title: [Phylogeny diversity of the nitrite reductase gene (nirS) in the sediments of the eutrophic East Lake, Wuhan].
abstract: OBJECTIVE
  The study aims to investigate the phylogeny diversity of the denitrification bacteria communities in the sediments of the eutrophic East Lake, Wuhan based on nitrite reductase gene (nirS) restriction fragment length polymorphism (RFLP) method and sequencing analysis, and to analyse community variation according to the environment parameters.
  
  
  METHODS
  We collected the sediment samples from the four typical sub-lake of East Lake in Wuhan, Guozheng Lake, Tangling Lake, Tuan Lake and Miao Lake, and measured the environmental parameters appropriately. After extracted the genomic DNA from the sediment, four nirS gene clone libraries were successfully constructed. The operation taxonomy units (OTUs) were determined by RFLP method and the representative fragment of every OTU was sequenced. The diversity, richness and evenness statistics of the NirS-like communities were calculated by using DOTUR software. Neighbor-joining phylogenetic tree was constructed basing on the amino acid sequences of NirS from the East Lake sediments and reference sequences retrieved from the GenBank database. The relationship between tested NirS communities and the references from different environments was also discussed.
  
  
  RESULTS
  Environmental parameters showed that Miao Lake sediment contains the highest amount of total nitrogen (TN) and NH4+ -N, while the Tuan Lake sediments contains the lowest amount. Among the four sub-lakes, Tuan Lake harbours the highest diversity and richness of NirS-like denitrifiers, while the denitrifiers in Miao Lake was the lowest. Phylogenic analyses suggested that sedimentary NirS-like denitrifiers in the East Lake could be distributed into three groups, Group I to III. Group I accounts for 67.7% of all tested communities. Eighty-one percent of sequences from Guozheng Lake were clustered into Group I, while 67.7% of sequences from Miao Lake were clustered into Group II. Comparative analysis of communities from East Lake and artificial wetland found there are phylogenetically related.
  
  
  CONCLUSIONS
  There are diverse and abundant NirS-like denitrifiers inhabited in the sediments of East Lake, Wuhan. The diversity indices and spatial distribution of these communities are affected by the content of TN, NH4- and NO3- nutrients in the sediments.
authors.affiliation: Key Laboratory of Molecular Bio-physics, Ministry of Education, China. zhanbingcheng@yahoo.cn
authors.forename: Zhanbing
authors.initials: Z
authors.lastname: Cheng
authors.forename: Jiangke
authors.initials: J
authors.lastname: Yang
authors.forename: He
authors.initials: H
authors.lastname: Li
authors.forename: Bing
authors.initials: B
authors.lastname: Zhu
authors.forename: Xiangjun
authors.initials: X
authors.lastname: Chen
authors.forename: Yunjun
authors.initials: Y
authors.lastname: Yan
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D001426:Bacterial Proteins / Q000235:genetics; D058440:Denitrification; D017753:Ecosystem; D005068:Eutrophication; D005618:Fresh Water / Q000382:microbiology*; D005819:Genetic Markers; D014644:Genetic Variation; D019015:Geologic Sediments / Q000382:microbiology*; D008969:Molecular Sequence Data; D009572:Nitrite Reductases / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D005819:Genetic Markers; D009572:Nitrite Reductases