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
Long-term nitrogen(N)fertilization imposes strong selection on nitrifying communities in agricultural soil,but how a progressively changing niche affects potentially active nitrifiers in the field remains poorly under...Long-term nitrogen(N)fertilization imposes strong selection on nitrifying communities in agricultural soil,but how a progressively changing niche affects potentially active nitrifiers in the field remains poorly understood.Using a 44-year grassland fertilization experiment,we investigated community shifts of active nitrifiers by DNA-based stable isotope probing(SIP)of field soils that received no fertilization(CK),high levels of organic cattle manure(HC),and chemical N fertilization(CF).Incubation of DNA-SIP microcosms showed significant nitrification activities in CF and HC soils,whereas no activity occurred in CK soils.The 44 years of inorganic N fertilization selected only 13C-ammonia-oxidizing bacteria(AOB),whereas cattle slurry applications created a niche in which both ammonia-oxidizing archaea(AOA)and AOB could be actively13C-labeled.Phylogenetic analysis indicated that Nitrosospira sp.62-like AOB dominated inorganically fertilized CF soils,while Nitrosospira sp.41-like AOB were abundant in organically fertilized HC soils.The 13C-AOA in HC soils were affiliated with the 29i4 lineage.The 13C-nitrite-oxidizing bacteria(NOB)were dominated by both Nitrospira-and Nitrobacter-like communities in CF soils,and the latter was overwhelmingly abundant in HC soils.The 13C-labeled nitrifying communities in SIP microcosms of CF and HC soils were largely similar to those predominant under field conditions.These results provide direct evidence for a strong selection of distinctly active nitrifiers after 44 years of different fertilization regimes in the field.Our findings imply that niche differentiation of nitrifying communities could be assessed as a net result of microbial adaption over 44 years to inorganic and organic N fertilization in the field,where distinct nitrifiers have been shaped by intensified anthropogenic N input.展开更多
Conventional clear-cut timber harvest is a widespread industrial practice across the Pacific Northwest;however,information regarding how these practices impact soil microbial community structure at the regional scale ...Conventional clear-cut timber harvest is a widespread industrial practice across the Pacific Northwest;however,information regarding how these practices impact soil microbial community structure at the regional scale is limited.With evidence of consistent and substantial impact of harvest on soil microbial functional profiles across the region(despite a range of environmental conditions),the objective of this study was to determine the extent to which harvest also influences the structure of prokaryotic and fungal soil microbial communities,and how generalized these trends are throughout the geographic region.Paired soil samples were collected one year before and after harvest across nine second-growth Douglas-fir forests in the Pacific Northwest.Total community DNA was extracted from the soils,and high-throughput targeted gene sequencing of the 16 S r RNA gene for prokaryotes and the internal transcribed spacer(ITS)gene for fungi was performed.Alpha diversity was consistently and significantly higher after harvest;it was moderately so for fungal communities(+14.6%),but only marginally so for prokaryotic communities(+2.0%).Similarly,on average,a greater proportion of the variation in the community structure of fungi(20.1%)at each site was associated with forest harvest compared to that of prokaryotes(13.2%).Overall,the greatest influence of timber harvest on soil microbial communities appeared to be a relative depletion of ectomycorrhizal fungi,with a concomitant enrichment of saprotrophic fungi.Understanding the short-term responses of soil microbial communities across the region,particularly those of tree root-associated symbionts,may aid our understanding of the role soil microbial communities play in ecological succession.展开更多
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.
基金the National Natural Science Foundation of China(Nos.41530857 and 41471208)the National Key Basic Research Program of China(No.2015CB150501)+2 种基金the Department of Agriculture,Environment,and Rural Affairs(DAERA)in Northern Ireland,UK(No.700141499)the Strategic Priority Research Program of Chinese Academy of Sciences(No.XDB15040000)the Startup Foundation for Introducing Talent of the Nanjing University of Information Science and Technology(NUIST),China(No.S8113117001).
文摘Long-term nitrogen(N)fertilization imposes strong selection on nitrifying communities in agricultural soil,but how a progressively changing niche affects potentially active nitrifiers in the field remains poorly understood.Using a 44-year grassland fertilization experiment,we investigated community shifts of active nitrifiers by DNA-based stable isotope probing(SIP)of field soils that received no fertilization(CK),high levels of organic cattle manure(HC),and chemical N fertilization(CF).Incubation of DNA-SIP microcosms showed significant nitrification activities in CF and HC soils,whereas no activity occurred in CK soils.The 44 years of inorganic N fertilization selected only 13C-ammonia-oxidizing bacteria(AOB),whereas cattle slurry applications created a niche in which both ammonia-oxidizing archaea(AOA)and AOB could be actively13C-labeled.Phylogenetic analysis indicated that Nitrosospira sp.62-like AOB dominated inorganically fertilized CF soils,while Nitrosospira sp.41-like AOB were abundant in organically fertilized HC soils.The 13C-AOA in HC soils were affiliated with the 29i4 lineage.The 13C-nitrite-oxidizing bacteria(NOB)were dominated by both Nitrospira-and Nitrobacter-like communities in CF soils,and the latter was overwhelmingly abundant in HC soils.The 13C-labeled nitrifying communities in SIP microcosms of CF and HC soils were largely similar to those predominant under field conditions.These results provide direct evidence for a strong selection of distinctly active nitrifiers after 44 years of different fertilization regimes in the field.Our findings imply that niche differentiation of nitrifying communities could be assessed as a net result of microbial adaption over 44 years to inorganic and organic N fertilization in the field,where distinct nitrifiers have been shaped by intensified anthropogenic N input.
基金supported by Weyerhaeuser Natural Resource Company.
文摘Conventional clear-cut timber harvest is a widespread industrial practice across the Pacific Northwest;however,information regarding how these practices impact soil microbial community structure at the regional scale is limited.With evidence of consistent and substantial impact of harvest on soil microbial functional profiles across the region(despite a range of environmental conditions),the objective of this study was to determine the extent to which harvest also influences the structure of prokaryotic and fungal soil microbial communities,and how generalized these trends are throughout the geographic region.Paired soil samples were collected one year before and after harvest across nine second-growth Douglas-fir forests in the Pacific Northwest.Total community DNA was extracted from the soils,and high-throughput targeted gene sequencing of the 16 S r RNA gene for prokaryotes and the internal transcribed spacer(ITS)gene for fungi was performed.Alpha diversity was consistently and significantly higher after harvest;it was moderately so for fungal communities(+14.6%),but only marginally so for prokaryotic communities(+2.0%).Similarly,on average,a greater proportion of the variation in the community structure of fungi(20.1%)at each site was associated with forest harvest compared to that of prokaryotes(13.2%).Overall,the greatest influence of timber harvest on soil microbial communities appeared to be a relative depletion of ectomycorrhizal fungi,with a concomitant enrichment of saprotrophic fungi.Understanding the short-term responses of soil microbial communities across the region,particularly those of tree root-associated symbionts,may aid our understanding of the role soil microbial communities play in ecological succession.
