Silver nanoparticles（Ag NPs）are among the most extensively used engineered nanomaterials because of their wellestablished antimicrobial and unique physicochemical properties（Yin et al.,2015）.Applications of AgNPs ...Silver nanoparticles（Ag NPs）are among the most extensively used engineered nanomaterials because of their wellestablished antimicrobial and unique physicochemical properties（Yin et al.,2015）.Applications of AgNPs have now been expanded beyond their initial use in medicine to industry, agriculture, and households.展开更多
Contaminated sites from electronic waste(e-waste)dismantling and coking plants feature high concentrations of heavy metals(HMs)and/or polycyclic aromatic hydrocarbons(PAHs)in soil.Mixed contamination(HMsþPAHs)hi...Contaminated sites from electronic waste(e-waste)dismantling and coking plants feature high concentrations of heavy metals(HMs)and/or polycyclic aromatic hydrocarbons(PAHs)in soil.Mixed contamination(HMsþPAHs)hinders land reclamation and affects the microbial diversity and function of soil microbiomes.In this study,we analyzed HM and PAH contamination from an e-waste dismantling plant and a coking plant and evaluated the influences of HM and PAH contamination on soil microbiomes.It was noticed that HMs and PAHs were found in all sites,although the major contaminants of the e-waste dismantling plant site were HMs(such as Cu at 5,947.58±433.44 mg kg^(-1),Zn at 4,961.38±436.51 mg kg^(-1),and Mn at 2,379.07±227.46 mg kg^(-1)),and the major contaminants of the coking plant site were PAHs(such as fluorene at 11,740.06±620.1 mg kg^(-1),acenaphthylene at 211.69±7.04 mg kg^(-1),and pyrene at 183.14±18.89 mg kg^(-1)).The microbiomes(diversity and abundance)of all sites were determined via high-throughput sequencing of 16S rRNA genes,and redundancy analysis was conducted to investigate the relations between soil microbiomes and contaminants.The results showed that the microbiomes of the contaminated sites divergently responded to HMs and PAHs.The abundances of the bacterial genera Sulfuritalea,Pseudomonas,and Sphingobium were positively related to PAHs,while the abundances of the bacterial genera Bryobacter,Nitrospira,and Steroidobacter were positively related to HMs.This study promotes an understanding of how soil microbiomes respond to single and mixed contamination with HMs and PAHs.展开更多
Straw is widely incorporated into soil worldwide,but most studies have concentrated on the effects of straw mulching or incorporation with topsoil.To determine the effect of depth of straw incorporation on bacterial a...Straw is widely incorporated into soil worldwide,but most studies have concentrated on the effects of straw mulching or incorporation with topsoil.To determine the effect of depth of straw incorporation on bacterial and fungal communities,we established a field experiment in a region in Northeast China with Haplic Chernozems using four treatments:conventional tillage(CT,tillage to a depth of 15 cm with no straw incorporation),straw incorporation with conventional tillage(SCT,tillage to a depth of 15 cm),inversion tillage(IT,tillage to a depth of 35 cm)and straw incorporation with inversion tillage(SIT,tillage to a depth of 35 cm).The soils were managed by inversion to a depth of 15 or 35 cm after harvest.The results show that soil organic carbon content was significantly higher and pH and bulk density were significantly lower in the 15–35 cm layer in IT and SIT than CT and SCT.Fungal abundance was higher with straw incorporation,but fungal diversity was lower in the 0–15 cm layer in SCT and SIT than in CT and IT.Path length in the bacterial network was shorter and connectivity was higher in CT+SCT than in IT+SIT,leading to a more complex ecosystem,and the fungal network had opposite patterns.The key taxa in the phylum Actinobacteriota and Ascomycota in the microbial networks changed dramatically at the genus level following inversion tillage with straw amendment,which may increase bacterial network resistance to environmental disturbances and unstable fungal networks,resulting in large changes in the fungal community involved in the decomposition of recalcitrant straw-derived C and the more efficient acquisition of limiting resources.展开更多
Apple replant disease(ARD)is a complex agricultural problem caused by multiple stressors that can lead to increased reactive oxygen species(ROS)levels and limited nutrient utilization in plants.However,existing counte...Apple replant disease(ARD)is a complex agricultural problem caused by multiple stressors that can lead to increased reactive oxygen species(ROS)levels and limited nutrient utilization in plants.However,existing countermeasures cannot effectively address this challenge.Here,we used Malus hupehensis as a test organism to investigate whether the pleiotropic molecule dopamine can alleviate ARD using pot experiments.Exogenous application of 100μmol L-1 dopamine significantly promoted the growth of apple seedlings in the replanted soil,with a relative growth rate increase of 17.44%.Our results revealed two major pathways by which dopamine regulates ARD resistance in apple trees.First,dopamine effectively reduces the level of ROS and activates the expression of genes related to nitrogen(N)transport and metabolism.Among those genes,MdNLP5,MdNRT1.1,MdNLP2,MdNRT2.5,MdNLP3,MdNRT2.4,MdNADH-GAGOT,and MdFd-GAGOT were strongly regulated by dopamine.These regulatory effects promoted the uptake and utilization of soil N by the plants.Second,dopamine improved the physical and chemical properties,enhanced microbial community diversity,and promoted mutual cooperation between microbial communities in the soil.Furthermore,dopamine altered the microbial structure of rhizosphere soil(upregulating Clostridiales,Gaiellales,Sordariales and Mortierellales;downregulating Micrococcales,Longimicrobiales,Hypocreales and Cystobasidiales).Notably,dopamine significantly upregulated the abundances of Gaiella and Mortierella,both of which were positively correlated with soil urease activity,soil available N content,plant growth and N uptake.Dopamine also significantly downregulated the abundance of the plant pathogen Gibberella(by 11.71-fold)in replant soil.Our results provide insights into the mechanisms by which dopamine promotes ARD resistance,and can promote the sustainable development of the apple industry.展开更多
The soil microbiome that plays important ecological roles in mountains and forests is influenced by anthropogenic and natural causes.Human activity,particularly harvesting or thinning,affects the soil microbiome in fo...The soil microbiome that plays important ecological roles in mountains and forests is influenced by anthropogenic and natural causes.Human activity,particularly harvesting or thinning,affects the soil microbiome in forests by altering environmental conditions,such as vegetation,microclimate,and soil physicochemical properties.The purpose of this study was to investigate the effects on forest thinning on the diversity and composition of the soil bacterial community.From next-generation sequencing results of the 16S rRNA gene,we examined differences in soil bacterial diversity and community composition before and after thinning at Mt.Janggunbong,South Korea.We identified 40 phyla,103 classes,192 orders,412families,947 genera,and 3,145 species from the soil samples.Acidobacteria and Proteobacteria were the most dominant bacterial phyla in the forest soil of Mt.Janggunbong.Soil bacterial diversity measures(richness,Shannon diversity index,and evenness)at the phylum level increased after thinning,whereas species-level taxonomic richness decreased after thinning.Thinning provided new opportunities for bacterial species in Chloroflexi,Verrucomicrobia,Nitrospirae,and other nondominant bacterial taxa,especially for those not found in Mt.Janggunbong before thinning,to settle and adapt to the changing environment.Our results suggested that thinning affected the diversity and composition of soil bacterial communities in forests and mountains.展开更多
Metagenomic studies of various soil environments have previously revealed the widespread distribution of antibiotic resistance genes(ARGs)around the globe.In this study,we applied shotgun metagenomics to investigate d...Metagenomic studies of various soil environments have previously revealed the widespread distribution of antibiotic resistance genes(ARGs)around the globe.In this study,we applied shotgun metagenomics to investigate differences in microbial communities and resistomes in Chernozem soils that have been under long-term organic and conventional cropping practices.The organic cropping system was seeded with Triticum spelta without any fertilizer.The conventional cropping system was seeded with Tríticum durum Desf and used mineral fertilizer(NPK),that resulted in an increased amount of total and available carbon and nitrogen in soils.Across all samples,we identified a total of 21 ARG classes,among which the dominant were vancomycin,tetracycline and multidrug.Profiling of soil microbial communities revealed differences between the studied fields in the relative abundances of 14 and 53 genera in topsoil and subsoil,respectively.Correlation analysis showed significant correlations(positive and negative)among 18 genera and 6 ARGs,as well as between these ARGs and some chemical properties of soils.The analysis of metagenome-assembled genomes revealed that Nitrospirota,Thermoproteota,Actinobacteriota and Binatota phyla of archaea and bacteria serve as hosts for glycopeptide and fluoroquinolone/tetracycline ARGs.Collectively,the data obtained enrich knowledge about the consequences of human agricultural activities in terms of soil microbiome modification and highlight the role of nitrogen cycling taxa,including uncultivated genera,in the formation of soil resistome.展开更多
Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites,i.e.,metabolomes,in the soil.Soil metabolites,including fatty acids,amino acids,lipids,organic acids,sugars,and volatile organ...Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites,i.e.,metabolomes,in the soil.Soil metabolites,including fatty acids,amino acids,lipids,organic acids,sugars,and volatile organic compounds,often contain essential nutrients such as nitrogen,phosphorus,and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms.This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling.We describe important applications of metabolomics in studying soil carbon cycling and sequestration,and the response of soil organic pools to changing environmental conditions.This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome,as well as responses of soil metabolome to plant and environmental stresses such as soil contamination.We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.展开更多
Plant health and performance are highly dependent on the root microbiome.The impact of agricultural management on the soil microbiome has been studied extensively.However,a comprehensive understanding of how soil type...Plant health and performance are highly dependent on the root microbiome.The impact of agricultural management on the soil microbiome has been studied extensively.However,a comprehensive understanding of how soil types and fertilization regimes affect both soil and root microbiome is still lacking,such as how fertilization regimes affect the root microbiome's stability,and whether it follows the same patterns as the soil microbiome.In this study,we carried out a longterm experiment to see how different soil types,plant varieties,and fertilizer regimens affected the soil and root bacterial communities.Our results revealed higher stability of microbial networks under combined organic-inorganic fertilization than those relied solely on inorganic or organic fertilization.The root microbiome variation was predominantly caused by total nitrogen,while the soil microbiome variation was primarily caused by pH and soil organic matter.Bacteroidetes and Firmicutes were major drivers when the soil was amended with organic fertilizer,but Actinobacteria was found to be enriched in the soil when the soil was treated with inorganic fertilizer.Our findings demonstrate how the soil and root microbiome respond to diverse fertilizing regimes,and hence contribute to a better understanding of smart fertilizer as a strategy for sustainable agriculture.展开更多
Secondary metabolites(SMs)produced by soil bacteria,for instance antimicrobials and siderophores,play a vital role in bacterial adaptation to soil and root ecosystems and can contribute to plant health.Many SMs are no...Secondary metabolites(SMs)produced by soil bacteria,for instance antimicrobials and siderophores,play a vital role in bacterial adaptation to soil and root ecosystems and can contribute to plant health.Many SMs are non-ribosomal peptides and polyketides,assembled by non-ribosomal peptides synthetase(NRPS)and polyketide synthase(PKS)and encoded by biosynthetic gene clusters(BGCs).Despite their ecological importance,little is known about the occurrence and diversity of NRPs and PKs in soil.We extracted NRPS-and PKS-encodiing BGCs from 20 publicly available soil and root-associated metagenomes and annotated them using antiSMASH-DB.We found that the overall abundance of NRPSs and PKSs is similar in both environments,however NRPSs and PKSs were significantly clustered between soil and root samples.Moreover,the majority of identified sequences were unique to either soil-or root-associated datasets and had low identity to known BGCs,suggesting their novelty.Overall,this study illuminates the huge untapped diversity of predicted SMs in soil and root microbiomes,and indicates presence of specific SMs,which may play a role in inter-and intra-bacteriial interactions in root ecosystems.展开更多
Soil is inhabited by a myriad of microorganisms,many of which can form supracellular structures,called biofilms,comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance th...Soil is inhabited by a myriad of microorganisms,many of which can form supracellular structures,called biofilms,comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival.Biofilms enable intensive inter-and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins.Here,we first discuss organization,dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome.Social interactions among bacteria,such as cooperation and competition,are discussed.We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms.Microfluidic platforms,which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with highthroughput screening and novel measurements,are also highlighted.This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.展开更多
Protists are essential components of soil biodiversity and ecosystem functioning. They play a vital role in the microbial food web as consumers of bacteria, fungi, and other small eukaryotes and are also involved in m...Protists are essential components of soil biodiversity and ecosystem functioning. They play a vital role in the microbial food web as consumers of bacteria, fungi, and other small eukaryotes and are also involved in maintaining soil fertility and plant productivity. Protists also contribute to regulating and shaping the bacterial community in terrestrial ecosystems via specific prey spectra. They play a role in plant growth promotion and plant health improvement,mostly via nutrient cycling, grazing, and the activation of bacterial genes required for plant growth and phytopathogen suppression. Thus, protists may prove to be a useful inoculant as biofertilizer and biocontrol agent. They can also be applied as model organisms as bioindicators of soil health. Despite their usefulness and essentiality, they are often forgotten and under-researched components of the soil microbiome, as most of our research focuses on bacteria and fungi. In this review, we provide an overview of the role of protists in plant productivity and plant health management and in shifts in soil bacterial community composition, as well as their roles as bioindicator. We also discuss the perspectives of knowledge gaps and future prospects to further improve soil biology.More research in soil protistology will provide insights into sustainable agriculture and environmental health alongside the study of bacteria and fungi.展开更多
Rice sheath blight pathogen,Rhizoctonia solani,produces numerous sclerotia to overwinter.As a rich source of nutrients in the soil,sclerotia may lead to the change of soil microbiota.For this purpose,we amended the sc...Rice sheath blight pathogen,Rhizoctonia solani,produces numerous sclerotia to overwinter.As a rich source of nutrients in the soil,sclerotia may lead to the change of soil microbiota.For this purpose,we amended the sclerotia of R.solani in soil and analyzed the changes in bacterial microbiota within the soil at different time points.At the phyla level,Proteobacteria,Acidobacteria,Bacteroidetes,Actinobacteria,Chloroflexi and Firmicutes showed varied abundance in the amended soil samples compared to those in the control.An increased abundance of ammonia-oxidizing bacterium(AOB)Nitrosospira and Nitrite oxidizing bacteria(NOB)i.e.,Nitrospira was observed,where the latter is reportedly involved in the nitrifier denitrification.Moreover,Thiobacillus,Gemmatimonas,Anaeromyxobacter and Geobacter,the vital players in denitrification,N2O reduction and reductive nitrogen transformation,respectively,depicted enhanced abundance in R.solani sclerotia-amended samples.Furthermore,asymbiotic nitrogen-fixing bacteria,notably,Azotobacter as well as Microvirga and Phenylobacterium with nitrogen-fixing potential also enriched in the amended samples compared to the control.Plant growth promoting bacteria,such as Kribbella,Chitinophaga and Flavisolibacter also enriched in the sclerotia-amended soil.As per our knowledge,this study is of its kind where pathogenic fungal sclerotia activated microbes with a potential role in N transformation and provided clues about the ecological functions of R.solani sclerotia on the stimulation of bacterial genera involved in different processes of N-cycle within the soil in the absence of host plants.展开更多
Managing plant health is a great challenge formodern food production and is further complicated by thelack of common ground between the many disciplinesinvolved in disease control. Here we present the concept ofrhizos...Managing plant health is a great challenge formodern food production and is further complicated by thelack of common ground between the many disciplinesinvolved in disease control. Here we present the concept ofrhizosphere immunity, in which plant health is consideredas an ecosystem level property emerging from networks ofinteractions between plants, microbiota and the surround-ing soil matrix. These interactions can potentially extendthe innate plant immune system to a point where therhizosphere immunity can fulfil all four core functions ofafull immune system: pathogen prevention, recognition,response and homeostasis. We suggest that consideringplant health from a meta-organism perspective will help indeveloping multidisciplinary pathogen management stra-tegies that focus on steering the whole plant-microbe-soilnetworks instead of individual components. This might beachieved by bringing together the latest discoveries inphytopathology, microbiome research, soil science andagronomy to pave the way toward more sustainable andproductive agriculture.展开更多
文摘Silver nanoparticles（Ag NPs）are among the most extensively used engineered nanomaterials because of their wellestablished antimicrobial and unique physicochemical properties（Yin et al.,2015）.Applications of AgNPs have now been expanded beyond their initial use in medicine to industry, agriculture, and households.
基金the National Natural Science Foundation of China(Grants No.41991333 and 31861133002)the European Unions Horizon 2020 Research and Innovation Program Under Grant Agreement(No.826244)+1 种基金the CAS Engineering Laboratory for Advanced Microbial Technology of Agriculture,Chinese Academy of Sciences(KFJ-PTXM-016)the Science and Technology Basic Resources Survey Special Project(2019FY100700).
文摘Contaminated sites from electronic waste(e-waste)dismantling and coking plants feature high concentrations of heavy metals(HMs)and/or polycyclic aromatic hydrocarbons(PAHs)in soil.Mixed contamination(HMsþPAHs)hinders land reclamation and affects the microbial diversity and function of soil microbiomes.In this study,we analyzed HM and PAH contamination from an e-waste dismantling plant and a coking plant and evaluated the influences of HM and PAH contamination on soil microbiomes.It was noticed that HMs and PAHs were found in all sites,although the major contaminants of the e-waste dismantling plant site were HMs(such as Cu at 5,947.58±433.44 mg kg^(-1),Zn at 4,961.38±436.51 mg kg^(-1),and Mn at 2,379.07±227.46 mg kg^(-1)),and the major contaminants of the coking plant site were PAHs(such as fluorene at 11,740.06±620.1 mg kg^(-1),acenaphthylene at 211.69±7.04 mg kg^(-1),and pyrene at 183.14±18.89 mg kg^(-1)).The microbiomes(diversity and abundance)of all sites were determined via high-throughput sequencing of 16S rRNA genes,and redundancy analysis was conducted to investigate the relations between soil microbiomes and contaminants.The results showed that the microbiomes of the contaminated sites divergently responded to HMs and PAHs.The abundances of the bacterial genera Sulfuritalea,Pseudomonas,and Sphingobium were positively related to PAHs,while the abundances of the bacterial genera Bryobacter,Nitrospira,and Steroidobacter were positively related to HMs.This study promotes an understanding of how soil microbiomes respond to single and mixed contamination with HMs and PAHs.
基金Under the auspices of Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA28070100)the National Key Research and Development Program of China(No.2022YFD1500100)+1 种基金the National Natural Science Foundation of China(No.41807085)the Earmarked Fund for China Agriculture Research System(No.CARS04)。
文摘Straw is widely incorporated into soil worldwide,but most studies have concentrated on the effects of straw mulching or incorporation with topsoil.To determine the effect of depth of straw incorporation on bacterial and fungal communities,we established a field experiment in a region in Northeast China with Haplic Chernozems using four treatments:conventional tillage(CT,tillage to a depth of 15 cm with no straw incorporation),straw incorporation with conventional tillage(SCT,tillage to a depth of 15 cm),inversion tillage(IT,tillage to a depth of 35 cm)and straw incorporation with inversion tillage(SIT,tillage to a depth of 35 cm).The soils were managed by inversion to a depth of 15 or 35 cm after harvest.The results show that soil organic carbon content was significantly higher and pH and bulk density were significantly lower in the 15–35 cm layer in IT and SIT than CT and SCT.Fungal abundance was higher with straw incorporation,but fungal diversity was lower in the 0–15 cm layer in SCT and SIT than in CT and IT.Path length in the bacterial network was shorter and connectivity was higher in CT+SCT than in IT+SIT,leading to a more complex ecosystem,and the fungal network had opposite patterns.The key taxa in the phylum Actinobacteriota and Ascomycota in the microbial networks changed dramatically at the genus level following inversion tillage with straw amendment,which may increase bacterial network resistance to environmental disturbances and unstable fungal networks,resulting in large changes in the fungal community involved in the decomposition of recalcitrant straw-derived C and the more efficient acquisition of limiting resources.
基金supported by National Natural Science Foundation of China(31901964)the Science and Technology Project of Hebei Education Department,China(BJK2022012)+3 种基金the Innovation Ability Training Project for Graduate Student of Hebei Province,China(CXZZBS2023071)the Introduced Talents Project of Hebei Agricultural University,China(YJ201904)the Key Research and Development Project of Hebei Province,China(21326308D-02-03)the Earmarked Fund for the China Agricultural Research System,China(CARS-27).
文摘Apple replant disease(ARD)is a complex agricultural problem caused by multiple stressors that can lead to increased reactive oxygen species(ROS)levels and limited nutrient utilization in plants.However,existing countermeasures cannot effectively address this challenge.Here,we used Malus hupehensis as a test organism to investigate whether the pleiotropic molecule dopamine can alleviate ARD using pot experiments.Exogenous application of 100μmol L-1 dopamine significantly promoted the growth of apple seedlings in the replanted soil,with a relative growth rate increase of 17.44%.Our results revealed two major pathways by which dopamine regulates ARD resistance in apple trees.First,dopamine effectively reduces the level of ROS and activates the expression of genes related to nitrogen(N)transport and metabolism.Among those genes,MdNLP5,MdNRT1.1,MdNLP2,MdNRT2.5,MdNLP3,MdNRT2.4,MdNADH-GAGOT,and MdFd-GAGOT were strongly regulated by dopamine.These regulatory effects promoted the uptake and utilization of soil N by the plants.Second,dopamine improved the physical and chemical properties,enhanced microbial community diversity,and promoted mutual cooperation between microbial communities in the soil.Furthermore,dopamine altered the microbial structure of rhizosphere soil(upregulating Clostridiales,Gaiellales,Sordariales and Mortierellales;downregulating Micrococcales,Longimicrobiales,Hypocreales and Cystobasidiales).Notably,dopamine significantly upregulated the abundances of Gaiella and Mortierella,both of which were positively correlated with soil urease activity,soil available N content,plant growth and N uptake.Dopamine also significantly downregulated the abundance of the plant pathogen Gibberella(by 11.71-fold)in replant soil.Our results provide insights into the mechanisms by which dopamine promotes ARD resistance,and can promote the sustainable development of the apple industry.
基金support of R&D Program for Forest Science Technology (Project No. 2013069D10-1719-AA03) provided by Korea Forest Service (Korea Forestry Promotion Institute)
文摘The soil microbiome that plays important ecological roles in mountains and forests is influenced by anthropogenic and natural causes.Human activity,particularly harvesting or thinning,affects the soil microbiome in forests by altering environmental conditions,such as vegetation,microclimate,and soil physicochemical properties.The purpose of this study was to investigate the effects on forest thinning on the diversity and composition of the soil bacterial community.From next-generation sequencing results of the 16S rRNA gene,we examined differences in soil bacterial diversity and community composition before and after thinning at Mt.Janggunbong,South Korea.We identified 40 phyla,103 classes,192 orders,412families,947 genera,and 3,145 species from the soil samples.Acidobacteria and Proteobacteria were the most dominant bacterial phyla in the forest soil of Mt.Janggunbong.Soil bacterial diversity measures(richness,Shannon diversity index,and evenness)at the phylum level increased after thinning,whereas species-level taxonomic richness decreased after thinning.Thinning provided new opportunities for bacterial species in Chloroflexi,Verrucomicrobia,Nitrospirae,and other nondominant bacterial taxa,especially for those not found in Mt.Janggunbong before thinning,to settle and adapt to the changing environment.Our results suggested that thinning affected the diversity and composition of soil bacterial communities in forests and mountains.
基金performed using resources of the Research Resource Center&Natural Resource Management and Physico-Chemical Research(University of Tyumen).
文摘Metagenomic studies of various soil environments have previously revealed the widespread distribution of antibiotic resistance genes(ARGs)around the globe.In this study,we applied shotgun metagenomics to investigate differences in microbial communities and resistomes in Chernozem soils that have been under long-term organic and conventional cropping practices.The organic cropping system was seeded with Triticum spelta without any fertilizer.The conventional cropping system was seeded with Tríticum durum Desf and used mineral fertilizer(NPK),that resulted in an increased amount of total and available carbon and nitrogen in soils.Across all samples,we identified a total of 21 ARG classes,among which the dominant were vancomycin,tetracycline and multidrug.Profiling of soil microbial communities revealed differences between the studied fields in the relative abundances of 14 and 53 genera in topsoil and subsoil,respectively.Correlation analysis showed significant correlations(positive and negative)among 18 genera and 6 ARGs,as well as between these ARGs and some chemical properties of soils.The analysis of metagenome-assembled genomes revealed that Nitrospirota,Thermoproteota,Actinobacteriota and Binatota phyla of archaea and bacteria serve as hosts for glycopeptide and fluoroquinolone/tetracycline ARGs.Collectively,the data obtained enrich knowledge about the consequences of human agricultural activities in terms of soil microbiome modification and highlight the role of nitrogen cycling taxa,including uncultivated genera,in the formation of soil resistome.
基金supported by the Youth Innovation Promotion Association,CAS(2021309)the Natural Sciences and Engineering Research Council of Canada(NSERC,RGPIN-2018-05700)+1 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA28010501)the National Natural Science Foundation of China(42277303,42107244).
文摘Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites,i.e.,metabolomes,in the soil.Soil metabolites,including fatty acids,amino acids,lipids,organic acids,sugars,and volatile organic compounds,often contain essential nutrients such as nitrogen,phosphorus,and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms.This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling.We describe important applications of metabolomics in studying soil carbon cycling and sequestration,and the response of soil organic pools to changing environmental conditions.This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome,as well as responses of soil metabolome to plant and environmental stresses such as soil contamination.We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.
基金supported by the National Key Research and Development Program of China(Grant No.2021YFD1700900)the National Natural Science Foundation of China(Grant No.31972519)the Taishan Industry Leading Talents HighEfficiency Agriculture Innovation Project(Grant No.LJNY202125).
文摘Plant health and performance are highly dependent on the root microbiome.The impact of agricultural management on the soil microbiome has been studied extensively.However,a comprehensive understanding of how soil types and fertilization regimes affect both soil and root microbiome is still lacking,such as how fertilization regimes affect the root microbiome's stability,and whether it follows the same patterns as the soil microbiome.In this study,we carried out a longterm experiment to see how different soil types,plant varieties,and fertilizer regimens affected the soil and root bacterial communities.Our results revealed higher stability of microbial networks under combined organic-inorganic fertilization than those relied solely on inorganic or organic fertilization.The root microbiome variation was predominantly caused by total nitrogen,while the soil microbiome variation was primarily caused by pH and soil organic matter.Bacteroidetes and Firmicutes were major drivers when the soil was amended with organic fertilizer,but Actinobacteria was found to be enriched in the soil when the soil was treated with inorganic fertilizer.Our findings demonstrate how the soil and root microbiome respond to diverse fertilizing regimes,and hence contribute to a better understanding of smart fertilizer as a strategy for sustainable agriculture.
文摘Secondary metabolites(SMs)produced by soil bacteria,for instance antimicrobials and siderophores,play a vital role in bacterial adaptation to soil and root ecosystems and can contribute to plant health.Many SMs are non-ribosomal peptides and polyketides,assembled by non-ribosomal peptides synthetase(NRPS)and polyketide synthase(PKS)and encoded by biosynthetic gene clusters(BGCs).Despite their ecological importance,little is known about the occurrence and diversity of NRPs and PKs in soil.We extracted NRPS-and PKS-encodiing BGCs from 20 publicly available soil and root-associated metagenomes and annotated them using antiSMASH-DB.We found that the overall abundance of NRPSs and PKSs is similar in both environments,however NRPSs and PKSs were significantly clustered between soil and root samples.Moreover,the majority of identified sequences were unique to either soil-or root-associated datasets and had low identity to known BGCs,suggesting their novelty.Overall,this study illuminates the huge untapped diversity of predicted SMs in soil and root microbiomes,and indicates presence of specific SMs,which may play a role in inter-and intra-bacteriial interactions in root ecosystems.
基金supported by the National Natural Science Foundation of China(41877029)the National Basic Research Program of China(2016YFD0800206)the Fundamental Research Funds for the Central Universities(2662017JC008).
文摘Soil is inhabited by a myriad of microorganisms,many of which can form supracellular structures,called biofilms,comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival.Biofilms enable intensive inter-and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins.Here,we first discuss organization,dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome.Social interactions among bacteria,such as cooperation and competition,are discussed.We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms.Microfluidic platforms,which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with highthroughput screening and novel measurements,are also highlighted.This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.
基金supported by the Department of Science and Technology, Science and Engineering Research Board (DST-SERB), New Delhi, India under an ECRA grant for researchers to NA (ECR/2017/001977)。
文摘Protists are essential components of soil biodiversity and ecosystem functioning. They play a vital role in the microbial food web as consumers of bacteria, fungi, and other small eukaryotes and are also involved in maintaining soil fertility and plant productivity. Protists also contribute to regulating and shaping the bacterial community in terrestrial ecosystems via specific prey spectra. They play a role in plant growth promotion and plant health improvement,mostly via nutrient cycling, grazing, and the activation of bacterial genes required for plant growth and phytopathogen suppression. Thus, protists may prove to be a useful inoculant as biofertilizer and biocontrol agent. They can also be applied as model organisms as bioindicators of soil health. Despite their usefulness and essentiality, they are often forgotten and under-researched components of the soil microbiome, as most of our research focuses on bacteria and fungi. In this review, we provide an overview of the role of protists in plant productivity and plant health management and in shifts in soil bacterial community composition, as well as their roles as bioindicator. We also discuss the perspectives of knowledge gaps and future prospects to further improve soil biology.More research in soil protistology will provide insights into sustainable agriculture and environmental health alongside the study of bacteria and fungi.
基金funded by the National Key R&D Program(grant number No.2017YFD0200600)and the earmarked fund for CARS-12.
文摘Rice sheath blight pathogen,Rhizoctonia solani,produces numerous sclerotia to overwinter.As a rich source of nutrients in the soil,sclerotia may lead to the change of soil microbiota.For this purpose,we amended the sclerotia of R.solani in soil and analyzed the changes in bacterial microbiota within the soil at different time points.At the phyla level,Proteobacteria,Acidobacteria,Bacteroidetes,Actinobacteria,Chloroflexi and Firmicutes showed varied abundance in the amended soil samples compared to those in the control.An increased abundance of ammonia-oxidizing bacterium(AOB)Nitrosospira and Nitrite oxidizing bacteria(NOB)i.e.,Nitrospira was observed,where the latter is reportedly involved in the nitrifier denitrification.Moreover,Thiobacillus,Gemmatimonas,Anaeromyxobacter and Geobacter,the vital players in denitrification,N2O reduction and reductive nitrogen transformation,respectively,depicted enhanced abundance in R.solani sclerotia-amended samples.Furthermore,asymbiotic nitrogen-fixing bacteria,notably,Azotobacter as well as Microvirga and Phenylobacterium with nitrogen-fixing potential also enriched in the amended samples compared to the control.Plant growth promoting bacteria,such as Kribbella,Chitinophaga and Flavisolibacter also enriched in the sclerotia-amended soil.As per our knowledge,this study is of its kind where pathogenic fungal sclerotia activated microbes with a potential role in N transformation and provided clues about the ecological functions of R.solani sclerotia on the stimulation of bacterial genera involved in different processes of N-cycle within the soil in the absence of host plants.
基金the National Natural Science Foundation of China (41922053, 41671248,ZW)the Fundamental Research Funds for the Central Universities KYXK202009-KYXK202012+2 种基金the National Key Research and DevelopmentProgram of China (2018YFD1000800,ZW)the National Key BasicResearch Program of China (2015CB150503,QS)AJ is supported by the Netherlands Organization for Scientific Research project ALW.870.15.050 and the H2020 project “Viroplant”. VPF is supported by Royal SocietyResearch Grants (RSG\R1\180213 and CHL\R1\180031) at the University of York.
文摘Managing plant health is a great challenge formodern food production and is further complicated by thelack of common ground between the many disciplinesinvolved in disease control. Here we present the concept ofrhizosphere immunity, in which plant health is consideredas an ecosystem level property emerging from networks ofinteractions between plants, microbiota and the surround-ing soil matrix. These interactions can potentially extendthe innate plant immune system to a point where therhizosphere immunity can fulfil all four core functions ofafull immune system: pathogen prevention, recognition,response and homeostasis. We suggest that consideringplant health from a meta-organism perspective will help indeveloping multidisciplinary pathogen management stra-tegies that focus on steering the whole plant-microbe-soilnetworks instead of individual components. This might beachieved by bringing together the latest discoveries inphytopathology, microbiome research, soil science andagronomy to pave the way toward more sustainable andproductive agriculture.
