Malaria remains a global health problem.The relationship between Plasmodium spp.and the gut microbiota as well as the impact of Plasmodium spp.on the gut microbiota in vertebrate hosts is unclear.The aim of the curren...Malaria remains a global health problem.The relationship between Plasmodium spp.and the gut microbiota as well as the impact of Plasmodium spp.on the gut microbiota in vertebrate hosts is unclear.The aim of the current study was to evaluate the effect of blood-stage Plasmodium parasites on the gut microbiota of mice.The gut microbiota was analyzed by 16S rRNA sequencing and bioinformatic analyses at three stages.The gut microbiota changed during the three phases:the healthy stage,the infection stage,and the cure stage(on the 9th day after malarial elimination).Moreover,the gut microbiota of these infected animals did not recover after malaria infection.There were 254 operational taxonomic units(OTUs)across all three stages,and there were unique strains or OTUs at each stage of the experiment.The percentages of community abundance of 8 OTUs changed significantly(P<0.05).The dominant OTU in both the healthy mice and the mice with malaria was OTU265,while that in the cured mice was OTU234.In addition,the changes in OTU147 were the most noteworthy.Its percentage of community abundance varied greatly,with higher values during malaria than before malaria infection and after malaria elimination.These results indicated that the external environment influenced the gut microbiota after host C57BL/6 mice were infected with blood-stage P.berghei ANKA and that the same was true during and after elimination of blood-stage P.berghei ANKA.In addition,we could not isolate OTU147 for further study.This study identified gut microbiota components that were reconstructed after infection by and elimination of blood-stage P.berghei ANKA in host C57BL/6 mice,and this process was affected by P.berghei ANKA and the external environment of the host.展开更多
Objective:To explore the structural and functional characteristics of microbiota in oropharynx of subhealthy children with gastrointestinal heat retention syndrome(GHRS)differentiated by traditional Chinese medicine,a...Objective:To explore the structural and functional characteristics of microbiota in oropharynx of subhealthy children with gastrointestinal heat retention syndrome(GHRS)differentiated by traditional Chinese medicine,and screen the biometric operational taxonomic units(OTUs)to assist the clinical diagnosis.Methods:We recruited children according to the“GHRS diagnostic scale”,collected their oropharyngeal swabs,and sequenced the 16 SrDNA V4 region.We described the bacterial structure with alpha-indexes,beta-distances,and relative abundances;moreover,we screened the differential genera/OTUs with Wilcoxon rank-sum test,Metagenome Seq analysis,and linear discriminant analysis effect size(LEf Se)analysis,in which biometric OTUs were selected to construct the receiver operating characteristic curve to verify the diagnostic value.The bacterial function was predicted with Kyoto Encyclopedia of Genes and Genomes pathways according to 16S rDNA gene by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States.Results:The study population was composed of 10 children with GHRS and 10 healthy control children.GHRS children were more likely to overeat(gluttony,P=.033).Alpha-indexes,such as Sobs,abundancebased coverage estimator,Bootstrap,and Qstat,were significantly higher in the GHRS group,while betadistances did not exhibit any significant intergroup differences.There were 9 differently distributed nonpredominant genera between the groups in Wilcoxon rank-sum test,as well as 13 non-predominant genera in Metagenome Seq analysis and 3 non-predominant OTUs in LEfSe analysis.OTU44 and OTU196 were used to construct the receiver operating characteristic curve,and the area under curve was 0.92.Predicted functions showed that pathways related to oxidative phosphorylation and carbon metabolism were enriched in healthy control samples,while the pathway related to renin secretion was remarkably enriched in GHRS samples.Conclusion:Unique oropharyngeal microbial structure and function were identified in GHRS children.OTU44 and OTU196 were specific OTUs,which could be used as biomarkers of GHRS to assist clinical diagnosis.展开更多
Sthenoteuthis oualaniensis is known for its complex population structure with three major transoceanic forms(viz.middle-sized,dwarf,and giant forms)whose taxonomic status has been disputed for decades.This integrated ...Sthenoteuthis oualaniensis is known for its complex population structure with three major transoceanic forms(viz.middle-sized,dwarf,and giant forms)whose taxonomic status has been disputed for decades.This integrated taxonomic study examines these prevenient morphotypes gathered on cruises in the Indian Ocean to ascertain their status in the evolutionary history of the species.Molecular analyses employing mitochondrial(COI,ND2)and nuclear(H3)markers revealed four genetically distinct and novel lineages of the species in the Indian Ocean,representing three morphotypes from the Arabian Sea and one from the Southern Indian Ocean.The mitochondrial-based phylograms revealed two distinct clades in the species:“dwarf forms+giant form”and“middle-sized forms,”which further branch into geographically structured evolutionary units.Species delimitation analyses recovered five distinct clades,namely,the Arabian Sea giant and dwarf forms,Equatorial,Eastern Typical,and Other Middle-sized forms,representing the consensus molecular operational taxonomic units.H3 being heterozygous could not resolve the phylogeny.Haplotype network and AMOVA analysis of mtDNA genes indicated explicit phylogeographic structuring of haplotypes,whereas these outputs and PCA results were incongruent with the morphological grouping.Phenetic features distinguishing the morphotypes were sometimes plastic and mismatched with the genotypes.The giant form was genetically close to the dwarf forms,contradicting the earlier notion that it descended from the middle-sized form.It may be assumed that the dwarf form evolved following sympatric speciation and adaptation to warm equatorial waters,while the focal features of the Western Arabian Sea guide toward allopatric speciation of the giant form.展开更多
Phosphorus(P) limitation in the coming decades calls for the utilization of alternative fertilizers in agriculture. Struvite is a promising P source, but its potential role as a fertilizer is dependent on different ph...Phosphorus(P) limitation in the coming decades calls for the utilization of alternative fertilizers in agriculture. Struvite is a promising P source, but its potential role as a fertilizer is dependent on different physical, chemical, and biological properties, which are very heterogeneous in soil, complicating the prediction of the best soil conditions for its application. Here, we evaluated the solubility of struvite in soil, its redistribution into P fractions, and its potential abiotic and biotic drivers in 62 globally distributed soils with contrasting properties through an incubation assay. We found that after 40 d, about 35% of struvite P was redistributed into soil fractions more accessible to plants and microbes. Phosphorus redistribution from struvite was driven by a complex suite of soil physical, chemical, and microbial properties as well as environmental factors that varied across soils. Soil texture played a critical role in determining the redistribution of P in struvite-amended soils in soluble(H2O extraction), labile(NaHCO3 extraction), and moderately labile(NaOH extraction) fractions.In addition, the soil solution cation concentration was one of the most important drivers of available struvite-derived P fractions. The great importance of texture and cations in determining struvite-derived P fractions in soil was contrasted with the relatively minor role of pH. At the microbial level, the number of bacterial operational taxonomic units(OTUs) from the unfertilized soils that correlated with struvite-derived P fractions was higher than that of fungi. The number of OTUs that correlated with the struvite-derived soluble P fraction was dominated by fungi, whereas the number of OTUs that correlated with the struvite-derived labile P fraction was dominated by bacteria. Overall, this study provided a predictive framework for the potential use of struvite as a P fertilizer in contrasting soils.展开更多
Ammonia-oxidizing archaea(AOA) are important in converting ammonia into nitrate in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic p...Ammonia-oxidizing archaea(AOA) are important in converting ammonia into nitrate in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has poorly been understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogenetic null modelling approach was used to calculate the beta nearest taxon index to quantify the influence of stochastic and deterministic processes. We found that spatial distance between samples predicted the perceived processes involved in community structuring, with stochastic processes dominating at local scales. At greater distances, stochasticity became weaker. However, soil pH, which was also the strongest determinant of AOA community, was a much stronger predictor of community structuring, leaving the distance effect redundant as an explanation of community structuring processes. The communities of AOA differing by less than 1 pH unit differed mainly stochastically in terms of operational taxonomic unit composition. At larger pH differences, deterministic processes based on heterogeneous selection between clades became increasingly dominant. It appears that AOA community composition is largely determined by the environment. However, very similar pH environments are the exception. In environments with very close pH values, stochastic effects dominantly cause differences in community composition, whether spatially near or far.展开更多
Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat...Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational tax- onomic unit (OTU) levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ulti- mately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interac- tion among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe-microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe-microbe inter- action networks.展开更多
The use of green manures contributes to sustainable soil and nutrient management in agriculture;however, the responses of soil microbial communities to different fertilization regimes at the regional scale are uncerta...The use of green manures contributes to sustainable soil and nutrient management in agriculture;however, the responses of soil microbial communities to different fertilization regimes at the regional scale are uncertain. A study was undertaken across multiple sites and years in Hunan, Jiangxi, Anhui, Henan,Hubei, and Fujian provinces of South China to investigate the effects of green manuring on the structure and function of soil bacterial communities in rice-green manure cropping systems. The study included four treatments: winter fallow with no chemical fertilizer as a control(NF), milk vetch as green manure without chemical fertilizer(GM), winter fallow and chemical fertilizer(CF), and a combination of chemical fertilizer and milk vetch(GMCF).Significant differences were found in the responses of soil microbial communities at different sites, with sampling sites explaining 72.33%(F = 36.59,P = 0.001) of the community composition variation. The bacterial communities in the soils from Anhui, Henan, and Hubei were broadly similar, while those from Hunan were distinctly different from other locations. The analysis of Weighted UniFrac distances showed that milk vetch changed soil microbial communities compared with winter fallow. Proteobacteria and Chloroflexi predominated in these paddy soils;however, the application of green manures increased the relative abundance of Actinobacteria. There was evidence showing that the functional microbes which play important roles in the cycling of soil carbon, nitrogen(N), and sulfur(S) changed after several years of milk vetch utilization(linear discriminant analysis score > 2). The abundance of methane-oxidizing bacteria and S-reducing bacteria increased, and microbes involved in N fixation, nitrification, and denitrification also increased in some provinces. We concluded that the application of milk vetch changed the bacterial community structure and affected the functional groups related to nutrient transformation in soils at a regional scale.展开更多
The sequencing revolution driven by high-throughput technologies has generated a huge amount of marine microbial sequences which hide the interaction patterns among microbial species and environment factors. Exploring...The sequencing revolution driven by high-throughput technologies has generated a huge amount of marine microbial sequences which hide the interaction patterns among microbial species and environment factors. Exploring these patterns is helpful for exploiting the marine resources. In this paper, we use the complex network approach to mine and analyze the interaction patterns of marine taxa and environments in spring, summer, fall and winter seasons. With the 16S rRNA pyrosequencing data of 76 time point taken monthly over 6 years, we first use our MtHc clustering algorithm to generate the operational taxonomic units (OTUs). Then, employ the k-means method to divide 76 time point samples into four seasonal groups, and utilize mutual information (MI) to construct the four correlation networks among microbial species and environment factors. Finally, we adopt the symmetrical non-negative matrix factorization method to detect the interaction patterns, and analysis the relationship between marine species and environment factors. The results show that the four seasonal microbial interaction networks have the characters of complex networks, and interaction patterns are related with the seasonal variability; the same environmental factor influences different species in the four seasons; the four environmental factors of day length, photosynthetically active radiation, NO2+ NO3 and silicate may have stronger influences on microbes than other environment factors.展开更多
Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos tea.Symbiotic interactions between A.linearis and...Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos tea.Symbiotic interactions between A.linearis and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor,acidic fynbos soil.The aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown A.linearis,as well as the effect of seasonal changes on these communities.Bacterial communities were characterized using high throughput amplicon sequencing,and their correlations with soil chemical properties were investigated.The N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain reaction.Actinobacteria,Proteobacteria,and Acidobacteria were the most dominant bacterial phyla detected in this study.Highly similar bacterial communities were associated with natural and commercially grown plants.Significant differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season,while no significant differences were detected in the wet season.This study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important A.linearis.展开更多
基金the Nature Science Foundation of Hainan Province(No.817145)College Student Innovation and Entrepreneurship Project(No.201611810082,No.HYCX2015063).
文摘Malaria remains a global health problem.The relationship between Plasmodium spp.and the gut microbiota as well as the impact of Plasmodium spp.on the gut microbiota in vertebrate hosts is unclear.The aim of the current study was to evaluate the effect of blood-stage Plasmodium parasites on the gut microbiota of mice.The gut microbiota was analyzed by 16S rRNA sequencing and bioinformatic analyses at three stages.The gut microbiota changed during the three phases:the healthy stage,the infection stage,and the cure stage(on the 9th day after malarial elimination).Moreover,the gut microbiota of these infected animals did not recover after malaria infection.There were 254 operational taxonomic units(OTUs)across all three stages,and there were unique strains or OTUs at each stage of the experiment.The percentages of community abundance of 8 OTUs changed significantly(P<0.05).The dominant OTU in both the healthy mice and the mice with malaria was OTU265,while that in the cured mice was OTU234.In addition,the changes in OTU147 were the most noteworthy.Its percentage of community abundance varied greatly,with higher values during malaria than before malaria infection and after malaria elimination.These results indicated that the external environment influenced the gut microbiota after host C57BL/6 mice were infected with blood-stage P.berghei ANKA and that the same was true during and after elimination of blood-stage P.berghei ANKA.In addition,we could not isolate OTU147 for further study.This study identified gut microbiota components that were reconstructed after infection by and elimination of blood-stage P.berghei ANKA in host C57BL/6 mice,and this process was affected by P.berghei ANKA and the external environment of the host.
基金supported by the National Natural Science Foundation of China(81373769)the Scientific Research and Postgraduate Training Co-construction Project of Beijing Municipal Education Commission(1000062520115)the Province Natural Science Foundation of Beijing(7172131)。
文摘Objective:To explore the structural and functional characteristics of microbiota in oropharynx of subhealthy children with gastrointestinal heat retention syndrome(GHRS)differentiated by traditional Chinese medicine,and screen the biometric operational taxonomic units(OTUs)to assist the clinical diagnosis.Methods:We recruited children according to the“GHRS diagnostic scale”,collected their oropharyngeal swabs,and sequenced the 16 SrDNA V4 region.We described the bacterial structure with alpha-indexes,beta-distances,and relative abundances;moreover,we screened the differential genera/OTUs with Wilcoxon rank-sum test,Metagenome Seq analysis,and linear discriminant analysis effect size(LEf Se)analysis,in which biometric OTUs were selected to construct the receiver operating characteristic curve to verify the diagnostic value.The bacterial function was predicted with Kyoto Encyclopedia of Genes and Genomes pathways according to 16S rDNA gene by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States.Results:The study population was composed of 10 children with GHRS and 10 healthy control children.GHRS children were more likely to overeat(gluttony,P=.033).Alpha-indexes,such as Sobs,abundancebased coverage estimator,Bootstrap,and Qstat,were significantly higher in the GHRS group,while betadistances did not exhibit any significant intergroup differences.There were 9 differently distributed nonpredominant genera between the groups in Wilcoxon rank-sum test,as well as 13 non-predominant genera in Metagenome Seq analysis and 3 non-predominant OTUs in LEfSe analysis.OTU44 and OTU196 were used to construct the receiver operating characteristic curve,and the area under curve was 0.92.Predicted functions showed that pathways related to oxidative phosphorylation and carbon metabolism were enriched in healthy control samples,while the pathway related to renin secretion was remarkably enriched in GHRS samples.Conclusion:Unique oropharyngeal microbial structure and function were identified in GHRS children.OTU44 and OTU196 were specific OTUs,which could be used as biomarkers of GHRS to assist clinical diagnosis.
基金This work was funded under the projects National Agricultural Innovation Project(Ref No.NAIP code:2000035101)ICAR-CMFRI Institute Project(Code:FISHCMFRISIL 201200600006).
文摘Sthenoteuthis oualaniensis is known for its complex population structure with three major transoceanic forms(viz.middle-sized,dwarf,and giant forms)whose taxonomic status has been disputed for decades.This integrated taxonomic study examines these prevenient morphotypes gathered on cruises in the Indian Ocean to ascertain their status in the evolutionary history of the species.Molecular analyses employing mitochondrial(COI,ND2)and nuclear(H3)markers revealed four genetically distinct and novel lineages of the species in the Indian Ocean,representing three morphotypes from the Arabian Sea and one from the Southern Indian Ocean.The mitochondrial-based phylograms revealed two distinct clades in the species:“dwarf forms+giant form”and“middle-sized forms,”which further branch into geographically structured evolutionary units.Species delimitation analyses recovered five distinct clades,namely,the Arabian Sea giant and dwarf forms,Equatorial,Eastern Typical,and Other Middle-sized forms,representing the consensus molecular operational taxonomic units.H3 being heterozygous could not resolve the phylogeny.Haplotype network and AMOVA analysis of mtDNA genes indicated explicit phylogeographic structuring of haplotypes,whereas these outputs and PCA results were incongruent with the morphological grouping.Phenetic features distinguishing the morphotypes were sometimes plastic and mismatched with the genotypes.The giant form was genetically close to the dwarf forms,contradicting the earlier notion that it descended from the middle-sized form.It may be assumed that the dwarf form evolved following sympatric speciation and adaptation to warm equatorial waters,while the focal features of the Western Arabian Sea guide toward allopatric speciation of the giant form.
基金the financial support by the Fundacion General CSIC, Spain (Programa ComFuturo)the project PID2020114942RB-I00 funded by MCIN/AEI//10.13039/5011000 11033+3 种基金supported by a project from the Spanish Ministry of Science and Innovation (No. PID2020-115813RA-I00)a project of the Fondo Europeo de Desarrollo Regional (FEDER)the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014-2020 Objetivo temático “01— Refuerzo de la investigación, el desarrollo tecnológico y la innovación”, ANDABIOMA, No. P20_00879)supported by a postdoctoral scholarship as part of the FCT-funded project “Soil Ecosystems in the XXI Century: Drivers, Conservation and Future Scenarios” (No. FCT-PTDC/BIACBI/2340/2020) led by IPVC, Portugal。
文摘Phosphorus(P) limitation in the coming decades calls for the utilization of alternative fertilizers in agriculture. Struvite is a promising P source, but its potential role as a fertilizer is dependent on different physical, chemical, and biological properties, which are very heterogeneous in soil, complicating the prediction of the best soil conditions for its application. Here, we evaluated the solubility of struvite in soil, its redistribution into P fractions, and its potential abiotic and biotic drivers in 62 globally distributed soils with contrasting properties through an incubation assay. We found that after 40 d, about 35% of struvite P was redistributed into soil fractions more accessible to plants and microbes. Phosphorus redistribution from struvite was driven by a complex suite of soil physical, chemical, and microbial properties as well as environmental factors that varied across soils. Soil texture played a critical role in determining the redistribution of P in struvite-amended soils in soluble(H2O extraction), labile(NaHCO3 extraction), and moderately labile(NaOH extraction) fractions.In addition, the soil solution cation concentration was one of the most important drivers of available struvite-derived P fractions. The great importance of texture and cations in determining struvite-derived P fractions in soil was contrasted with the relatively minor role of pH. At the microbial level, the number of bacterial operational taxonomic units(OTUs) from the unfertilized soils that correlated with struvite-derived P fractions was higher than that of fungi. The number of OTUs that correlated with the struvite-derived soluble P fraction was dominated by fungi, whereas the number of OTUs that correlated with the struvite-derived labile P fraction was dominated by bacteria. Overall, this study provided a predictive framework for the potential use of struvite as a P fertilizer in contrasting soils.
文摘Ammonia-oxidizing archaea(AOA) are important in converting ammonia into nitrate in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has poorly been understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogenetic null modelling approach was used to calculate the beta nearest taxon index to quantify the influence of stochastic and deterministic processes. We found that spatial distance between samples predicted the perceived processes involved in community structuring, with stochastic processes dominating at local scales. At greater distances, stochasticity became weaker. However, soil pH, which was also the strongest determinant of AOA community, was a much stronger predictor of community structuring, leaving the distance effect redundant as an explanation of community structuring processes. The communities of AOA differing by less than 1 pH unit differed mainly stochastically in terms of operational taxonomic unit composition. At larger pH differences, deterministic processes based on heterogeneous selection between clades became increasingly dominant. It appears that AOA community composition is largely determined by the environment. However, very similar pH environments are the exception. In environments with very close pH values, stochastic effects dominantly cause differences in community composition, whether spatially near or far.
基金supported by Indian Council of Medical Research (Grant No.2013-1551G)Department of Biotechnology,India for providing Ramalingaswami Fellowship (BT/RLF/Re-entry/11/2011)
文摘Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational tax- onomic unit (OTU) levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ulti- mately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interac- tion among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe-microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe-microbe inter- action networks.
基金supported by the earmarked fund for Modern Agro-industry Technology Research System-Green Manure,China (No.CARS-22)the National Natural Science Foundation of China (No.42007071)。
文摘The use of green manures contributes to sustainable soil and nutrient management in agriculture;however, the responses of soil microbial communities to different fertilization regimes at the regional scale are uncertain. A study was undertaken across multiple sites and years in Hunan, Jiangxi, Anhui, Henan,Hubei, and Fujian provinces of South China to investigate the effects of green manuring on the structure and function of soil bacterial communities in rice-green manure cropping systems. The study included four treatments: winter fallow with no chemical fertilizer as a control(NF), milk vetch as green manure without chemical fertilizer(GM), winter fallow and chemical fertilizer(CF), and a combination of chemical fertilizer and milk vetch(GMCF).Significant differences were found in the responses of soil microbial communities at different sites, with sampling sites explaining 72.33%(F = 36.59,P = 0.001) of the community composition variation. The bacterial communities in the soils from Anhui, Henan, and Hubei were broadly similar, while those from Hunan were distinctly different from other locations. The analysis of Weighted UniFrac distances showed that milk vetch changed soil microbial communities compared with winter fallow. Proteobacteria and Chloroflexi predominated in these paddy soils;however, the application of green manures increased the relative abundance of Actinobacteria. There was evidence showing that the functional microbes which play important roles in the cycling of soil carbon, nitrogen(N), and sulfur(S) changed after several years of milk vetch utilization(linear discriminant analysis score > 2). The abundance of methane-oxidizing bacteria and S-reducing bacteria increased, and microbes involved in N fixation, nitrification, and denitrification also increased in some provinces. We concluded that the application of milk vetch changed the bacterial community structure and affected the functional groups related to nutrient transformation in soils at a regional scale.
基金ACKNOWLEDGEMENTS This paper was supported by the National Natural Science Foundation of China (Nos. 91430111, 61473232 and 61170134).
文摘The sequencing revolution driven by high-throughput technologies has generated a huge amount of marine microbial sequences which hide the interaction patterns among microbial species and environment factors. Exploring these patterns is helpful for exploiting the marine resources. In this paper, we use the complex network approach to mine and analyze the interaction patterns of marine taxa and environments in spring, summer, fall and winter seasons. With the 16S rRNA pyrosequencing data of 76 time point taken monthly over 6 years, we first use our MtHc clustering algorithm to generate the operational taxonomic units (OTUs). Then, employ the k-means method to divide 76 time point samples into four seasonal groups, and utilize mutual information (MI) to construct the four correlation networks among microbial species and environment factors. Finally, we adopt the symmetrical non-negative matrix factorization method to detect the interaction patterns, and analysis the relationship between marine species and environment factors. The results show that the four seasonal microbial interaction networks have the characters of complex networks, and interaction patterns are related with the seasonal variability; the same environmental factor influences different species in the four seasons; the four environmental factors of day length, photosynthetically active radiation, NO2+ NO3 and silicate may have stronger influences on microbes than other environment factors.
基金supported by the National Research Foundation Biodiversity Information Program:Biodiversity Surveys in Priority Inland Areas(FBIP)(South Africa)(No.87602)the National Research Foundation for funding the equipment based at the Central Analytical Facilities of Stellenbosch University,South Africa(No.74452)
文摘Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos tea.Symbiotic interactions between A.linearis and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor,acidic fynbos soil.The aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown A.linearis,as well as the effect of seasonal changes on these communities.Bacterial communities were characterized using high throughput amplicon sequencing,and their correlations with soil chemical properties were investigated.The N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain reaction.Actinobacteria,Proteobacteria,and Acidobacteria were the most dominant bacterial phyla detected in this study.Highly similar bacterial communities were associated with natural and commercially grown plants.Significant differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season,while no significant differences were detected in the wet season.This study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important A.linearis.