A sediment sample was collected from a deep-sea hydrothermal vent field located at a depth of 2 951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community using polymerase c...A sediment sample was collected from a deep-sea hydrothermal vent field located at a depth of 2 951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community using polymerase chain reaction（PCR） amplification of the 16 S rRNA and nifH genes. Within the Archaea, the dominant clones were from marine benthic group E（MBGE） and marine group I（MGI） belonging to the phyla Euryarchaeota and Thaumarchaeota, respectively. More than half of the bacterial clones belonged to the Proteobacteria, and most fell within the Gammaproteobacteria. No epsilonproteobacterial sequence was observed. Additional phyla were detected including the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3 and TM6, confirming their existence in hydrothermal vent environments. The detection of nifH gene suggests that biological nitrogen fixation may occur in the hydrothermal vent field of the Southwest Indian Ridge. Phylogenetic analysis indicated that only Clusters I and III NifH were present. This is consistent with the phylogenetic analysis of the microbial 16 S rRNA genes, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment.展开更多
A field experiment involving cry1Ab transgenic rice(GM) and its parental non-cry1Ab rice(M) has been on-going since 2014. The diversity of the bacterial communities and the abundance of the microbial functional genes ...A field experiment involving cry1Ab transgenic rice(GM) and its parental non-cry1Ab rice(M) has been on-going since 2014. The diversity of the bacterial communities and the abundance of the microbial functional genes which drive the conversion of nitrogen in paddy soil were analyzed during the growth period of rice in the fifth year of the experiment, using 16 S rRNAbased Illumina Mi Seq and real-time PCR on the amoA, nirS and nirK genes. The results showed no differences in the alpha diversity indexes of the bacterial communities, including Chao1, Shannon and Simpson, between the fields cultivated with line GM and cultivar M at any of the growth stages of rice. However, the bacterial communities in the paddy soil with line GM were separated from those of paddy soil with cultivar M at each of the growth stages of rice, based on the unweighted Uni Frac NMDS or PCoA. In addition, the analyses of ADONIS and ANOSIM, based on the unweighted Uni Frac distance, indicated that the above separations between line GM and cultivar M were statistically significant(P<0.05) during the growth season of rice. The increases in the relative abundances of Acidobacteria or Bacteroidetes, in the paddy soils with line GM or cultivar M, respectively, led to the differences in the bacterial communities between them. At the same time, functional gene prediction based on Illumina Mi Seq data suggested that the abundance of many functional genes increased in the paddy soil with line GM at the maturity stage of rice, such as genes related to the metabolism of starch, amino acids and nitrogen. Otherwise, the copies of bacterial amo A gene, archaeal amo A gene and denitrifying bacterial nir K gene significantly increased(P<0.05 or 0.01) in the paddy soil with line GM. In summary, the release of cry1Ab transgenic rice had effects on either the composition of bacterial communities or the abundance of microbial functional genes in the paddy soil.展开更多
Based on long-term dynamic tracing of dissolved inorganic carbon(DIC)and stable carbon isotope(δ13CDIC)in produced water from 20 coalbed methane(CBM)wells in western Guizhou,the spatial-temporal dynamic variations of...Based on long-term dynamic tracing of dissolved inorganic carbon(DIC)and stable carbon isotope(δ13CDIC)in produced water from 20 coalbed methane(CBM)wells in western Guizhou,the spatial-temporal dynamic variations ofδ13CDIC of the GP well group produced in multi-layer commingled manner were analyzed,and the relationship between the value ofδ13CDIC and CBM productivity was examined.The produced water samples of typical wells in the GP well group were amplified and sequenced using 16S rDNA,and a geological response model ofδ13CDIC in produced water from CBM wells with multi-coal seams was put forward.The research shows that:δ13CDIC in produced water from medium-rank coal seams commonly show positive anomalies,the produced water contains more than 15 species of methanogens,and Methanobacterium is the dominant genus.The dominant methanogens sequence numbers in the produced water are positively correlated withδ13CDIC,and the positive anomaly of v is caused by reduction of methanogens,and especially hydrogenotrophic methanogens.Vertical segmentation of sedimentary facies and lithology in stratum with multi-coal seams will result in permeability and water cut segmentation,which will lead to the segmentation ofδ13CDIC and archaea community in produced water,so in the strata with better permeability and high water cut,theδ13CDIC of the produced water is abnormally enriched,and the dominant archaea is mainly Methanobacterium.In the strata with weak permeability and low water cut,theδ13CDIC of the produced water is small,and the microbial action is weak.The shallow layer close to the coal seam outcrop is likely to be affected by meteoric precipitation,so theδ13CDIC of the produced water is smaller.The geological response model ofδ13CDIC in produced water from multi-coal seams CBM wells in the medium-rank coal reveals the geological mechanism and microbial action mechanism of theδ13CDIC difference in the produced water from the multi-coal seams CBM wells.It also provides effective geochemical evidence for the superimposed fluid system controlled by sedimentary facies,and can also be used for the contribution analysis of the produced gas and water by the multi-layer CBM wells.展开更多
The microbial quality of urban recreational water is of great concern to public health.The monitoring of indicator organisms and several pathogens alone is not sufficient to accurately and comprehensively identify mic...The microbial quality of urban recreational water is of great concern to public health.The monitoring of indicator organisms and several pathogens alone is not sufficient to accurately and comprehensively identify microbial risks.To assess the levels of bacterial pathogens and health risks in urban recreational water,we analyzed pathogen diversity and quantified four pathogens in 46 water samples collected from waterbodies in Beijing Olympic Forest Park in one year.The pathogen diversity revealed by 16 S r RNA gene targeted next-generation sequencing（NGS） showed that 16 of 40 genera and 13 of 76 reference species were present.The most abundant species were Acinetobacter johnsonii,Mycobacterium avium and Aeromonas spp.Quantitative polymerase chain reaction（q PCR） of Escherichia coli（uid A）,Aeromonas（aer A）,M.avium（16S r RNA）,Pseudomonas aeruginosa（oaa） and Salmonella（inv A） showed that the aer A genes were the most abundant,occurring in all samples with concentrations of 10^（4–6） genome copies/100 m L,followed by oaa,inv A and M.avium.In total,34.8% of the samples harbored all genes,indicating the prevalence of these pathogens in this recreational waterbody.Based on the q PCR results,a quantitative microbial risk assessment（QMRA） showed that the annual infection risks of Salmonella,M.avium and P.aeruginosa in five activities were mostly greater than the U.S.EPA risk limit for recreational contacts,and children playing with water may be exposed to the greatest infection risk.Our findings provide a comprehensive understanding of bacterial pathogen diversity and pathogen abundance in urban recreational water by applying both NGS and q PCR.展开更多
Ammonia（NH3） volatilization is one of the primary pathways of nitrogen（N） loss from soils after chemical fertilizer is applied, especially from the alkaline soils in Northern China, which results in lower efficien...Ammonia（NH3） volatilization is one of the primary pathways of nitrogen（N） loss from soils after chemical fertilizer is applied, especially from the alkaline soils in Northern China, which results in lower efficiency for chemical fertilizers. Therefore, we conducted an incubation experiment using an alkaline soil from Tianjin（p H 8.37–8.43） to evaluate the suppression effect of Trichoderma viride（T. viride） biofertilizer on NH3 volatilization, and compared the differences in microbial community structure among all samples. The results showed that viable T. viride biofertilizer（T） decreased NH3 volatilization by 42.21% compared with conventional fertilizer（（CK）, urea）, while nonviable T. viride biofertilizer（TS） decreased NH3 volatilization by 32.42%. NH3 volatilization was significantly higher in CK and sweet potato starch wastewater（SPSW） treatments during the peak period. T. viride biofertilizer also improved the transfer of ammonium from soil to sweet sorghum. Plant dry weights increased 91.23% and 61.08% for T and TS, respectively, compared to CK. Moreover, T. viride biofertilizer enhanced nitrification by increasing the abundance of ammonium-oxidizing archaea（AOA） and ammonium-oxidizing bacteria（AOB）. The results of high-throughput sequencing indicated that the microbial community structure and composition were significantly changed by the application of T. viride biofertilizer. This study demonstrated the immense potential of T. viride biofertilizer in reducing NH3 volatilization from alkaline soil and simultaneously improving the utilization of fertilizer N by sweet sorghum.展开更多
Water washing is a meaningful method to improve the surface’characteristic of hydrochar produced using hydrothermal carbonization and minimize the negative effect on crop growth.However,the greenhouse effect resultin...Water washing is a meaningful method to improve the surface’characteristic of hydrochar produced using hydrothermal carbonization and minimize the negative effect on crop growth.However,the greenhouse effect resulting from water-washed hydrochar application was unclear in agricultural ecosystems.Hence,the effect of water-washed hydrochar on methane and nitrous oxide emissions was analyzed in an infertile paddy soil based on a soil-column experiment.Sawdust-derived hydro-char(WSH)and wheat straw-derived hydrochar(WWH)after water washing were selected and applied with low(5‰,w/w;8.5 t ha^(−1))or high addition rate(15‰,w/w;25.5 t ha^(−1)).The study indicated that water-washed hydrochar could increase the grain yield;the difference between WWH with 5‰application rate and CKU treatments was significant.WSH signifi-cantly decreased CH4 and N2O emissions in comparison with WWH addition treatments.For the same material,there were trends in reducing greenhouse gas(GHG)emissions at low application rate,although the differences were not significant.Compared with all treatments,WSH with 5‰application rate achieved the lowest seasonal emissions for both GHGs.The mcrA gene was the critical factor affecting CH4 emission;soil NO_(3)^(−)-N concentration and the copy numbers of nirK,nirS,and nosZ jointly affected N2O emissions.Benefits from the high yield and low global warming potential,GHG emission intensity(GHGI)at low application rate was lower than at high application rate for WSH.Overall,the response of GHG emissions to water-washed hydrochar varies with the derived feedstock;WSH is a good additive for the mitigation of GHGI.展开更多
基金The China Ocean Mineral Resources R&D Association(COMRA)Special Foundation under contract No.DY125-15-R-03the National Natural Science Foundation of China under contract Nos 41276173 and 41206104the Scientific Research Fund of the Second Institute of Oceanography,State Oceanic Administration under contract No.JT1011
文摘A sediment sample was collected from a deep-sea hydrothermal vent field located at a depth of 2 951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community using polymerase chain reaction（PCR） amplification of the 16 S rRNA and nifH genes. Within the Archaea, the dominant clones were from marine benthic group E（MBGE） and marine group I（MGI） belonging to the phyla Euryarchaeota and Thaumarchaeota, respectively. More than half of the bacterial clones belonged to the Proteobacteria, and most fell within the Gammaproteobacteria. No epsilonproteobacterial sequence was observed. Additional phyla were detected including the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3 and TM6, confirming their existence in hydrothermal vent environments. The detection of nifH gene suggests that biological nitrogen fixation may occur in the hydrothermal vent field of the Southwest Indian Ridge. Phylogenetic analysis indicated that only Clusters I and III NifH were present. This is consistent with the phylogenetic analysis of the microbial 16 S rRNA genes, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment.
基金the National Science and Technology Major Project of the Ministry of Science and Technology of China (2016ZX08001-001)。
文摘A field experiment involving cry1Ab transgenic rice(GM) and its parental non-cry1Ab rice(M) has been on-going since 2014. The diversity of the bacterial communities and the abundance of the microbial functional genes which drive the conversion of nitrogen in paddy soil were analyzed during the growth period of rice in the fifth year of the experiment, using 16 S rRNAbased Illumina Mi Seq and real-time PCR on the amoA, nirS and nirK genes. The results showed no differences in the alpha diversity indexes of the bacterial communities, including Chao1, Shannon and Simpson, between the fields cultivated with line GM and cultivar M at any of the growth stages of rice. However, the bacterial communities in the paddy soil with line GM were separated from those of paddy soil with cultivar M at each of the growth stages of rice, based on the unweighted Uni Frac NMDS or PCoA. In addition, the analyses of ADONIS and ANOSIM, based on the unweighted Uni Frac distance, indicated that the above separations between line GM and cultivar M were statistically significant(P<0.05) during the growth season of rice. The increases in the relative abundances of Acidobacteria or Bacteroidetes, in the paddy soils with line GM or cultivar M, respectively, led to the differences in the bacterial communities between them. At the same time, functional gene prediction based on Illumina Mi Seq data suggested that the abundance of many functional genes increased in the paddy soil with line GM at the maturity stage of rice, such as genes related to the metabolism of starch, amino acids and nitrogen. Otherwise, the copies of bacterial amo A gene, archaeal amo A gene and denitrifying bacterial nir K gene significantly increased(P<0.05 or 0.01) in the paddy soil with line GM. In summary, the release of cry1Ab transgenic rice had effects on either the composition of bacterial communities or the abundance of microbial functional genes in the paddy soil.
基金Supported by the National Natural Science Foundation of China(41772155)the National Science and Technology Major Project of China(2016ZX05044-002)
文摘Based on long-term dynamic tracing of dissolved inorganic carbon(DIC)and stable carbon isotope(δ13CDIC)in produced water from 20 coalbed methane(CBM)wells in western Guizhou,the spatial-temporal dynamic variations ofδ13CDIC of the GP well group produced in multi-layer commingled manner were analyzed,and the relationship between the value ofδ13CDIC and CBM productivity was examined.The produced water samples of typical wells in the GP well group were amplified and sequenced using 16S rDNA,and a geological response model ofδ13CDIC in produced water from CBM wells with multi-coal seams was put forward.The research shows that:δ13CDIC in produced water from medium-rank coal seams commonly show positive anomalies,the produced water contains more than 15 species of methanogens,and Methanobacterium is the dominant genus.The dominant methanogens sequence numbers in the produced water are positively correlated withδ13CDIC,and the positive anomaly of v is caused by reduction of methanogens,and especially hydrogenotrophic methanogens.Vertical segmentation of sedimentary facies and lithology in stratum with multi-coal seams will result in permeability and water cut segmentation,which will lead to the segmentation ofδ13CDIC and archaea community in produced water,so in the strata with better permeability and high water cut,theδ13CDIC of the produced water is abnormally enriched,and the dominant archaea is mainly Methanobacterium.In the strata with weak permeability and low water cut,theδ13CDIC of the produced water is small,and the microbial action is weak.The shallow layer close to the coal seam outcrop is likely to be affected by meteoric precipitation,so theδ13CDIC of the produced water is smaller.The geological response model ofδ13CDIC in produced water from multi-coal seams CBM wells in the medium-rank coal reveals the geological mechanism and microbial action mechanism of theδ13CDIC difference in the produced water from the multi-coal seams CBM wells.It also provides effective geochemical evidence for the superimposed fluid system controlled by sedimentary facies,and can also be used for the contribution analysis of the produced gas and water by the multi-layer CBM wells.
基金supported by the Key Program of the National Natural Science Foundation of China(No.51138006)the National Key Research on Water Environment Pollution Control in China(No.2012ZX07301-001)
文摘The microbial quality of urban recreational water is of great concern to public health.The monitoring of indicator organisms and several pathogens alone is not sufficient to accurately and comprehensively identify microbial risks.To assess the levels of bacterial pathogens and health risks in urban recreational water,we analyzed pathogen diversity and quantified four pathogens in 46 water samples collected from waterbodies in Beijing Olympic Forest Park in one year.The pathogen diversity revealed by 16 S r RNA gene targeted next-generation sequencing（NGS） showed that 16 of 40 genera and 13 of 76 reference species were present.The most abundant species were Acinetobacter johnsonii,Mycobacterium avium and Aeromonas spp.Quantitative polymerase chain reaction（q PCR） of Escherichia coli（uid A）,Aeromonas（aer A）,M.avium（16S r RNA）,Pseudomonas aeruginosa（oaa） and Salmonella（inv A） showed that the aer A genes were the most abundant,occurring in all samples with concentrations of 10^（4–6） genome copies/100 m L,followed by oaa,inv A and M.avium.In total,34.8% of the samples harbored all genes,indicating the prevalence of these pathogens in this recreational waterbody.Based on the q PCR results,a quantitative microbial risk assessment（QMRA） showed that the annual infection risks of Salmonella,M.avium and P.aeruginosa in five activities were mostly greater than the U.S.EPA risk limit for recreational contacts,and children playing with water may be exposed to the greatest infection risk.Our findings provide a comprehensive understanding of bacterial pathogen diversity and pathogen abundance in urban recreational water by applying both NGS and q PCR.
基金supported by the National Science Fund Projects (Nos. 41371266 and 31670507)Innovation in Cross-functional Team Program of the Chinese Academy of Sciences (No. 2015)+1 种基金the Key Research Program of Chinese Academy of Sciences (No. ZDRW-ZS-2016-5)the Key State Science and Technology Program of China (No. 2015ZX07206-006)
文摘Ammonia（NH3） volatilization is one of the primary pathways of nitrogen（N） loss from soils after chemical fertilizer is applied, especially from the alkaline soils in Northern China, which results in lower efficiency for chemical fertilizers. Therefore, we conducted an incubation experiment using an alkaline soil from Tianjin（p H 8.37–8.43） to evaluate the suppression effect of Trichoderma viride（T. viride） biofertilizer on NH3 volatilization, and compared the differences in microbial community structure among all samples. The results showed that viable T. viride biofertilizer（T） decreased NH3 volatilization by 42.21% compared with conventional fertilizer（（CK）, urea）, while nonviable T. viride biofertilizer（TS） decreased NH3 volatilization by 32.42%. NH3 volatilization was significantly higher in CK and sweet potato starch wastewater（SPSW） treatments during the peak period. T. viride biofertilizer also improved the transfer of ammonium from soil to sweet sorghum. Plant dry weights increased 91.23% and 61.08% for T and TS, respectively, compared to CK. Moreover, T. viride biofertilizer enhanced nitrification by increasing the abundance of ammonium-oxidizing archaea（AOA） and ammonium-oxidizing bacteria（AOB）. The results of high-throughput sequencing indicated that the microbial community structure and composition were significantly changed by the application of T. viride biofertilizer. This study demonstrated the immense potential of T. viride biofertilizer in reducing NH3 volatilization from alkaline soil and simultaneously improving the utilization of fertilizer N by sweet sorghum.
基金This research is supported by The National Natural Science Foundation of China(4187709042077092)+3 种基金The National Key R&D Program,Ministry of Science and Technology,China(2017YFD0300104)Open Project of Key Laboratory for Crop and Animal Integrated Farming of Ministry of Agriculture and Rural Affairs,P.R.China(202001)The National Key Research and Development Program,P.R.China(2016YFD0300908-02)Baoshan Xing acknowledges the UMass Amherst Conti Faculty Fellowship。
文摘Water washing is a meaningful method to improve the surface’characteristic of hydrochar produced using hydrothermal carbonization and minimize the negative effect on crop growth.However,the greenhouse effect resulting from water-washed hydrochar application was unclear in agricultural ecosystems.Hence,the effect of water-washed hydrochar on methane and nitrous oxide emissions was analyzed in an infertile paddy soil based on a soil-column experiment.Sawdust-derived hydro-char(WSH)and wheat straw-derived hydrochar(WWH)after water washing were selected and applied with low(5‰,w/w;8.5 t ha^(−1))or high addition rate(15‰,w/w;25.5 t ha^(−1)).The study indicated that water-washed hydrochar could increase the grain yield;the difference between WWH with 5‰application rate and CKU treatments was significant.WSH signifi-cantly decreased CH4 and N2O emissions in comparison with WWH addition treatments.For the same material,there were trends in reducing greenhouse gas(GHG)emissions at low application rate,although the differences were not significant.Compared with all treatments,WSH with 5‰application rate achieved the lowest seasonal emissions for both GHGs.The mcrA gene was the critical factor affecting CH4 emission;soil NO_(3)^(−)-N concentration and the copy numbers of nirK,nirS,and nosZ jointly affected N2O emissions.Benefits from the high yield and low global warming potential,GHG emission intensity(GHGI)at low application rate was lower than at high application rate for WSH.Overall,the response of GHG emissions to water-washed hydrochar varies with the derived feedstock;WSH is a good additive for the mitigation of GHGI.
