Leaves of terrestrial and aquatic plants are home to a wide diversity of bacterial species. However, the diversity and variability of epiphytic bacteria on their submerged plant hosts remains poorly understood. We inv...Leaves of terrestrial and aquatic plants are home to a wide diversity of bacterial species. However, the diversity and variability of epiphytic bacteria on their submerged plant hosts remains poorly understood. We investigated the diversity and composition of epiphytic bacteria from two common submerged macrophytes: Vallisneria natans and Hydrilla verticillata in Taihu Lake, Jiangsu, China, using methods of terminal restriction fragment length polymorphisms (T-RFLP) and clone library analyses targeted at bacterial 16S rRNA genes. The results show that: (1) the libraries of the two waterweeds contain wide phylogenetic distribution of bacteria, and that the sequences of the two libraries can be separated into 93 OTUs (at 97% similar value); (2) Betaproteobacteria, including Burkholderiales, was the most abundant bacterial group on both plants. Cyanobacteria and Gammaproteobacteria were the second largest groups on V. natans and H. verticillata, respectively. Both clone libraries included some sequences related to those of methanotrophs and nitrogen-fixing bacteria; (3) Cluster analysis of the T-RFLP profiles showed two distinct clusters corresponding to the two plant populations. Both ANOSIM of the T-RFLP data and Libshuff analysis of the two clone libraries indicated a significant difference in epiphytic bacterial communities between the two plants. Therefore, the epiphytic bacterial communities on submerged macrophytes appear to be diverse and host-specific, which may aid in understanding the ecological functions of submerged macrophytes in general.展开更多
The relaxation property of both Eigen model and Crow-Kimura model with a single peak fitness landscape is studied from phase transition point of view. We first analyze the eigenvalue spectra of the replication mutatio...The relaxation property of both Eigen model and Crow-Kimura model with a single peak fitness landscape is studied from phase transition point of view. We first analyze the eigenvalue spectra of the replication mutation matrices. For sufficiently long sequences, the almost crossing point between the largest and seeond-largest eigenvalues locates the error threshold at which critical slowing down behavior appears. We calculate the critical exponent in the limit of infinite sequence lengths and compare it with the result from numerical curve fittings at sufficiently long sequences. We find that for both models the relaxation time diverges with exponent 1 at the error （mutation） threshold point. Results obtained from both methods agree quite well. From the unlimited correlation length feature, the first order phase transition is further confirmed. Finally with linear stability theory, we show that the two model systems are stable for all ranges of mutation rate. The Igigen model is asymptotically stable in terms of mutant classes, and the Crow-Kimura model is completely stable.展开更多
Di-n-butyl phthalate (DBP),one of phthalate acid esters (PAEs),was investigated to determine its biodegradation rate using Xiangjiang River sediment and find potential DBP degraders in the enrichment culture of the se...Di-n-butyl phthalate (DBP),one of phthalate acid esters (PAEs),was investigated to determine its biodegradation rate using Xiangjiang River sediment and find potential DBP degraders in the enrichment culture of the sediment. The sediment sample was incubated with an initial concentration of DBP of 100 mg/L for 5 d. The biodegradation rate of DBP was detected using HPLC and the degraded products were analyzed by GC/MS. Subsequently,the microbial diversity of the enrichment culture was analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The results reveal that almost 100% of DBP is degraded after merely 3 d,generating two main degraded products:mono-butyl phthalate (MBP) and 9-octadecenoic acid. After a six-month enrichment period under the pressure of DBP,the dominant family in the final enrichment culture is clustered with the Comamonas sp.,the remaining are affiliated with Sphingomonas sp.,Hydrogenophaga sp.,Rhizobium sp.,and Acidovorax sp. The results show the potential of these bacteria to be used in the bioremediation of DBP in the environment.展开更多
Haliotis diversicolor Reeve is one of the most important mollusks cultured in South China. Preliminary genetic linkage maps were constructed with amplified fragment length polymorphism (AFLP) markers. A total of 2 596...Haliotis diversicolor Reeve is one of the most important mollusks cultured in South China. Preliminary genetic linkage maps were constructed with amplified fragment length polymorphism (AFLP) markers. A total of 2 596 AFLP markers were obtained from 28 primer combinations in two parents and 78 offsprings. Among them, 412 markers (15.9%) were polymorphic and segregated in the mapping family. Chi-square tests showed that 151 (84.4%) markers segregated according to the expected 1:1 Mendelian ratio (P<0.05) in the female parent, and 200 (85.8%) in the male parent. For the female map, 179 markers were used for linkage analysis and 90 markers were assigned to 17 linkage groups with an average interval length of 25.7 cm. For the male map, 233 markers were used and 94 were mapped into 18 linkage groups, with an average interval of 25.0 cm. The estimated genome length was 2 773.0 cm for the female and 2 817.1 cm for the male map. The observed length of the linkage map was 1 875.2 cm and 1 896.5 cm for the female and male maps, respectively. When doublets were considered, the map length increased to 2 152.8 cm for the female and 2 032.7 cm for the male map, corresponding to genome coverage of 77.6% and 72.2%, respectively.展开更多
基金Supported by the National Natural Science Foundation of China(No.40730528)the National Basic Research Program of China(973Program)(No.2008CB418104)+2 种基金the Knowledge Innovation Project of Chinese Academy of Sciences(No.KZCX2-YW-JC302)the Jiangsu Provincial Science Foundation(No.BK2009024)the Frontier Foundation of Nanjing Institute of Geography & Limnology,Chinese Academy of Sciences(No.09SL021001)
文摘Leaves of terrestrial and aquatic plants are home to a wide diversity of bacterial species. However, the diversity and variability of epiphytic bacteria on their submerged plant hosts remains poorly understood. We investigated the diversity and composition of epiphytic bacteria from two common submerged macrophytes: Vallisneria natans and Hydrilla verticillata in Taihu Lake, Jiangsu, China, using methods of terminal restriction fragment length polymorphisms (T-RFLP) and clone library analyses targeted at bacterial 16S rRNA genes. The results show that: (1) the libraries of the two waterweeds contain wide phylogenetic distribution of bacteria, and that the sequences of the two libraries can be separated into 93 OTUs (at 97% similar value); (2) Betaproteobacteria, including Burkholderiales, was the most abundant bacterial group on both plants. Cyanobacteria and Gammaproteobacteria were the second largest groups on V. natans and H. verticillata, respectively. Both clone libraries included some sequences related to those of methanotrophs and nitrogen-fixing bacteria; (3) Cluster analysis of the T-RFLP profiles showed two distinct clusters corresponding to the two plant populations. Both ANOSIM of the T-RFLP data and Libshuff analysis of the two clone libraries indicated a significant difference in epiphytic bacterial communities between the two plants. Therefore, the epiphytic bacterial communities on submerged macrophytes appear to be diverse and host-specific, which may aid in understanding the ecological functions of submerged macrophytes in general.
基金Supported in part by the National natural Science Foundation of China under Grant No.10675170Major State Basic Research Developing Program under Gant No.2007CB815003
文摘The relaxation property of both Eigen model and Crow-Kimura model with a single peak fitness landscape is studied from phase transition point of view. We first analyze the eigenvalue spectra of the replication mutation matrices. For sufficiently long sequences, the almost crossing point between the largest and seeond-largest eigenvalues locates the error threshold at which critical slowing down behavior appears. We calculate the critical exponent in the limit of infinite sequence lengths and compare it with the result from numerical curve fittings at sufficiently long sequences. We find that for both models the relaxation time diverges with exponent 1 at the error （mutation） threshold point. Results obtained from both methods agree quite well. From the unlimited correlation length feature, the first order phase transition is further confirmed. Finally with linear stability theory, we show that the two model systems are stable for all ranges of mutation rate. The Igigen model is asymptotically stable in terms of mutant classes, and the Crow-Kimura model is completely stable.
基金Project(50621063) supported by the National Nature Science Foundation of ChinaProject(NCET-06-0691) supported by the Program for New Century Excellent Talents in University
文摘Di-n-butyl phthalate (DBP),one of phthalate acid esters (PAEs),was investigated to determine its biodegradation rate using Xiangjiang River sediment and find potential DBP degraders in the enrichment culture of the sediment. The sediment sample was incubated with an initial concentration of DBP of 100 mg/L for 5 d. The biodegradation rate of DBP was detected using HPLC and the degraded products were analyzed by GC/MS. Subsequently,the microbial diversity of the enrichment culture was analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The results reveal that almost 100% of DBP is degraded after merely 3 d,generating two main degraded products:mono-butyl phthalate (MBP) and 9-octadecenoic acid. After a six-month enrichment period under the pressure of DBP,the dominant family in the final enrichment culture is clustered with the Comamonas sp.,the remaining are affiliated with Sphingomonas sp.,Hydrogenophaga sp.,Rhizobium sp.,and Acidovorax sp. The results show the potential of these bacteria to be used in the bioremediation of DBP in the environment.
基金Supported by the National Basic Research Program of China (973 Program) (Nos. 2010CB126405 and 2009CB126005)the Key Project for International Science and Technology Cooperation, Ministry of Science and Technology of China (No. 2004DFA07200)+2 种基金the Great Science and Technique Program of Hainan Province (No. 06120)the Hainan Key Laboratory of Tropical Hydrobiological Technology (No. shkyjj0810)supported by the Rutgers University
文摘Haliotis diversicolor Reeve is one of the most important mollusks cultured in South China. Preliminary genetic linkage maps were constructed with amplified fragment length polymorphism (AFLP) markers. A total of 2 596 AFLP markers were obtained from 28 primer combinations in two parents and 78 offsprings. Among them, 412 markers (15.9%) were polymorphic and segregated in the mapping family. Chi-square tests showed that 151 (84.4%) markers segregated according to the expected 1:1 Mendelian ratio (P<0.05) in the female parent, and 200 (85.8%) in the male parent. For the female map, 179 markers were used for linkage analysis and 90 markers were assigned to 17 linkage groups with an average interval length of 25.7 cm. For the male map, 233 markers were used and 94 were mapped into 18 linkage groups, with an average interval of 25.0 cm. The estimated genome length was 2 773.0 cm for the female and 2 817.1 cm for the male map. The observed length of the linkage map was 1 875.2 cm and 1 896.5 cm for the female and male maps, respectively. When doublets were considered, the map length increased to 2 152.8 cm for the female and 2 032.7 cm for the male map, corresponding to genome coverage of 77.6% and 72.2%, respectively.
