The input of organic substances(e.g.,rice straw)in rice field soils usually stimulates the production and emission of the greenhouse gas methane(CH4).However,the amount of CH4 derived from the applied rice straw,as we...The input of organic substances(e.g.,rice straw)in rice field soils usually stimulates the production and emission of the greenhouse gas methane(CH4).However,the amount of CH4 derived from the applied rice straw,as well as the response of bacterial and archaeal communities during the methanogenic phase,are poorly understood for different rice field soils.In this study,samples of five different rice soils were amended with 13^C-labeled rice straw(RS)under methanogenic conditions.Immediately after RS addition,the RS-derived CH4 production rates were higher in soils(Uruguay,Fuyang)that possessed a stronger inherent CH4 production potential compared with other soils with lower inherent potentials(Changsha,the Philippines,Vercelli).However,soils with higher inherent potential did not necessarily produce higher amounts of CH4 from the RS applied,or vice versa.Quantitative PCR showed copy numbers of both bacteria and methanogens increased in straw-amended soils.High-throughput sequencing of 16 S rRNA genes showed distinct bacterial communities among the unamended soil samples,which also changed differently in response to RS addition.Nevertheless,RS addition generally resulted in all the rice field soils in a relative increase of primary fermenters belonging to Anaerolineaceae and Ruminococcaceae.Meanwhile,RS addition also generally resulted in a relative increase of Methanosarcinaceae and/or Methanocellaceae.Our results suggest that after RS addition the total amounts of RSderived CH4 are distinct in different rice field soils under methanogenic conditions.Meanwhile,there are potential core bacterial populations that are often involved in primary fermentation of RS under methanogenic conditions.展开更多
Microbial methanogenesis is a major source of the greenhouse gas methane(CH4).It is the final step in the anaerobic degradation of organic matter when inorganic electron acceptors such as nitrate,ferric iron,or sulfat...Microbial methanogenesis is a major source of the greenhouse gas methane(CH4).It is the final step in the anaerobic degradation of organic matter when inorganic electron acceptors such as nitrate,ferric iron,or sulfate have been depleted.Knowledge of this degradation pathway is important for the creation of mechanistic models,prediction of future CH4 emission scenarios,and development of mitigation strategies.In most anoxic environments,CH4 is produced from either acetate(aceticlastic methanogenesis)or hydrogen(H2)plus carbon dioxide(CO2)(hydrogenotrophic methanogenesis).Hydrogen can be replaced by other CO2-type methanogenesis,using formate,carbon monoxide(CO),or alcohols as substrates.The ratio of these two pathways is tightly constrained by the stoichiometry of conversion processes.If the degradation of organic matter is complete(e.g.,degradation of straw in rice paddies),then fermentation eventually results in production of acetate and H2 at a ratio of>67%aceticlastic and<33%hydrogenotrophic methanogensis.However,acetate production can be favored when heterotrophic or chemolithotrophic acetogenesis is enhanced,and H2 production can be favored when syntrophic acetate oxidation is enhanced.This typically occurs at low and elevated temperatures,respectively.Thus,temperature can strongly influence the methanogenic pathway,which may range from 100%aceticlastic methanogenesis at low temperatures to 100%hydrogenotrophic methanogenesis at high temperatures.However,if the degradation of organic matter is not complete(e.g.,degradation of soil organic matter),the stoichiometry of fermentation is not tightly constrained,resulting,for example,in the preferential production of H2,followed by hydrogenotrophic methanogenesis.Preferential production of CH4 by either aceticlastic or hydrogenotrophic methanogenesis can also happen if one of the methanogenic substrates is not consumed by methanogens but is,instead,accumulated,volatilized,or utilized otherwise.Methylotrophic methanogens,which can use methanol as a substrate,are widespread,but it is unlikely that methanol is produced in similar quantities as acetate,CO2,and H2.Methylotrophic methanogenesis is important in saline environments,where compatible solutes are degraded to methyl compounds(trimethyl amine and dimethyl sulfide)and then serve as non-competitive substrates,while acetate and hydrogen are degraded by non-methanogenic processes,e.g.,sulfate reduction.展开更多
Microbes are simple single-cell organisms,but have an enormous practical significance for human kind.Soil microbes make our planet habitable,and the planet's rapidly changing environments in turn have a profound i...Microbes are simple single-cell organisms,but have an enormous practical significance for human kind.Soil microbes make our planet habitable,and the planet's rapidly changing environments in turn have a profound impact on the soil microbial communities,both positively and negatively.It is thus crucial to better understand how abiotic and biotic factors interact to assemble microbiomes under the given environmental conditions,and how they modulate the intrinsic link between microbial diversity and ecosystem function.From a functional viewpoint.展开更多
Volcanism is a primary process of land formation.It provides a model for understanding soil-forming processes and the role of pioneer bacteria and/or archaea as early colonizers in those new environments.The objective...Volcanism is a primary process of land formation.It provides a model for understanding soil-forming processes and the role of pioneer bacteria and/or archaea as early colonizers in those new environments.The objective of this study was to identify the microbial communities involved in soil formation.DNA was extracted from soil samples from the Llaima volcano in Chile at sites destroyed by lava in different centuries(1640,1751,and 1957).Bacterial and archaeal 16 S r RNA genes were analyzed using quantitative polymerase chain reaction(q PCR)and Illumina Mi Seq sequencing.Results showed that microbial diversity increased with soil age,particularly between the 1751 and 1640 soils.For archaeal communities,Thaumarchaeota was detected in similar abundances in all soils,but Euryarchaeota was rare in the older soils.The analysis of bacterial 16 S r RNA genes showed high abundances of Chloroflexi(37%),Planctomycetes(18%),and Verrucomicrobia(10%)in the youngest soil.Proteobacteria and Acidobacteria were highly abundant in the older soils(16%in 1640 and 15%in 1751 for Acidobacteria;38%in 1640 and 27%in 1751 for Proteobacteria).The microbial profiles in the youngest soils were unusual,with a high abundance of bacteria belonging to the order Ktedonobacterales(Chloroflexi)in the 1957 soil(37%)compared with the 1751(18%)and 1640(7%)soils.In this study,we show that there is a gradual establishment of the microbial community in volcanic soils following an eruption and that specific microbial groups can colonize during the early stages of recovery.展开更多
基金the National Natural Science Foundation of China(41573083)the Construction Program of Biology First-class Discipline in Guizhou(GNYL[2017]009FX1KT09),China+1 种基金the LOEWE center for synthetic microbiology(SYNMIKRO),Germanythe German Research Foundation as part of the ICON consortium(CO 141/4-1)。
文摘The input of organic substances(e.g.,rice straw)in rice field soils usually stimulates the production and emission of the greenhouse gas methane(CH4).However,the amount of CH4 derived from the applied rice straw,as well as the response of bacterial and archaeal communities during the methanogenic phase,are poorly understood for different rice field soils.In this study,samples of five different rice soils were amended with 13^C-labeled rice straw(RS)under methanogenic conditions.Immediately after RS addition,the RS-derived CH4 production rates were higher in soils(Uruguay,Fuyang)that possessed a stronger inherent CH4 production potential compared with other soils with lower inherent potentials(Changsha,the Philippines,Vercelli).However,soils with higher inherent potential did not necessarily produce higher amounts of CH4 from the RS applied,or vice versa.Quantitative PCR showed copy numbers of both bacteria and methanogens increased in straw-amended soils.High-throughput sequencing of 16 S rRNA genes showed distinct bacterial communities among the unamended soil samples,which also changed differently in response to RS addition.Nevertheless,RS addition generally resulted in all the rice field soils in a relative increase of primary fermenters belonging to Anaerolineaceae and Ruminococcaceae.Meanwhile,RS addition also generally resulted in a relative increase of Methanosarcinaceae and/or Methanocellaceae.Our results suggest that after RS addition the total amounts of RSderived CH4 are distinct in different rice field soils under methanogenic conditions.Meanwhile,there are potential core bacterial populations that are often involved in primary fermentation of RS under methanogenic conditions.
基金the Fonds der Chemischen Industrie (Fonds of the Chemical Industry), Germany.
文摘Microbial methanogenesis is a major source of the greenhouse gas methane(CH4).It is the final step in the anaerobic degradation of organic matter when inorganic electron acceptors such as nitrate,ferric iron,or sulfate have been depleted.Knowledge of this degradation pathway is important for the creation of mechanistic models,prediction of future CH4 emission scenarios,and development of mitigation strategies.In most anoxic environments,CH4 is produced from either acetate(aceticlastic methanogenesis)or hydrogen(H2)plus carbon dioxide(CO2)(hydrogenotrophic methanogenesis).Hydrogen can be replaced by other CO2-type methanogenesis,using formate,carbon monoxide(CO),or alcohols as substrates.The ratio of these two pathways is tightly constrained by the stoichiometry of conversion processes.If the degradation of organic matter is complete(e.g.,degradation of straw in rice paddies),then fermentation eventually results in production of acetate and H2 at a ratio of>67%aceticlastic and<33%hydrogenotrophic methanogensis.However,acetate production can be favored when heterotrophic or chemolithotrophic acetogenesis is enhanced,and H2 production can be favored when syntrophic acetate oxidation is enhanced.This typically occurs at low and elevated temperatures,respectively.Thus,temperature can strongly influence the methanogenic pathway,which may range from 100%aceticlastic methanogenesis at low temperatures to 100%hydrogenotrophic methanogenesis at high temperatures.However,if the degradation of organic matter is not complete(e.g.,degradation of soil organic matter),the stoichiometry of fermentation is not tightly constrained,resulting,for example,in the preferential production of H2,followed by hydrogenotrophic methanogenesis.Preferential production of CH4 by either aceticlastic or hydrogenotrophic methanogenesis can also happen if one of the methanogenic substrates is not consumed by methanogens but is,instead,accumulated,volatilized,or utilized otherwise.Methylotrophic methanogens,which can use methanol as a substrate,are widespread,but it is unlikely that methanol is produced in similar quantities as acetate,CO2,and H2.Methylotrophic methanogenesis is important in saline environments,where compatible solutes are degraded to methyl compounds(trimethyl amine and dimethyl sulfide)and then serve as non-competitive substrates,while acetate and hydrogen are degraded by non-methanogenic processes,e.g.,sulfate reduction.
文摘Microbes are simple single-cell organisms,but have an enormous practical significance for human kind.Soil microbes make our planet habitable,and the planet's rapidly changing environments in turn have a profound impact on the soil microbial communities,both positively and negatively.It is thus crucial to better understand how abiotic and biotic factors interact to assemble microbiomes under the given environmental conditions,and how they modulate the intrinsic link between microbial diversity and ecosystem function.From a functional viewpoint.
文摘Volcanism is a primary process of land formation.It provides a model for understanding soil-forming processes and the role of pioneer bacteria and/or archaea as early colonizers in those new environments.The objective of this study was to identify the microbial communities involved in soil formation.DNA was extracted from soil samples from the Llaima volcano in Chile at sites destroyed by lava in different centuries(1640,1751,and 1957).Bacterial and archaeal 16 S r RNA genes were analyzed using quantitative polymerase chain reaction(q PCR)and Illumina Mi Seq sequencing.Results showed that microbial diversity increased with soil age,particularly between the 1751 and 1640 soils.For archaeal communities,Thaumarchaeota was detected in similar abundances in all soils,but Euryarchaeota was rare in the older soils.The analysis of bacterial 16 S r RNA genes showed high abundances of Chloroflexi(37%),Planctomycetes(18%),and Verrucomicrobia(10%)in the youngest soil.Proteobacteria and Acidobacteria were highly abundant in the older soils(16%in 1640 and 15%in 1751 for Acidobacteria;38%in 1640 and 27%in 1751 for Proteobacteria).The microbial profiles in the youngest soils were unusual,with a high abundance of bacteria belonging to the order Ktedonobacterales(Chloroflexi)in the 1957 soil(37%)compared with the 1751(18%)and 1640(7%)soils.In this study,we show that there is a gradual establishment of the microbial community in volcanic soils following an eruption and that specific microbial groups can colonize during the early stages of recovery.
