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Frontiers of Environmental Science & Engineering

ISSN 2095-2201

ISSN 2095-221X(Online)

CN 10-1013/X

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Front. Environ. Sci. Eng.    2016, Vol. 10 Issue (6) : 16    https://doi.org/10.1007/s11783-016-0888-0
RESEARCH ARTICLE
Effect of salinity on community structure and naphthalene dioxygenase gene diversity of a halophilic bacterial consortium
Tingting Fang1,Ruisong Pan2,Jing Jiang1,Fen He1,Hui Wang1()
1. State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing100084, China
2. Development and Promotion Center of Environmental Science and Technology, Changzhou 213001, China
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Abstract

Various salinities affected the PAH-biodegrading community structure.

Various salinities affected the growth of strains with different salt tolerance.

The two ndo genes belonged to a new divergent cluster of the known nah-like genes.

The two main ndo genes had correlations with the phenanthrene degradation.

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 salinities ranging 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 nah-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.
Keywords Phenanthrene      Halophilic bacteria      Gene diversity      Naphthalene dioxygenase genes     
PACS:     
Fund: 
Corresponding Author(s): Hui Wang   
Issue Date: 25 November 2016
 Cite this article:   
Tingting Fang,Ruisong Pan,Jing Jiang, et al. Effect of salinity on community structure and naphthalene dioxygenase gene diversity of a halophilic bacterial consortium[J]. Front. Environ. Sci. Eng., 2016, 10(6): 16.
 URL:  
https://academic.hep.com.cn/fese/EN/10.1007/s11783-016-0888-0
https://academic.hep.com.cn/fese/EN/Y2016/V10/I6/16
Fig.1  The biodegradation of phenanthrene by microbial consortium at SSDMY with different salinity
Fig.2  DGGE banding pattern (a) and cluster analysis (b) (Ward method, Dice coefficients of similarity) of DGGE gel image of bacterial 16S rRNA gene extracted from enrichments grown at different salinities. 0%–25% represented sampling salinity and S1 represented the soil sample. The numbers correspond to bands were identified by 16S rRNA gene sequence analysis (Table 2)
lane 0.1% 1% 5% 10% 15% 20% 25% S1
0.1% 100.0 77.6 72.9 60.6 67.1 65.6 64.5 45.5
1% 77.6 100.0 74.2 70.4 66.6 66.8 63.6 44.0
5% 72.9 74.2 100.0 77.1 85.8 80.3 79.6 34.8
10% 60.6 70.4 77.1 100.0 75.7 83.6 84.4 33.3
15% 67.1 66.6 85.8 75.7 100.0 88.3 83.3 35.7
20% 65.6 66.8 80.3 83.6 88.3 100.0 91.3 31.5
25% 64.5 63.6 79.6 84.4 83.3 91.3 100.0 31.1
S1 45.5 44.0 34.8 33.3 35.7 31.5 31.1 100.0
Tab.1  The similarity matrix of DGGE lanes
number similarity closest sequence match(Genbankaccession) relevant characteristics,origin and reference
y1 92% uncultured bacterium (DQ424439) unpublished
y2 98% Halomonas sp. ZB-2007 (EF421176) PAH-degrading, oil contaminated hypersaline soil, unpublished
y3 99% Marinobacter sp. B (EF571249) phenanthrene-degrading, Oil contaminated hypersaline soil [13]
y4 99% Idiomarina seosinensis (AY635468) hypersaline water [18]
y5 100% Alcanivorax venustensis (EU440999) PAH-degrading, deep- sea water of The Indian Ocean, unpublished
y6 96% Idiomarina baltica (AJ440215) sea water [19]
y7 99% Alcanivorax venustensis MARC4Q (DQ768632) PAH-degrading, Atlantic sediments [17]
y8 98% Halomonas gomseomensis M12 (AM229314) saline water [20]
y9 98% Halomonas sp. TAG C4 (AB042501) The Atlantic [21]
y10 98% Marinobacter szutsaonensis (EU164778) unpublished
y11 99% Alcanivorax dieselolei (EU440990) unpublished
y12 100% Uncultured bacterium (EU236842) India seaside, unpublished
y13 99% Uncultured bacterium (EU328060) crude oil-degrading, oil contaminated soil, unpublished
y14 100% Martelella mediterranea MACL11 (AY649762) underground salt lake [22]
y15 98% Salinimicrobium xinjiangense (EF520007) Xinjiang Province of China [23]
y16 98% uncultured bacterium (EU328031) crude oil-degrading, oil contaminated soil, unpublished
y17 96% uncultured bacterium (DQ015780) Antarctic lake bonney, unpublished
y18 99% uncultured bacterium (AM935386) Aliphatic hydrocarbon-degrading, Oil contaminated soil [24]
y19 96% Halospina denitrificans(FJ152879) Alkaline saline lake [25]
y20 94% Halospina denitrificans(FJ152880) Alkaline saline lake [25]
Tab.2  Sequence analysis of bands from DGGE banding pattern from bacteria 16S rRNA gene
Fig.3  DGGE fingerprints of ndo gene fragments amplified from different salinities of DNA templates. 0%–25% represented sampling salinity and N1and N2 represented dominant bands
Fig.4  Phylogenetic tree of amplified ndo gene fragments based on the analysis of the deduced amino acid sequences (258 residues). The N1 and N2 represent ndo gene sequence from the enrichment culture. Reference sequences from GenBank include the accession number in brackets. The scale bar corresponds to 0.1 substitutions per amino acid position. Bootstrap values were calculated as percentage of 1000 replicates, and only values greater than 70% were shown above or near the relevant nodes
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