The contamination of methyl ten-butyl ether （MTBE） in underground waters has become a widely concerned problem all over the world. In this study, a novel dosed culture system with oxygen supplied by H2O2 was introdu...The contamination of methyl ten-butyl ether （MTBE） in underground waters has become a widely concerned problem all over the world. In this study, a novel dosed culture system with oxygen supplied by H2O2 was introduced for MTBE aerobic biodegradation. After 7 d, almost all MTBE was degraded by a pure culture, a member of β-Proteobacteria named as PMI, in a closed system with oxygen supply, while only 40% MTBE was degraded in one without oxygen supply. Dissolved oxygen （DO） levels of the broth in closed systems respectively with and without H2O2 were about 5-6 and 4 mg/L. Higher DO may improve the activity of monooxygemase, which is the key enzyme of metabolic pathway from MTBE to tert-butyl alcohol and finally to CO2, and may result in the increase of the degrading activity of PM1 cell. The purge and trap GC-MS result of the broth in closed systems showed that tea-butyl alcohol, isopronol and acetone were the main intermediate products.展开更多
The phylogeny of γ-proteobacteria was inferred from nucleotide sequence comparisons of a short 232 nucleotide sequence marker. A total of 64 γ-proteobacterial strains from 13 Orders, 22 families, 40 genera and 59 sp...The phylogeny of γ-proteobacteria was inferred from nucleotide sequence comparisons of a short 232 nucleotide sequence marker. A total of 64 γ-proteobacterial strains from 13 Orders, 22 families, 40 genera and 59 species were analyzed. The short 232 nucleotide sequence marker used here was a combination of a 157 nucleotide sequence at the 3’ end of the 16S rRNA gene and a 75 nucleotide sequence at the 5’ end of the 16S-23S Internal Transcribed Spacer (ITS) sequence. Comparative analyses of the 3’ end of the 16S rRNA gene nucleotide sequence showed that the last 157 bp were conserved among strains from same species and less conserved in more distantly related species. This 157 bp sequence was selected as the first part in the construction of our nucleotide sequence marker. A bootstrapped neighbor-joining tree based on the alignment of this 157 bp was constructed. This 157 bp could distinguish γ-proteobacterial species from different genera from same family. Closely related species could not be distinguished. Next, an alignment of the 16S-23S ITS nucleotide sequences of alleles from same bacterial strain was performed. The first 75 bp at the 5’ end of the 16S-23S ITS was highly conserved at the intra-strain level. It was selected as the second part in the construction of our nucleotide sequence marker. Finally, a bootstrapped neighbor-joining tree based on the alignment of this 232 bp sequence was constructed. Based on the topology of the neighbour-joining tree, four major Groups, Group I to IV, were revealed with several sub-groups and clusters. Our results, based on the 232 bp sequence were, in general, in agreement with the phylogeny of γ-proteobacteria based on the 16S rRNA gene. The use of this 232 bp sequence as a phylogenetic marker presents several advantages over the use of the entire 16S rRNA gene or the generation of extensive phenotypic and genotypic data in phylogenetic analyses. First, this marker is not allele-dependant. Second, this 232 bp marker contains 157 bp from the 3’ end of the 16S rRNA gene and 75 bp from the 5’ end of the 16S-23S ITS. The 157 bp allows discrimination among distantly related species. Owing to its higher rate of nucleotide substitutions, the 75 bp adds discriminating power among closely related species from same genus and closely related genera from same family. Because of its higher percentage of nucleotide sequence divergence than the 16S rRNA gene, the 232 bp marker can better discriminate among closely related γ-proteobacterial species. Third, the method is simple, rapid, suited to large screening programs and easily accessible to most laboratories. Fourth, this marker can also reveal γ-proteobacterial species which may appear misassigned and for which additional characterization appear warranted.展开更多
Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with dr...Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with drought, advancing desertification and degraded soils. Most restoration efforts involve revegetation, which in the past has met with limited success. Microbial communities of soils play a pivotal role in soil fertility and plant cover. We conducted the first metagenomic amplicon sequencing study, comparing two soil depths to determine whether soil bacteria abundance and diversity in the harsh bare soils were sufficient to sustain greening efforts. The goal was to glean insights to guide microbial inoculant formulation needed in the region. Samples from top (0 - 15 cm) and sub (16 - 65 cm) soils were collected from five strategic locations in the state. Using next generation Illumina sequencing protocols, total DNA extracted directly from the soils was sequenced and analyzed by QIIME. Metadata collected from site showed scorching temperatures of over 46?C, near zero moisture level and a pH of about 6 for top soil. At 65 cm depth, the temperature averaged 32?C with a pH of 5 and significantly higher soil moisture of 0.1%. The bacterial community structure was unexpectedly very diverse at both soil depths samples, recording a ChaO1 index ranging from 909 to 4296 and a Shannon diversity range of 3.54 to 6.33. The most abundant phyla in both soil depths were the Firmicutes and Proteobacteria;however the relative abundance of composite lower taxa was strikingly different. Operational taxonomic units and diversity indices were highest for top soils and were dominated by members of resilient groups of Actinobacteria, Firmucutes, Acidobacteria and numerous other less well-known taxa whose individual relative abundance did not exceed 3% of total population. The high diversity and richness of Proteobacteria (at 65 cm depth), some of which are key to soil fertility, suggest that revegetation efforts could be improved by shifting the gradient of these microbiota upwards using shades and micro-irrigation. Soils in semi-arid regions in Nigeria contain numerous operational taxonomic bacterial groups with potential thermophilic and drought genetic resources to be mined. Microbial community structure beneath the top soil appears stable and should be the target sample for the assessments of climatic change impact on microbial community structure in environments like this.展开更多
Cold seeps are oases for biological communities on the sea floor around hydrocarbon emission pathways.Microbial utilization of methane and other hydrocarbons yield products that fuel rich chemosynthetic communities at...Cold seeps are oases for biological communities on the sea floor around hydrocarbon emission pathways.Microbial utilization of methane and other hydrocarbons yield products that fuel rich chemosynthetic communities at these sites.One such site in the cold seep ecosystem of Krishna-Godavari basin(K-G basin)along the east coast of India,discovered in Feb 2018 at a depth of 1800 m was assessed for its bacterial diversity.The seep bacterial communities were dominated by phylum Proteobacteria(57%),Firmicutes(16%)and unclassified species belonging to the family Helicobacteriaceae.The surface sediments of the seep had maximum OTUs(operational taxonomic units)(2.27×10^(3))with a Shannon alpha diversity index of 8.06.In general,environmental parameters like total organic carbon(p<0.01),sulfate(p<0.001),sulfide(p<0.05)and methane(p<0.01)were responsible for shaping the bacterial community of the cold seep ecosystem in the K-G Basin.Environmental parameters play a significant role in changing the bacterial diversity richness between different cold seep environments in the oceans.展开更多
以黄海和渤海代表性刺参养殖池塘秋、冬季海水和沉积物基因组DNA为模板,以细菌16S r DNA通用引物进行PCR扩增,构建16S r DNA文库并进行测序分析,研究了秋、冬季刺参养殖池塘菌群的多样性。结果表明:海水和沉积物中主要包括11个门类的细...以黄海和渤海代表性刺参养殖池塘秋、冬季海水和沉积物基因组DNA为模板,以细菌16S r DNA通用引物进行PCR扩增,构建16S r DNA文库并进行测序分析,研究了秋、冬季刺参养殖池塘菌群的多样性。结果表明:海水和沉积物中主要包括11个门类的细菌,即变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)、拟杆菌门(Bacteroidetes)、疣微菌门(Verrucomicrobia)、厚壁菌门(Firmicutes)、梭杆菌门(Fusobacteria)、蓝细菌门(Cyanobacteria)、浮霉菌门(Planctomycetes)、脱铁杆菌门(Deferribacteres)、绿弯菌门(Chloroflexi);黄海和渤海刺参养殖池塘海水和沉积物中优势类群均为变形菌(变形菌比例>48%);用Shannon指数及Simpson优势度指数分析细菌的多样性,黄、渤海刺参养殖池塘中,冬季沉积物细菌Simpson优势度指数均最低,分别为0.014 89和0.016 50,Shannon指数均最高,分别为6.312和5.695。研究表明,黄海和渤海刺参养殖池塘中,冬季沉积物细菌多样性均最高。展开更多
分别于2011年6月和11月,在武汉东湖和南湖采集沉积物,作为夏季和冬季样品的代表,采用PCR-DGGE(Denaturing gradient gel electrophoresis,变性梯度凝胶电泳)和克隆测序方法研究沉积物中微生物多样性及其季节变化.结果显示,城市湖泊沉积...分别于2011年6月和11月,在武汉东湖和南湖采集沉积物,作为夏季和冬季样品的代表,采用PCR-DGGE(Denaturing gradient gel electrophoresis,变性梯度凝胶电泳)和克隆测序方法研究沉积物中微生物多样性及其季节变化.结果显示,城市湖泊沉积物中微生物多样性十分丰富,冬季两个湖泊沉积物的DGGE条带总数为287条,夏季为317条.冬季和夏季,东湖的平均丰度分别为27.4和31.0,Shannon-Wiener指数分别为2.32和2.78;南湖的平均丰度分别为30.0和32.2,Shannon-Winner指数分别为2.83和2.86.两个湖泊的夏季微生物丰度和多样性指数均高于冬季;同一湖泊各样点之间的相似性更强,说明湖泊内部形成了自身特有的微生物群落结构.克隆测序的结果表明东湖、南湖微生物主要归属于3个细菌类群,其中,变形菌门占有优势地位,其次为拟杆菌门和厚壁菌门,分别占序列总数的77%、17%和6%.变形菌门中,β-变形菌纲和γ-变形菌纲为优势菌种,占序列总数的35%和31%.综上,东湖和南湖沉积物夏季微生物丰度和多样性指数均高于冬季,季节性变化影响了沉积物微生物群落的丰度和结构;本研究结果丰富了对城市富营养化湖泊沉积物微生物多样性的认识.展开更多
基金Project supported by the National Natural Science Foundation of China (No. 20476099) Zhejiang Provincial Natural Science Foundation (No. Y504272).
文摘The contamination of methyl ten-butyl ether （MTBE） in underground waters has become a widely concerned problem all over the world. In this study, a novel dosed culture system with oxygen supplied by H2O2 was introduced for MTBE aerobic biodegradation. After 7 d, almost all MTBE was degraded by a pure culture, a member of β-Proteobacteria named as PMI, in a closed system with oxygen supply, while only 40% MTBE was degraded in one without oxygen supply. Dissolved oxygen （DO） levels of the broth in closed systems respectively with and without H2O2 were about 5-6 and 4 mg/L. Higher DO may improve the activity of monooxygemase, which is the key enzyme of metabolic pathway from MTBE to tert-butyl alcohol and finally to CO2, and may result in the increase of the degrading activity of PM1 cell. The purge and trap GC-MS result of the broth in closed systems showed that tea-butyl alcohol, isopronol and acetone were the main intermediate products.
文摘The phylogeny of γ-proteobacteria was inferred from nucleotide sequence comparisons of a short 232 nucleotide sequence marker. A total of 64 γ-proteobacterial strains from 13 Orders, 22 families, 40 genera and 59 species were analyzed. The short 232 nucleotide sequence marker used here was a combination of a 157 nucleotide sequence at the 3’ end of the 16S rRNA gene and a 75 nucleotide sequence at the 5’ end of the 16S-23S Internal Transcribed Spacer (ITS) sequence. Comparative analyses of the 3’ end of the 16S rRNA gene nucleotide sequence showed that the last 157 bp were conserved among strains from same species and less conserved in more distantly related species. This 157 bp sequence was selected as the first part in the construction of our nucleotide sequence marker. A bootstrapped neighbor-joining tree based on the alignment of this 157 bp was constructed. This 157 bp could distinguish γ-proteobacterial species from different genera from same family. Closely related species could not be distinguished. Next, an alignment of the 16S-23S ITS nucleotide sequences of alleles from same bacterial strain was performed. The first 75 bp at the 5’ end of the 16S-23S ITS was highly conserved at the intra-strain level. It was selected as the second part in the construction of our nucleotide sequence marker. Finally, a bootstrapped neighbor-joining tree based on the alignment of this 232 bp sequence was constructed. Based on the topology of the neighbour-joining tree, four major Groups, Group I to IV, were revealed with several sub-groups and clusters. Our results, based on the 232 bp sequence were, in general, in agreement with the phylogeny of γ-proteobacteria based on the 16S rRNA gene. The use of this 232 bp sequence as a phylogenetic marker presents several advantages over the use of the entire 16S rRNA gene or the generation of extensive phenotypic and genotypic data in phylogenetic analyses. First, this marker is not allele-dependant. Second, this 232 bp marker contains 157 bp from the 3’ end of the 16S rRNA gene and 75 bp from the 5’ end of the 16S-23S ITS. The 157 bp allows discrimination among distantly related species. Owing to its higher rate of nucleotide substitutions, the 75 bp adds discriminating power among closely related species from same genus and closely related genera from same family. Because of its higher percentage of nucleotide sequence divergence than the 16S rRNA gene, the 232 bp marker can better discriminate among closely related γ-proteobacterial species. Third, the method is simple, rapid, suited to large screening programs and easily accessible to most laboratories. Fourth, this marker can also reveal γ-proteobacterial species which may appear misassigned and for which additional characterization appear warranted.
文摘Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with drought, advancing desertification and degraded soils. Most restoration efforts involve revegetation, which in the past has met with limited success. Microbial communities of soils play a pivotal role in soil fertility and plant cover. We conducted the first metagenomic amplicon sequencing study, comparing two soil depths to determine whether soil bacteria abundance and diversity in the harsh bare soils were sufficient to sustain greening efforts. The goal was to glean insights to guide microbial inoculant formulation needed in the region. Samples from top (0 - 15 cm) and sub (16 - 65 cm) soils were collected from five strategic locations in the state. Using next generation Illumina sequencing protocols, total DNA extracted directly from the soils was sequenced and analyzed by QIIME. Metadata collected from site showed scorching temperatures of over 46?C, near zero moisture level and a pH of about 6 for top soil. At 65 cm depth, the temperature averaged 32?C with a pH of 5 and significantly higher soil moisture of 0.1%. The bacterial community structure was unexpectedly very diverse at both soil depths samples, recording a ChaO1 index ranging from 909 to 4296 and a Shannon diversity range of 3.54 to 6.33. The most abundant phyla in both soil depths were the Firmicutes and Proteobacteria;however the relative abundance of composite lower taxa was strikingly different. Operational taxonomic units and diversity indices were highest for top soils and were dominated by members of resilient groups of Actinobacteria, Firmucutes, Acidobacteria and numerous other less well-known taxa whose individual relative abundance did not exceed 3% of total population. The high diversity and richness of Proteobacteria (at 65 cm depth), some of which are key to soil fertility, suggest that revegetation efforts could be improved by shifting the gradient of these microbiota upwards using shades and micro-irrigation. Soils in semi-arid regions in Nigeria contain numerous operational taxonomic bacterial groups with potential thermophilic and drought genetic resources to be mined. Microbial community structure beneath the top soil appears stable and should be the target sample for the assessments of climatic change impact on microbial community structure in environments like this.
文摘Cold seeps are oases for biological communities on the sea floor around hydrocarbon emission pathways.Microbial utilization of methane and other hydrocarbons yield products that fuel rich chemosynthetic communities at these sites.One such site in the cold seep ecosystem of Krishna-Godavari basin(K-G basin)along the east coast of India,discovered in Feb 2018 at a depth of 1800 m was assessed for its bacterial diversity.The seep bacterial communities were dominated by phylum Proteobacteria(57%),Firmicutes(16%)and unclassified species belonging to the family Helicobacteriaceae.The surface sediments of the seep had maximum OTUs(operational taxonomic units)(2.27×10^(3))with a Shannon alpha diversity index of 8.06.In general,environmental parameters like total organic carbon(p<0.01),sulfate(p<0.001),sulfide(p<0.05)and methane(p<0.01)were responsible for shaping the bacterial community of the cold seep ecosystem in the K-G Basin.Environmental parameters play a significant role in changing the bacterial diversity richness between different cold seep environments in the oceans.
文摘以黄海和渤海代表性刺参养殖池塘秋、冬季海水和沉积物基因组DNA为模板,以细菌16S r DNA通用引物进行PCR扩增,构建16S r DNA文库并进行测序分析,研究了秋、冬季刺参养殖池塘菌群的多样性。结果表明:海水和沉积物中主要包括11个门类的细菌,即变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)、拟杆菌门(Bacteroidetes)、疣微菌门(Verrucomicrobia)、厚壁菌门(Firmicutes)、梭杆菌门(Fusobacteria)、蓝细菌门(Cyanobacteria)、浮霉菌门(Planctomycetes)、脱铁杆菌门(Deferribacteres)、绿弯菌门(Chloroflexi);黄海和渤海刺参养殖池塘海水和沉积物中优势类群均为变形菌(变形菌比例>48%);用Shannon指数及Simpson优势度指数分析细菌的多样性,黄、渤海刺参养殖池塘中,冬季沉积物细菌Simpson优势度指数均最低,分别为0.014 89和0.016 50,Shannon指数均最高,分别为6.312和5.695。研究表明,黄海和渤海刺参养殖池塘中,冬季沉积物细菌多样性均最高。
文摘分别于2011年6月和11月,在武汉东湖和南湖采集沉积物,作为夏季和冬季样品的代表,采用PCR-DGGE(Denaturing gradient gel electrophoresis,变性梯度凝胶电泳)和克隆测序方法研究沉积物中微生物多样性及其季节变化.结果显示,城市湖泊沉积物中微生物多样性十分丰富,冬季两个湖泊沉积物的DGGE条带总数为287条,夏季为317条.冬季和夏季,东湖的平均丰度分别为27.4和31.0,Shannon-Wiener指数分别为2.32和2.78;南湖的平均丰度分别为30.0和32.2,Shannon-Winner指数分别为2.83和2.86.两个湖泊的夏季微生物丰度和多样性指数均高于冬季;同一湖泊各样点之间的相似性更强,说明湖泊内部形成了自身特有的微生物群落结构.克隆测序的结果表明东湖、南湖微生物主要归属于3个细菌类群,其中,变形菌门占有优势地位,其次为拟杆菌门和厚壁菌门,分别占序列总数的77%、17%和6%.变形菌门中,β-变形菌纲和γ-变形菌纲为优势菌种,占序列总数的35%和31%.综上,东湖和南湖沉积物夏季微生物丰度和多样性指数均高于冬季,季节性变化影响了沉积物微生物群落的丰度和结构;本研究结果丰富了对城市富营养化湖泊沉积物微生物多样性的认识.
