Investigating ecological interactions within microbial ecosystems is essential for enhancing our comprehension of key ecological issues,such as community stability,keystone species identification,and the manipulation ...Investigating ecological interactions within microbial ecosystems is essential for enhancing our comprehension of key ecological issues,such as community stability,keystone species identification,and the manipulation of community structures.However,exploring these interactions proves challenging within complex natural ecosys-tems.With advances in synthetic biology,the design of synthetic microbial ecosystems has received increasing attention due to their reduced complexity and enhanced controllability.Various ecological relationships,includ-ing commensalism,amensalism,mutualism,competition,and predation have been established within synthetic ecosystems.These relationships are often context-dependent and shaped by physical and chemical environmental factors,as well as by interacting populations and surrounding species.This review consolidates current knowl-edge of synthetic microbial ecosystems and factors influencing their ecological dynamics.A deeper understanding of how these ecosystems function and respond to different variables will advance our understanding of microbial-community interactions.展开更多
Zhenjiang aromatic vinegar(ZAV),known for its distinctive flavors,is produced through traditional solid-state fermentation involving multiple strains.The development of functional microbial communities during repeated...Zhenjiang aromatic vinegar(ZAV),known for its distinctive flavors,is produced through traditional solid-state fermentation involving multiple strains.The development of functional microbial communities during repeated batch acetic acid fermentation(AAF)is crucial for flavor formation in ZAV.Hence,investigating the two pivotal factors,namely flavor synthesis and microbial strains,within the vinegar ecosystem is essential for the vinegar industry to modulate the metabolic function of vinegar microbiota,monitor the fermentation process,and maintain the desired flavor quality of the final product.This study aimed to explore the ecological interactions of Bacillus within the vinegar Pei and examine the correlation between the Bacillus community and the characteristic aroma components of ZAV.The findings demonstrated that the dynamic of Bacillus community was drove by environmental factors represented by temperature and acidity,together with the interactions between microorganisms.Moreover,Bacillus exhibited a significant positive correlation with 34 volatile flavor components,including 7 alcohols,1 acid,20 esters,3 aldehydes,2 ketones,and 1 phenol.The characteristic aroma components strongly associated with Bacillus were identified as lactic acid,six ethyl esters,namely ethyl acetate,benzeneacetaldehyde,and 3-methylbutyraldehyde.Overall,this study revealed the crucial role of Bacillus in maintaining fermentation system stability and facilitating flavor synthesis.The detailed insights provided here contributed to a better understanding of the fermentation mechanisms underlying ZAV.展开更多
Stoichiometry has long been addressed in the studies of ecosystem ecology, but it was almost ignored for a long time. Until recently, ecologists have become aware that stoichiometry could provide a new tool to study e...Stoichiometry has long been addressed in the studies of ecosystem ecology, but it was almost ignored for a long time. Until recently, ecologists have become aware that stoichiometry could provide a new tool to study ecology from genes to the biosphere. Among this trend, N:P stoichiometry is used actively in ecological interactions since nitrogen (N) and phosphorus (P) are the two most important elements in most ecosystems. This article reviews the application of N:P stoichiometry to the studies of ecological problems at different levels, including ecosystem, community and species. Meanwhile, we also provide the cellular basis of N:P stoichiometry, identify the shortages in the use of N:P stoichiometry theory, and put forward some perspectives for future research to be conducted.展开更多
Anammox （ANaerobic AMMonia OXidation） is a newly discovered pathway in the nitrogen cycle. This discovery has increased our knowledge of the global nitrogen cycle and triggered intense interest for anammox-based app...Anammox （ANaerobic AMMonia OXidation） is a newly discovered pathway in the nitrogen cycle. This discovery has increased our knowledge of the global nitrogen cycle and triggered intense interest for anammox-based applications. Anammox bacteria are almost ubiquitous in the suboxic zones of almost all types of natural ecosystems and contribute significant to the global total nitrogen loss. In this paper, their ecological distributions and contributions to the nitrogen loss in marine, wetland, terrestrial ecosystems, and even extreme environments were reviewed. The unique metabolic mechanism of anammox bacteria was well described, including the particular cellular structures and genome compositions, which indicate the special evolutionary status of anammox bacteria. Finally, the ecological interactions among anammox bacteria and other organisms were discussed based on substrate availability and spatial organizations. This review attempts to summarize the fundamental understanding of anammox, provide an up-to-date summary of the knowledge of the overall anammox status, and propose future prospects for anammox. Based on novel findings, the metagenome has become a powerful tool for the genomic analysis of communities containing anammox bacteria; the metabolic diversity and biogeochemistry in the global nitrogen budget require more comprehensive studies.展开更多
Sugar beet fiber(SBF)is a promising prebiotic candidate,yet its comprehensive impact on gut microbiota and metabolic profiles remains unclear.Here,we conducted in vitro fecal fermentation using samples from six health...Sugar beet fiber(SBF)is a promising prebiotic candidate,yet its comprehensive impact on gut microbiota and metabolic profiles remains unclear.Here,we conducted in vitro fecal fermentation using samples from six healthy donors to evaluate the microbial and metabolic impacts of SBF compared to a carbohydrate-free control(CON group).SBF significantly altered the overall gut microbiota composition and diversity(p<0.05).Keystone SBFresponsive taxa were identified,including the enrichment of Bifidobacterium,Parasutterella,Sutterella,Bifidobacterium longum subsp.longum,and Lactobacillus salivarius,alongside the reduction of Escherichia-Shigella.Network analysis revealed a functional guild of primary degraders actively foraging SBF.Metabolically,SBF supplementation significantly increased acetate,propionate,and butyrate production(p<0.05),while selectively modulating organic acids by elevating pyruvate and reducing 3-phosphoglycerate and citrate(p<0.05).Targeted metabolomics showed increased levels of indole-3-propionic acid(SBF:4.8797 mg/L vs.CON:4.4508 mg/L,p=0.0138)and tryptamine(SBF:8.2855 mg/L vs.CON:7.3250 mg/L,p=0.0030),along with a significant reduction in the secondary bile acid deoxycholic acid(p=0.0138).Non-targeted metabolomics further highlighted fatty acid biosynthesis as a key SBF-responsive pathway.These findings demonstrate that SBF promotes the growth of beneficial microbial taxa,enhances the production of short-chain fatty acids and indole derivatives,and remodels bile acid metabolism,supporting its potential as a novel prebiotic fiber for gut health improvement.展开更多
Agaricus bisporus is the most widely consumed edible mushroom and an important source of dietary protein and bioactive compounds.The casing layer plays a critical role in its cultivation,where microbial communities an...Agaricus bisporus is the most widely consumed edible mushroom and an important source of dietary protein and bioactive compounds.The casing layer plays a critical role in its cultivation,where microbial communities and metabolic activities strongly affect yield and quality,however,the stage-resolved research gap remains that it is still unclear which microbial and metabolic shifts in the casing layer are associated with primordia initiation and subsequent quality formation.In this study,the ecological and metabolic basis of mushroom quality formation was investigated by the combination of microbiome sequencing,non-targeted metabolomics,and functional genomics.Microbial communities exhibited stage-specific dynamics,with significant restructuring during primordia formation,when community cohesion and niche breadth reached their highest levels(0.68±0.06 and 4.48±1.05,respectively).A total of 1108 non-volatile metabolites were identified from metabolomic profiling.The adenosine and tryptophan exhibited significant changes and were enriched in energy and amino acid metabolism pathways.A representative strain,Pseudomonas putida AT130,was isolated from the genus Pseu-domonas.The gene clusters related to phosphate solubilization,potassium mobilization,lignin degradation,and indole-3-acetic acid biosynthesis were revealed by genome analysis with the multifunctional activities being confirmed through in vitro assays.Pot experiments further showed that AT130 inoculation improved mushroom performance,increasing fruiting body yield by 123.55%and enhancing nutritional traits(protein and soluble sugars increased,whereas ash decreased)relative to the control.These findings linked casing-layer microbiota with mushroom quality and identified AT130 as a promising food-grade bioinoculant to enhance A.bisporus nutritional value and productivity.展开更多
Ecological interactions are evolutionarily conserved,indicating a tendency of closely related species to interact with similar partners.Arbuscular mycorrhizal(AM)fungi form obligate symbioses with the roots of most la...Ecological interactions are evolutionarily conserved,indicating a tendency of closely related species to interact with similar partners.Arbuscular mycorrhizal(AM)fungi form obligate symbioses with the roots of most land plants.Local host preference is frequently reported as a factor in structuring AM fungal communities.There lacks study about whether AM fungi-host preference could structure AM fungal communities at the regional scales.Here,AM fungal communities of 296 root samples were revealed,encompassing 76 plant species from 29 plant families,which were sampled in steppe in the Xilingol Grassland in northern China.The relative importance of plant phylogeny,geographical distance,and environmental variables were characterized on phylogenetic turnover of AM fungal communities with GLMM-MCMC(the generalized linear mixed model using Markov chain Monte Carlo)and Mantel test approaches.Geographic distance appeared to be more important to the phylogenetic turnover of AM fungal communities than plant phylogeny and environmental variables,evidencing the role of dispersal limitation in shaping the root AM fungal communities.A great majority of phylogenetic beta diversity(betaNTI and betaNRI)is distributed between−2 and+2,which also suggested a random pattern of AM fungal communities.Here,empirical evidence supporting that dispersal limitation is the main determinant of AM fungal communities at the landscape scale is provided and it is suggested that AM fungal communities are mainly structured by stochastic events.展开更多
Recently,Chen and colleagues from Shanghai Institute of Plant Physiology and Ecology of Chinese Academy of Sciences,in collaboration with scientists from Nanjing Agricultural University and from the US,have identified...Recently,Chen and colleagues from Shanghai Institute of Plant Physiology and Ecology of Chinese Academy of Sciences,in collaboration with scientists from Nanjing Agricultural University and from the US,have identified a homeodomain（HOX）-containing transcription factor that plays a central role in controlling cotton fiber elongation.展开更多
基金supported by the Hainan Province Science and Tech-nology Special Fund(ZDYF2024XDNY164)National Natural Science Foundation of China(32470065,31971336)+4 种基金Shandong Provincial Nat-ural Science Foundation(ZR2022QC222)Shandong Province Medical and Health Science and Technology Project(202404070807)Science and Technology Development Program of Jinan Municipal Health Com-mission(2024102001)Youth Science Foundation of Shandong First Medical University(202201-132)Talent Introduction of Jinan Cen-tral Hospital(YJRC2022002).
文摘Investigating ecological interactions within microbial ecosystems is essential for enhancing our comprehension of key ecological issues,such as community stability,keystone species identification,and the manipulation of community structures.However,exploring these interactions proves challenging within complex natural ecosys-tems.With advances in synthetic biology,the design of synthetic microbial ecosystems has received increasing attention due to their reduced complexity and enhanced controllability.Various ecological relationships,includ-ing commensalism,amensalism,mutualism,competition,and predation have been established within synthetic ecosystems.These relationships are often context-dependent and shaped by physical and chemical environmental factors,as well as by interacting populations and surrounding species.This review consolidates current knowl-edge of synthetic microbial ecosystems and factors influencing their ecological dynamics.A deeper understanding of how these ecosystems function and respond to different variables will advance our understanding of microbial-community interactions.
基金the National Natural Science Foundation of China(No.32072202)the Graduate Research and Innovation Projects of Jiangsu Province(No.1182162203)for financial support.
文摘Zhenjiang aromatic vinegar(ZAV),known for its distinctive flavors,is produced through traditional solid-state fermentation involving multiple strains.The development of functional microbial communities during repeated batch acetic acid fermentation(AAF)is crucial for flavor formation in ZAV.Hence,investigating the two pivotal factors,namely flavor synthesis and microbial strains,within the vinegar ecosystem is essential for the vinegar industry to modulate the metabolic function of vinegar microbiota,monitor the fermentation process,and maintain the desired flavor quality of the final product.This study aimed to explore the ecological interactions of Bacillus within the vinegar Pei and examine the correlation between the Bacillus community and the characteristic aroma components of ZAV.The findings demonstrated that the dynamic of Bacillus community was drove by environmental factors represented by temperature and acidity,together with the interactions between microorganisms.Moreover,Bacillus exhibited a significant positive correlation with 34 volatile flavor components,including 7 alcohols,1 acid,20 esters,3 aldehydes,2 ketones,and 1 phenol.The characteristic aroma components strongly associated with Bacillus were identified as lactic acid,six ethyl esters,namely ethyl acetate,benzeneacetaldehyde,and 3-methylbutyraldehyde.Overall,this study revealed the crucial role of Bacillus in maintaining fermentation system stability and facilitating flavor synthesis.The detailed insights provided here contributed to a better understanding of the fermentation mechanisms underlying ZAV.
文摘Stoichiometry has long been addressed in the studies of ecosystem ecology, but it was almost ignored for a long time. Until recently, ecologists have become aware that stoichiometry could provide a new tool to study ecology from genes to the biosphere. Among this trend, N:P stoichiometry is used actively in ecological interactions since nitrogen (N) and phosphorus (P) are the two most important elements in most ecosystems. This article reviews the application of N:P stoichiometry to the studies of ecological problems at different levels, including ecosystem, community and species. Meanwhile, we also provide the cellular basis of N:P stoichiometry, identify the shortages in the use of N:P stoichiometry theory, and put forward some perspectives for future research to be conducted.
文摘Anammox （ANaerobic AMMonia OXidation） is a newly discovered pathway in the nitrogen cycle. This discovery has increased our knowledge of the global nitrogen cycle and triggered intense interest for anammox-based applications. Anammox bacteria are almost ubiquitous in the suboxic zones of almost all types of natural ecosystems and contribute significant to the global total nitrogen loss. In this paper, their ecological distributions and contributions to the nitrogen loss in marine, wetland, terrestrial ecosystems, and even extreme environments were reviewed. The unique metabolic mechanism of anammox bacteria was well described, including the particular cellular structures and genome compositions, which indicate the special evolutionary status of anammox bacteria. Finally, the ecological interactions among anammox bacteria and other organisms were discussed based on substrate availability and spatial organizations. This review attempts to summarize the fundamental understanding of anammox, provide an up-to-date summary of the knowledge of the overall anammox status, and propose future prospects for anammox. Based on novel findings, the metagenome has become a powerful tool for the genomic analysis of communities containing anammox bacteria; the metabolic diversity and biogeochemistry in the global nitrogen budget require more comprehensive studies.
基金financial support from the National Natural Sci-ence Foundation of China(No.32202059)Natural Science Foundation of Jiangsu Province(BK20221070)+3 种基金the China National Postdoctoral Program for Innovative Talents(BX20230146)China Postdoctoral Science Foundation(2023M731338)the Fundamental Research Funds for the Central Universities(JUSRP123051)the Program of Collaborative Innovation Centre of Food Safety and Quality Control in Jiangsu Province.
文摘Sugar beet fiber(SBF)is a promising prebiotic candidate,yet its comprehensive impact on gut microbiota and metabolic profiles remains unclear.Here,we conducted in vitro fecal fermentation using samples from six healthy donors to evaluate the microbial and metabolic impacts of SBF compared to a carbohydrate-free control(CON group).SBF significantly altered the overall gut microbiota composition and diversity(p<0.05).Keystone SBFresponsive taxa were identified,including the enrichment of Bifidobacterium,Parasutterella,Sutterella,Bifidobacterium longum subsp.longum,and Lactobacillus salivarius,alongside the reduction of Escherichia-Shigella.Network analysis revealed a functional guild of primary degraders actively foraging SBF.Metabolically,SBF supplementation significantly increased acetate,propionate,and butyrate production(p<0.05),while selectively modulating organic acids by elevating pyruvate and reducing 3-phosphoglycerate and citrate(p<0.05).Targeted metabolomics showed increased levels of indole-3-propionic acid(SBF:4.8797 mg/L vs.CON:4.4508 mg/L,p=0.0138)and tryptamine(SBF:8.2855 mg/L vs.CON:7.3250 mg/L,p=0.0030),along with a significant reduction in the secondary bile acid deoxycholic acid(p=0.0138).Non-targeted metabolomics further highlighted fatty acid biosynthesis as a key SBF-responsive pathway.These findings demonstrate that SBF promotes the growth of beneficial microbial taxa,enhances the production of short-chain fatty acids and indole derivatives,and remodels bile acid metabolism,supporting its potential as a novel prebiotic fiber for gut health improvement.
基金supported by the Key Science&Technology Project of Anhui Province(202423m10050005).
文摘Agaricus bisporus is the most widely consumed edible mushroom and an important source of dietary protein and bioactive compounds.The casing layer plays a critical role in its cultivation,where microbial communities and metabolic activities strongly affect yield and quality,however,the stage-resolved research gap remains that it is still unclear which microbial and metabolic shifts in the casing layer are associated with primordia initiation and subsequent quality formation.In this study,the ecological and metabolic basis of mushroom quality formation was investigated by the combination of microbiome sequencing,non-targeted metabolomics,and functional genomics.Microbial communities exhibited stage-specific dynamics,with significant restructuring during primordia formation,when community cohesion and niche breadth reached their highest levels(0.68±0.06 and 4.48±1.05,respectively).A total of 1108 non-volatile metabolites were identified from metabolomic profiling.The adenosine and tryptophan exhibited significant changes and were enriched in energy and amino acid metabolism pathways.A representative strain,Pseudomonas putida AT130,was isolated from the genus Pseu-domonas.The gene clusters related to phosphate solubilization,potassium mobilization,lignin degradation,and indole-3-acetic acid biosynthesis were revealed by genome analysis with the multifunctional activities being confirmed through in vitro assays.Pot experiments further showed that AT130 inoculation improved mushroom performance,increasing fruiting body yield by 123.55%and enhancing nutritional traits(protein and soluble sugars increased,whereas ash decreased)relative to the control.These findings linked casing-layer microbiota with mushroom quality and identified AT130 as a promising food-grade bioinoculant to enhance A.bisporus nutritional value and productivity.
基金supported by the Central Public-interest Scientific Institution Basal Research Fund(CAFYBB2019QB001,CAFYBB2020ZB001)the Natural Science Foundation of China(Grant No.31870099)the Strategic Priority Research Program of Chinese Academy of Sciences(XDA26020102).
文摘Ecological interactions are evolutionarily conserved,indicating a tendency of closely related species to interact with similar partners.Arbuscular mycorrhizal(AM)fungi form obligate symbioses with the roots of most land plants.Local host preference is frequently reported as a factor in structuring AM fungal communities.There lacks study about whether AM fungi-host preference could structure AM fungal communities at the regional scales.Here,AM fungal communities of 296 root samples were revealed,encompassing 76 plant species from 29 plant families,which were sampled in steppe in the Xilingol Grassland in northern China.The relative importance of plant phylogeny,geographical distance,and environmental variables were characterized on phylogenetic turnover of AM fungal communities with GLMM-MCMC(the generalized linear mixed model using Markov chain Monte Carlo)and Mantel test approaches.Geographic distance appeared to be more important to the phylogenetic turnover of AM fungal communities than plant phylogeny and environmental variables,evidencing the role of dispersal limitation in shaping the root AM fungal communities.A great majority of phylogenetic beta diversity(betaNTI and betaNRI)is distributed between−2 and+2,which also suggested a random pattern of AM fungal communities.Here,empirical evidence supporting that dispersal limitation is the main determinant of AM fungal communities at the landscape scale is provided and it is suggested that AM fungal communities are mainly structured by stochastic events.
文摘Recently,Chen and colleagues from Shanghai Institute of Plant Physiology and Ecology of Chinese Academy of Sciences,in collaboration with scientists from Nanjing Agricultural University and from the US,have identified a homeodomain（HOX）-containing transcription factor that plays a central role in controlling cotton fiber elongation.
