundant picocyanobacteria in marine ecosystem,and the absence of Prochlorococcus would make it indispensable as a primary producer in the Bohai Sea,North China.However,the abundance d...Synechococcus is one of the most abundant picocyanobacteria in marine ecosystem,and the absence of Prochlorococcus would make it indispensable as a primary producer in the Bohai Sea,North China.However,the abundance distribution and genetic diversity of Synechococcus in this region have rarely been reported.In this study,the distribution pattern of Synechococcus abundance was investigated during four cruises in April,June,August,and November from 2018 to 2019,moreover,its phenogenetic diversity was studied based on high-throughput sequencing of the cpe BA operon.The results demonstrate that phycoerythrin-containing Synechococcus was most abundant in August when temperature was high and oxygen saturation was low.During this period,Synechococcus pigment type(PT)2 was abundant in the Bohai Bay and Laizhou Bay under conditions of high nutrient concentration,temperature,and turbidity.In comparison,PT3,especially those clusters characterized with high or variable ratio of phycourobilin and phycoerythrobilin,was predominant in the Bohai Strait and Liaodong Bay under conditions of high salinity,pH,and oxygen saturation.Furthermore,co-occurrence correlations using network analysis revealed that Synechococcus PTs were related to 15.37%-43.48%of the prokaryotic genera.Synechococcus PT3c/PT3d and PT2 were the most important PTs in the network.The hierarchical clustering revealed that taxa co-occurred with Synechococcus PTs diff ered among samples.It could be attributed to the substance exchange and the environmental impact,which calls for more studies in the future.展开更多
Synechococcus is a widely distributed photosynthetic pico-phytoplankton,which contributes mainly to carbon fixation and maintains the stability of the marine ecosystem.To investigate its distribution patterns in the Y...Synechococcus is a widely distributed photosynthetic pico-phytoplankton,which contributes mainly to carbon fixation and maintains the stability of the marine ecosystem.To investigate its distribution patterns in the Yellow Sea,seawater samples were collected during September 2018.Results of flow cytometry analysis showed that the Synechococcus abundance ranged from 6.36×10^(2) to 4.51×10^(4) cells mL^(−1),which correlated with salinity(P<0.01)and temperature(P<0.05).At deeper off-shore sites,Synecho-coccus showed high abundance at the subsurface thermo-halocline,which was in accordance with chlorophyll a(Chl a)content along the vertical column.Based on the high-throughput sequencing data of rpoC1(partial gene encoding RNA polymerase),two Synechococcus subclusters,S5.1 and S5.2,were found to coexist in the studied area.Several clades of S5.1,including Clades I,II,and III,were the dominant components,accounting for 6.63%,26.11%,and 45.5%of the total genus,respectively.Redundancy analysis(RDA)showed that nitrite was the main environmental factor that explained the genus composition among samples.Fur-thermore,co-occurrence network revealed that the main phyla that coexisted with Synechococcus were Proteobacteria,Bacteroidetes,Actinobacteria,Planctomycetes,and Verrucomicrobia,which were involved in the carbon(C),nitrogen(N),sulfur(S),and manga-nese(Mn)cycles.Overall,Synechococcus exhibited biogeographic distribution correlated with temperature-salinity and nitrite in the Yellow Sea,and their geochemical function showed diverse but should be further verified in the future.展开更多
Complex network theory has been increasingly used in various research areas,including agroecosystems.This paper summarizes the basic concepts and approaches commonly used in complex network theory,and then reviews rec...Complex network theory has been increasingly used in various research areas,including agroecosystems.This paper summarizes the basic concepts and approaches commonly used in complex network theory,and then reviews recent studies on the applications in agroecosystems of three types of common ecological networks,i.e.,food webs,pollination networks and microbial co-occurrence networks.In general,agricultural intensification is considered to be a key driver of the change of agroecosystems.It causes the simplification of landscape,leads to the loss of biocontrol through cascading effect in food webs,and also reduces the complexity and connectance of soil food webs.For pollination networks,agricultural intensification impaired the robustness by reducing specialization and enhancing generality.The microbial co-occurrence networks with high connectance and low modularity generally corresponded to high efficiency in utilization of nutrients,and high resistance to crop pathogens.This review aims to show the readers the advances of ecological networks in agroecosystems and inspire the researchers to conduct their studies in a new network perspective.展开更多
The public content increasingly available on the Internet, especially in online forums, enables researchers to study society in new ways. However, qualitative analysis of online forums is very time consuming and most ...The public content increasingly available on the Internet, especially in online forums, enables researchers to study society in new ways. However, qualitative analysis of online forums is very time consuming and most content is not related to researchers’ interest. Consequently, analysts face the following problem: how to efficiently explore and select the content to be analyzed? This article introduces a new process to support analysts in solving this problem. This process is based on unsupervised machine learning techniques like hierarchical clustering and term co-occurrence network. A tool that helps to apply the proposed process was created to provide consolidated and structured results. This includes measurements and a content exploration interface.展开更多
Responses of soil DIRB to lignocellulosic fractions during a 6-week microcosm incubation were investigated.Anaeromyxobacter,Bacillus,and Clostridium maintained their domi-nance throughout the incubation.Distinct DIRB ...Responses of soil DIRB to lignocellulosic fractions during a 6-week microcosm incubation were investigated.Anaeromyxobacter,Bacillus,and Clostridium maintained their domi-nance throughout the incubation.Distinct DIRB groups proliferated under specific lignocellulosic fraction amendments.Limits of insufficient ferric iron on the proliferation varied by DIRB group.Dissimilatory iron reducing bacteria(DIRB)are phylogenetically and physi-ologically diverse in paddy soils,where iron reduction closely couples with the oxidation of rice straw-derived carbon in the straw returning scenarios.However,few studies have addressed the niche differentiation within DIRB groups during the degradation of lignocellulosic fractions of rice straw.This study conducted a 6-week microcosm incubation experiment to reveal the distinct responses of DIRB groups under specific lignocellulosic fraction amendments with and without ferrihydrite(Fh)addition in a flooded paddy Ultisol.Results showed that the total absolute abundance of the 19 detected DIRB groups did not vary significantly during the incubation.Anaeromyxobacter,Bacillus,and Clostridium were the dominant DIRB groups for all lignocellulosic treatments whereas Thermincola was dominant but only under xylan amendment with Fh addition.DIRB-nodes in the co-occurrence networks of bacterial community mainly belonged to Anaeromyxobacter and Bacillus.Clostridium and Thermincola,Alkaliphilus and Anaeromyxobacter,and Alicyclobacillus,Desulfobulbus,and Desulfosporosinus were specifically proliferated under xylan,cellulose,and lignin amendments,respectively.Whether the proliferation was limited by insufficient ferric iron varied by bacterial group.These findings suggested the lignocellulosic fraction-induced niche differentiation within DIRB groups,which advanced our understanding of the ecology of DIRB in paddy soils under straw returning.展开更多
The nirS-type denitrifying bacterial community is the main drivers of the nitrogen loss process in drinking water reservoir ecosystems.The temporal patterns in nirS gene abundance and nirS-type denitrifying bacterial ...The nirS-type denitrifying bacterial community is the main drivers of the nitrogen loss process in drinking water reservoir ecosystems.The temporal patterns in nirS gene abundance and nirS-type denitrifying bacterial community harbored in aerobic water layers of drinking water reservoirs have not been studied well.In this study,quantitative polymerase chain reaction(qPCR)and Illumina Miseq sequencing were employed to explore the nirS gene abundance and denitrifying bacterial community structure in two drinking water reservoirs.The overall results showed that the water quality parameters in two reservoirs had obvious differences.The qPCR results suggested that nirS gene abundance ranged from(2.61±0.12)×10^(5) to(3.68±0.16)×10^(5) copies/mL and(3.01±0.12)×10^(5) to(5.36±0.31)×10^(5) copies/mL in Jinpen and Lijiahe reservoirs,respectively.The sequencing results revealed that Paracoccus sp.,Azoarcus sp.,Dechloromonas sp.and Thauera sp.were the dominant genera observed.At species level,Cupriavidus necator,Dechloromonas sp.R-28400,Paracoccus denitrificans and Pseudomonas stutzeri accounted for more proportions in two reservoirs.More importantly,the co-occurrence network analysis demonstrated that Paracoccus sp.R-24615 and Staphylococcus sp.N23 were the keystone species observed in Jinpen and Lijiahe reservoirs,respectively.Redundancy analysis indicated that water quality(particularly turbidity,water temperature,pH and Chlorophyll a)and sampling time had significant influence on the nirS-type denitrifying bacterial community in both reservoirs.These results will shed new lights on exploring the dynamics of nirS-type denitrifying bacteria in aerobic water layers of drinking water reservoirs.展开更多
Symbiotic microbiomes of Sphagnum have been confirmed to play a fundamental role in carbon and nitrogen cycles, however, little is known about microbiomes associated with other bryophytes in subtropical peatland ecosy...Symbiotic microbiomes of Sphagnum have been confirmed to play a fundamental role in carbon and nitrogen cycles, however, little is known about microbiomes associated with other bryophytes in subtropical peatland ecosystems. To explore the differences in community structure, metabolic potential and interaction relationship of bacterial microbiomes associated with different bryophytes species, the gametophytes of three bryophyte species(Sphagnum palustre, Aulacomnium androgynum, and Polytrichum commune) and their underlying peat sediments were collected from the subtropical Dajiuhu Peatland and subjected to Illumina high-throughout sequencing of 16S r RNA gene. Results showed that bacterial diversity was lowest in S. palustre, the dominant moss species, among the three moss species investigated in Dajiuhu Peatland. Bacterial communities from bryophytes clearly separated with those from sediments as indicated by both phylogenetic and taxonomical approaches. Linear discriminant analysis effect size(LEf Se) identified 30 and 36 indicator taxa in mosses and peat sediments. Bacteroidetes, Verrucomicrobia and Thermoleophilia significantly enriched in S. palustre, A. androgynum and P. commune, Chloroflexi, Proteobacteria and Acidobacteria subgroup 6 was indicator taxa for corresponding underlying sediments, respectively. Despite of these differences in compositions, bacterial functional structures were similar among all bryophytes, such as abundant aerobic heterotrophs, rare nitrifiers and denitrifiers. This phenomenon was also observed among the underlying sediments. Network analysis indicated that Proteobacteria and Acidobacteria located in the center of network and exerted strong interactions to other taxa. The sub-network of bacterial communities in sediments was more connected and microbial groups were more competitive than those in bryophytes subnetwork. Our results offer new insight into the community structure, ecological function and interaction pattern of bacterial microbiomes in the Dajiuhu Peatland across different habitats.展开更多
Reservoirs have been served as the major source of drinking water for dozens of years.The water quality safety of large andmedium reservoirs increasingly becomes the focus of public concern.Field test has proved that ...Reservoirs have been served as the major source of drinking water for dozens of years.The water quality safety of large andmedium reservoirs increasingly becomes the focus of public concern.Field test has proved that water-lifting and aeration system(WLAS)is a piece of effective equipment for in situ control and improvement of water quality.However,its intrinsic bioremediation mechanism,especially for nitrogen removal,still lacks in-depth investigation.Hence,the dynamic changes inwater quality parameters,carbon source metabolism,species compositions and co-occurrence patterns ofmicrobial communitieswere systematically studied in Jinpen Reservoir within a wholeWLAS running cycle.TheWLAS operation could efficiently reduce organic carbon(19.77%),nitrogen(21.55%)and phosphorus(65.60%),respectively.Biolog analysis revealed that the microbialmetabolic capacitieswere enhanced viaWLAS operation,especially in bottomwater.High-throughput sequencing demonstrated that WLAS operation altered the diversity and distributions of microbial communities in the source water.The most dominant genus accountable for aerobic denitrification was identified as Dechloromonas.Furthermore,network analysis revealed that microorganisms interacted more closely through WLAS operation.Oxidation-reduction potential(ORP)and total nitrogen(TN)were regarded as the two main physicochemical parameters influencing microbial community structures,as confirmed by redundancy analysis(RDA)and Mantel test.Overall,the results will provide a scientific basis and an effective way for strengthening the in-situ bioremediation of micro-polluted source water.展开更多
Background The study purpose was to characterize the mycobiome and its associations with the expression of pathogenic genes in esophageal squamous cell carcinoma(ESCC).Methods Patients with primary ESCC were recruited...Background The study purpose was to characterize the mycobiome and its associations with the expression of pathogenic genes in esophageal squamous cell carcinoma(ESCC).Methods Patients with primary ESCC were recruited from two central hospitals.We performed internal transcribed spacer 1(ITS1)ribosomal DNA sequencing analysis.We compared differential fungi and explored the ecology of fungi and the interaction of bacteria and fungi.Results The mycobiota diversity was significantly different between tumors and tumor-adjacent samples.We further analysed the differences between the two groups,at the species level,confirming that Rhodotorula toruloides,Malassezia dermatis,Hanseniaspora lachancei,and Spegazzinia tessarthra were excessively colonized in the tumor samples,whereas Preussia persica,Fusarium solani,Nigrospora oryzae,Acremonium furcatum,Golovinomyces artemisiae,and Tausonia pullulans were significantlymore abundant in tumor-adjacent samples.The fungal co-occurrence network in tumor-adjacent samples was larger and denser than that in tumors.Similarly,themore complex bacterial–fungal interactions in tumor-adjacent samples were also detected.The expression ofmechanistic target of rapamycin kinase was positively correlated with the abundance of N.oryzae and T.pullulans in tumor-adjacent samples.In tumors,the expression ofMET proto-oncogene,receptor tyrosine kinase(MET)had a negative correlation and a positive correlation with the abundance of R.toruloides and S.tessarthra,respectively.Conclusion This study revealed the landscape of the esophageal mycobiome characterized by an altered fungal composition and bacterial and fungal ecology in ESCC.展开更多
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 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(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.
基金supported by the National Natural Science Foundation of China(32001733)the Earmarked fund for CARS(CARS-47)+3 种基金Guangxi Natural Science Foundation Program(2021GXNSFAA196023)Guangdong Basic and Applied Basic Research Foundation(2021A1515010833)Young Talent Support Project of Guangzhou Association for Science and Technology(QT20220101142)the Special Scientific Research Funds for Central Non-profit Institutes,Chinese Academy of Fishery Sciences(2020TD69)。
文摘Popular fermented golden pomfret(Trachinotus ovatus)is prepared via spontaneous fermentation;however,the mechanisms underlying the regulation of its flavor development remain unclear.This study shows the roles of the complex microbiota and the dynamic changes in microbial community and flavor compounds during fish fermentation.Single-molecule real-time sequencing and molecular networking analysis revealed the correlations among different microbial genera and the relationships between microbial taxa and volatile compounds.Mechanisms underlying flavor development were also elucidated via KEGG based functional annotations.Clostridium,Shewanella,and Staphylococcus were the dominant microbial genera.Forty-nine volatile compounds were detected in the fermented fish samples,with thirteen identified as characteristic volatile compounds(ROAV>1).Volatile profiles resulted from the interactions among the microorganisms and derived enzymes,with the main metabolic pathways being amino acid biosynthesis/metabolism,carbon metabolism,and glycolysis/gluconeogenesis.This study demonstrated the approaches for distinguishing key microbiota associated with volatile compounds and monitoring the industrial production of high-quality fermented fish products.
基金supported by the National Science Foundation of China(No.31770672 and 3137062)the National Basic Research Program of China(No.2010CB950602)。
文摘Atmospheric nitrogen(N)deposition is predicted to increase,especially in the subtropics.However,the responses of soil microorganisms to long-term N addition at the molecular level in N-rich subtropical forests have not been clarified.A long-term nutrient addition experiment was conducted in a subtropical evergreen old-growth forest in China.The four treatments were:control,low N(50 kg N ha^(-1)a^(-1)),high N(100 kg N ha^(-1)a^(-1)),and combined N and phosphorus(P)(100 kg N ha^(-1)a^(-1)+50 kg P ha^(-1)a^(-1)).Metagenomic sequencing characterized diversity and composition of soil microbial communities and used to construct bacterial/fungal co-occurrence networks.Nutrient-treated soils were more acidic and had higher levels of dissolved organic carbon than controls.There were no significant differences in microbial diversity and community composition across treatments.The addition of nutrients increased the abundance of copiotrophic bacteria and potentially beneficial microorganisms(e.g.,Gemmatimonadetes,Chaetomium,and Aureobasidium).Low N addition increased microbiome network connectivity.Three rare fungi were identified as module hubs under nutrient addition,indicating that low abundance fungi were more sensitive to increased nutrients.The results indicate that the overall composition of microbial communities was stable but not static to long-term N addition.Our findings provide new insights that can aid predictions of the response of soil microbial communities to long-term N addition.
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Supported by the National Natural Science Foundation of China(Nos.42177253,41807476,41706186)Natural Science Foundation of Guangdong Province,China(No.2022A1515010197)。
文摘The microbial communities colonized on microplastics(MPs)have attracted widespread attention.However,few studies focused on the MPs impacts on mangrove ecosystems,particularly on bacterial communities.We investigated the MPs pollution in mangrove of Zhujiang(Pearl)River estuary(ZRE).To study the potential risk posed by MPs to the mangrove ecosystems,the differences in bacterial communities,functions,and complexity between MPs and sediment samples were reported for the first time.Microplastics(2991±1586 items/kg dry weight(dw))in sediment were mainly fibers and polyethylene,mostly transparent,and in size less than 0.5 mm.Bacterial communities and functions significantly differed from MPs in mangrove sediment.Compared with sediment,MPs significantly enriched members of Proteobacteria,Bacteroidetes,and Actinobacteria,as well as the bacteria associated with plastic-degrading and human diseases on their surface,suggesting that microbial communities on MPs may promote MPs degradation and the spread of diseases,posing potential risk to mangrove ecosystems and human health.Although bacteria on MPs exhibited a lower diversity,the co-occurrence network analysis indicated that network of bacteria colonized on MPs was bigger and more complex than those of mangrove sediment,illustrating that MPs can act as a distinct habitat in this special ecosystem.This study provides a new perspective for increasing our understanding of microplastic pollution in mangrove ecosystems.
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This research was supported by the National Natural Science Foundation of China(Nos.32270010,U2003211 and 31870008)Beijing Forestry University Outstanding Young Talent Cultivation Project(No.2019JQ03016).
文摘Soil fungi in forest ecosystems have great potential to enhance host plant growth and systemic ecological functions and services.Reforestation at Saihanba Mechanized Forest Farm,the world's largest artificial plantation,has been integral to global forest ecosystem preservation since the 1950s.To better assess the ecological effects of soil microbiology after afforestation,fungal diversity and community structure(using Illumina sequencing)from forests dominated by Larix gmelinii var.principis-rupprechtii,Pinus sylvestris var.mongolica and Picea asperata,and from grassland were surveyed.In total,4,540 operational taxonomic units(OTUs)were identified,with Mortierella and Solicoccozyma being the dominant genera of grassland soil and Inocybe,Cortinarius,Piloderma,Tomentella,Sebacina,Hygrophorus and Saitozyma dominating the plantation soil.Principle coordinate analysis(PCoA)and co-occurrence networks revealed differences in fungal structure after afforestation.Significantly,more symbiotroph guilds were dominated by ectomycorrhizal fungi in plantations under the prediction of FUNGuild.The community composition and diversity of soil fungi were significantly influenced by pH via redundancy analysis(RDA)and the Mantel test(p<0.01).This finding emphasizes that soil pH has a strong effect on the transition of fungal communities and functional taxa from grassland to plantation,providing a novel indicator for forest restoration.
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 Key Deployment Project of Centre for Ocean Mega-Research of Science,Chinese Academy of Sciences(No.COMS2020Q09)the National Key Research and Development Program of China(No.2018YFD0901102)the Science and Technology program of Yantai(No.2017ZH095)。
文摘Synechococcus is one of the most abundant picocyanobacteria in marine ecosystem,and the absence of Prochlorococcus would make it indispensable as a primary producer in the Bohai Sea,North China.However,the abundance distribution and genetic diversity of Synechococcus in this region have rarely been reported.In this study,the distribution pattern of Synechococcus abundance was investigated during four cruises in April,June,August,and November from 2018 to 2019,moreover,its phenogenetic diversity was studied based on high-throughput sequencing of the cpe BA operon.The results demonstrate that phycoerythrin-containing Synechococcus was most abundant in August when temperature was high and oxygen saturation was low.During this period,Synechococcus pigment type(PT)2 was abundant in the Bohai Bay and Laizhou Bay under conditions of high nutrient concentration,temperature,and turbidity.In comparison,PT3,especially those clusters characterized with high or variable ratio of phycourobilin and phycoerythrobilin,was predominant in the Bohai Strait and Liaodong Bay under conditions of high salinity,pH,and oxygen saturation.Furthermore,co-occurrence correlations using network analysis revealed that Synechococcus PTs were related to 15.37%-43.48%of the prokaryotic genera.Synechococcus PT3c/PT3d and PT2 were the most important PTs in the network.The hierarchical clustering revealed that taxa co-occurred with Synechococcus PTs diff ered among samples.It could be attributed to the substance exchange and the environmental impact,which calls for more studies in the future.
基金supported by the Key Deployment Project of Center for Ocean Mega-Science,Chinese Academy of Sciences(No.COMS2020Q09)the National Key Re-search and Development Program of China(No.2018 YFD0901102)the Science and Technology Program of Yantai(No.2017ZH095).
文摘Synechococcus is a widely distributed photosynthetic pico-phytoplankton,which contributes mainly to carbon fixation and maintains the stability of the marine ecosystem.To investigate its distribution patterns in the Yellow Sea,seawater samples were collected during September 2018.Results of flow cytometry analysis showed that the Synechococcus abundance ranged from 6.36×10^(2) to 4.51×10^(4) cells mL^(−1),which correlated with salinity(P<0.01)and temperature(P<0.05).At deeper off-shore sites,Synecho-coccus showed high abundance at the subsurface thermo-halocline,which was in accordance with chlorophyll a(Chl a)content along the vertical column.Based on the high-throughput sequencing data of rpoC1(partial gene encoding RNA polymerase),two Synechococcus subclusters,S5.1 and S5.2,were found to coexist in the studied area.Several clades of S5.1,including Clades I,II,and III,were the dominant components,accounting for 6.63%,26.11%,and 45.5%of the total genus,respectively.Redundancy analysis(RDA)showed that nitrite was the main environmental factor that explained the genus composition among samples.Fur-thermore,co-occurrence network revealed that the main phyla that coexisted with Synechococcus were Proteobacteria,Bacteroidetes,Actinobacteria,Planctomycetes,and Verrucomicrobia,which were involved in the carbon(C),nitrogen(N),sulfur(S),and manga-nese(Mn)cycles.Overall,Synechococcus exhibited biogeographic distribution correlated with temperature-salinity and nitrite in the Yellow Sea,and their geochemical function showed diverse but should be further verified in the future.
基金funded by the National Key Research and Development Program of China(2021YFD190090307)the National Natural Science Foundation of China(31901108)+1 种基金the Beijing Natural Science Foundation(5222014)the 2115 Talent Development Program of China Agricultural University。
文摘Complex network theory has been increasingly used in various research areas,including agroecosystems.This paper summarizes the basic concepts and approaches commonly used in complex network theory,and then reviews recent studies on the applications in agroecosystems of three types of common ecological networks,i.e.,food webs,pollination networks and microbial co-occurrence networks.In general,agricultural intensification is considered to be a key driver of the change of agroecosystems.It causes the simplification of landscape,leads to the loss of biocontrol through cascading effect in food webs,and also reduces the complexity and connectance of soil food webs.For pollination networks,agricultural intensification impaired the robustness by reducing specialization and enhancing generality.The microbial co-occurrence networks with high connectance and low modularity generally corresponded to high efficiency in utilization of nutrients,and high resistance to crop pathogens.This review aims to show the readers the advances of ecological networks in agroecosystems and inspire the researchers to conduct their studies in a new network perspective.
基金sponsored by CNPq(Brazilian Council for Research and Development),process 142620/2009-2FAPESP(State of Sao Paulo Research Foundation),process 2010/20564-8 and 2011/19850-9.
文摘The public content increasingly available on the Internet, especially in online forums, enables researchers to study society in new ways. However, qualitative analysis of online forums is very time consuming and most content is not related to researchers’ interest. Consequently, analysts face the following problem: how to efficiently explore and select the content to be analyzed? This article introduces a new process to support analysts in solving this problem. This process is based on unsupervised machine learning techniques like hierarchical clustering and term co-occurrence network. A tool that helps to apply the proposed process was created to provide consolidated and structured results. This includes measurements and a content exploration interface.
基金funded by the National Natural Science Foundation of China(Grant Nos.41730753 and 42177033)the Natural Science Foundation of the Higher Education Institutions of Jiangsu Province(Grant No.21KJB210010)the Natural ScienceFoundationof Jiangxi Province(Grant No.20224BAB203033).
文摘Responses of soil DIRB to lignocellulosic fractions during a 6-week microcosm incubation were investigated.Anaeromyxobacter,Bacillus,and Clostridium maintained their domi-nance throughout the incubation.Distinct DIRB groups proliferated under specific lignocellulosic fraction amendments.Limits of insufficient ferric iron on the proliferation varied by DIRB group.Dissimilatory iron reducing bacteria(DIRB)are phylogenetically and physi-ologically diverse in paddy soils,where iron reduction closely couples with the oxidation of rice straw-derived carbon in the straw returning scenarios.However,few studies have addressed the niche differentiation within DIRB groups during the degradation of lignocellulosic fractions of rice straw.This study conducted a 6-week microcosm incubation experiment to reveal the distinct responses of DIRB groups under specific lignocellulosic fraction amendments with and without ferrihydrite(Fh)addition in a flooded paddy Ultisol.Results showed that the total absolute abundance of the 19 detected DIRB groups did not vary significantly during the incubation.Anaeromyxobacter,Bacillus,and Clostridium were the dominant DIRB groups for all lignocellulosic treatments whereas Thermincola was dominant but only under xylan amendment with Fh addition.DIRB-nodes in the co-occurrence networks of bacterial community mainly belonged to Anaeromyxobacter and Bacillus.Clostridium and Thermincola,Alkaliphilus and Anaeromyxobacter,and Alicyclobacillus,Desulfobulbus,and Desulfosporosinus were specifically proliferated under xylan,cellulose,and lignin amendments,respectively.Whether the proliferation was limited by insufficient ferric iron varied by bacterial group.These findings suggested the lignocellulosic fraction-induced niche differentiation within DIRB groups,which advanced our understanding of the ecology of DIRB in paddy soils under straw returning.
基金supported by the National Nature Science Foundation of China (Nos. 51979217, 51978561)grant from Youth Innovation Team of Shaanxi Universities in 2020 (PI: Dr. Haihan Zhang)
文摘The nirS-type denitrifying bacterial community is the main drivers of the nitrogen loss process in drinking water reservoir ecosystems.The temporal patterns in nirS gene abundance and nirS-type denitrifying bacterial community harbored in aerobic water layers of drinking water reservoirs have not been studied well.In this study,quantitative polymerase chain reaction(qPCR)and Illumina Miseq sequencing were employed to explore the nirS gene abundance and denitrifying bacterial community structure in two drinking water reservoirs.The overall results showed that the water quality parameters in two reservoirs had obvious differences.The qPCR results suggested that nirS gene abundance ranged from(2.61±0.12)×10^(5) to(3.68±0.16)×10^(5) copies/mL and(3.01±0.12)×10^(5) to(5.36±0.31)×10^(5) copies/mL in Jinpen and Lijiahe reservoirs,respectively.The sequencing results revealed that Paracoccus sp.,Azoarcus sp.,Dechloromonas sp.and Thauera sp.were the dominant genera observed.At species level,Cupriavidus necator,Dechloromonas sp.R-28400,Paracoccus denitrificans and Pseudomonas stutzeri accounted for more proportions in two reservoirs.More importantly,the co-occurrence network analysis demonstrated that Paracoccus sp.R-24615 and Staphylococcus sp.N23 were the keystone species observed in Jinpen and Lijiahe reservoirs,respectively.Redundancy analysis indicated that water quality(particularly turbidity,water temperature,pH and Chlorophyll a)and sampling time had significant influence on the nirS-type denitrifying bacterial community in both reservoirs.These results will shed new lights on exploring the dynamics of nirS-type denitrifying bacteria in aerobic water layers of drinking water reservoirs.
基金jointly supported by National Natural Science Foundation of China (No. 41572325)China University of Geosciences (Wuhan) (Nos. CUGCJ1703 and CUGQY1922)。
文摘Symbiotic microbiomes of Sphagnum have been confirmed to play a fundamental role in carbon and nitrogen cycles, however, little is known about microbiomes associated with other bryophytes in subtropical peatland ecosystems. To explore the differences in community structure, metabolic potential and interaction relationship of bacterial microbiomes associated with different bryophytes species, the gametophytes of three bryophyte species(Sphagnum palustre, Aulacomnium androgynum, and Polytrichum commune) and their underlying peat sediments were collected from the subtropical Dajiuhu Peatland and subjected to Illumina high-throughout sequencing of 16S r RNA gene. Results showed that bacterial diversity was lowest in S. palustre, the dominant moss species, among the three moss species investigated in Dajiuhu Peatland. Bacterial communities from bryophytes clearly separated with those from sediments as indicated by both phylogenetic and taxonomical approaches. Linear discriminant analysis effect size(LEf Se) identified 30 and 36 indicator taxa in mosses and peat sediments. Bacteroidetes, Verrucomicrobia and Thermoleophilia significantly enriched in S. palustre, A. androgynum and P. commune, Chloroflexi, Proteobacteria and Acidobacteria subgroup 6 was indicator taxa for corresponding underlying sediments, respectively. Despite of these differences in compositions, bacterial functional structures were similar among all bryophytes, such as abundant aerobic heterotrophs, rare nitrifiers and denitrifiers. This phenomenon was also observed among the underlying sediments. Network analysis indicated that Proteobacteria and Acidobacteria located in the center of network and exerted strong interactions to other taxa. The sub-network of bacterial communities in sediments was more connected and microbial groups were more competitive than those in bryophytes subnetwork. Our results offer new insight into the community structure, ecological function and interaction pattern of bacterial microbiomes in the Dajiuhu Peatland across different habitats.
基金This work was supported by the National Key Research and Development Program of China(No.2019YFD1100101)the National Natural Science Foundation of China(No.51979217)+2 种基金the Shaanxi Provincial Key Research and Development Program(No.2019ZDLSF06-03)the Youth Innovation Team of Shaanxi Universities in 2020(PI:Dr.Haihan Zhang)the Youth Innovation Team of Shaanxi Universities in 2021(No.21JP061).
文摘Reservoirs have been served as the major source of drinking water for dozens of years.The water quality safety of large andmedium reservoirs increasingly becomes the focus of public concern.Field test has proved that water-lifting and aeration system(WLAS)is a piece of effective equipment for in situ control and improvement of water quality.However,its intrinsic bioremediation mechanism,especially for nitrogen removal,still lacks in-depth investigation.Hence,the dynamic changes inwater quality parameters,carbon source metabolism,species compositions and co-occurrence patterns ofmicrobial communitieswere systematically studied in Jinpen Reservoir within a wholeWLAS running cycle.TheWLAS operation could efficiently reduce organic carbon(19.77%),nitrogen(21.55%)and phosphorus(65.60%),respectively.Biolog analysis revealed that the microbialmetabolic capacitieswere enhanced viaWLAS operation,especially in bottomwater.High-throughput sequencing demonstrated that WLAS operation altered the diversity and distributions of microbial communities in the source water.The most dominant genus accountable for aerobic denitrification was identified as Dechloromonas.Furthermore,network analysis revealed that microorganisms interacted more closely through WLAS operation.Oxidation-reduction potential(ORP)and total nitrogen(TN)were regarded as the two main physicochemical parameters influencing microbial community structures,as confirmed by redundancy analysis(RDA)and Mantel test.Overall,the results will provide a scientific basis and an effective way for strengthening the in-situ bioremediation of micro-polluted source water.
基金from Nature Science Foundation of Fujian Province[no.2021J01733,no.2021J01726]central government-led local science and technology development special project[no.2019L3006,no.2020L3009]Startup Fund for scientific research,Fujian Medical University(no.2020QH2008).
文摘Background The study purpose was to characterize the mycobiome and its associations with the expression of pathogenic genes in esophageal squamous cell carcinoma(ESCC).Methods Patients with primary ESCC were recruited from two central hospitals.We performed internal transcribed spacer 1(ITS1)ribosomal DNA sequencing analysis.We compared differential fungi and explored the ecology of fungi and the interaction of bacteria and fungi.Results The mycobiota diversity was significantly different between tumors and tumor-adjacent samples.We further analysed the differences between the two groups,at the species level,confirming that Rhodotorula toruloides,Malassezia dermatis,Hanseniaspora lachancei,and Spegazzinia tessarthra were excessively colonized in the tumor samples,whereas Preussia persica,Fusarium solani,Nigrospora oryzae,Acremonium furcatum,Golovinomyces artemisiae,and Tausonia pullulans were significantlymore abundant in tumor-adjacent samples.The fungal co-occurrence network in tumor-adjacent samples was larger and denser than that in tumors.Similarly,themore complex bacterial–fungal interactions in tumor-adjacent samples were also detected.The expression ofmechanistic target of rapamycin kinase was positively correlated with the abundance of N.oryzae and T.pullulans in tumor-adjacent samples.In tumors,the expression ofMET proto-oncogene,receptor tyrosine kinase(MET)had a negative correlation and a positive correlation with the abundance of R.toruloides and S.tessarthra,respectively.Conclusion This study revealed the landscape of the esophageal mycobiome characterized by an altered fungal composition and bacterial and fungal ecology in ESCC.
