Core Microbiome:The Hidden Organ Essential for Human Health The core microbiome,often described as a‘hidden organ’,has captivated researchers as a fundamental key to understanding the intimate relationship between m...Core Microbiome:The Hidden Organ Essential for Human Health The core microbiome,often described as a‘hidden organ’,has captivated researchers as a fundamental key to understanding the intimate relationship between microbial ecosystems and human health(Turnbaugh and Gordon 2009).This specialized subset of microbial entities,ever-present across populations,transcends the variations of genetics,diet,and lifestyle to act as a stabilizing force in the gut.展开更多
The unique gut habitat led to a core intestinal micro-biome in diverse soil ecosystems.The collembolan guts may help eliminate soil pathogens.Host-selection carried more weight on community assembly of gut microbiome....The unique gut habitat led to a core intestinal micro-biome in diverse soil ecosystems.The collembolan guts may help eliminate soil pathogens.Host-selection carried more weight on community assembly of gut microbiome.Soil invertebrates are widely distributed in the ecosystem and are essential for soil ecological processes.Inverte-brate gut microbiome plays an important role in host health and has been considered as a hidden microbial repository.However,little is known about how gut microbiome in soil invertebrates respond to diverse soil ecosystems.Based on a laboratory microcosm experiment,we characterized the assembling of microbiome of soil collembolans(Folsomia candida)from six representative regions of the soil ecosystem which they inhabit.Results showed that collembolan gut microbial communities differed significantly from their surrounding soil microbial communities.A dominant core gut microbiome was identified in gut habitat.Community analyses indicated that deterministic process dominated in the community assembly of collembolan gut microbiome.The results further demonstrate a dominant contribution of host selection in shaping gut microbiome.It is also worthy to mention that pathogens,such as common agricultural phytopathogenic fungi Fusarium,were involved in core microbiome,indicating that collembolans could act as vectors of pathogens.Our results unravelled the existence of gut core microbiome of collembolans in soil ecosystems and provided new insights for under-standing the crucial role of gut microbiome of soil fauna in maintaining microbial biodiversity and stability of soil ecosystems.展开更多
Phyllosphere microbiome plays an irreplaceable role in maintaining plant health under stress,but its structure and functions in heavy metal-hyperaccumulating plants remain elusive.Here,the phyllosphere microbiome,inha...Phyllosphere microbiome plays an irreplaceable role in maintaining plant health under stress,but its structure and functions in heavy metal-hyperaccumulating plants remain elusive.Here,the phyllosphere microbiome,inhabiting hyperaccumulating(HE)and non-hyperaccumulating ecotype(NHE)of Sedum alfredii grown in soils with varying heavy metal concentration,was characterized.Compared with NHE,the microbial communityα-diversity was greater in HE.Core phyllosphere taxa with high relative abundance(>10%),including Streptomyces and Nocardia(bacteria),Cladosporium and Acremonium(fungi),were significantly related to cadmium(Cd)and zinc(Zn)concentration and biomass of host plants.Moreover,microbial co-occurrence networks in HE exhibited greater complexity than those in NHE.Additionally,proportions of positive associations in HE bacterial networks increased with the rising heavy metal concentration,indicating a higher resistance of HE phyllosphere microbiome to heavy metal stress.Furthermore,in contrast to NHE,microbial community functions,primarily involved in heavy metal stress resistance,were more abundant in HE,in which microbiome assisted hosts to resist heavy metal stress better.Collectively,this study indicated that phyllosphere microbiome of the hyperaccumulator played an indispensable role in assisting hosts to resist heavy metal stress,and provided new insights into phyllosphere microbial application potential in phytoremediation.展开更多
Domestication and genetic improvement of maize improve yield and stress tolerance due to changes in morphological and physiological properties, which likely alter rhizosphere microbial diversity. Understanding how the...Domestication and genetic improvement of maize improve yield and stress tolerance due to changes in morphological and physiological properties, which likely alter rhizosphere microbial diversity. Understanding how the evolution of maize germplasm impacts its rhizobacterial traits during the growth stage is important for optimizing plant-microbe associations and obtaining yield gain in domesticated germplasms. In this study, a total of nine accessions representing domestication and subsequent genetic improvement were selected. We then sequenced the plant DNA and rhizobacterial DNA of teosinte, landraces and inbred lines at the seedling, flowering and maturity stages in a field trial. Moreover, the soil chemical properties were determined at the respective stages to explore the associations of soil characteristics with bacterial community structures. The results showed that domestication and genetic improvement increased the rhizobacterial diversity and substantially altered the rhizobacterial community composition. The core microbiome in the rhizosphere differed among germplasm groups. The co-occurrence network analysis demonstrated that the modularity in the bacterial network of the inbred lines was greater than those of teosinte and the landraces. In conclusion, the increased diversity of the rhizobacterial community with domestication and genetic improvement may improve maize resilience to biotic stresses and soil nutrient availability to plants.展开更多
Trimethoprim(TMP)is an antibiotic frequently detected in various environments.Microorganisms are the main drivers of emerging antibiotic contaminant degradation in the environment.However,the feasibility and stability...Trimethoprim(TMP)is an antibiotic frequently detected in various environments.Microorganisms are the main drivers of emerging antibiotic contaminant degradation in the environment.However,the feasibility and stability of the anaerobic biodegradation of TMP with sulfate as an electron acceptor remain poorly understood.Here,TMP-degrading microbial consortia were successfully enriched from municipal activated sludge(AS)and river sediment(RS)as the initial inoculums.The acclimated consortia were capable of transforming TMP through demethylation,and the hydroxyl-substituted demethylated product(4-desmethyl-TMP)was further degraded.The biodegradation ofTMP followed a 3-parameter sigmoid kinetic model.The potential degraders(Acetobacterium,Desulfovibrio,Desulfbbulbus,and unidentified Peptococcaceae)and fermenters(Lentimicrobium and Petrimonas)were significantly enriched in the acclimated consortia.The AS-and RS-acclimated TMP-degrading consortia had similar core microbiomes.The anaerobic biodegradation ofTMP could be coupled with sulfate respiration,which gives new insights into the antibiotic fate in real environments and provides a new route for the bioremediation of antibiotic-contaminated environments.展开更多
Synthetic microbial community has widely concerned in the fields of agriculture,food and environment over the past few years.However,there is little consensus on the method to synthetic microbial community from constr...Synthetic microbial community has widely concerned in the fields of agriculture,food and environment over the past few years.However,there is little consensus on the method to synthetic microbial community from construction to functional verification.Here,we review the concept,characteristics,history and applications of synthetic microbial community,summarizing several methods for synthetic microbial community construction,such as isolation culture,core microbiome mining,automated design,and gene editing.In addition,we also systematically summarized the design concepts,technological thresholds,and applicable scenarios of various construction methods,and highlighted their advantages and limitations.Ultimately,this review provides four efficient,detailed,easy-to-understand and-follow steps for synthetic microbial community construction,with major implications for agricultural practices,food production,and environmental governance.展开更多
文摘Core Microbiome:The Hidden Organ Essential for Human Health The core microbiome,often described as a‘hidden organ’,has captivated researchers as a fundamental key to understanding the intimate relationship between microbial ecosystems and human health(Turnbaugh and Gordon 2009).This specialized subset of microbial entities,ever-present across populations,transcends the variations of genetics,diet,and lifestyle to act as a stabilizing force in the gut.
基金supported by the National Natural Science Foundation of China(No.42277102).
文摘The unique gut habitat led to a core intestinal micro-biome in diverse soil ecosystems.The collembolan guts may help eliminate soil pathogens.Host-selection carried more weight on community assembly of gut microbiome.Soil invertebrates are widely distributed in the ecosystem and are essential for soil ecological processes.Inverte-brate gut microbiome plays an important role in host health and has been considered as a hidden microbial repository.However,little is known about how gut microbiome in soil invertebrates respond to diverse soil ecosystems.Based on a laboratory microcosm experiment,we characterized the assembling of microbiome of soil collembolans(Folsomia candida)from six representative regions of the soil ecosystem which they inhabit.Results showed that collembolan gut microbial communities differed significantly from their surrounding soil microbial communities.A dominant core gut microbiome was identified in gut habitat.Community analyses indicated that deterministic process dominated in the community assembly of collembolan gut microbiome.The results further demonstrate a dominant contribution of host selection in shaping gut microbiome.It is also worthy to mention that pathogens,such as common agricultural phytopathogenic fungi Fusarium,were involved in core microbiome,indicating that collembolans could act as vectors of pathogens.Our results unravelled the existence of gut core microbiome of collembolans in soil ecosystems and provided new insights for under-standing the crucial role of gut microbiome of soil fauna in maintaining microbial biodiversity and stability of soil ecosystems.
基金supported by the National Natural Science Foundation of China(Nos.42177008,and 42377005)the fellowship of China Postdoctoral Science Foundation(No.2022M712770)the Fundamental Research Funds for the Central Universities.
文摘Phyllosphere microbiome plays an irreplaceable role in maintaining plant health under stress,but its structure and functions in heavy metal-hyperaccumulating plants remain elusive.Here,the phyllosphere microbiome,inhabiting hyperaccumulating(HE)and non-hyperaccumulating ecotype(NHE)of Sedum alfredii grown in soils with varying heavy metal concentration,was characterized.Compared with NHE,the microbial communityα-diversity was greater in HE.Core phyllosphere taxa with high relative abundance(>10%),including Streptomyces and Nocardia(bacteria),Cladosporium and Acremonium(fungi),were significantly related to cadmium(Cd)and zinc(Zn)concentration and biomass of host plants.Moreover,microbial co-occurrence networks in HE exhibited greater complexity than those in NHE.Additionally,proportions of positive associations in HE bacterial networks increased with the rising heavy metal concentration,indicating a higher resistance of HE phyllosphere microbiome to heavy metal stress.Furthermore,in contrast to NHE,microbial community functions,primarily involved in heavy metal stress resistance,were more abundant in HE,in which microbiome assisted hosts to resist heavy metal stress better.Collectively,this study indicated that phyllosphere microbiome of the hyperaccumulator played an indispensable role in assisting hosts to resist heavy metal stress,and provided new insights into phyllosphere microbial application potential in phytoremediation.
基金supported by the Key Area Research and Development Program of Guangdong Province,China(2018B020202013)the National Key R&D Program of China(2018YFD1000903)the Natural Science Foundation of Guangdong Province,China(2018A030313865)。
文摘Domestication and genetic improvement of maize improve yield and stress tolerance due to changes in morphological and physiological properties, which likely alter rhizosphere microbial diversity. Understanding how the evolution of maize germplasm impacts its rhizobacterial traits during the growth stage is important for optimizing plant-microbe associations and obtaining yield gain in domesticated germplasms. In this study, a total of nine accessions representing domestication and subsequent genetic improvement were selected. We then sequenced the plant DNA and rhizobacterial DNA of teosinte, landraces and inbred lines at the seedling, flowering and maturity stages in a field trial. Moreover, the soil chemical properties were determined at the respective stages to explore the associations of soil characteristics with bacterial community structures. The results showed that domestication and genetic improvement increased the rhizobacterial diversity and substantially altered the rhizobacterial community composition. The core microbiome in the rhizosphere differed among germplasm groups. The co-occurrence network analysis demonstrated that the modularity in the bacterial network of the inbred lines was greater than those of teosinte and the landraces. In conclusion, the increased diversity of the rhizobacterial community with domestication and genetic improvement may improve maize resilience to biotic stresses and soil nutrient availability to plants.
基金supported by the National Natural Science Foundation of China(Grant No.51808537)the China Postdoctoral Science Foundation(No.2019M650866)+3 种基金the Key Research Program of the Chinese Academy of Sciences(No.KFZD-SW-219)the Youth Technology Fund Project of Gansu Province(No.18JR3RA023)the Provincial Science and Technology Plan Projects of Gansu Province(No.2015017)the Youth Science and Technology Foundation of Gansu Province(No.1506RJYA154).
文摘Trimethoprim(TMP)is an antibiotic frequently detected in various environments.Microorganisms are the main drivers of emerging antibiotic contaminant degradation in the environment.However,the feasibility and stability of the anaerobic biodegradation of TMP with sulfate as an electron acceptor remain poorly understood.Here,TMP-degrading microbial consortia were successfully enriched from municipal activated sludge(AS)and river sediment(RS)as the initial inoculums.The acclimated consortia were capable of transforming TMP through demethylation,and the hydroxyl-substituted demethylated product(4-desmethyl-TMP)was further degraded.The biodegradation ofTMP followed a 3-parameter sigmoid kinetic model.The potential degraders(Acetobacterium,Desulfovibrio,Desulfbbulbus,and unidentified Peptococcaceae)and fermenters(Lentimicrobium and Petrimonas)were significantly enriched in the acclimated consortia.The AS-and RS-acclimated TMP-degrading consortia had similar core microbiomes.The anaerobic biodegradation ofTMP could be coupled with sulfate respiration,which gives new insights into the antibiotic fate in real environments and provides a new route for the bioremediation of antibiotic-contaminated environments.
基金supported by the Natural Science Foundation of China(32360029,32260003)Gui Da Tegang He Zi(2022)57,“Hundred”Talent Projects of Guizhou Province(Qian Ke He[2020]6005).
文摘Synthetic microbial community has widely concerned in the fields of agriculture,food and environment over the past few years.However,there is little consensus on the method to synthetic microbial community from construction to functional verification.Here,we review the concept,characteristics,history and applications of synthetic microbial community,summarizing several methods for synthetic microbial community construction,such as isolation culture,core microbiome mining,automated design,and gene editing.In addition,we also systematically summarized the design concepts,technological thresholds,and applicable scenarios of various construction methods,and highlighted their advantages and limitations.Ultimately,this review provides four efficient,detailed,easy-to-understand and-follow steps for synthetic microbial community construction,with major implications for agricultural practices,food production,and environmental governance.
