Bacterial communities play a crucial role in permafrost biogeochemical cycling and ecosystem function maintenance.Bacterial interaction is one of the main factors in shaping soil bacterial communities.However,how woul...Bacterial communities play a crucial role in permafrost biogeochemical cycling and ecosystem function maintenance.Bacterial interaction is one of the main factors in shaping soil bacterial communities.However,how would bacterial interaction influence the bacterial communities in permafrost of the Qinghai-Tibet Plateau(QTP)remains largely unknown.Here we collected paired soil samples from both the active and permafrost layers of two typical QTP permafrost regions in October 2020 for Tuotuohe River(TTH)and May 2022 for Aerjin(ARJ),and investigated the bacterial communities and the role of interactions in structuring the bacterial community and its assembly process through amplicon sequencing of the 16S rRNA gene.Our study revealed distinct bacterial communities,with significant differences in the relative abundances of Proteobacteria(P<0.05),Acidobacteriota(P<0.001),Bacteroidota(P<0.05),and Planctomycetota(P<0.001)between the active layer and the permafrost layer.More importantly,we found that interspecies interactions,including both positive and negative associations,were strongly correlated with bacterial alpha-diversity and played a significant role in community variation and assembly process.Our findings also showed that the community assembly in both the active and permafrost layers was primarily driven by homogeneous selection of deterministic processes,with interspecies interactions accounting for more than 58%and 63%of all assembly mechanisms,respectively.This is the first study to quantify the contribution of bacterial interactions in shaping the bacterial community and its assembly process in permafrost of QTP,highlighting the importance of considering interspecies interactions in future modeling efforts.Our work also emphasizes the necessity of including interspecies interactions in microbial process projections to reduce uncertainty.展开更多
Rice seedling blight,caused by various fungi,including Fusarium oxysporum,poses a severe threat to rice production.As awareness grows regarding the environmental and safety hazards associated with the application of f...Rice seedling blight,caused by various fungi,including Fusarium oxysporum,poses a severe threat to rice production.As awareness grows regarding the environmental and safety hazards associated with the application of fungicides for managing rice seedling blight,there has been a shift in focus towards biological control agents.In this study,we isolated biocontrol bacteria from paddy fields that significantly inhibited the growth of F.oxysporum in vitro and identified the strains as Bacillus amyloliquefaciens T40 and Bacillus pumilus T208.Additionally,our findings indicated that the combined application of these Bacillus strains in soil was more effective in reducing the incidence of rice seedling blight than their individual use.Analysis of 16S and internal transcribed spacer rRNA gene sequencing data revealed that the mixture of the T40 and T208 strains exhibited the lowest average clustering coefficients,which were negatively correlated with the biomass of F.oxysporum-inoculated rice seedlings.Furthermore,this mixture led to higher stochastic assembly(average|βNTI|<2)and reduced selection pressures on rice rhizosphere bacteria compared with individual strain applications.The mixture of the T40 and T208 strains also significantly increased the expression of defense-related genes.In conclusion,the mixture of the T40 and T208 strains effectively modulates microbial community structures,enhances microbial network stability,and boosts the resistance against rice seedling blight.Our study supports the development and utilization of biological resources for crop protection.展开更多
Soil microbes play a critical role in maintaining the health and stability of these ecosystems. However, the ecological assembly processes of soil microbial communities remain poorly understood. This study explores th...Soil microbes play a critical role in maintaining the health and stability of these ecosystems. However, the ecological assembly processes of soil microbial communities remain poorly understood. This study explores the changes in ecological components across original and degraded patches of alpine meadows in Sanjiangyuan National Park and analyzed soil microbial community structure using high-throughput sequencing techniques. Results showed that alpine meadows degradation increased vegetation species diversity, significantly reduced aboveground productivity, and made the soil more barren and alkaline. Although the dominant phyla of soil microorganisms were similar across different degradation states, degradation significantly increased the relative abundance of oligotrophic bacteria and decreased the relative abundance of dominant fungi. Additionally, microbial communities exhibited significant β-diversity. Degradation also led to an increase in microbial α-diversity, heightened microbial taxa competition and a more complex microbial co-occurrence network. However, vegetation-soil variables explained only a small portion of the variation in soil microbes. Through the study of microbial ecological assembly processes, we found that degradation enhanced the stochastic processes of soil microbial communities, and the changes in soil microbial communities were mainly driven by the variations inherent in the microbes themselves. These findings highlight the complex ecological interactions between above- and belowground components and emphasize the critical role of microbial community dynamics qin mediating ecosystem functions.展开更多
The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution.However,the patterns of phylogenetic diversity(PD) and phylogenetic beta diversity...The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution.However,the patterns of phylogenetic diversity(PD) and phylogenetic beta diversity(PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America(EA-ENA disjuncts) and their associated factors remain unknown.Here we investigated the standardized effect size of PD(SES-PD),PBD,and potentially associated factors in 11natural mixed forest sites(five in EA and six in ENA) where abundant EA-ENA disjuncts occur.We found that the disjuncts in ENA possessed higher SES-PD than those in EA at the continental scale(1.96vs-1.12),even though the number of disjunct species in ENA is much lower than in EA(128 vs 263).SESPD of the EA-ENA disjuncts tended to decrease with increasing latitude in 11 sites.The latitudinal diversity gradient of SES-PD was stronger in EA sites than in ENA sites.Based on the unweighted unique fraction metric(UniFrac) distance and the phylogenetic community dissimilarity,PBD showed that the two northern sites in EA were more similar to the six-site ENA group than to the remaining southern EA sites.Based on the standardized effect size of mean pairwise distances(SES-MPD),nine of eleven studied sites showed a neutral community structure(-1.96 ≤SES-MPD ≤1.96).Both Pearson’s r and structural equation modeling suggested that SES-PD of the EA-ENA disjuncts was mostly associated with mean divergence time.Moreover,SES-PD of the EA-ENA disjuncts was positively correlated with temperaturerelated climatic factors,although negatively correlated with mean diversification rate and community structure.By applying approaches from phylogenetics and community ecology,our work sheds light on historical patterns of the EA-ENA disjunction and paves the way for further research.展开更多
Background:The regional species pool and local community assembly processes shape the biogeographic patterns of soil bacterial community diversity.However,how community assembly mechanisms regulate biogeographic patte...Background:The regional species pool and local community assembly processes shape the biogeographic patterns of soil bacterial community diversity.However,how community assembly mechanisms regulate biogeographic patterns in rare and abundant bacterial communities remains unclear.Methods:Soil samples of 16 grassland habitats across the Inner Mongolian Plateau and Qinghai-Tibet Plateau(QTP)transects were collected to investigate the variation ofβ-diversity in rare taxa(RT)and abundant taxa(AT).Highthroughput sequencing analysis of 16S rRNA gene amplicons was implemented on an Ilumina MiSeq platform.Results:Significant distance-decay relationships ofβ-diversity in RT and AT were observed at transect and habitat scales,and the turnover rate increased from desert to meadow steppe in both taxa.For variations ofβ-diversity along environmental gradient,the regional species pool had a limited effect on both taxa except RT in QTP.Deterministic processes,including homogeneous selection(85.1%-97.3%)and heterogenous selection(48.1%-64.2%),dominated the assembly of RT at both the transect and habitat scales.In contrast,the assembly of AT exhibited habitat specificity and was dominated by homogeneous selection(47.2%-80.6%),heterogenous selection(42.1%-54.2%),and dispersal limitation(41.8%)in different transects and habitats.Moreover,the local assembly processes of the AT community were more stochastic than those of the RT community.Mean annual precipitation(MAP)was the dominant driver of community assembly at the transect scale,with extreme MAP(<200 or>400 mm)resulting in more deterministic processes and a moderate level of MAP(200-400 mm)leading to more stochastic processes.However,the effects of geographical distance and soil properties on different grassland habitats cannot be ignored.Conclusions:Although both bacterial taxa exhibited significant distance-decay patterns,different assembly mechanisms shaped theβ-diversity of AT and RT communities in grassland soils.Our results suggested that MAP can mediate community assembly of soil bacteria on a large scale.展开更多
基金supported by grants from the National Natural Science Foundation of China for Excellent Young Scientists Fund Program(No.42222105)the National Natural Science Foundation of China General Program(No.42171144)+1 种基金the Assessment of Ecosystem Carbon Stock and Turnover Patterns in Qinghai Province(No.2021-SFA7-1-1)the Second Tibetan Plateau Scientific Expedition and Research Program(STEP)(No.2021QZKK0100)。
文摘Bacterial communities play a crucial role in permafrost biogeochemical cycling and ecosystem function maintenance.Bacterial interaction is one of the main factors in shaping soil bacterial communities.However,how would bacterial interaction influence the bacterial communities in permafrost of the Qinghai-Tibet Plateau(QTP)remains largely unknown.Here we collected paired soil samples from both the active and permafrost layers of two typical QTP permafrost regions in October 2020 for Tuotuohe River(TTH)and May 2022 for Aerjin(ARJ),and investigated the bacterial communities and the role of interactions in structuring the bacterial community and its assembly process through amplicon sequencing of the 16S rRNA gene.Our study revealed distinct bacterial communities,with significant differences in the relative abundances of Proteobacteria(P<0.05),Acidobacteriota(P<0.001),Bacteroidota(P<0.05),and Planctomycetota(P<0.001)between the active layer and the permafrost layer.More importantly,we found that interspecies interactions,including both positive and negative associations,were strongly correlated with bacterial alpha-diversity and played a significant role in community variation and assembly process.Our findings also showed that the community assembly in both the active and permafrost layers was primarily driven by homogeneous selection of deterministic processes,with interspecies interactions accounting for more than 58%and 63%of all assembly mechanisms,respectively.This is the first study to quantify the contribution of bacterial interactions in shaping the bacterial community and its assembly process in permafrost of QTP,highlighting the importance of considering interspecies interactions in future modeling efforts.Our work also emphasizes the necessity of including interspecies interactions in microbial process projections to reduce uncertainty.
基金supported by the Zhejiang Provincial Natural Science Foundation,China(Grant No.LQ24C010007)Zhejiang Science and Technology Major Program on Rice New Variety Breeding,China(Grant No.2021C02063)+4 种基金the Agricultural Sciences and Technologies Innovation Program,China(Grant No.CAAS-CSCB-202301)the Key Projects of Zhejiang Provincial Natural Science Foundation,China(Grant No.LZ23C130002)the Youth Innovation Program of Chinese Academy of Agricultural Sciences(Grant No.Y2023QC22)the Joint Open Competitive Project of the Yazhou Bay Seed Laboratory and China National Seed Company Limited(Grant Nos.B23YQ1514 and B23CQ15EP)the External Cooperation Projects of Biotechnology Research Institute,Fujian Academy of Agricultural Sciences,China(Grant No.DWHZ2024-07).
文摘Rice seedling blight,caused by various fungi,including Fusarium oxysporum,poses a severe threat to rice production.As awareness grows regarding the environmental and safety hazards associated with the application of fungicides for managing rice seedling blight,there has been a shift in focus towards biological control agents.In this study,we isolated biocontrol bacteria from paddy fields that significantly inhibited the growth of F.oxysporum in vitro and identified the strains as Bacillus amyloliquefaciens T40 and Bacillus pumilus T208.Additionally,our findings indicated that the combined application of these Bacillus strains in soil was more effective in reducing the incidence of rice seedling blight than their individual use.Analysis of 16S and internal transcribed spacer rRNA gene sequencing data revealed that the mixture of the T40 and T208 strains exhibited the lowest average clustering coefficients,which were negatively correlated with the biomass of F.oxysporum-inoculated rice seedlings.Furthermore,this mixture led to higher stochastic assembly(average|βNTI|<2)and reduced selection pressures on rice rhizosphere bacteria compared with individual strain applications.The mixture of the T40 and T208 strains also significantly increased the expression of defense-related genes.In conclusion,the mixture of the T40 and T208 strains effectively modulates microbial community structures,enhances microbial network stability,and boosts the resistance against rice seedling blight.Our study supports the development and utilization of biological resources for crop protection.
基金financially supported by the Special Project on National Science and Technology Basic Resources Investigation of China (2021FY100705)Leading Plan Project of Academic Team of Minzu University of China (2024XSYL04)the Second Tibetan Plateau Scientific Expedition and Research (STEP) Program (2019QZKK040104, 2019QZKK0302)。
文摘Soil microbes play a critical role in maintaining the health and stability of these ecosystems. However, the ecological assembly processes of soil microbial communities remain poorly understood. This study explores the changes in ecological components across original and degraded patches of alpine meadows in Sanjiangyuan National Park and analyzed soil microbial community structure using high-throughput sequencing techniques. Results showed that alpine meadows degradation increased vegetation species diversity, significantly reduced aboveground productivity, and made the soil more barren and alkaline. Although the dominant phyla of soil microorganisms were similar across different degradation states, degradation significantly increased the relative abundance of oligotrophic bacteria and decreased the relative abundance of dominant fungi. Additionally, microbial communities exhibited significant β-diversity. Degradation also led to an increase in microbial α-diversity, heightened microbial taxa competition and a more complex microbial co-occurrence network. However, vegetation-soil variables explained only a small portion of the variation in soil microbes. Through the study of microbial ecological assembly processes, we found that degradation enhanced the stochastic processes of soil microbial communities, and the changes in soil microbial communities were mainly driven by the variations inherent in the microbes themselves. These findings highlight the complex ecological interactions between above- and belowground components and emphasize the critical role of microbial community dynamics qin mediating ecosystem functions.
基金supported by the National Natural Science Foundation of China (Grant No.31461123001 to C.X.F.)the US National Science Foundation Dimensions of Biodiversity US-China Program (DEB-1442280 to P.S.S.and D.E.S.)+1 种基金the HZAU Talent Start-up Fund (Grant no.11042210014 to M.S.)the China Scholarship Council (Grant no.201806320056 to H.Y.L.)。
文摘The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution.However,the patterns of phylogenetic diversity(PD) and phylogenetic beta diversity(PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America(EA-ENA disjuncts) and their associated factors remain unknown.Here we investigated the standardized effect size of PD(SES-PD),PBD,and potentially associated factors in 11natural mixed forest sites(five in EA and six in ENA) where abundant EA-ENA disjuncts occur.We found that the disjuncts in ENA possessed higher SES-PD than those in EA at the continental scale(1.96vs-1.12),even though the number of disjunct species in ENA is much lower than in EA(128 vs 263).SESPD of the EA-ENA disjuncts tended to decrease with increasing latitude in 11 sites.The latitudinal diversity gradient of SES-PD was stronger in EA sites than in ENA sites.Based on the unweighted unique fraction metric(UniFrac) distance and the phylogenetic community dissimilarity,PBD showed that the two northern sites in EA were more similar to the six-site ENA group than to the remaining southern EA sites.Based on the standardized effect size of mean pairwise distances(SES-MPD),nine of eleven studied sites showed a neutral community structure(-1.96 ≤SES-MPD ≤1.96).Both Pearson’s r and structural equation modeling suggested that SES-PD of the EA-ENA disjuncts was mostly associated with mean divergence time.Moreover,SES-PD of the EA-ENA disjuncts was positively correlated with temperaturerelated climatic factors,although negatively correlated with mean diversification rate and community structure.By applying approaches from phylogenetics and community ecology,our work sheds light on historical patterns of the EA-ENA disjunction and paves the way for further research.
基金National Natural Science Foundation of China,Grant/Award Numbers:32271619,32192461。
文摘Background:The regional species pool and local community assembly processes shape the biogeographic patterns of soil bacterial community diversity.However,how community assembly mechanisms regulate biogeographic patterns in rare and abundant bacterial communities remains unclear.Methods:Soil samples of 16 grassland habitats across the Inner Mongolian Plateau and Qinghai-Tibet Plateau(QTP)transects were collected to investigate the variation ofβ-diversity in rare taxa(RT)and abundant taxa(AT).Highthroughput sequencing analysis of 16S rRNA gene amplicons was implemented on an Ilumina MiSeq platform.Results:Significant distance-decay relationships ofβ-diversity in RT and AT were observed at transect and habitat scales,and the turnover rate increased from desert to meadow steppe in both taxa.For variations ofβ-diversity along environmental gradient,the regional species pool had a limited effect on both taxa except RT in QTP.Deterministic processes,including homogeneous selection(85.1%-97.3%)and heterogenous selection(48.1%-64.2%),dominated the assembly of RT at both the transect and habitat scales.In contrast,the assembly of AT exhibited habitat specificity and was dominated by homogeneous selection(47.2%-80.6%),heterogenous selection(42.1%-54.2%),and dispersal limitation(41.8%)in different transects and habitats.Moreover,the local assembly processes of the AT community were more stochastic than those of the RT community.Mean annual precipitation(MAP)was the dominant driver of community assembly at the transect scale,with extreme MAP(<200 or>400 mm)resulting in more deterministic processes and a moderate level of MAP(200-400 mm)leading to more stochastic processes.However,the effects of geographical distance and soil properties on different grassland habitats cannot be ignored.Conclusions:Although both bacterial taxa exhibited significant distance-decay patterns,different assembly mechanisms shaped theβ-diversity of AT and RT communities in grassland soils.Our results suggested that MAP can mediate community assembly of soil bacteria on a large scale.
