Lake littoral zones are characterized by heterogeneity in the biogeochemistry of nutrient elements. This study aimed to explore the relationship between the nitrous oxide reductase gene （nosZ）-encoding denitrifier c...Lake littoral zones are characterized by heterogeneity in the biogeochemistry of nutrient elements. This study aimed to explore the relationship between the nitrous oxide reductase gene （nosZ）-encoding denitrifier community composition/abundance and N2O reduction. Five samples （deep sediment, near-transition sediment, transition site, near-transition land and land soil） were collected along a littoral gradient of eutrophic Baiyangdian Lake, North China. To investigate the relationship between the nosZ-encoding denitrifier community structure and N20 reduction, the nosZ-encoding denitrifier community composition/abundance, potential denitrification rate （DNR） and potential N20 production rate （pN20） were investigated using molecular biological technologies and laboratory incubation experiments. The results showed that the average DNR of sediments was about 25 times higher than that of land soils, reaching 282.5 nmol N/（g dry weight （dw）.hr） and that the average pN20 of sediments was about 3.5 times higher than that of land soils, reaching 15.7 nmol N/（g dw-hr）. In the land area, the nosZ gene abundance showed a negative correlation with the N20/（N20＋N2） ratio, indicating that nosZ gene abundance dominated N20 reduction both in the surface soils of the land area and in the soil core of the transition site. Phylogenetic analysis showed that all the nosZ sequences recovered from sediment clustered closely with the isolates Azospirillum largimobile and Azospirillum irakense affiliated to Rhodospirillaceae in alpha-Proteobacteria, while about 92.3% （12/13） of the nosZ sequences recovered from land soil affiliated to Rhizobiaceae and Bradyrhizobiaceae in a-Proteobacteria. The community composition of nosZ gene-encoding denitrifiers appeared to be coupled with N20 reduction along the littoral gradient.展开更多
Low availability of phosphorus(P) is a major constraint for optimal crop production, as P is mostly present in its insoluble form in soil. Therefore,phosphate-solubilizing bacteria(PSB) from paddy field soils of the I...Low availability of phosphorus(P) is a major constraint for optimal crop production, as P is mostly present in its insoluble form in soil. Therefore,phosphate-solubilizing bacteria(PSB) from paddy field soils of the Indo-Gangetic Plain, India were isolated, and their abundance was attempted to be correlated with the physicochemical characteristics of the soils. Ninety-four PSB were isolated on Pikovskaya’s agar medium, and quantitative phosphate solubilization was evaluated using NBRIP medium. The isolates solubilized P up to a concentration of 1 006 μg mL-1 from tricalcium phosphate with the secretion of organic acids. These isolates were identified by 16 S rRNA gene sequence comparison, and they belonged to Gammaproteobacteria(56 isolates),Firmicutes(28 isolates), Actinobacteria(8 isolates), and Alphaproteobacteria(2 isolates). Phylogenetic analysis confirmed the identification by clustering the isolates in the clade of the respective reference organisms. The correlation analysis between PSB abundance and physicochemical characteristics revealed that the PSB population increased with increasing levels of soil organic carbon, insoluble P, K+, and Mg2+. The promising PSB explored in this study can be further evaluated for their biofertilizer potential in the field and for their use as potent bio-inoculants.展开更多
Rapid,precise,and tunable regulation of protein abundance would be significantly useful in a variety of biotechnologies and biomedical applications.Here,we describe a system that allows tunable and rapid drug control ...Rapid,precise,and tunable regulation of protein abundance would be significantly useful in a variety of biotechnologies and biomedical applications.Here,we describe a system that allows tunable and rapid drug control of gene expression for either gene activation or inactivation in mammalian cells.We construct the system by coupling Tet-on 3 G and small molecule-assisted shutoff systems,which can respectively induce transcriptional activation and protein degradation in the presence of corresponding small molecules.This dual-input drug inducer regulation system facilitates a bidirectional control of gene expression.The gene of interest can be precisely controlled by dual small molecules in a broad dynamic range of expression from overexpression to complete silence,allowing gene function study in a comprehensive expression profile.Our results reveal that the bidirectional control system enables sensitive dosage-and time-dependent regulation for either turn-on or shutoff of gene expression.We also apply this system for inducible genome editing and gene activation mediated by clustered regularly interspaced short palindromic repeats.The system provides an integrated platform for studying multiple biological processes by manipulating gene expression in a more flexible way.展开更多
The combined use of plants and bacteria is a promising approach for the remediation of soil contaminated with organic pollutants. Different biotic and abiotie factors can affect the survival and activity of the applie...The combined use of plants and bacteria is a promising approach for the remediation of soil contaminated with organic pollutants. Different biotic and abiotie factors can affect the survival and activity of the applied bacteria and consequently plant growth and phy- toremediation efficiency. The effect of inoculum density on the abundance and expression of alkune-degrading genes in the rhizosphere of plant vegetated in hydrocarbon-contaminated soil has been rarely observed. In this study, an alkane-degrading bacterium （Pantoea sp. strain BTRH79）, at different inoculum densities （10^5 to 10^8 cells cm^-3 soil）, was inoculated to ryegrass （Lolium perenne） vegetated in diesel-contaminated soil to find the optimum inoculum density needed for its efficient colonization and hydrocarbon degradation activity. Bacterial inoculation improved plant growth and hydrocarbon degradation. Maximum plant growth and hydrocarbon degra- dation were observed with the inoculum having the highest cell density （10^8 cells cm^-3 soil）. Moreover, the inoculum with higher cell density exhibited more abundance and expression of alkane hydroxylase gene, CYP153. This study suggests that the inoculum density is one of the main factors that can affect bacterial colonization and activity during phytoremediation.展开更多
The effects of nitrogen （N） addition on microbial biomass, bacterial abundance, and community composition in sediment colonized by Suaeda heteroptera were examined by chloroform fumigation extraction method, real-ti...The effects of nitrogen （N） addition on microbial biomass, bacterial abundance, and community composition in sediment colonized by Suaeda heteroptera were examined by chloroform fumigation extraction method, real-time quantitative polymerase chain reaction, and denaturing gradient gel electrophoresis （DGGE） in a salt marsh located in Shuangtai Estuary, China. The sediment samples were collected from plots treated with different amounts of a single N fertilizer （urea supplied at 0.1, 0.2, 0.4 and 0.8 g/kg （nitrogen content in sediment） and different forms of N fertilizers （urea, （NH4）2SO4, and NH4NO3, each supplied at 0.2 g/kg （calculated by nitrogen）. The fertilizers were applied 1-4 times during the plant-growing season in May, luly, August, and September of 2013. Untreated plots were included as a control. The results showed that both the amount and form of N positively influenced microbial biomass carbon, microbial biomass nitrogen, and bacterial abundance. The DGGE profiles revealed that the bacterial community composition was also affected by the amount and form of N. Thus, our findings indicate that short-term N amendment increases microbial biomass and bacterial abundance, and alters the structure of bacterial community.展开更多
Background： A main goal of metagenomics is taxonomic characterization of microbial communities. Although sequence comparison has been the main method for the taxonomic classification, there is not a clear agreement o...Background： A main goal of metagenomics is taxonomic characterization of microbial communities. Although sequence comparison has been the main method for the taxonomic classification, there is not a clear agreement on similarity calculation and similarity thresholds, especially at higher taxonomic levels such as phylum and class. Thus taxonomic classification of novel metagenomic sequences without close homologs in the biological databases poses a challenge. Methods： In this study, we propose to use the co-abundant associations between taxa/operational taxonomic units （OTU） across complex and diverse communities to assist taxonomic classification. We developed a Markov Random Field model to predict taxa of unknown microorganisms using co-abundant associations. Results： Although such associations are intrinsically functional associations, we demonstrate that they are strongly correlated with taxonomic associations and can be combined with sequence comparison methods to predict taxonomic origins of unknown microorganisms at phylum and class levels. Conclusions： With the ever-increasing accumulation of sequence data from microbial communities, we now take the first step to explore these associations for taxonomic identification beyond sequence similarity. Availability and Implementation： Source codes of TACO are freely available at the following URL： https：//github.com/ baharvand/OTU-Taxonomy-Identification implemented in C＋＋, supported on Linux and MS Windows.展开更多
基金supported by the National Natural Science Foundation of China (No.21077119)the National Basic Research Program of China(No. 2009CB421103)+3 种基金the Key Project of Water Pollution Control and Management of China (No.2008ZX07209-006, 2009ZX07209-005 and 2008ZX07421-001)the Special Fund of Tianjin Science and Technology Innovation Project (No. 08FDZDSF03200)the support of the Beijing Nova Program (No. 2011095)the K. C. Wong Education Foundation, Hong Kong, China
文摘Lake littoral zones are characterized by heterogeneity in the biogeochemistry of nutrient elements. This study aimed to explore the relationship between the nitrous oxide reductase gene （nosZ）-encoding denitrifier community composition/abundance and N2O reduction. Five samples （deep sediment, near-transition sediment, transition site, near-transition land and land soil） were collected along a littoral gradient of eutrophic Baiyangdian Lake, North China. To investigate the relationship between the nosZ-encoding denitrifier community structure and N20 reduction, the nosZ-encoding denitrifier community composition/abundance, potential denitrification rate （DNR） and potential N20 production rate （pN20） were investigated using molecular biological technologies and laboratory incubation experiments. The results showed that the average DNR of sediments was about 25 times higher than that of land soils, reaching 282.5 nmol N/（g dry weight （dw）.hr） and that the average pN20 of sediments was about 3.5 times higher than that of land soils, reaching 15.7 nmol N/（g dw-hr）. In the land area, the nosZ gene abundance showed a negative correlation with the N20/（N20＋N2） ratio, indicating that nosZ gene abundance dominated N20 reduction both in the surface soils of the land area and in the soil core of the transition site. Phylogenetic analysis showed that all the nosZ sequences recovered from sediment clustered closely with the isolates Azospirillum largimobile and Azospirillum irakense affiliated to Rhodospirillaceae in alpha-Proteobacteria, while about 92.3% （12/13） of the nosZ sequences recovered from land soil affiliated to Rhizobiaceae and Bradyrhizobiaceae in a-Proteobacteria. The community composition of nosZ gene-encoding denitrifiers appeared to be coupled with N20 reduction along the littoral gradient.
文摘Low availability of phosphorus(P) is a major constraint for optimal crop production, as P is mostly present in its insoluble form in soil. Therefore,phosphate-solubilizing bacteria(PSB) from paddy field soils of the Indo-Gangetic Plain, India were isolated, and their abundance was attempted to be correlated with the physicochemical characteristics of the soils. Ninety-four PSB were isolated on Pikovskaya’s agar medium, and quantitative phosphate solubilization was evaluated using NBRIP medium. The isolates solubilized P up to a concentration of 1 006 μg mL-1 from tricalcium phosphate with the secretion of organic acids. These isolates were identified by 16 S rRNA gene sequence comparison, and they belonged to Gammaproteobacteria(56 isolates),Firmicutes(28 isolates), Actinobacteria(8 isolates), and Alphaproteobacteria(2 isolates). Phylogenetic analysis confirmed the identification by clustering the isolates in the clade of the respective reference organisms. The correlation analysis between PSB abundance and physicochemical characteristics revealed that the PSB population increased with increasing levels of soil organic carbon, insoluble P, K+, and Mg2+. The promising PSB explored in this study can be further evaluated for their biofertilizer potential in the field and for their use as potent bio-inoculants.
基金supported by the National Natural Science Foundation of China(81800555,81701580,and 31972926)the National Key R&D Program of China(2018YFC1106400)+1 种基金the Science and Technology Planning Project of Guangdong Province(2015B020229002)the Natural Science Foundation of Guangdong Province(2014A030312013 and 2018A030313128)
文摘Rapid,precise,and tunable regulation of protein abundance would be significantly useful in a variety of biotechnologies and biomedical applications.Here,we describe a system that allows tunable and rapid drug control of gene expression for either gene activation or inactivation in mammalian cells.We construct the system by coupling Tet-on 3 G and small molecule-assisted shutoff systems,which can respectively induce transcriptional activation and protein degradation in the presence of corresponding small molecules.This dual-input drug inducer regulation system facilitates a bidirectional control of gene expression.The gene of interest can be precisely controlled by dual small molecules in a broad dynamic range of expression from overexpression to complete silence,allowing gene function study in a comprehensive expression profile.Our results reveal that the bidirectional control system enables sensitive dosage-and time-dependent regulation for either turn-on or shutoff of gene expression.We also apply this system for inducible genome editing and gene activation mediated by clustered regularly interspaced short palindromic repeats.The system provides an integrated platform for studying multiple biological processes by manipulating gene expression in a more flexible way.
基金supported by the Higher Education Commission (HEC), Pakistan (No. 20-2011-1997)
文摘The combined use of plants and bacteria is a promising approach for the remediation of soil contaminated with organic pollutants. Different biotic and abiotie factors can affect the survival and activity of the applied bacteria and consequently plant growth and phy- toremediation efficiency. The effect of inoculum density on the abundance and expression of alkune-degrading genes in the rhizosphere of plant vegetated in hydrocarbon-contaminated soil has been rarely observed. In this study, an alkane-degrading bacterium （Pantoea sp. strain BTRH79）, at different inoculum densities （10^5 to 10^8 cells cm^-3 soil）, was inoculated to ryegrass （Lolium perenne） vegetated in diesel-contaminated soil to find the optimum inoculum density needed for its efficient colonization and hydrocarbon degradation activity. Bacterial inoculation improved plant growth and hydrocarbon degradation. Maximum plant growth and hydrocarbon degra- dation were observed with the inoculum having the highest cell density （10^8 cells cm^-3 soil）. Moreover, the inoculum with higher cell density exhibited more abundance and expression of alkane hydroxylase gene, CYP153. This study suggests that the inoculum density is one of the main factors that can affect bacterial colonization and activity during phytoremediation.
基金The National Natural Science Foundation of China under contract No.41171389the Public Science and Technology Research Funds Projects of Ocean under contract No.201305043Program for Liaoning Excellent Talents in University under contract No.LR2013035
文摘The effects of nitrogen （N） addition on microbial biomass, bacterial abundance, and community composition in sediment colonized by Suaeda heteroptera were examined by chloroform fumigation extraction method, real-time quantitative polymerase chain reaction, and denaturing gradient gel electrophoresis （DGGE） in a salt marsh located in Shuangtai Estuary, China. The sediment samples were collected from plots treated with different amounts of a single N fertilizer （urea supplied at 0.1, 0.2, 0.4 and 0.8 g/kg （nitrogen content in sediment） and different forms of N fertilizers （urea, （NH4）2SO4, and NH4NO3, each supplied at 0.2 g/kg （calculated by nitrogen）. The fertilizers were applied 1-4 times during the plant-growing season in May, luly, August, and September of 2013. Untreated plots were included as a control. The results showed that both the amount and form of N positively influenced microbial biomass carbon, microbial biomass nitrogen, and bacterial abundance. The DGGE profiles revealed that the bacterial community composition was also affected by the amount and form of N. Thus, our findings indicate that short-term N amendment increases microbial biomass and bacterial abundance, and alters the structure of bacterial community.
文摘Background： A main goal of metagenomics is taxonomic characterization of microbial communities. Although sequence comparison has been the main method for the taxonomic classification, there is not a clear agreement on similarity calculation and similarity thresholds, especially at higher taxonomic levels such as phylum and class. Thus taxonomic classification of novel metagenomic sequences without close homologs in the biological databases poses a challenge. Methods： In this study, we propose to use the co-abundant associations between taxa/operational taxonomic units （OTU） across complex and diverse communities to assist taxonomic classification. We developed a Markov Random Field model to predict taxa of unknown microorganisms using co-abundant associations. Results： Although such associations are intrinsically functional associations, we demonstrate that they are strongly correlated with taxonomic associations and can be combined with sequence comparison methods to predict taxonomic origins of unknown microorganisms at phylum and class levels. Conclusions： With the ever-increasing accumulation of sequence data from microbial communities, we now take the first step to explore these associations for taxonomic identification beyond sequence similarity. Availability and Implementation： Source codes of TACO are freely available at the following URL： https：//github.com/ baharvand/OTU-Taxonomy-Identification implemented in C＋＋, supported on Linux and MS Windows.
