To explore the relationships between community composition and the environment in a reservoir ecosystem, plankton communities from the Three Gorges Reservoir Region were studied by PCR-denaturing gradient gel electrop...To explore the relationships between community composition and the environment in a reservoir ecosystem, plankton communities from the Three Gorges Reservoir Region were studied by PCR-denaturing gradient gel electrophoresis fingerprinting. Bacterial and eukaryotic operational taxonomic units （OTUs）, generated by DGGE analysis of the PCR-amplified 16S and 18S rRNA genes, were used as surrogates for the dominant ＂biodiversity units＂. OTU composition among the sites was heterogeneous; 46.7% of the total bacterial OTUs （45） and 64.1% of the eukaryotic OTUs （39） were identified in less than half of the sampling sites. Unweighted pair group method with arithmetic averages （UPGMA） clustering of the OTUs suggested that the plankton communities in the Xiangxi Rive sites were not always significantly different from those from the Yangtze River sites, despite clear differences in their environmental characterizations. Canonical correspondence analysis （CCA） was applied to further investigate the relationships between OTU composition and the environmental factors. The first two CCA ordination axes suggested that the bacterial community composition was primarily correlated with the variables of NO3^--N, dissolved oxygen （DO）, and SiO3^2--Si, whereas, the eukaryotic community was mainly correlated with the concentrations of DO, PO4^3--P, and SiO3^2--Si.展开更多
In order to investigate the correlation between reactor performance and the microorganisms,an integrated A/O reactor was operated for 72 days to treat diluted livestock wastewater.Chemical oxygen demand （COD） remova...In order to investigate the correlation between reactor performance and the microorganisms,an integrated A/O reactor was operated for 72 days to treat diluted livestock wastewater.Chemical oxygen demand （COD） removal efficiency increased from 79% to 94%,with total nitrogen （TN） removal efficiency from 37% to 50% （HRT 7.4 hr） when the influent COD and TN were ca.1500 mg/L and 95 mg/L,respectively,and the outlet COD concentration was less than 100 mg/L at the end.Microbial community was monitored during start-up period by denaturing gradient gel electrophoresis （DGGE） based on 16S rRNA gene.DGGE profiles showed that microbial community had changed significantly during the start-up and these shifts were in accordance with the reactor performance.UPGMA clustering analysis showed that 14 anaerobic samples fell into five main groups and so did the aerobic ones,but the grouping patterns were different.Phylogenetic analysis indicated that microbial populations in the anaerobic compartment belonged to Firmicutes,Proteobacteria,Chloroflexi and Bacteroidetes,while Proteobacteria,Bacteroidetes,Firmicutes,Verrucomicrobiae and Nitrospira were present in the aerobic compartment.In the anaerobic compartment,more fermentative and acetogenic bacteria were detected during the start-up while denitrifying bacteria faded away.Two functional populations such as Nitrospira defluvii and Dechloromonas denitrificans were observed when nitrogen removal was high,indicating that simultaneous nitrification and denitrification occurred in the aerobic compartment.展开更多
The intestinal bacteria of vertebrates form a close relationship with their host.External and internal conditions of the host,including its habitat,affect the intestinal bacterial community.Similarly,the intestinal ba...The intestinal bacteria of vertebrates form a close relationship with their host.External and internal conditions of the host,including its habitat,affect the intestinal bacterial community.Similarly,the intestinal bacterial community can,in turn,influence the host,particularly with respect to disease resistance.We compared the intestinal bacterial communities of grass carp that were collected from farm-ponds or a lake.We conducted denaturing gradient gel electrophoresis of amplified 16S rRNA genes,from which 66 different operational taxonomic units were identified.Using both the unweighted pair-group method with arithmetic means clustering and principal component analysis ordination,we found that the intestinal bacterial communities from the two groups of pond fish were clustered together and inset into the clusters of wild fish,except for DF-7,and there was no significant correlation between genetic diversity of grass carp and their intestinal bacterial communities(Mantel one-tailed test,R=0.157,P=0.175).Cetobacterium appeared more frequently in the intestine of grass carp collected from pond.A more thorough understanding of the role played by intestinal microbiota on fish health would be of considerable benefit to the aquaculture industry.展开更多
A lab-scale sequencing batch reactor （SBR） was set-up and the aerobic granular sludge was successfully incubated using anaerobic granular sludge as seed sludge. Nitrogen was partially removed by simultaneous nitrifi...A lab-scale sequencing batch reactor （SBR） was set-up and the aerobic granular sludge was successfully incubated using anaerobic granular sludge as seed sludge. Nitrogen was partially removed by simultaneous nitrification and denitrification （SND） via nitrite with free ammonia （FA） of about 10 mg/L. The denaturing gradient gel electrophoresis （DGGE） method was used to investigate community structure of α-Proteobacteria, β-Proteobacteria, ammonia oxidizing bacteria （AOB）, and Nitrospira populations during start-up. The population sizes of bacteria, AOB and Nitrospira were examined using real-time PCR method. The analysis of community structure and Shannon index showed that stable structure of AOB population was obtained at day 35, while the communities of α- Proteobacteria, β-Proteobacteria, and Nitrospira became stable after day 45. At stable stage, the average cell densities were 1.1× 10^12, 2.2×10^10 and 1.0×10^10 cells/L for bacteria, AOB and Nitrospira, respectively. The relationship between characteristics of nitrifying bacteria community and nitrogenous substrate utilization constant was discussed by calculating Pearson correlation. Certain correlation seemed to exist between population size, biodiversity, and degradation constant. And the influence of population size might be greater than that of biodiversity.展开更多
Soil microbial biomass and community structures are commonly used as indicators for soil quality and fertility. A investigation was performed to study the effects of long-term natural restoration, cropping, and bare f...Soil microbial biomass and community structures are commonly used as indicators for soil quality and fertility. A investigation was performed to study the effects of long-term natural restoration, cropping, and bare fallow managements on the soil microbial biomass and bacterial community structures in depths of 0-10, 20 30, and 40-50 cm in a black soil （Mollisol）. Microbial biomass was estimated from chloroform fumigation-extraction, and bacterial community structures were determined by analysis of 16S rDNA using polymerase chain reaction-denaturing gradient gel electrophoresis （PCR- DGGE）. Experimental results showed that microbial biomass significantly declined with soil depth in the managements of restoration and cropping, but not in the bare fallow. DGGE profiles indicated that the band number in top 0-10 cm soils was less than that in depth of 20-30 or 40-50 cm. These suggested that the microbial population was high but the bacterial community structure was simple in the topsoil. Cluster and principle component analysis based on DGGE banding patterns showed that the bacterial community structure was affected by soil depth more primarily than by managements, and the succession of bacterial community as increase of soil depth has a similar tendency in the three managements. Fourteen predominating DGGE bands were excised and sequenced, in which 6 bands were identified as the taxa of Verrueomicrobia, 2 bands as Actinobacteria, 2 bands as α-Proteobacteria, and the other 4 bands as 8-Proteobacteria, Aeidobacteria, Nitrospira, and unclassified bacteria. In addition, the sequences of 11 DGGE bands were closely related to uncultured bacteria. Thus, the bacterial community structure in black soil was stable, and the predominating bacterial groups were uncultured.展开更多
Fusarium wilt is one of the most serious diseases of banana plants caused by soil-borne pathogen Fusarium oxysporum f.sp. cubense(FOC). In this study a pot experiment was conducted to evaluate the effects of different...Fusarium wilt is one of the most serious diseases of banana plants caused by soil-borne pathogen Fusarium oxysporum f.sp. cubense(FOC). In this study a pot experiment was conducted to evaluate the effects of different bio-organic fertilizers(BIOs) on Fusarium wilt of banana, including the investigations of disease incidence, chitinase and β-1,3-glucanase activities of banana plants, and FOC populations as well as soil rhizosphere microbial community. Five fertilization treatments were considered, including chemical fertilizer containing the same N, P and K concentrations as the BIO(control), and matured compost mixed with antagonists Paenibacillus polymyxa SQR-21 and Trichoderma harzianum T37(BIO1), Bacillus amyloliquefaciens N6(BIO2), Bacillus subtilis N11(BIO3), and the combination of N6 and N11(BIO4). The results indicated that the application of BIOs significantly decreased the incidence rate of Fusarium wilt by up to 80% compared with the control. BIOs also significantly promoted plant growth, and increased chitinase andβ-1,3-glucanase activities by 55%–65% and 17.3%–120.1%, respectively, in the banana roots. The population of FOC in the rhizosphere soil was decreased significantly to about 104 colony forming units g-1with treatment of BIOs. Serial dilution plating and denaturing gradient gel electrophoresis analysis revealed that the application of BIOs increased the densities of bacteria and actinomycetes but decreased the number of fungi in the rhizosphere soil. In general, the application of BIOs revealed a great potential for the control of Fusarium wilt disease of banana plants.展开更多
Interactions between bacteria and cyanobacteria have been suggested to have a potential to influence harmful algal bloom dynamics; however, little information on these interactions has been reported. In this study, th...Interactions between bacteria and cyanobacteria have been suggested to have a potential to influence harmful algal bloom dynamics; however, little information on these interactions has been reported. In this study, the bacterial communities associated with five strains of Microcystis aeruginosa, three species of other Microcystis spp., and four representative species of non-Microcystis cyanobacteria were compared. Bacterial 16S rDNA fragments were amplified and separated by denaturing gradient gel electrophoresis （DGGE） followed by DNA sequence analysis. The similarities among bacterial communities associated with these cyanobacteria were compared to the digitized DGGE profiles using the cluster analyses. The bacterial community structure of all cyanobacterial cultures differed. Cluster analysis showed that the similarity values among M. aeruginosa cultures were higher than those of other cyanobacterial cultures. Sequence analysis of DGGE fragments indicated the presence of bacteria including, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria in the cyanobacterial cultures. Members of the Sphingomonadales were the prevalent group among the Microcystis-associated bacteria. The results provided further evidence for species-specific associations between cyanoabcteria and heterotrophic bacteria, which are useful for understanding interactions between Microcystis and their associated bacteria.展开更多
This study investigated the effect of dietary supplementation of yeast nucleotides on the growth, nonspecific immunity, intestine growth and intestinal microbiota of juvenile hybrid tilapia. Tilapia(initial average we...This study investigated the effect of dietary supplementation of yeast nucleotides on the growth, nonspecific immunity, intestine growth and intestinal microbiota of juvenile hybrid tilapia. Tilapia(initial average weight of 8.02 g) was fed test diets supplemented with a yeast-originated nucleotide mixture(0,0.15, 0.30, 0.60, and 1.20 g/100 g diet) for 8 weeks. Fish fed the diet with 0.60% nucleotide had significantly higher weight gain than the control group(P < 0.05). Feed efficiency was improved in the fish fed 0.60 and 1.20% nucleotide compared with that in the control group. The optimal doses of nucleotides supplementation for growth and feed efficiency of fish were determined as 0.63 and 0.81%, respectively.Intestinal growth was improved in the 0.30 and 0.60% groups, as indicated by significant increase in intestine length. The fish fed 0.60 and 1.20% nucleotide showed higher super oxide dismutase(SOD)activity and lower malondialdehyde(MDA) level in the liver than the control fish, indicating enhancement of the anti-oxidant status. Serum lysozyme activity was significantly increased in the 0.15 and 0.3%nucleotide supplementation groups, suggesting an enhancement effect on the non-specific immune response. Lastly, dietary nucleotides supplementation exerted moderate influence on the intestinal microbiota of hybrid tilapia. A reduction in the cumulative abundance of putative butyrate-producing species was observed in the intestinal microbiota of fish fed diets with 0.60% nucleotide compared with the control, implying an interaction between dietary nucleotides and butyrate production. Briefly, dietary supplementation with 0.60% nucleotide improve the growth performance, immune activity and intestine growth in tilapia.展开更多
Methamidophos was widely used a pesticide in northern China. The potential influences of methamidophos on soil fungal community in black soil were assessed by plate count, 28S rDNA-PCR-DGGE, and clone library analysis...Methamidophos was widely used a pesticide in northern China. The potential influences of methamidophos on soil fungal community in black soil were assessed by plate count, 28S rDNA-PCR-DGGE, and clone library analysis. Three methamidophos levels （50, 150, and 250 mg/kg） were tested in soil microcosms. Results from plate count during a 60-d microcosm experiment showed that high concentrations of methamidophos （250 mg/kg） could significantly stimulate fungal populations. DGGE （denaturing gradient gel electrophoresis） fingerprinting patterns showed a significant difference between the responses of culturable and total fungi communities under the stress of methamidophos. Shannon diversity indices calculated from DGGE profiles indicated that culturable fungi in all microcosms with methamidophos treatment increased after 1 week of incubation. However, the diversity indices of total fungi decreased in the first week, as compared to the stimulation of culturable fungi. At the 8th week, however, all the microcosms treated by methamidophos were similar to the control microcosms in community structure as suggested by the Shannon diversity indices for both culturable and total fungi. In contrast, after 1 week the fungal structure of culturable and unculturable both were disturbed to different extent under the stresses of methamidophos by clustering analysis. Clone sequencing analysis indicated the stimulation of pathogenic and unculturable fungal populations by methamidophos treatment, suggetsing potential risks of plant disease outbreak.展开更多
Objective To analyze the structure of bacteria in drinking water by molecular biological techniques, Methods DNA of bacteria in drinking water was directly extracted without culture. 16S ribosomal DNA fragments, inclu...Objective To analyze the structure of bacteria in drinking water by molecular biological techniques, Methods DNA of bacteria in drinking water was directly extracted without culture. 16S ribosomal DNA fragments, including V-6, -7, and -8 regions, were amplified with universal primers （EUBf933CJC and EUBr1387） and analyzed by DGGE. Results DGGE indicated that amplification products could be separated, The results showed that DGGE could be used in the separation of different microbial 16SrRNA genes extracted from drinkng water. Though there were special bacteria in different water samples, the predominant bacteria were essentially the same. Three sequences of the reclaimed specific bands were obtained, and phylogenetic tree of these bands was made. Conclusion Bacterial diversity in drinking water is identified by molecular biological techniques.展开更多
The bacterial strain Paracoccus denitrificans W12, which could utilize pyridine as its sole source of carbon and nitrogen, was added into a membrane bioreactor （MBR） to enhance the treatment of a pharmaceutical wast...The bacterial strain Paracoccus denitrificans W12, which could utilize pyridine as its sole source of carbon and nitrogen, was added into a membrane bioreactor （MBR） to enhance the treatment of a pharmaceutical wastewater. The treatment efliciencies investigated showed that the removal of chemical oxygen demand, total nitrogen, and total phosphorus were similar between bioaugmented and non-bioaugmented MBRs, however, significant removal of pyridine was obtained in the bioaugmented reactor. When the hydraulic retention time was 60 hr and the influent concentration of pyridine was 250-500 mg/L, the mean effluent concentration of pyridine without adding W12 was 57.2 mg/L, while the pyridine was degraded to an average of 10.2 mg/L with addition of W12. The bacterial community structure of activated sludge during the bioaugmented treatment was analyzed using polymerase chain reaction-denaturing gradient gel electrophoresis （PCR-DGGE）. The results showed that the W12 inoculum reversed the decline of microbial community diversity, however, the similarity between bacterial community structure of the original sludge and that of the sludge after bioaugmentation decreased steadily during the wastewater treatment. Sequencing of the DNA recovered from DGGE gel indicated that sp., Sphingobium sp., Comamonas sp., and Hyphomicrobium sp. were the dominant organisms in time sequence in the bacterial community in the bioaugmented MBR. This implied that the bioaugmentation was affected by the adjustment of whole bacterial community structure in the inhospitable environment, rather than being due solely to the degradation performance of the bacterium added.展开更多
This study evaluated the microbial community dynamics and maturation time of two compost systems： biogas slurry compost and cow manure compost, with the aim of evaluating the potential utility of a biogas slurry comp...This study evaluated the microbial community dynamics and maturation time of two compost systems： biogas slurry compost and cow manure compost, with the aim of evaluating the potential utility of a biogas slurry compost system. Denaturing gradient gel electrophoresis （DGGE）, gene clone library, temperature, C/N ratio, and the germination index were employed for the investigation, cow manure compost was used as the control. Results showed that the basic strip and dominant strips of the DGGE bands for biogas slurry compost were similar to those of cow manure compost, but the brightness of the respective strips for each system were different. Shannon-Weaver indices of the two compost systems differed, possessing only 22% similarity in the primary and maturity stages of the compost process. Using bacterial 16S rRNA gene clone library analysis, 88 bacterial clones were detected. Further, 18 and 13 operational taxonomic units （OTUs） were present in biogas slurry and cow manure compost, respectively. The 18 OTUs of the biogas slurry compost belonged to nine bacterial genera, of which the dominant strains were Bacillus sp. and Carnobacterium sp.; the 13 OTUs of the cow manure compost belonged to eight bacterial genera, of which the dominant strains were Psychrobacter sp., Pseudomonas sp., and Clostridium sp. Results demonstrated that the duration of the thermophilic phase （more than 50°C） for biogas slurry compost was 8 d less than the according duration for cow manure compost, and the maturation times for biogas slurry and cow manure compost were 45 and 60 d, respectively. It is an effective biogas slurry assimilate technology by application of biogas slurry as nitrogen additives in the manufacture of organic fertilizer.展开更多
Vertical diversity of sediment bacterial communities in 2 different trophic states （macrophyte-dominated and algae-dominated） of the large shallow eutrophic Lake Taihu, China, were investigated using denaturing grad...Vertical diversity of sediment bacterial communities in 2 different trophic states （macrophyte-dominated and algae-dominated） of the large shallow eutrophic Lake Taihu, China, were investigated using denaturing gradient gel electropfioresis （DGGE） and 16S rRNA sequence analysis. Clustering analysis of DGGE profiles showed that different clusters were recognized in different depths of sediment cores in the 2 lake trophic states. Analyses of the bacterial diversity, as estimated by the Shannon index （H＇）, showed that different sediment layers of the macrophyte-dominated state had higher diversity than the algae-dominated state. In addition, bacterial diversity of the sediment in the macrophyte-dominated state changed abruptly throughout the layers, but bacterial diversity of the algae-dominated state decreased gradually with sediment depth. Phylogenetic analysis showed that Proteobacteria was the most abundant phylum in the middle sediment of the 2 lake trophic states. In the macrophyte-dominated state, clone sequences related to Betaproteobacteria （50.0%） were the most abundant, followed by Epsilonproteobacteria （21.1%）, Acidobacteria （7.9%）, Deltaproteobacteria （7.9%）, Chloroflexi （7.9%）, and Bacteroidetes （5.3%）; whereas in the algae-dominated state, sequences affiliated with Betaproteobacteria （84.4%） were predominant, followed by Deltaproteobacteria （12.5%） and Acidobacteria （3.1%）. Canonical correspondence analysis showed that organic matter and pH play key roles in driving the vertical changes of bacterial community composition.展开更多
Zoige wetland is one of the most important methane emission centers in China. The oxidation of methane in the wetland affects global warming, soil ecology and atmospheric chemistry. Despite their global significance, ...Zoige wetland is one of the most important methane emission centers in China. The oxidation of methane in the wetland affects global warming, soil ecology and atmospheric chemistry. Despite their global significance, microorganisms that consume methane in Zoige wetland remain poorly characterized. In this study, we investigated methanotrophs diversity in soil samples from both anaerobic site and aerobic site in Zoige wetland using pmoA gene as a molecular marker. The cloning library was constructed according to the pmoA sequences detected. Four clusters of methanotrophs were detected. The phylogenetic tree showed that all four clusters detected were affiliated to type I methanotrophs. Two novel clusters （cluster 1, cluster 2） were found to relate to none of the recognized genera of methanotrophs. These clusters have no cultured representatives and reveal an ecological adaptation of particular uncultured methanotrophs in Zoige wetland. Two clusters were belonging to Methylobacter and Methylococcus separately. Denaturing gradient gel electrophoresis gel bands pattern retrieved from these two samples revealed that the community compositions of anaerobic soil and aerobic soil were different from each other while anaerobic soil showed a higher metanotrophs diversity. Real-time PCR assays of the two samples demonstrated that aerobic soil sample in Zoige wetland was 1.5 times as much copy numbers as anaerobic soil. These data illustrated that methanotrophs are a group of microorganisms influence the methane consumption in Zoige wetland.展开更多
The expressed prostatic secretions （EPSs） of men with chronic prostatitis/chronic pelvic pain syndrome （CP/CPPS）, infertile men and normal men were subjected to microbiological study. EPSs were collected from the ...The expressed prostatic secretions （EPSs） of men with chronic prostatitis/chronic pelvic pain syndrome （CP/CPPS）, infertile men and normal men were subjected to microbiological study. EPSs were collected from the subjects, which included 26 normal men, 11 infertile patients and 51 CP/CPPS patients. DNA was extracted from each specimen, and the V3 regions of the 16S rRNA genes were amplified using universal bacterial primers. The results showed that the EPS 16S rRNA gene-positive rate in the CP/CPPS and infertile patients was much higher than in the normal men, but without any difference among the three patient groups. The denaturing gradient gel electrophoresis （DGGE） method was used to characterize the EPS bacterial community structure of the prostate fluid from patients with CP/CPPS or infertility issues. Principal component analysis （PCA） and partial least squares （PLS） analyses of PCR-DGGE profiles revealed that the EPS bacterial community structure differed among the three groups. Three bands were identified as the key factors responsible for the discrepancy between CP/CPPS patients and infertile patients （P〈O.05）. Two bands were identified as priority factors in the discrepancy of category IliA and category IIIB prostatitis patients （P〈O.05）. According to this research, the ecological balance of the prostate and low urethra tract, when considered as a microenvironment, might play an important role in the maintenance of a healthy male reproductive tract.展开更多
Objective It aims to investigate the changes in composition and structure of bacterial communities de-veloping on biological activated carbon （BAC） particles, and the bacterial functions. Method A pilot plant had be...Objective It aims to investigate the changes in composition and structure of bacterial communities de-veloping on biological activated carbon （BAC） particles, and the bacterial functions. Method A pilot plant had been in service for 180 days, aiming to develop bacterial communities on acti-vated carbon naturally. After 180 days of operation, the bacterial communities were determined by dena-turing gradient gel electrophoresis （DGGE） analyses of PCR-amplified 16S rRNA genes. The study on community composition and the phylogenetic relationships of the organisms was complemented by a se-quence analysis of cloned PCR products from 16S rRNA genes. Gas chromatorgaphy-mass （GC-MS） mea-surement was used to determine organic chemical composition of inflow and outflow water on the 300th day. TOC and NH 4 ＋ -N were also tested in this experiment. Results It showed that the stable bacterial structure did not develop on BAC particles until the 9th month during running time of the BAC filter. The communities were finally dominated by Pseudomonas sp., Ba-cillus sp., Nitrospira sp., and an uncultured bacterium. Stable bacterial communities played an important role in removal of NH 4 ＋ -N and total organic carbon （TOC）. Results from gas chromatorgaphy-mass （GC-MS） showed that 36 kinds of chemicals in feed water were eliminated, and concentrations of 5 kinds of chemicals decreased. These chemicals served as nutrients for the dominant bacteria. Conclusion The findings from the study suggested that the stability of microbial structure was beneficial for improving NH 4 ＋ -N and TOC removal efficiencies. The dominant bacteria had the advantage of biode-grading a wide range of organic chemicals and NH 4 ＋ -N.展开更多
The insulin-like growth factor binding protein-3 （IGFBP-3） was known as a key factor that regulates the effect of insulin- like growth factors （IGF-1 and IGF-2） on pig growth and development. We first identified 3...The insulin-like growth factor binding protein-3 （IGFBP-3） was known as a key factor that regulates the effect of insulin- like growth factors （IGF-1 and IGF-2） on pig growth and development. We first identified 38 single nucleotide polymorphisms （SNPs） from a fragment of the IGFBP-3 gene spanning 1 823 bp using the denaturing high-performance liquid chromatography （DHPLC） method and confirmed them by direct sequencing. Among these SNPs, 36 located in introns and the remaining 2 in the 3 prime untranslated region （3UTR）. In addition, 16 PCR-RFLP polymorphisms were identified within these SNPs. Three SNPs were then selected to genotype 272 F2 individuals with PCR-RFLP method and the association of polymorphism with growth and carcass traits were analyzed. The results showed that no significant associations were observed between polymorphisms of A265G and A952G and traits. However, the A2670G significantly related with live body length, loin muscle area, and skin and fat percentage （P〈0.05）; highly significantly associated with weight of carcass lean and lean percentage （P〈 0.01）.展开更多
Molecular diversity and development of the Lactobacillus community in the intestinal tract, as influenced by age and intestinal compartment, were studied in one litter of 12 conventionally raised piglets. Piglets were...Molecular diversity and development of the Lactobacillus community in the intestinal tract, as influenced by age and intestinal compartment, were studied in one litter of 12 conventionally raised piglets. Piglets were euthanized at each week （3 animals per time）. Digesta and tissue samples from stomach, duodenum, jejunum, ileum, caecum, colon, and rectum were collected and analysed by using 16S ribosomal RNA-based methods. DGGE （denaturing gradient gel electrophoresis） profiles revealed that the Lactobacillus communities throughout the GI tract from duodenum to rectum showed good stability at same age. This indicates that fecal Lactobacillus communities can effectively represent the intestinal community. Two dominant bands were found in tissue samples of the small intestine, suggesting that the lactobacilli can adhere to the small intestinal wall. The Lactobacillus communities in different GI tract compartments developed over time. A successional change of Lactobacillus communities was observed from birth, through creep feeding to one week after weaning, showing a trend from simple to complex and back to simple. Furthermore, a clone library of Lactobacillus spp. 16S rRNA gene sequences were generated from jejunal and colonic chymes. Six dominant DGGE bands generated from jejunal chymes were matched with sequences that show 94-98% similarity to the bands derived from L. reuteri, L. delbrueckii, and L. crispatus. Seven dominant DGGE bands generated from colon chymes were matched with sequences that show 88-99% similarity to those derived from L. reuteri, L. delbrueckii, L. amylovorus/L. sobrius, and L. acidophilus. Amplicons related to L. reuteri were found in all DGGE fingerprints from jejunal digesta of age of weeks 1, 3, and 4. Amplicons related to L. amylovorus/L. sobrius were present in all DGGE fingerprints from colonic digesta of age of week 1, 3, and 4. Amplicons related to L. delbrueckii were found before weaning, L. crispatus after creep feeding before weaning and L. acidophilus after weaning. Thi展开更多
Taking two important agricultural soils with different pH, brown soil （Hap-Udic Luvisol） and cinnamon soil （Hap-Ustic Luvisol）, from Northeast China, a pot culture experiment with spring maize （Zea mays L.） was ...Taking two important agricultural soils with different pH, brown soil （Hap-Udic Luvisol） and cinnamon soil （Hap-Ustic Luvisol）, from Northeast China, a pot culture experiment with spring maize （Zea mays L.） was conducted to study the dynamic changes in the abundance and diversity of soil ammonia-oxidizing bacteria （AOB） and ammonia-oxidizing archaea （AOA） populations during maize growth period in response to the additions of nitrification inhibitors dicyandiamide （DCD） and 3,4-dimethylpyrazole phosphate （DMPP） by the methods of real-time polymerase chain reaction （PCR） assay, PCR-denaturing gradient gel electrophoresis （DGGE）, and construction of clone library targeting the amoA gene. Four treatments were established, i.e., no urea （control）, urea, urea plus DCD, and urea plus DMPP. Both DCD and DMPP inhibited growth of AOB significantly, compared to applying urea alone. Soil bacterial amoA gene copies had a significant positive linear correlation with soil nitrate content, but soil archaeal amoA gene copies did not. In both soils, all AOB sequences fell within Nitrosospira or Nitrosospira-like groups, and all AOA sequences belonged to group 1.1b crenaxchaea. With the application of DCD or DMPP, community composition of AOB and AOA in the two soils had less change except that the AOB community composition in Hap-Udic Luvisol changed at the last two growth stages of maize under the application of DCD. AOB rather than AOA likely dominated soil ammonia oxidation in these two agricultural soils.展开更多
基金This work was supported by the National Natural Science Foundation of China(No.30490232,30570240)the Major State Basic Research Development Program of China(No.2002CB412308).
文摘To explore the relationships between community composition and the environment in a reservoir ecosystem, plankton communities from the Three Gorges Reservoir Region were studied by PCR-denaturing gradient gel electrophoresis fingerprinting. Bacterial and eukaryotic operational taxonomic units （OTUs）, generated by DGGE analysis of the PCR-amplified 16S and 18S rRNA genes, were used as surrogates for the dominant ＂biodiversity units＂. OTU composition among the sites was heterogeneous; 46.7% of the total bacterial OTUs （45） and 64.1% of the eukaryotic OTUs （39） were identified in less than half of the sampling sites. Unweighted pair group method with arithmetic averages （UPGMA） clustering of the OTUs suggested that the plankton communities in the Xiangxi Rive sites were not always significantly different from those from the Yangtze River sites, despite clear differences in their environmental characterizations. Canonical correspondence analysis （CCA） was applied to further investigate the relationships between OTU composition and the environmental factors. The first two CCA ordination axes suggested that the bacterial community composition was primarily correlated with the variables of NO3^--N, dissolved oxygen （DO）, and SiO3^2--Si, whereas, the eukaryotic community was mainly correlated with the concentrations of DO, PO4^3--P, and SiO3^2--Si.
基金supported by the National Postdoctoral Fundation of China (No. 20070410881)the National Natural Science Fundation of China (No. 50878063)the National Natural Science Key Fundation of China (No.50638020)
文摘In order to investigate the correlation between reactor performance and the microorganisms,an integrated A/O reactor was operated for 72 days to treat diluted livestock wastewater.Chemical oxygen demand （COD） removal efficiency increased from 79% to 94%,with total nitrogen （TN） removal efficiency from 37% to 50% （HRT 7.4 hr） when the influent COD and TN were ca.1500 mg/L and 95 mg/L,respectively,and the outlet COD concentration was less than 100 mg/L at the end.Microbial community was monitored during start-up period by denaturing gradient gel electrophoresis （DGGE） based on 16S rRNA gene.DGGE profiles showed that microbial community had changed significantly during the start-up and these shifts were in accordance with the reactor performance.UPGMA clustering analysis showed that 14 anaerobic samples fell into five main groups and so did the aerobic ones,but the grouping patterns were different.Phylogenetic analysis indicated that microbial populations in the anaerobic compartment belonged to Firmicutes,Proteobacteria,Chloroflexi and Bacteroidetes,while Proteobacteria,Bacteroidetes,Firmicutes,Verrucomicrobiae and Nitrospira were present in the aerobic compartment.In the anaerobic compartment,more fermentative and acetogenic bacteria were detected during the start-up while denitrifying bacteria faded away.Two functional populations such as Nitrospira defluvii and Dechloromonas denitrificans were observed when nitrogen removal was high,indicating that simultaneous nitrification and denitrification occurred in the aerobic compartment.
基金Supported by the National Basic Research Program of China(973 Program)(No.2009CB118705)the National Natural Science Foundation of China(No.30970358)
文摘The intestinal bacteria of vertebrates form a close relationship with their host.External and internal conditions of the host,including its habitat,affect the intestinal bacterial community.Similarly,the intestinal bacterial community can,in turn,influence the host,particularly with respect to disease resistance.We compared the intestinal bacterial communities of grass carp that were collected from farm-ponds or a lake.We conducted denaturing gradient gel electrophoresis of amplified 16S rRNA genes,from which 66 different operational taxonomic units were identified.Using both the unweighted pair-group method with arithmetic means clustering and principal component analysis ordination,we found that the intestinal bacterial communities from the two groups of pond fish were clustered together and inset into the clusters of wild fish,except for DF-7,and there was no significant correlation between genetic diversity of grass carp and their intestinal bacterial communities(Mantel one-tailed test,R=0.157,P=0.175).Cetobacterium appeared more frequently in the intestine of grass carp collected from pond.A more thorough understanding of the role played by intestinal microbiota on fish health would be of considerable benefit to the aquaculture industry.
基金Project supported by the New Century Excellent Talent Scholarship of China(No.NCET-05-0387)the Doctodal Unit Scholarship of China(No.20050247016).
文摘A lab-scale sequencing batch reactor （SBR） was set-up and the aerobic granular sludge was successfully incubated using anaerobic granular sludge as seed sludge. Nitrogen was partially removed by simultaneous nitrification and denitrification （SND） via nitrite with free ammonia （FA） of about 10 mg/L. The denaturing gradient gel electrophoresis （DGGE） method was used to investigate community structure of α-Proteobacteria, β-Proteobacteria, ammonia oxidizing bacteria （AOB）, and Nitrospira populations during start-up. The population sizes of bacteria, AOB and Nitrospira were examined using real-time PCR method. The analysis of community structure and Shannon index showed that stable structure of AOB population was obtained at day 35, while the communities of α- Proteobacteria, β-Proteobacteria, and Nitrospira became stable after day 45. At stable stage, the average cell densities were 1.1× 10^12, 2.2×10^10 and 1.0×10^10 cells/L for bacteria, AOB and Nitrospira, respectively. The relationship between characteristics of nitrifying bacteria community and nitrogenous substrate utilization constant was discussed by calculating Pearson correlation. Certain correlation seemed to exist between population size, biodiversity, and degradation constant. And the influence of population size might be greater than that of biodiversity.
基金Project supported by the National Natural Science Foundation of China (No.40671099)
文摘Soil microbial biomass and community structures are commonly used as indicators for soil quality and fertility. A investigation was performed to study the effects of long-term natural restoration, cropping, and bare fallow managements on the soil microbial biomass and bacterial community structures in depths of 0-10, 20 30, and 40-50 cm in a black soil （Mollisol）. Microbial biomass was estimated from chloroform fumigation-extraction, and bacterial community structures were determined by analysis of 16S rDNA using polymerase chain reaction-denaturing gradient gel electrophoresis （PCR- DGGE）. Experimental results showed that microbial biomass significantly declined with soil depth in the managements of restoration and cropping, but not in the bare fallow. DGGE profiles indicated that the band number in top 0-10 cm soils was less than that in depth of 20-30 or 40-50 cm. These suggested that the microbial population was high but the bacterial community structure was simple in the topsoil. Cluster and principle component analysis based on DGGE banding patterns showed that the bacterial community structure was affected by soil depth more primarily than by managements, and the succession of bacterial community as increase of soil depth has a similar tendency in the three managements. Fourteen predominating DGGE bands were excised and sequenced, in which 6 bands were identified as the taxa of Verrueomicrobia, 2 bands as Actinobacteria, 2 bands as α-Proteobacteria, and the other 4 bands as 8-Proteobacteria, Aeidobacteria, Nitrospira, and unclassified bacteria. In addition, the sequences of 11 DGGE bands were closely related to uncultured bacteria. Thus, the bacterial community structure in black soil was stable, and the predominating bacterial groups were uncultured.
基金Supported by the National High Technology Research and Development Program(863 Program)of China(No.2010AA10Z401)
文摘Fusarium wilt is one of the most serious diseases of banana plants caused by soil-borne pathogen Fusarium oxysporum f.sp. cubense(FOC). In this study a pot experiment was conducted to evaluate the effects of different bio-organic fertilizers(BIOs) on Fusarium wilt of banana, including the investigations of disease incidence, chitinase and β-1,3-glucanase activities of banana plants, and FOC populations as well as soil rhizosphere microbial community. Five fertilization treatments were considered, including chemical fertilizer containing the same N, P and K concentrations as the BIO(control), and matured compost mixed with antagonists Paenibacillus polymyxa SQR-21 and Trichoderma harzianum T37(BIO1), Bacillus amyloliquefaciens N6(BIO2), Bacillus subtilis N11(BIO3), and the combination of N6 and N11(BIO4). The results indicated that the application of BIOs significantly decreased the incidence rate of Fusarium wilt by up to 80% compared with the control. BIOs also significantly promoted plant growth, and increased chitinase andβ-1,3-glucanase activities by 55%–65% and 17.3%–120.1%, respectively, in the banana roots. The population of FOC in the rhizosphere soil was decreased significantly to about 104 colony forming units g-1with treatment of BIOs. Serial dilution plating and denaturing gradient gel electrophoresis analysis revealed that the application of BIOs increased the densities of bacteria and actinomycetes but decreased the number of fungi in the rhizosphere soil. In general, the application of BIOs revealed a great potential for the control of Fusarium wilt disease of banana plants.
基金supported by the National Basic Research Program (973) of China (No. 2008CB418004)the Natural Science Foundation of Jiangsu Province (No.BK2007150)the China Postdoctoral Science Foundation (No. 20070410345)
文摘Interactions between bacteria and cyanobacteria have been suggested to have a potential to influence harmful algal bloom dynamics; however, little information on these interactions has been reported. In this study, the bacterial communities associated with five strains of Microcystis aeruginosa, three species of other Microcystis spp., and four representative species of non-Microcystis cyanobacteria were compared. Bacterial 16S rDNA fragments were amplified and separated by denaturing gradient gel electrophoresis （DGGE） followed by DNA sequence analysis. The similarities among bacterial communities associated with these cyanobacteria were compared to the digitized DGGE profiles using the cluster analyses. The bacterial community structure of all cyanobacterial cultures differed. Cluster analysis showed that the similarity values among M. aeruginosa cultures were higher than those of other cyanobacterial cultures. Sequence analysis of DGGE fragments indicated the presence of bacteria including, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria in the cyanobacterial cultures. Members of the Sphingomonadales were the prevalent group among the Microcystis-associated bacteria. The results provided further evidence for species-specific associations between cyanoabcteria and heterotrophic bacteria, which are useful for understanding interactions between Microcystis and their associated bacteria.
基金supported by grants from the National Science and Technology Support Program Project of China (2014CB138600, 2012BAD25B02, 2015CB150605)the National Natural Science Foundation of China (31272672 to ZGZ)the Beijing Earmarked Fund for Modern Agro-industry Technology Research System (SCGWZJ20141104-4)
文摘This study investigated the effect of dietary supplementation of yeast nucleotides on the growth, nonspecific immunity, intestine growth and intestinal microbiota of juvenile hybrid tilapia. Tilapia(initial average weight of 8.02 g) was fed test diets supplemented with a yeast-originated nucleotide mixture(0,0.15, 0.30, 0.60, and 1.20 g/100 g diet) for 8 weeks. Fish fed the diet with 0.60% nucleotide had significantly higher weight gain than the control group(P < 0.05). Feed efficiency was improved in the fish fed 0.60 and 1.20% nucleotide compared with that in the control group. The optimal doses of nucleotides supplementation for growth and feed efficiency of fish were determined as 0.63 and 0.81%, respectively.Intestinal growth was improved in the 0.30 and 0.60% groups, as indicated by significant increase in intestine length. The fish fed 0.60 and 1.20% nucleotide showed higher super oxide dismutase(SOD)activity and lower malondialdehyde(MDA) level in the liver than the control fish, indicating enhancement of the anti-oxidant status. Serum lysozyme activity was significantly increased in the 0.15 and 0.3%nucleotide supplementation groups, suggesting an enhancement effect on the non-specific immune response. Lastly, dietary nucleotides supplementation exerted moderate influence on the intestinal microbiota of hybrid tilapia. A reduction in the cumulative abundance of putative butyrate-producing species was observed in the intestinal microbiota of fish fed diets with 0.60% nucleotide compared with the control, implying an interaction between dietary nucleotides and butyrate production. Briefly, dietary supplementation with 0.60% nucleotide improve the growth performance, immune activity and intestine growth in tilapia.
文摘Methamidophos was widely used a pesticide in northern China. The potential influences of methamidophos on soil fungal community in black soil were assessed by plate count, 28S rDNA-PCR-DGGE, and clone library analysis. Three methamidophos levels （50, 150, and 250 mg/kg） were tested in soil microcosms. Results from plate count during a 60-d microcosm experiment showed that high concentrations of methamidophos （250 mg/kg） could significantly stimulate fungal populations. DGGE （denaturing gradient gel electrophoresis） fingerprinting patterns showed a significant difference between the responses of culturable and total fungi communities under the stress of methamidophos. Shannon diversity indices calculated from DGGE profiles indicated that culturable fungi in all microcosms with methamidophos treatment increased after 1 week of incubation. However, the diversity indices of total fungi decreased in the first week, as compared to the stimulation of culturable fungi. At the 8th week, however, all the microcosms treated by methamidophos were similar to the control microcosms in community structure as suggested by the Shannon diversity indices for both culturable and total fungi. In contrast, after 1 week the fungal structure of culturable and unculturable both were disturbed to different extent under the stresses of methamidophos by clustering analysis. Clone sequencing analysis indicated the stimulation of pathogenic and unculturable fungal populations by methamidophos treatment, suggetsing potential risks of plant disease outbreak.
基金This research was supported by grants from Chinese National Science Foundation (50478086). The 10th Five-year Key Programs for Science and Technology Development of China (2002AA601120).
文摘Objective To analyze the structure of bacteria in drinking water by molecular biological techniques, Methods DNA of bacteria in drinking water was directly extracted without culture. 16S ribosomal DNA fragments, including V-6, -7, and -8 regions, were amplified with universal primers （EUBf933CJC and EUBr1387） and analyzed by DGGE. Results DGGE indicated that amplification products could be separated, The results showed that DGGE could be used in the separation of different microbial 16SrRNA genes extracted from drinkng water. Though there were special bacteria in different water samples, the predominant bacteria were essentially the same. Three sequences of the reclaimed specific bands were obtained, and phylogenetic tree of these bands was made. Conclusion Bacterial diversity in drinking water is identified by molecular biological techniques.
基金supported by the"863"Exploration Projectof the Ministry of Science and Technology of China(No.2009AA06Z309)the National Natural Science Foundation of China(No.51178002)the Science andTechnology Project of Zhejiang Province of China(No.2011C23064)
文摘The bacterial strain Paracoccus denitrificans W12, which could utilize pyridine as its sole source of carbon and nitrogen, was added into a membrane bioreactor （MBR） to enhance the treatment of a pharmaceutical wastewater. The treatment efliciencies investigated showed that the removal of chemical oxygen demand, total nitrogen, and total phosphorus were similar between bioaugmented and non-bioaugmented MBRs, however, significant removal of pyridine was obtained in the bioaugmented reactor. When the hydraulic retention time was 60 hr and the influent concentration of pyridine was 250-500 mg/L, the mean effluent concentration of pyridine without adding W12 was 57.2 mg/L, while the pyridine was degraded to an average of 10.2 mg/L with addition of W12. The bacterial community structure of activated sludge during the bioaugmented treatment was analyzed using polymerase chain reaction-denaturing gradient gel electrophoresis （PCR-DGGE）. The results showed that the W12 inoculum reversed the decline of microbial community diversity, however, the similarity between bacterial community structure of the original sludge and that of the sludge after bioaugmentation decreased steadily during the wastewater treatment. Sequencing of the DNA recovered from DGGE gel indicated that sp., Sphingobium sp., Comamonas sp., and Hyphomicrobium sp. were the dominant organisms in time sequence in the bacterial community in the bioaugmented MBR. This implied that the bioaugmentation was affected by the adjustment of whole bacterial community structure in the inhospitable environment, rather than being due solely to the degradation performance of the bacterium added.
基金supported by the National 863 Program of China(2012AA101803)the National Key Technology R&D Program of China(2012BAD14B06,2012BAD14B01)
文摘This study evaluated the microbial community dynamics and maturation time of two compost systems： biogas slurry compost and cow manure compost, with the aim of evaluating the potential utility of a biogas slurry compost system. Denaturing gradient gel electrophoresis （DGGE）, gene clone library, temperature, C/N ratio, and the germination index were employed for the investigation, cow manure compost was used as the control. Results showed that the basic strip and dominant strips of the DGGE bands for biogas slurry compost were similar to those of cow manure compost, but the brightness of the respective strips for each system were different. Shannon-Weaver indices of the two compost systems differed, possessing only 22% similarity in the primary and maturity stages of the compost process. Using bacterial 16S rRNA gene clone library analysis, 88 bacterial clones were detected. Further, 18 and 13 operational taxonomic units （OTUs） were present in biogas slurry and cow manure compost, respectively. The 18 OTUs of the biogas slurry compost belonged to nine bacterial genera, of which the dominant strains were Bacillus sp. and Carnobacterium sp.; the 13 OTUs of the cow manure compost belonged to eight bacterial genera, of which the dominant strains were Psychrobacter sp., Pseudomonas sp., and Clostridium sp. Results demonstrated that the duration of the thermophilic phase （more than 50°C） for biogas slurry compost was 8 d less than the according duration for cow manure compost, and the maturation times for biogas slurry and cow manure compost were 45 and 60 d, respectively. It is an effective biogas slurry assimilate technology by application of biogas slurry as nitrogen additives in the manufacture of organic fertilizer.
基金supported by the Key Program of Nanjing Institute of Geography and Limnology,Chinese Academy of Sciences (No. NIGLAS2012135002)the National Key Natural Science Foundation of China (No. 41230744)the Open Foundation from the State Key Laboratory of Nanjing Institute of Geography and Limnology,Chinese Academy of Sciences (No. 2010SKL008)
文摘Vertical diversity of sediment bacterial communities in 2 different trophic states （macrophyte-dominated and algae-dominated） of the large shallow eutrophic Lake Taihu, China, were investigated using denaturing gradient gel electropfioresis （DGGE） and 16S rRNA sequence analysis. Clustering analysis of DGGE profiles showed that different clusters were recognized in different depths of sediment cores in the 2 lake trophic states. Analyses of the bacterial diversity, as estimated by the Shannon index （H＇）, showed that different sediment layers of the macrophyte-dominated state had higher diversity than the algae-dominated state. In addition, bacterial diversity of the sediment in the macrophyte-dominated state changed abruptly throughout the layers, but bacterial diversity of the algae-dominated state decreased gradually with sediment depth. Phylogenetic analysis showed that Proteobacteria was the most abundant phylum in the middle sediment of the 2 lake trophic states. In the macrophyte-dominated state, clone sequences related to Betaproteobacteria （50.0%） were the most abundant, followed by Epsilonproteobacteria （21.1%）, Acidobacteria （7.9%）, Deltaproteobacteria （7.9%）, Chloroflexi （7.9%）, and Bacteroidetes （5.3%）; whereas in the algae-dominated state, sequences affiliated with Betaproteobacteria （84.4%） were predominant, followed by Deltaproteobacteria （12.5%） and Acidobacteria （3.1%）. Canonical correspondence analysis showed that organic matter and pH play key roles in driving the vertical changes of bacterial community composition.
基金supported by the Knowledge InnovationGrant of the Chinese Academy of Sciences (No. kzcx2-yw-418-03)
文摘Zoige wetland is one of the most important methane emission centers in China. The oxidation of methane in the wetland affects global warming, soil ecology and atmospheric chemistry. Despite their global significance, microorganisms that consume methane in Zoige wetland remain poorly characterized. In this study, we investigated methanotrophs diversity in soil samples from both anaerobic site and aerobic site in Zoige wetland using pmoA gene as a molecular marker. The cloning library was constructed according to the pmoA sequences detected. Four clusters of methanotrophs were detected. The phylogenetic tree showed that all four clusters detected were affiliated to type I methanotrophs. Two novel clusters （cluster 1, cluster 2） were found to relate to none of the recognized genera of methanotrophs. These clusters have no cultured representatives and reveal an ecological adaptation of particular uncultured methanotrophs in Zoige wetland. Two clusters were belonging to Methylobacter and Methylococcus separately. Denaturing gradient gel electrophoresis gel bands pattern retrieved from these two samples revealed that the community compositions of anaerobic soil and aerobic soil were different from each other while anaerobic soil showed a higher metanotrophs diversity. Real-time PCR assays of the two samples demonstrated that aerobic soil sample in Zoige wetland was 1.5 times as much copy numbers as anaerobic soil. These data illustrated that methanotrophs are a group of microorganisms influence the methane consumption in Zoige wetland.
文摘The expressed prostatic secretions （EPSs） of men with chronic prostatitis/chronic pelvic pain syndrome （CP/CPPS）, infertile men and normal men were subjected to microbiological study. EPSs were collected from the subjects, which included 26 normal men, 11 infertile patients and 51 CP/CPPS patients. DNA was extracted from each specimen, and the V3 regions of the 16S rRNA genes were amplified using universal bacterial primers. The results showed that the EPS 16S rRNA gene-positive rate in the CP/CPPS and infertile patients was much higher than in the normal men, but without any difference among the three patient groups. The denaturing gradient gel electrophoresis （DGGE） method was used to characterize the EPS bacterial community structure of the prostate fluid from patients with CP/CPPS or infertility issues. Principal component analysis （PCA） and partial least squares （PLS） analyses of PCR-DGGE profiles revealed that the EPS bacterial community structure differed among the three groups. Three bands were identified as the key factors responsible for the discrepancy between CP/CPPS patients and infertile patients （P〈O.05）. Two bands were identified as priority factors in the discrepancy of category IliA and category IIIB prostatitis patients （P〈O.05）. According to this research, the ecological balance of the prostate and low urethra tract, when considered as a microenvironment, might play an important role in the maintenance of a healthy male reproductive tract.
基金supported by grants from National Natural Science Foundation of China (50678046)Heilongjiang Provincial Natural Science Foundation for Distinguished Young Scholars (JC200708)
文摘Objective It aims to investigate the changes in composition and structure of bacterial communities de-veloping on biological activated carbon （BAC） particles, and the bacterial functions. Method A pilot plant had been in service for 180 days, aiming to develop bacterial communities on acti-vated carbon naturally. After 180 days of operation, the bacterial communities were determined by dena-turing gradient gel electrophoresis （DGGE） analyses of PCR-amplified 16S rRNA genes. The study on community composition and the phylogenetic relationships of the organisms was complemented by a se-quence analysis of cloned PCR products from 16S rRNA genes. Gas chromatorgaphy-mass （GC-MS） mea-surement was used to determine organic chemical composition of inflow and outflow water on the 300th day. TOC and NH 4 ＋ -N were also tested in this experiment. Results It showed that the stable bacterial structure did not develop on BAC particles until the 9th month during running time of the BAC filter. The communities were finally dominated by Pseudomonas sp., Ba-cillus sp., Nitrospira sp., and an uncultured bacterium. Stable bacterial communities played an important role in removal of NH 4 ＋ -N and total organic carbon （TOC）. Results from gas chromatorgaphy-mass （GC-MS） showed that 36 kinds of chemicals in feed water were eliminated, and concentrations of 5 kinds of chemicals decreased. These chemicals served as nutrients for the dominant bacteria. Conclusion The findings from the study suggested that the stability of microbial structure was beneficial for improving NH 4 ＋ -N and TOC removal efficiencies. The dominant bacteria had the advantage of biode-grading a wide range of organic chemicals and NH 4 ＋ -N.
基金the projects under the National High Technology Research and Development Program of China(2006CB 102107)the National Natu-ral Science Foundation of China(30571327)the Key Program of Science and Technology of Guangdong Province,China(2006B20201051).
文摘The insulin-like growth factor binding protein-3 （IGFBP-3） was known as a key factor that regulates the effect of insulin- like growth factors （IGF-1 and IGF-2） on pig growth and development. We first identified 38 single nucleotide polymorphisms （SNPs） from a fragment of the IGFBP-3 gene spanning 1 823 bp using the denaturing high-performance liquid chromatography （DHPLC） method and confirmed them by direct sequencing. Among these SNPs, 36 located in introns and the remaining 2 in the 3 prime untranslated region （3UTR）. In addition, 16 PCR-RFLP polymorphisms were identified within these SNPs. Three SNPs were then selected to genotype 272 F2 individuals with PCR-RFLP method and the association of polymorphism with growth and carcass traits were analyzed. The results showed that no significant associations were observed between polymorphisms of A265G and A952G and traits. However, the A2670G significantly related with live body length, loin muscle area, and skin and fat percentage （P〈0.05）; highly significantly associated with weight of carcass lean and lean percentage （P〈 0.01）.
基金supported by the National Natural Science Foundation of China (30771570)the Natural Science Foundation of Jiangsu Province, China(BK2006143)
文摘Molecular diversity and development of the Lactobacillus community in the intestinal tract, as influenced by age and intestinal compartment, were studied in one litter of 12 conventionally raised piglets. Piglets were euthanized at each week （3 animals per time）. Digesta and tissue samples from stomach, duodenum, jejunum, ileum, caecum, colon, and rectum were collected and analysed by using 16S ribosomal RNA-based methods. DGGE （denaturing gradient gel electrophoresis） profiles revealed that the Lactobacillus communities throughout the GI tract from duodenum to rectum showed good stability at same age. This indicates that fecal Lactobacillus communities can effectively represent the intestinal community. Two dominant bands were found in tissue samples of the small intestine, suggesting that the lactobacilli can adhere to the small intestinal wall. The Lactobacillus communities in different GI tract compartments developed over time. A successional change of Lactobacillus communities was observed from birth, through creep feeding to one week after weaning, showing a trend from simple to complex and back to simple. Furthermore, a clone library of Lactobacillus spp. 16S rRNA gene sequences were generated from jejunal and colonic chymes. Six dominant DGGE bands generated from jejunal chymes were matched with sequences that show 94-98% similarity to the bands derived from L. reuteri, L. delbrueckii, and L. crispatus. Seven dominant DGGE bands generated from colon chymes were matched with sequences that show 88-99% similarity to those derived from L. reuteri, L. delbrueckii, L. amylovorus/L. sobrius, and L. acidophilus. Amplicons related to L. reuteri were found in all DGGE fingerprints from jejunal digesta of age of weeks 1, 3, and 4. Amplicons related to L. amylovorus/L. sobrius were present in all DGGE fingerprints from colonic digesta of age of week 1, 3, and 4. Amplicons related to L. delbrueckii were found before weaning, L. crispatus after creep feeding before weaning and L. acidophilus after weaning. Thi
基金Supported by the National Natural Science Foundation of China(No.41101242)the National Basic Research Program(973 Program)of China(No.2011CB100504)the National Key Technology R&D Program of China(Nos.2011BAD11B04 and 2012BAD14B04)
文摘Taking two important agricultural soils with different pH, brown soil （Hap-Udic Luvisol） and cinnamon soil （Hap-Ustic Luvisol）, from Northeast China, a pot culture experiment with spring maize （Zea mays L.） was conducted to study the dynamic changes in the abundance and diversity of soil ammonia-oxidizing bacteria （AOB） and ammonia-oxidizing archaea （AOA） populations during maize growth period in response to the additions of nitrification inhibitors dicyandiamide （DCD） and 3,4-dimethylpyrazole phosphate （DMPP） by the methods of real-time polymerase chain reaction （PCR） assay, PCR-denaturing gradient gel electrophoresis （DGGE）, and construction of clone library targeting the amoA gene. Four treatments were established, i.e., no urea （control）, urea, urea plus DCD, and urea plus DMPP. Both DCD and DMPP inhibited growth of AOB significantly, compared to applying urea alone. Soil bacterial amoA gene copies had a significant positive linear correlation with soil nitrate content, but soil archaeal amoA gene copies did not. In both soils, all AOB sequences fell within Nitrosospira or Nitrosospira-like groups, and all AOA sequences belonged to group 1.1b crenaxchaea. With the application of DCD or DMPP, community composition of AOB and AOA in the two soils had less change except that the AOB community composition in Hap-Udic Luvisol changed at the last two growth stages of maize under the application of DCD. AOB rather than AOA likely dominated soil ammonia oxidation in these two agricultural soils.
