Paddy fields play an important role in global carbon(C) cycling and are an important source of methane(CH_(4)) emissions. Insights into the processes influencing the dynamics of soil organic C(SOC) in paddy fields are...Paddy fields play an important role in global carbon(C) cycling and are an important source of methane(CH_(4)) emissions. Insights into the processes influencing the dynamics of soil organic C(SOC) in paddy fields are essential for maintaining global soil C stocks and mitigating climate change. Periphytic biofilms composed of microalgae, bacteria, and other microorganisms are ubiquitous in paddy fields, where they directly mediate the transfer of elements at the soil-water interface. However, their contributions to C turnover and exchange have been largely neglected. Periphytic biofilms affect and participate in soil C dynamics by altering both abiotic(e.g., pH and redox potential) and biotic conditions(e.g., microbial community composition and metabolism). This review summarizes the contributions of periphytic biofilms to soil C cycling processes, including carbon dioxide fixation, SOC mineralization, and CH_(4) emissions. Future research should be focused on: i) the mechanisms underlying periphytic biofilm-induced C fixation and turnover and ii) quantifying the contributions of periphytic biofilms to soil C uptake, stabilization, and sequestration in paddy fields.展开更多
The nitrogen cycle plays a vital role in sustaining productive and healthy ecosystems,with the microbial nitrogen cycle being a focal point in agriculture and eco-environmental protection.Among these microbially media...The nitrogen cycle plays a vital role in sustaining productive and healthy ecosystems,with the microbial nitrogen cycle being a focal point in agriculture and eco-environmental protection.Among these microbially mediated processes is ammonium(NH_(4)^(+))oxidation,the gatekeeper of the nitrogen cycle.Our understanding of ammonium oxidation is continuously evolving,thanks to recent research breakthroughs like comammox,Feammox,and dirammox[1-6].The increasing complexity of ammonium oxidation necessitates more precise and well-focused research tools beyond those commonly used today.展开更多
Rice paddies are major contributors to anthropogenic greenhouse gas emissions via methane(CH_(4))flux.The accurate quantification of CH_(4)emissions from rice paddies remains problematic,in part due to uncertainties a...Rice paddies are major contributors to anthropogenic greenhouse gas emissions via methane(CH_(4))flux.The accurate quantification of CH_(4)emissions from rice paddies remains problematic,in part due to uncertainties and omissions in the contribution of microbial aggregates on the soil surface to carbon fluxes.Herein,we comprehensively evaluated the contribution of one form of microbial aggregates,periphytic biofilm(PB),to carbon dioxide(CO_(2))and CH_(4)emissions from paddies distributed across three climatic zones,and quantified the pathways that drive net CH_(4)production as well as CO_(2)fixation.We found that PB accounted for 7.1%-38.5%of CH_(4)emissions and 7.2%-12.7%of CO_(2)fixation in the rice paddies.During their growth phase,PB fixed CO_(2)and increased the redox potential,which promoted aerobic CH_(4)oxidation.During the decay phase,PB degradation reduced redox potential and increased soil organic carbon availability,which promoted methanogenic microbial community growth and metabolism and increased CH_(4)emissions.Overall,PB acted as a biotic converter of atmospheric CO_(2)to CH_(4),and aggravated carbon emissions by up to 2,318 kg CO_(2)equiv ha^(-1)season^(-1).Our results provide proof-of-concept evidence for the discrimination of the contributions of surface microbial aggregates(i.e.,PB)from soil microbes,and a profound foundation for the estimation and simulation of carbon fluxes in a potential novel approach to the mitigation of CH_(4)emissions by manipulating PB growth.展开更多
Rice paddies are unique waterlogged wetlands artificially constructed for agricultural production.Periphytic biofilms(PBs)at the soil–water interface play an important role in rice paddies characterized by high nutri...Rice paddies are unique waterlogged wetlands artificially constructed for agricultural production.Periphytic biofilms(PBs)at the soil–water interface play an important role in rice paddies characterized by high nutrient input but low utilization efficiency.PBs are composed of microbial aggregates,including a wide variety of microorganisms(algae,bacteria,fungi,protozoa,and metazoa),extracellular polymeric substances and minerals(iron,aluminum,and calcium),which form an integrated food web and energy flux within a relatively stable micro-ecosystem.PBs are crucial to regulate and streamline the nitrogen cycle by neutralizing nitrogen losses and improving rice production since PBs can serve as both a sink by capturing surplus nitrogen and a source by slowly re-releasing this nitrogen for reutilization.Here the ecological advantages of PBs in regulating the nitrogen cycle in rice paddies are illustrated.We summarize the key functional importance of PBs,including the intricate and delicate community structure,microbial interactions among individual phylotypes,a wide diversity of selfproduced organics,the active adaptation of PBs to constantly changing environments,and the intricate mechanisms by which PBs regulate the nitrogen cycle.We also identify the future challenges of microbial interspecific cooperation in PBs and their quantitative contributions to agricultural sustainability,optimizing nitrogen utilization and crop yields in rice paddies.展开更多
Chronosequences of ancient rice terraces serve as an invaluable archive for reconstructions of historical human-environment interactions. Presently, however, these reconstructions are based on traditional soil physico...Chronosequences of ancient rice terraces serve as an invaluable archive for reconstructions of historical human-environment interactions. Presently, however, these reconstructions are based on traditional soil physico-chemical properties. The microorganisms in palaeosols have been unexplored. We hypothesized that microbial information can be used as an additional proxy to complement and consolidate archaeological interpretations. To test this hypothesis, the palaeoenvironmental methanogenic archaeal DNA in Longji Terraces, one of the famous ancient terraces in China, dating back to the late Yuan Dynasty(CE1361–1406), was chronosequenced by high-throughput sequencing. It was found that the methanogenic archaeal abundance, diversity and community composition were closely associated with the 630 years of rice cultivation and in line with changes in multi-proxy data. Particularly, the centennial-and decadalscale influences of known historical events, including social turbulences(The Taiping Rebellion, CE1850–1865), palaeoclimate changes(the Little Ice Age) and recorded natural disasters(earthquakes and inundation), on ancient agricultural society were clearly echoed in the microbial archives as variations in alpha and beta diversity. This striking correlation suggests that the microorganisms archived in palaeosols can be quantitatively and qualitatively analyzed to provide an additional proxy, and palaeo-microbial information could be routinely incorporated in the toolkit for archaeological interpretation.展开更多
Soil microorganisms play globally vital roles in the environment,ecology,and agriculture[1],and have become a research hotspot.Most research in these fields depends on microbial sequencing and analysis[2,3],which shou...Soil microorganisms play globally vital roles in the environment,ecology,and agriculture[1],and have become a research hotspot.Most research in these fields depends on microbial sequencing and analysis[2,3],which should ideally be conducted immediately after sample collection[4].However on-site DNA extraction and sequencing are often impractical.Therefore,freshly collected soil samples must be properly stored for transport before sequencing.While this sounds like a natural operation,proper transport of soil samples has been widely overlooked,challenging the accuracy of all related research.展开更多
基金financial support from the National Natural Science Foundation of China(Nos.41825021 and 42207447)the National Key Research and Development Program of China(No.2021YFD17008)+3 种基金the Provincial Natural Science Foundation of Jiangsu,China(No.BK20220004)the Postdoctoral Science Foundation of China(Nos.BX2021325 and 2022M723242)the State Key Laboratory of Lake Science and Environment Foundation,China(No.2022SKL008)EJ was supported by the TüBITAK program BIDEB2232 of Türkiye(No.118C250)。
文摘Paddy fields play an important role in global carbon(C) cycling and are an important source of methane(CH_(4)) emissions. Insights into the processes influencing the dynamics of soil organic C(SOC) in paddy fields are essential for maintaining global soil C stocks and mitigating climate change. Periphytic biofilms composed of microalgae, bacteria, and other microorganisms are ubiquitous in paddy fields, where they directly mediate the transfer of elements at the soil-water interface. However, their contributions to C turnover and exchange have been largely neglected. Periphytic biofilms affect and participate in soil C dynamics by altering both abiotic(e.g., pH and redox potential) and biotic conditions(e.g., microbial community composition and metabolism). This review summarizes the contributions of periphytic biofilms to soil C cycling processes, including carbon dioxide fixation, SOC mineralization, and CH_(4) emissions. Future research should be focused on: i) the mechanisms underlying periphytic biofilm-induced C fixation and turnover and ii) quantifying the contributions of periphytic biofilms to soil C uptake, stabilization, and sequestration in paddy fields.
基金supported by the National Natural Science Foundation of China(41825021 and 42320104002)the Natural Science Foundation of Jiangsu Province(BE2020731)+1 种基金the Jiangsu Agriculture Science and Technology Innovation Fund(JASTIF,CX(22)1003)the Original Innovation Project of Chinese Academy of Sciences(ZDBS-LY-DQC024)。
文摘The nitrogen cycle plays a vital role in sustaining productive and healthy ecosystems,with the microbial nitrogen cycle being a focal point in agriculture and eco-environmental protection.Among these microbially mediated processes is ammonium(NH_(4)^(+))oxidation,the gatekeeper of the nitrogen cycle.Our understanding of ammonium oxidation is continuously evolving,thanks to recent research breakthroughs like comammox,Feammox,and dirammox[1-6].The increasing complexity of ammonium oxidation necessitates more precise and well-focused research tools beyond those commonly used today.
基金supported by the National Natural Science Foundation of China(41825021,41961144010,and 31772396)the Natural Science Foundation of Jiangsu Province(BZ2019015 and BE2020731)the Original Innovation Project of the Chinese Academy of Sciences(ZDBS-LY-DQC024).
文摘Rice paddies are major contributors to anthropogenic greenhouse gas emissions via methane(CH_(4))flux.The accurate quantification of CH_(4)emissions from rice paddies remains problematic,in part due to uncertainties and omissions in the contribution of microbial aggregates on the soil surface to carbon fluxes.Herein,we comprehensively evaluated the contribution of one form of microbial aggregates,periphytic biofilm(PB),to carbon dioxide(CO_(2))and CH_(4)emissions from paddies distributed across three climatic zones,and quantified the pathways that drive net CH_(4)production as well as CO_(2)fixation.We found that PB accounted for 7.1%-38.5%of CH_(4)emissions and 7.2%-12.7%of CO_(2)fixation in the rice paddies.During their growth phase,PB fixed CO_(2)and increased the redox potential,which promoted aerobic CH_(4)oxidation.During the decay phase,PB degradation reduced redox potential and increased soil organic carbon availability,which promoted methanogenic microbial community growth and metabolism and increased CH_(4)emissions.Overall,PB acted as a biotic converter of atmospheric CO_(2)to CH_(4),and aggravated carbon emissions by up to 2,318 kg CO_(2)equiv ha^(-1)season^(-1).Our results provide proof-of-concept evidence for the discrimination of the contributions of surface microbial aggregates(i.e.,PB)from soil microbes,and a profound foundation for the estimation and simulation of carbon fluxes in a potential novel approach to the mitigation of CH_(4)emissions by manipulating PB growth.
基金supported by the National Natural Science Foundation of China(41825021 and 41961144010)the Natural Science Foundation of Jiangsu Province(BE2020731)the Original Innovation Project of Chinese Academy of Sciences(ZDBS-LY-DQC024).
文摘Rice paddies are unique waterlogged wetlands artificially constructed for agricultural production.Periphytic biofilms(PBs)at the soil–water interface play an important role in rice paddies characterized by high nutrient input but low utilization efficiency.PBs are composed of microbial aggregates,including a wide variety of microorganisms(algae,bacteria,fungi,protozoa,and metazoa),extracellular polymeric substances and minerals(iron,aluminum,and calcium),which form an integrated food web and energy flux within a relatively stable micro-ecosystem.PBs are crucial to regulate and streamline the nitrogen cycle by neutralizing nitrogen losses and improving rice production since PBs can serve as both a sink by capturing surplus nitrogen and a source by slowly re-releasing this nitrogen for reutilization.Here the ecological advantages of PBs in regulating the nitrogen cycle in rice paddies are illustrated.We summarize the key functional importance of PBs,including the intricate and delicate community structure,microbial interactions among individual phylotypes,a wide diversity of selfproduced organics,the active adaptation of PBs to constantly changing environments,and the intricate mechanisms by which PBs regulate the nitrogen cycle.We also identify the future challenges of microbial interspecific cooperation in PBs and their quantitative contributions to agricultural sustainability,optimizing nitrogen utilization and crop yields in rice paddies.
基金supported by National Natural Science Foundation of China(41671267,41430859 and 41271256)the CAS Strategic Priority Research Program Grant(XDB15020103)+2 种基金National Key R&D Program(2016YFD0200306)National Basic Research Program(973 Program)(2014CB954500)Knowledge Innovation Program of Chinese Academy of Sciences(ISSASIP1639)
文摘Chronosequences of ancient rice terraces serve as an invaluable archive for reconstructions of historical human-environment interactions. Presently, however, these reconstructions are based on traditional soil physico-chemical properties. The microorganisms in palaeosols have been unexplored. We hypothesized that microbial information can be used as an additional proxy to complement and consolidate archaeological interpretations. To test this hypothesis, the palaeoenvironmental methanogenic archaeal DNA in Longji Terraces, one of the famous ancient terraces in China, dating back to the late Yuan Dynasty(CE1361–1406), was chronosequenced by high-throughput sequencing. It was found that the methanogenic archaeal abundance, diversity and community composition were closely associated with the 630 years of rice cultivation and in line with changes in multi-proxy data. Particularly, the centennial-and decadalscale influences of known historical events, including social turbulences(The Taiping Rebellion, CE1850–1865), palaeoclimate changes(the Little Ice Age) and recorded natural disasters(earthquakes and inundation), on ancient agricultural society were clearly echoed in the microbial archives as variations in alpha and beta diversity. This striking correlation suggests that the microorganisms archived in palaeosols can be quantitatively and qualitatively analyzed to provide an additional proxy, and palaeo-microbial information could be routinely incorporated in the toolkit for archaeological interpretation.
基金supported by the National Natural Science Foundation of China(42320104002)the Jiangsu Agriculture Science and Technology Innovation Fund(JASTIF,CX(22)1003)the Original Innovation Project of Chinese Academy of Sciences(ZDBS-LY-DQC024)。
文摘Soil microorganisms play globally vital roles in the environment,ecology,and agriculture[1],and have become a research hotspot.Most research in these fields depends on microbial sequencing and analysis[2,3],which should ideally be conducted immediately after sample collection[4].However on-site DNA extraction and sequencing are often impractical.Therefore,freshly collected soil samples must be properly stored for transport before sequencing.While this sounds like a natural operation,proper transport of soil samples has been widely overlooked,challenging the accuracy of all related research.
