Plant roots are one of the major mediators that allocate carbon captured from the atmosphere to soils as rhizodeposits,including root exudates.Although rhizodeposition regulates both microbial activity and the biogeoc...Plant roots are one of the major mediators that allocate carbon captured from the atmosphere to soils as rhizodeposits,including root exudates.Although rhizodeposition regulates both microbial activity and the biogeochemical cycling of nutrients,the effects of particular exudate species on soil carbon fluxes and key rhizosphere microorganisms remain unclear.By combining high-throughput sequencing,q-PCR,and NanoSIMS analyses,we characterized the bacterial community structure,quantified total bacteria depending on root exudate chemistry,and analyzed the consequences on the mobility of mineral-protected carbon.Using well-controlled incubation experiments,we showed that the three most abundant groups of root exudates(amino acids,carboxylic acids,and sugars)have contrasting effects on the release of dissolved organic carbon(DOC)and bioavailable Fe in an Ultisol through the disruption of organo-mineral associations and the alteration of bacterial communities,thus priming organic matter decomposition in the rhizosphere.High resolution(down to 50 nm)NanoSIMS images of mineral particles indicated that iron and silicon colocalized significantly more organic carbon following amino acid inputs than treatments without exudates or with carboxylic acids.The application of sugar strongly reduced microbial diversity without impacting soil carbon mobilization.Carboxylic acids increased the prevalence of Actinobacteria and facilitated carbon mobilization,whereas amino acid addition increased the abundances of Proteobacteria that prevented DOC release.In summary,root exudate functions are defined by their chemical composition that regulates bacterial community composition and,consequently,the biogeochemical cycling of carbon in the rhizosphere.展开更多
Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge instudies on marine microbial community composition using high-throughput sequencing methods. Extens...Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge instudies on marine microbial community composition using high-throughput sequencing methods. Extensive mining ofthe compositional data has provided exciting new insights into marine microbial ecology from a number of perspectives.Both deterministic and stochastic processes contribute to microbial community assembly but their relative importance instructuring subcommunities, that are categorized by traits such as abundance, functional type and activity, differs. Throughcorrelation-based network analysis, significant progress has been made in unraveling microbial co-occurrence patterns anddynamics in response to environmental changes. Prediction of ecosystem functioning, based on microbial data, is receivingincreasing attention, as closely related microbes often share similar ecological traits and microbial diversity often exhibitssignificant correlations to ecosystem functioning. The ecosystem functioning is likely executed not by the whole community,but rather by an active fraction of a community, which can be inferred from the marker gene transcription level of communitymembers. Furthermore, the huge amount of microbial community data has significantly expanded the tree of lifeand illuminated microbial phylogenetic divergence and evolutionary history. This review summarizes important findingsin microbial assembly, interaction, functioning, activity and diversification, highlighting the interacting roles of differentaspects, derived from community compositional data.展开更多
Conventional biological treatment usually cannot achieve the same high water quality as advanced treatment when conducted under varied temperatures.Here,satisfactory wastewater treatment efficiency was observed in a m...Conventional biological treatment usually cannot achieve the same high water quality as advanced treatment when conducted under varied temperatures.Here,satisfactory wastewater treatment efficiency was observed in a microalgae-bacteria consortia(MBC)over a wide temperature range because of the predominance of microalgae.Microalgae contributed more toward wastewater treatment at low temperature because of the unsatisfactory performance of the accompanying bacteria,which experienced cold stress(e.g.,bacterial abundance below 3000 sequences)and executed defensive strategies(e.g.,enrichment of cold-shock proteins).A low abundance of amoA-C and hao indicated that conventional nitrogen removal was replaced through the involvement of microalgae.Diverse heterotrophic bacteria for nitrogen removal were identified at medium and high temperatures,implying this microbial niche treatment contained diverse flexible consortia with temperature variation.Additionally,pathogenic bacteria were eliminated through microalgal photosynthesis.After fitting the neutral community model and calculating the ecological niche,microalgae achieved a maximum niche breadth of 5.21 and the lowest niche overlap of 0.38,while the accompanying bacterial community in the consortia were shaped through deterministic processes.Finally,the maximum energy yield of 87.4 kJ L^(-1)and lipid production of 1.9 g L^(-1)were achieved at medium temperature.Altogether,this study demonstrates that advanced treatment and energy reclamation can be achieved through microalgae-bacteria niche strategies.展开更多
Lake mixing influences aquatic chemical properties and microbial community composition,and thus,we hypothesized that it would alter microbial community assembly and interac-tion.To clarify this issue,we explored the c...Lake mixing influences aquatic chemical properties and microbial community composition,and thus,we hypothesized that it would alter microbial community assembly and interac-tion.To clarify this issue,we explored the community assembly processes and cooccurrence networks in four seasons at two depths(epilimnion and hypolimnion)in a mesotrophic and stratified lake(Chenghai Lake),which formed stratification in the summer and turnover in the winter.During the stratification period,the epilimnion and hypolimnion went through contrary assembly processes but converged to similar assembly patterns in the mixing pe-riod.In a highly homogeneous selection environment,species with low niche breadth were filtered,resulting in decreased species richness.Water mixing in the winter homogenized the environment,resulting in a simpler microbial cooccurrence network.Interestingly,we observed a high abundance of the cyanobacterial genus Planktothrix in the winter,proba-bly due to nutrient redistribution and Planktothrix adaptivity to the winter environment in which mixing played important roles.Our study provides deeper fundamental insights into how environmental factors influence microbial community structure through community assembly processes.展开更多
Robinia pseudoacacia L.(RP)restoration has increased vegetation cover in semi-arid regions on the Loess Plateau of China,but ecological problems have also occurred due to RP restoration,such as reduced soil moisture.F...Robinia pseudoacacia L.(RP)restoration has increased vegetation cover in semi-arid regions on the Loess Plateau of China,but ecological problems have also occurred due to RP restoration,such as reduced soil moisture.Further,it is still uncertain how microbial diversity,composition and assembly processes change with RP restoration in semi-arid regions.Therefore,amplicon sequencing of small subunit ribosomal ribonucleic acid(16S rRNA)and internal transcribed spacer(ITS)genes was performed to study soil bacterial and fungal diversity,composition and assembly processes at four study sites with different stand ages of RP plantations(Y10,RP plantation with stand ages less than 10 a;Y15,RP plantation with stand ages approximately 15 a;Y25,RP plantation with stand ages approximately 25 a;and Y40,RP plantation with stand ages approximately 40 a)along a 40-a chronosequence on the Loess Plateau.The diversity of soil bacteria and fungi increased significantly during the restoration period from 10 to 15 a(P<0.05).However,compared with Y15,bacterial diversity was lower at Y25 and Y40,and fungal diversity remained stable during the restoration period between 25 and 40 a.The relative abundances of Proteobacteria and Ascomycota increased during the restoration period from 10 to 15 a.Conversely,after 15 a of restoration,they both decreased,whereas the relative abundances of Actinomycetes,Acidobacteria and Basidiomycota gradually increased.The variations in soil bacterial communities were mainly related to changes in soil total nitrogen,nitrate nitrogen and moisture contents,while soil fungal communities were mainly shaped by soil organic carbon and nitrate nitrogen contents.Bacterial communities were structured by the heterogeneous selection and stochastic process,while fungal communities were structured primarily by the stochastic process.The RP restoration induced an increase in the relative importance of heterogeneous selection on bacterial communities.Overall,this study reveals the changes in microbial diversity,community comp展开更多
基金supported by National Natural Science Foundation of China(Grants No.31902107 and 41977271)Natural Science Foundation of Jiangsu Province(Grant No.BK20211577)+3 种基金the Innovative Research Team Development Plan of the Ministry of Education of China(Grant No.IRT_17R56)supported by Qing Lan Project of Jiangsu Provincethe support by the RUDN University Strategic Academic Leadership Programthe WeChat subscription ID“meta-Genome”and“Micro-Bioinformatics and microflora”for the analysis methods.
文摘Plant roots are one of the major mediators that allocate carbon captured from the atmosphere to soils as rhizodeposits,including root exudates.Although rhizodeposition regulates both microbial activity and the biogeochemical cycling of nutrients,the effects of particular exudate species on soil carbon fluxes and key rhizosphere microorganisms remain unclear.By combining high-throughput sequencing,q-PCR,and NanoSIMS analyses,we characterized the bacterial community structure,quantified total bacteria depending on root exudate chemistry,and analyzed the consequences on the mobility of mineral-protected carbon.Using well-controlled incubation experiments,we showed that the three most abundant groups of root exudates(amino acids,carboxylic acids,and sugars)have contrasting effects on the release of dissolved organic carbon(DOC)and bioavailable Fe in an Ultisol through the disruption of organo-mineral associations and the alteration of bacterial communities,thus priming organic matter decomposition in the rhizosphere.High resolution(down to 50 nm)NanoSIMS images of mineral particles indicated that iron and silicon colocalized significantly more organic carbon following amino acid inputs than treatments without exudates or with carboxylic acids.The application of sugar strongly reduced microbial diversity without impacting soil carbon mobilization.Carboxylic acids increased the prevalence of Actinobacteria and facilitated carbon mobilization,whereas amino acid addition increased the abundances of Proteobacteria that prevented DOC release.In summary,root exudate functions are defined by their chemical composition that regulates bacterial community composition and,consequently,the biogeochemical cycling of carbon in the rhizosphere.
基金supported by the National NaturalScience Foundation of China (Grants Nos. 41976101, 41506154 and41730530)the Fundamental Research Funds for the Central Universities(Grants No. 201762017).
文摘Microorganisms play crucial roles in maintaining ecosystem stability. The last two decades have witnessed an upsurge instudies on marine microbial community composition using high-throughput sequencing methods. Extensive mining ofthe compositional data has provided exciting new insights into marine microbial ecology from a number of perspectives.Both deterministic and stochastic processes contribute to microbial community assembly but their relative importance instructuring subcommunities, that are categorized by traits such as abundance, functional type and activity, differs. Throughcorrelation-based network analysis, significant progress has been made in unraveling microbial co-occurrence patterns anddynamics in response to environmental changes. Prediction of ecosystem functioning, based on microbial data, is receivingincreasing attention, as closely related microbes often share similar ecological traits and microbial diversity often exhibitssignificant correlations to ecosystem functioning. The ecosystem functioning is likely executed not by the whole community,but rather by an active fraction of a community, which can be inferred from the marker gene transcription level of communitymembers. Furthermore, the huge amount of microbial community data has significantly expanded the tree of lifeand illuminated microbial phylogenetic divergence and evolutionary history. This review summarizes important findingsin microbial assembly, interaction, functioning, activity and diversification, highlighting the interacting roles of differentaspects, derived from community compositional data.
基金supported by the National Key Research and Development Program(No.2019YFC0408503)Fund Project of National and Local Joint Engineering Research Center for Biomass Energy Development and Utilization(Harbin Institute of Technology,Project No.2021A004).
文摘Conventional biological treatment usually cannot achieve the same high water quality as advanced treatment when conducted under varied temperatures.Here,satisfactory wastewater treatment efficiency was observed in a microalgae-bacteria consortia(MBC)over a wide temperature range because of the predominance of microalgae.Microalgae contributed more toward wastewater treatment at low temperature because of the unsatisfactory performance of the accompanying bacteria,which experienced cold stress(e.g.,bacterial abundance below 3000 sequences)and executed defensive strategies(e.g.,enrichment of cold-shock proteins).A low abundance of amoA-C and hao indicated that conventional nitrogen removal was replaced through the involvement of microalgae.Diverse heterotrophic bacteria for nitrogen removal were identified at medium and high temperatures,implying this microbial niche treatment contained diverse flexible consortia with temperature variation.Additionally,pathogenic bacteria were eliminated through microalgal photosynthesis.After fitting the neutral community model and calculating the ecological niche,microalgae achieved a maximum niche breadth of 5.21 and the lowest niche overlap of 0.38,while the accompanying bacterial community in the consortia were shaped through deterministic processes.Finally,the maximum energy yield of 87.4 kJ L^(-1)and lipid production of 1.9 g L^(-1)were achieved at medium temperature.Altogether,this study demonstrates that advanced treatment and energy reclamation can be achieved through microalgae-bacteria niche strategies.
基金This work was supported by the National Natural Science Foundation of China(No.51578537)Chinese Academy of Sciences(No.QYZDY-SSW-DQC004)。
文摘Lake mixing influences aquatic chemical properties and microbial community composition,and thus,we hypothesized that it would alter microbial community assembly and interac-tion.To clarify this issue,we explored the community assembly processes and cooccurrence networks in four seasons at two depths(epilimnion and hypolimnion)in a mesotrophic and stratified lake(Chenghai Lake),which formed stratification in the summer and turnover in the winter.During the stratification period,the epilimnion and hypolimnion went through contrary assembly processes but converged to similar assembly patterns in the mixing pe-riod.In a highly homogeneous selection environment,species with low niche breadth were filtered,resulting in decreased species richness.Water mixing in the winter homogenized the environment,resulting in a simpler microbial cooccurrence network.Interestingly,we observed a high abundance of the cyanobacterial genus Planktothrix in the winter,proba-bly due to nutrient redistribution and Planktothrix adaptivity to the winter environment in which mixing played important roles.Our study provides deeper fundamental insights into how environmental factors influence microbial community structure through community assembly processes.
基金supported by the National Natural Science Foundation of China(41471437)the National Key R&D Program of China(2016YFA0600801,2017YFC0504504)+1 种基金the West Light Foundation of the Chinese Academy of Science(XAB2016A04)the Key R&D Program of Ningxia Hui Autonomous Region,China(2022BBF02033)。
文摘Robinia pseudoacacia L.(RP)restoration has increased vegetation cover in semi-arid regions on the Loess Plateau of China,but ecological problems have also occurred due to RP restoration,such as reduced soil moisture.Further,it is still uncertain how microbial diversity,composition and assembly processes change with RP restoration in semi-arid regions.Therefore,amplicon sequencing of small subunit ribosomal ribonucleic acid(16S rRNA)and internal transcribed spacer(ITS)genes was performed to study soil bacterial and fungal diversity,composition and assembly processes at four study sites with different stand ages of RP plantations(Y10,RP plantation with stand ages less than 10 a;Y15,RP plantation with stand ages approximately 15 a;Y25,RP plantation with stand ages approximately 25 a;and Y40,RP plantation with stand ages approximately 40 a)along a 40-a chronosequence on the Loess Plateau.The diversity of soil bacteria and fungi increased significantly during the restoration period from 10 to 15 a(P<0.05).However,compared with Y15,bacterial diversity was lower at Y25 and Y40,and fungal diversity remained stable during the restoration period between 25 and 40 a.The relative abundances of Proteobacteria and Ascomycota increased during the restoration period from 10 to 15 a.Conversely,after 15 a of restoration,they both decreased,whereas the relative abundances of Actinomycetes,Acidobacteria and Basidiomycota gradually increased.The variations in soil bacterial communities were mainly related to changes in soil total nitrogen,nitrate nitrogen and moisture contents,while soil fungal communities were mainly shaped by soil organic carbon and nitrate nitrogen contents.Bacterial communities were structured by the heterogeneous selection and stochastic process,while fungal communities were structured primarily by the stochastic process.The RP restoration induced an increase in the relative importance of heterogeneous selection on bacterial communities.Overall,this study reveals the changes in microbial diversity,community comp
