Microbial community structure and nitrogenase gene diversity of sediment from a deep-sea hydrothermal vent field on the Southwest Indian Ridge

A sediment sample was collected from a deep-sea hydrothermal vent field located at a depth of 2 951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community using polymerase chain reaction（PCR） amplification of the 16 S rRNA and nifH genes. Within the Archaea, the dominant clones were from marine benthic group E（MBGE） and marine group I（MGI） belonging to the phyla Euryarchaeota and Thaumarchaeota, respectively. More than half of the bacterial clones belonged to the Proteobacteria, and most fell within the Gammaproteobacteria. No epsilonproteobacterial sequence was observed. Additional phyla were detected including the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3 and TM6, confirming their existence in hydrothermal vent environments. The detection of nifH gene suggests that biological nitrogen fixation may occur in the hydrothermal vent field of the Southwest Indian Ridge. Phylogenetic analysis indicated that only Clusters I and III NifH were present. This is consistent with the phylogenetic analysis of the microbial 16 S rRNA genes, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment.

Diversity of bacterial lactase genes in intestinal contents of mice with antibiotics-induced diarrhea

AIM To investigate the diversity of bacterial lactase genes in the intestinal contents of mice with antibiotics-induced diarrhea.METHODS Following 2 d of adaptive feeding, 12 specific pathogenfree Kunming mice were randomly divided into the control group and model group. The mouse model of antibiotics-induced diarrhea was established by gastric perfusion with mixed antibiotics(23.33 m L·kg^(-1)·d^(-1)) composed of gentamicin sulfate and cephradine capsules administered for 5 days, and the control group was treated with an equal amount of sterile water. Contents of the jejunum and ileum were then collected and metagenomic DNA was extracted, after which analysis of bacterial lactase genes using operational taxonomic units(OTUs) was carried outafter amplification and sequencing.RESULTS OTUs were 871 and 963 in the model group and control group, respectively, and 690 of these were identical. There were significant differences in Chao1 and ACE indices between the two groups(P < 0.05). Principal component analysis, principal coordination analysis and nonmetric multidimensional scaling analyses showed that OTUs distribution in the control group was relatively intensive, and differences among individuals were small, while in the model group, they were widely dispersed and more diversified. Bacterial lactase genes from the intestinal contents of the control group were related to Proteobacteria, Actinobacteria, Firmicutes and unclassified bacteria. Of these, Proteobacteria was the most abundant phylum. In contrast, the bacterial population was less diverse and abundant in the model group, as the abundance of Bradyrhizobium sp. BTAi1, Agrobacterium sp. H13-3, Acidovorax sp. KKS102, Azoarcus sp. KH32 C and Aeromonas caviae was lower than that in the control group. In addition, of the known species, the control group and model group had their own unique genera, respectively.CONCLUSION Antibiotics reduce the diversity of bacterial lactase genes in the intestinal contents, decrease the abundance of lactase gene, change the lactase gene strains, and transform their structures.

Effect of salinity on community structure and naphthalene dioxygenase gene diversity of a halophilic bacterial consortium

The aim of this study is to analyze the effect of salinity on polycyclic aromatic hydrocarbons （PAHs） biodegradation, community structure and naphthalene dioxygenase gene （ndo） diversity of a halophilic bacterial consortium with the denaturing gradient gel electrophoresis （DGGE） approach. The consortium was developed from oil-contaminated saline soil after enrichment for six times, using phenanthrene as the substrate. The prominent species in the bacterial consortium at all salinities were identified as halophilic bacteria Halomonas, Alcanivorax, Marinobacter, Idiomarina, Martelella and uncultured bacteria. The predominant microbes gradually changed associating with the saline concentration fluctuations ranging from 0.1% to 25% （w/v）. Two ndo alpha subunits were dominant at salinities ranging, from 0.1% to 20%. while not been clearly detected at 25% salinity. Consistently. the biodegradation occurred at salmltles rangmg from 0.1% to 20%, while no at 25% salinity, suggesting the two ndo genes played an important role in the degradation. The phylogenetic analysis revealed that both of the two ndo alpha subunits were related to the classic nab-like gene from Pseudomonas stutzeri AN10 and Pseudomonas aeruginosa PaK1, while one with identity of about 82% and the other one with identity of 90% at amino acid sequence level. We concluded that salinity greatly affected halophilic bacterial community structure and also the functional genes which were more related to biodegradation.

The Genetic Structure and Diversity of Repomucenus curvicornis Inhabiting Liaoning Coast Based on Mitochondrial COⅠ Gene and Control Region

[Object] This study was conducted to explore the genetic diversity and structure of the wild Repomucenus curvicornis inhabiting Liaoning Coast, China. [Method] The mitochondrial COⅠ gene and control region（CR） were PCR amplified from the wild R. curvicornis populations from the Liaodong Bay（n=22） and the northern Yellow Sea（n=18）, sequenced and analyzed for genetic diversity. [Result] The contents of A, T, C and G of 624 bp COⅠ gene were 24.09%, 31.04%, 25.28%, and 19.59%, and those of 460 bp CR fragment were 32.96%, 32.80%, 14.86% and 19.38%, respectively. The total number of variable sites, average number of nucleotide differences（ k）, haplotype diversity（H） and nucleotide diversity（π） based on COⅠ gene were 38, 4.67,（0.96±0.02） and（0.007 5±0.004 2）, and those based on CR fragment were 26, 3.35,（0.97 ±0.02） and（0.007 3±0.004 3）, respectively. Based on mitochondrial COⅠ gene and CR, the genetic diversity of Liaodong Bay population was lower than that of the northern Yellow Sea population. The AMOVA analysis based on CR fragments revealed almost significant genetic divergence between the Liaodong Bay and the northern Yellow Sea populations, while there was no significant genetic divergence based on COⅠ gene. The results showed that CR and COⅠ gene are effective molecular markers for detecting the genetic diversity of R. curvicornis population, while CR is more reliable than COⅠ gene in detecting the genetic structure. [Conclusion] CR is an appropriate marker for genetic analysis of marine fish population.

Microbial diversity and functionally distinct groups in produced water from the Daqing Oilfield,China

The microbial community structure and functionally distinct groups in three kinds of produced water samples from the shallow,mesothermic and low-salinity Daqing oil reservoir were systematically evaluated using both culture-dependent and culture-independent methods.Sequence analysis of the 16S rRNA genes indicated that the bacterial library was dominated by Acinetobacter and Arcobacter and the archaeal community was dominated by Methanosaeta and Methanolinea.Two isolated methanogens were closely related with Methanothermobacter thermautotrophicus and Methanoculleus receptaculi.The fermentative bacteria were identified as Pseudomonas,Haloanaerobium,Alcalibacter,Arcobacter,and Pannonibacter.The predominant nitrate-reducing bacteria fell within the genus Pseudomonas.The dominant members of the cultured hydrocarbon-oxidizing bacteria were phylogenetically associated with Micrococcus,Pseudomonas,and Bacillus.Enrichments of biosurfactants and biopolymer producing groups mainly yielded Pseudomonas,Bacillus,and Acenitobacter-related members.The functional groups related to polymer degradation were also affiliated with Pseudomonas and Bacillus.Results from this study provide the fresh insight into the diversity of microbial communities in Daqing petroleum reservoirs.The vast pool of functional strains retrieved in this study was presumed to include the promising strains that could be applied in microbial-enhanced oil recovery in future.

Bacterial diversity in sediments of core MD05-2902 from the Xisha Trough,the South China Sea

A sediment core MD05-2902 was collected from the deep-sea basin of the Xisha Trough. The vertical distribution and diversity of bacteria in the core was investigated through ten sub-sampling with an interval of 1 m using bacterial 16 S rRNA gene as a phylogenetic bio-marker. Eighteen phylogenetic groups were identified from 16 S rRNA gene clone libraries. The dominant bacterial groups were JS1, Planctomycetes and Chloroflexi, which accounted for 30.6%, 16.6%, and 15.6% of bacterial clones in the libraries, respectively. In order to reveal the relationship between biotic and abiotic data, a nonmetric multidimensional scaling analysis was performed. The result revealed that the δ15N, δ13C, total organic carbon and total organic nitrogen possibly influenced the bacterial community structure. This study expanded our knowledge of the biogeochemical cycling in the Xisha Trough sediment.

Molecular Characterization of Sixty Local Mango Germplasm of Chapainawabganj

The experiment was conducted at Plant Genetic Resources Centre, Bangladesh Agricultural Research Institute (BARI) and the genotypes were collected from Chapainawabganj, the most mango variability rich district in Bangladesh. The molecular characters of mango germplasm were assessed by using six simple sequence repeat (SSR) markers. Polymerase chain reaction (PCR) amplification of the DNA isolated from 60 mango germplasm with 6 SSR primers was performed. The sizes of the alleles detected ranged from 112 to 221 bp. SSRs exhibited moderate values of polymorphic information content (PIC) range of 0.9405 to 0.6501. Genetic distances (D) between varieties were computed from combined data of the 6 primers, ranging from 0.5000 to 1.0000. Moderate degree of genetic diversity was obtained where the highest level of gene diversity value was noted 0.9433 in loci MIGA179 and the lowest level of gene diversity value was computed 0.6683 in loci MIGA253 with a mean diversity of 0.8842. The dendrogram generated from the unweighed pair group arithmetic average (UPGMA) cluster analysis broadly placed 60 mango cultivars into ten major clusters. The cluster size varied from 1 to 12 and cluster-VI was the largest cluster comprising of 9 cultivars. The tendency of clustering among mango cultivars revealed that they have strong affinity towards further breeding programme.

Characterization of root-associated bacterial community structures in soybean and corn using locked nucleic acid(LNA) oligonucleotide-PCR clamping and 454 pyrosequencing

supported in part by grants from the Strategic Priority Research Program of Chinese Academy of Sciences （XDB15010103）;the National Natural Science Foundation of China （41201247）

Persistent pollutants and the patchiness of urban green areas as drivers of genetic richness in the epiphytic moss Leptodon smithii

We determined genetic variation and metal and polycyclic aromatic hydrocarbon concentrations in Leptodon smithii moss collected in holm oak stands at cities, outskirts and remote areas of Campania and Tuscany（Italy） to investigate if anthropogenic pressure（pollutant emissions and land use change） affects moss genetic richness. In both regions, metal and polycyclic aromatic hydrocarbon concentrations reflected the trend urban 〉 outskirts 〉 remote areas, excepting Tuscany remote site. In both regions,the moss gene diversity increased from urban to remote areas. The findings suggest the extent and the fragmentation of urban green areas, as drivers of moss genetic richness.