Sebastiscus marmoratus is an important sedentary ovoviparous fish distributed in near-shore coastal waters from the coast of China to Japan. Candidate S. marmoratus microsatellite markers were developed in the present...Sebastiscus marmoratus is an important sedentary ovoviparous fish distributed in near-shore coastal waters from the coast of China to Japan. Candidate S. marmoratus microsatellite markers were developed in the present study using 454 pyrosequencing, and the marker profile was analyzed. A total of 2 000 000 raw sequence reads were assembled to reduce redundancy. Among them, 1 043 dinucleotide, 925 trinucleotide, 692 tetranucleotide, and 315 pentanucleotide repeats were detected. AC repeats were the most frequent motifs among the dinucleotide repeats, and AAT was the most abundant among the trinucleotide repeats. AAAT, ATAG, and ATCC were the three most common tetranucleotide motifs, and AAGAT and AATAT were the most dominant pentanucleotide motifs. The greatest numbers of loci and potentially amplifiable loci were found in dinucleotide repeats, whereas trinucleotide repeats had the fewest. In summary, a wide range of candidate microsatellite markers were identified in the present study using a rapid and efficient 454 pyrosequencing approach.展开更多
Biofouling, the accumulation of microorganisms, is a major problem in paper mills processing paper and cardboard. This leads to the production of lower quality recycled products. Several studies have focused on the mi...Biofouling, the accumulation of microorganisms, is a major problem in paper mills processing paper and cardboard. This leads to the production of lower quality recycled products. Several studies have focused on the microbial content in the paper mill and the final products. Our aim was to determine the microbial biota in a bale of collected cardboard prior to entering the paper mill. Total genomic DNA was isolated and analyzed using two different methods for comparison purposes: 454 pyrosequencing and clone library. A total of 3268 V6-V8 454 pyrosequencing reads and 322 cloned V6-V8 16S rRNA nucleotide sequences were obtained. Both methods showed the presence of three major bacterial genera: Bacillus, Solibacillus and Paenibacillus, all members of the spore-forming phylum Firmicutes. Pyrosequencing, however, revealed a richer and more diverse bacterial community than clone library. It showed the presence of additional minor Firmicute genera and of a small number of Proteobacteria. The sorting at the recycling plant, the storing, and the processing at the paper mill, the end uses, will all contribute to the bacterial microbiota present in a bale of collected cardboard as revealed here.展开更多
Based on the 454 pyrosequencing approach, this research evaluated the influence of coal mining subsi- dence on soil bacterial diversity and community structure in Chinese mining area. In order to characterize the bact...Based on the 454 pyrosequencing approach, this research evaluated the influence of coal mining subsi- dence on soil bacterial diversity and community structure in Chinese mining area. In order to characterize the bacterial community comparatively, this study selected a field experiment site with coal-excavated subsidence soils and an adjacent site with non-disturbed agricultural soils, respectively. The dataset com- prises 24512 sequences that are affiliated to the 7 phylogenetic groups： proteobacteria, actinobacteria, bacteroidetes, gemmatimonadetes, chlorofiexi, nitrospirae and unclassified phylum. Proteobacteria is the largest bacterial phylum in all samples, with a marked shift of the proportions of alpha-, beta-, and gammaproteobacteria. The results show that undisturbed soils are relatively more diverse and rich than subsided soils, and differences in abundances of dominant taxonomic groups between the two soil groups are visible. Compared with the control, soil nutrient contents decline achieves significant level in subsided soils. Correlational analysis showed bacterial diversity indices have significantly positive corre- lation with soil organic matter, total N, total P, and available K. but in negative relation with soil salinity. Ground subsidence noticeably affects the diversity and composition of soil microbial community. Degen- eration of soil fertility and soil salinization inhibits the sole-carbon-source metabolic ability of microbial community, leading to the simplification of advantage species and uneven distribution of microbial spe- cies. This work demonstrates the great potential of pyrosequencing technique in revealing microbial diversity and presents background information of microbial communities of mine subsidence land.展开更多
目的阐明非酒精性脂肪性肝病（NAFLD）患者肠道菌群结构特征。方法采用454焦磷酸测序技术,对47例经＂肝活检＂确诊的NAFLD患者和34例健康人新鲜粪便样品16S DNA V3-V5可变区进行测序,通过序列比较及操作分类单元（OTU）划分评价肠道菌...目的阐明非酒精性脂肪性肝病（NAFLD）患者肠道菌群结构特征。方法采用454焦磷酸测序技术,对47例经＂肝活检＂确诊的NAFLD患者和34例健康人新鲜粪便样品16S DNA V3-V5可变区进行测序,通过序列比较及操作分类单元（OTU）划分评价肠道菌群结构差异。结果 NAFLD患者OTUs为（88.32±28.27）,显著低于健康人[（109.65±30.65）,P〈0.01];在＂门＂水平,NAFLD患者厚壁菌门所占比例为（51.2±17.8）%,显著高于健康人的[（46.4±12.8）%,P=0.048],而拟杆菌门为（31.6±18.9）%,显著低于健康人的[（43.3±14.4）%,P〈0.001];在＂纲＂水平上,NAFLD组Erysipelotrichi纲占（3.2±5.1）%,显著高于健康人的[（1.0±1.2）%,P=0.009],而Bacteroidia纲占（31.0±18.8）%,显著低于对照组的[（42.3±14.0）%,P=0.004];在＂属＂水平上,NAFLD组乳球菌占（0.0038±0.0001）%,低于健康组的[（0.0145±0.001）%,P=0.003],普氏菌属也同样显著减少（P=0.022）,而链球菌（Streptococcus）在NAFLD占（1.50±0.03）%,显著高于对照组的[（0.21±0.24）%,P=0.004]。结论 NAFLD患者肠道菌群多样性减少,存在构成显著异常,是致病因素抑或其后果仍有待于进一步研究。展开更多
The kelp grouper (Epinephelus bruneus), belonging to one of the largest genera among the subfamily Epinephelinae, is a commercially important fish in Japan. There are limited data about the genomics of this species. T...The kelp grouper (Epinephelus bruneus), belonging to one of the largest genera among the subfamily Epinephelinae, is a commercially important fish in Japan. There are limited data about the genomics of this species. To provide tools for addressing both population genetics studies and gene mapping, dito pentanucleotide simple sequence repeat (SSR) markers were developed using 454 pyrosequencing. Among the 1466 SSR markers developed, 1244 primer sets produced strong PCR products, of which 905 (72.7%) were polymorphic in kelp grouper. Cross-species utility of the 905 polymorphic SSR markers was tested in four additional Epinephelinae species of Hyporthodus septemfasciatus, Plectropomus leopardus, Epinephelus lanceolatus and Epinephelus coioides. Results revealed that, respectively, 401 (44.3%), 136 (15.0%), 434 (49.0%) and 538 (59.4%) SSRs showed specific polymorphic products. Of these, 40 SSR markers (33 di-, 1 tri- and 6 tetra-nucleotides) showed polymorphism in all species tested. Additionally, three AGAT SSR motifs which accounted for 42.9% of the nondi-nucleotide markers were found in the 40 SSR markers. This indicates that the AGAT SSR motif has a high potential as a highly versatile SSR marker in grouper Epinephelinae. The SSR markers developed in this study can be employed to obtain reliable genetic variability estimates for groupers (Epinephelinae).展开更多
2-Phase anaerobic digestion（AD）, where the acidogenic phase was operated at 2 day hydraulic retention time（HRT） and the methanogenic phase at 10 days HRT, had been evaluated to determine if it could provide higher...2-Phase anaerobic digestion（AD）, where the acidogenic phase was operated at 2 day hydraulic retention time（HRT） and the methanogenic phase at 10 days HRT, had been evaluated to determine if it could provide higher organic reduction and methane production than the conventional single-stage AD（also operated at 12 days HRT）. 454 pyrosequencing was performed to determine and compare the microbial communities. The acidogenic reactor of the 2-phase system yielded a unique bacterial community of the lowest richness and diversity, while bacterial profiles of the methanogenic reactor closely followed the single-stage reactor. All reactors were predominated by hydrogenotrophic methanogens, mainly Methanolinea. Unusually, the acidogenic reactor contributed up to 24%of total methane production in the 2-phase system. This could be explained by the presence of Methanosarcina and Methanobrevibacter, and their activities could also help regulate reactor alkalinity during high loading conditions through carbon dioxide production. The enrichment of hydrolytic and acidogenic Porphyromonadaceae, Prevotellaceae, Ruminococcaceae and unclassified Bacteroidetes in the acidogenic reactor would have contributed to the improved sludge volatile solids degradation, and ultimately the overall 2-phase system＇s performance. Syntrophic acetogenic microorganisms were absent in the acidogenic reactor but present in the downstream methanogenic reactor, indicating the retention of various metabolic pathways also found in a single-stage system. The determination of key microorganisms further expands our understanding of the complex biological functions in AD process.展开更多
基金Supported by the Special Fund for Agro-scientific Research in the Public Interest(201303048)the National Natural Science Foundation of China(Nos.41176117,31172447)the National Infrastructure of Fishery Germplasm Resources
文摘Sebastiscus marmoratus is an important sedentary ovoviparous fish distributed in near-shore coastal waters from the coast of China to Japan. Candidate S. marmoratus microsatellite markers were developed in the present study using 454 pyrosequencing, and the marker profile was analyzed. A total of 2 000 000 raw sequence reads were assembled to reduce redundancy. Among them, 1 043 dinucleotide, 925 trinucleotide, 692 tetranucleotide, and 315 pentanucleotide repeats were detected. AC repeats were the most frequent motifs among the dinucleotide repeats, and AAT was the most abundant among the trinucleotide repeats. AAAT, ATAG, and ATCC were the three most common tetranucleotide motifs, and AAGAT and AATAT were the most dominant pentanucleotide motifs. The greatest numbers of loci and potentially amplifiable loci were found in dinucleotide repeats, whereas trinucleotide repeats had the fewest. In summary, a wide range of candidate microsatellite markers were identified in the present study using a rapid and efficient 454 pyrosequencing approach.
基金supported in part by the Natural Sciences and Engineering Research Council of Canada(grant EGP 436904-12).
文摘Biofouling, the accumulation of microorganisms, is a major problem in paper mills processing paper and cardboard. This leads to the production of lower quality recycled products. Several studies have focused on the microbial content in the paper mill and the final products. Our aim was to determine the microbial biota in a bale of collected cardboard prior to entering the paper mill. Total genomic DNA was isolated and analyzed using two different methods for comparison purposes: 454 pyrosequencing and clone library. A total of 3268 V6-V8 454 pyrosequencing reads and 322 cloned V6-V8 16S rRNA nucleotide sequences were obtained. Both methods showed the presence of three major bacterial genera: Bacillus, Solibacillus and Paenibacillus, all members of the spore-forming phylum Firmicutes. Pyrosequencing, however, revealed a richer and more diverse bacterial community than clone library. It showed the presence of additional minor Firmicute genera and of a small number of Proteobacteria. The sorting at the recycling plant, the storing, and the processing at the paper mill, the end uses, will all contribute to the bacterial microbiota present in a bale of collected cardboard as revealed here.
基金supported by the National Natural Science Foundation of China (No. 51174207)Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions of China (No. SZBF20116B35)
文摘Based on the 454 pyrosequencing approach, this research evaluated the influence of coal mining subsi- dence on soil bacterial diversity and community structure in Chinese mining area. In order to characterize the bacterial community comparatively, this study selected a field experiment site with coal-excavated subsidence soils and an adjacent site with non-disturbed agricultural soils, respectively. The dataset com- prises 24512 sequences that are affiliated to the 7 phylogenetic groups： proteobacteria, actinobacteria, bacteroidetes, gemmatimonadetes, chlorofiexi, nitrospirae and unclassified phylum. Proteobacteria is the largest bacterial phylum in all samples, with a marked shift of the proportions of alpha-, beta-, and gammaproteobacteria. The results show that undisturbed soils are relatively more diverse and rich than subsided soils, and differences in abundances of dominant taxonomic groups between the two soil groups are visible. Compared with the control, soil nutrient contents decline achieves significant level in subsided soils. Correlational analysis showed bacterial diversity indices have significantly positive corre- lation with soil organic matter, total N, total P, and available K. but in negative relation with soil salinity. Ground subsidence noticeably affects the diversity and composition of soil microbial community. Degen- eration of soil fertility and soil salinization inhibits the sole-carbon-source metabolic ability of microbial community, leading to the simplification of advantage species and uneven distribution of microbial spe- cies. This work demonstrates the great potential of pyrosequencing technique in revealing microbial diversity and presents background information of microbial communities of mine subsidence land.
文摘目的阐明非酒精性脂肪性肝病（NAFLD）患者肠道菌群结构特征。方法采用454焦磷酸测序技术,对47例经＂肝活检＂确诊的NAFLD患者和34例健康人新鲜粪便样品16S DNA V3-V5可变区进行测序,通过序列比较及操作分类单元（OTU）划分评价肠道菌群结构差异。结果 NAFLD患者OTUs为（88.32±28.27）,显著低于健康人[（109.65±30.65）,P〈0.01];在＂门＂水平,NAFLD患者厚壁菌门所占比例为（51.2±17.8）%,显著高于健康人的[（46.4±12.8）%,P=0.048],而拟杆菌门为（31.6±18.9）%,显著低于健康人的[（43.3±14.4）%,P〈0.001];在＂纲＂水平上,NAFLD组Erysipelotrichi纲占（3.2±5.1）%,显著高于健康人的[（1.0±1.2）%,P=0.009],而Bacteroidia纲占（31.0±18.8）%,显著低于对照组的[（42.3±14.0）%,P=0.004];在＂属＂水平上,NAFLD组乳球菌占（0.0038±0.0001）%,低于健康组的[（0.0145±0.001）%,P=0.003],普氏菌属也同样显著减少（P=0.022）,而链球菌（Streptococcus）在NAFLD占（1.50±0.03）%,显著高于对照组的[（0.21±0.24）%,P=0.004]。结论 NAFLD患者肠道菌群多样性减少,存在构成显著异常,是致病因素抑或其后果仍有待于进一步研究。
文摘The kelp grouper (Epinephelus bruneus), belonging to one of the largest genera among the subfamily Epinephelinae, is a commercially important fish in Japan. There are limited data about the genomics of this species. To provide tools for addressing both population genetics studies and gene mapping, dito pentanucleotide simple sequence repeat (SSR) markers were developed using 454 pyrosequencing. Among the 1466 SSR markers developed, 1244 primer sets produced strong PCR products, of which 905 (72.7%) were polymorphic in kelp grouper. Cross-species utility of the 905 polymorphic SSR markers was tested in four additional Epinephelinae species of Hyporthodus septemfasciatus, Plectropomus leopardus, Epinephelus lanceolatus and Epinephelus coioides. Results revealed that, respectively, 401 (44.3%), 136 (15.0%), 434 (49.0%) and 538 (59.4%) SSRs showed specific polymorphic products. Of these, 40 SSR markers (33 di-, 1 tri- and 6 tetra-nucleotides) showed polymorphism in all species tested. Additionally, three AGAT SSR motifs which accounted for 42.9% of the nondi-nucleotide markers were found in the 40 SSR markers. This indicates that the AGAT SSR motif has a high potential as a highly versatile SSR marker in grouper Epinephelinae. The SSR markers developed in this study can be employed to obtain reliable genetic variability estimates for groupers (Epinephelinae).
基金supported with funding from the National Research Foundation(NRF-CRP5-2009-02),Singapore for the project"Wastewater Treatment Plants as Urban Eco Power Stations"
文摘2-Phase anaerobic digestion（AD）, where the acidogenic phase was operated at 2 day hydraulic retention time（HRT） and the methanogenic phase at 10 days HRT, had been evaluated to determine if it could provide higher organic reduction and methane production than the conventional single-stage AD（also operated at 12 days HRT）. 454 pyrosequencing was performed to determine and compare the microbial communities. The acidogenic reactor of the 2-phase system yielded a unique bacterial community of the lowest richness and diversity, while bacterial profiles of the methanogenic reactor closely followed the single-stage reactor. All reactors were predominated by hydrogenotrophic methanogens, mainly Methanolinea. Unusually, the acidogenic reactor contributed up to 24%of total methane production in the 2-phase system. This could be explained by the presence of Methanosarcina and Methanobrevibacter, and their activities could also help regulate reactor alkalinity during high loading conditions through carbon dioxide production. The enrichment of hydrolytic and acidogenic Porphyromonadaceae, Prevotellaceae, Ruminococcaceae and unclassified Bacteroidetes in the acidogenic reactor would have contributed to the improved sludge volatile solids degradation, and ultimately the overall 2-phase system＇s performance. Syntrophic acetogenic microorganisms were absent in the acidogenic reactor but present in the downstream methanogenic reactor, indicating the retention of various metabolic pathways also found in a single-stage system. The determination of key microorganisms further expands our understanding of the complex biological functions in AD process.
