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Culture independent molecular analysis of bacterial communities in the mangrove sediment of Sundarban, India.

Ghosh A, Dey N, Bera A, Tiwari A, Sathyaniranjan K, Chakrabarti K, Chattopadhyay D - Saline Syst. (2010)

Bottom Line: The gammaproteobacteria were found to be the most abundant bacterial group in Sundarban sediment.The present study indicates a probable hydrocarbon and oil contamination in this sediment.In the present study, a number of clones were identified that have shown similarity with bacterial clones or isolates responsible for the maintenance of the S-cycle in the saline environment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Department of Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata- 700019, West Bengal, India. dhrubajyotic@gmail.com.

ABSTRACT

Background: Sundarban is the world's largest coastal sediment comprising of mangrove forest which covers about one million hectares in the south-eastern parts of India and southern parts of Bangladesh. The microbial diversity in this sediment is largely unknown till date. In the present study an attempt has been made to understand the microbial diversity in this sediment using a cultivation-independent molecular approach.

Results: Two 16 S rRNA gene libraries were constructed and partial sequencing of the selected clones was carried out to identify bacterial strains present in the sediment. Phylogenetic analysis of partially sequenced 16 S rRNA gene sequences revealed the diversity of bacterial strains in the Sundarban sediment. At least 8 different bacterial phyla were detected. The major divisions of detected bacterial phyla were Proteobacteria (alpha, beta, gamma, and delta), Flexibacteria (CFB group), Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, Planctomycetes and Gammatimonadates.

Conclusion: The gammaproteobacteria were found to be the most abundant bacterial group in Sundarban sediment. Many clones showed similarity with previously reported bacterial lineages recovered from various marine sediments. The present study indicates a probable hydrocarbon and oil contamination in this sediment. In the present study, a number of clones were identified that have shown similarity with bacterial clones or isolates responsible for the maintenance of the S-cycle in the saline environment.

No MeSH data available.


16S rRNA gene tree showing positions of proteobacterial sequences in D16S_pMOS library including the reference sequences retrieved from GenBank. 16S rRNA gene sequence of Bacillus subtilis 168 is used to assign an out-group species.
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Figure 1: 16S rRNA gene tree showing positions of proteobacterial sequences in D16S_pMOS library including the reference sequences retrieved from GenBank. 16S rRNA gene sequence of Bacillus subtilis 168 is used to assign an out-group species.

Mentions: The total DNA was extracted from the sediment of Netidhopani, Sundarban, using modified CTAB-SDS based DNA isolation technique. Two partial 16S rRNA gene clone libraries were established from the PCR amplified partial 16S rRNA gene sequences using 515F/1492R and uni-for/uni-rev primer sets, respectively. The recombinant clones in the libraries were selected based on α-complementation (blue-white screening) technique and also confirmed by the re-PCR analysis and restriction enzyme digestion. Our sequencing analysis included 85 clones from D16S_pMOS library and 110 clones from DUni_pMOS library. All the sequenced clones were screened for sequences that repeat more than once in the library. Our final analysis included 50 clones from D16S_pMOS library and 80 clones from DUni_pMOS library, respectively (Table1) (Figures 1, 2, 3 and 4). Methylophaga spp. was found to be abundant in both the libraries. We also found four non bacterial chloroplastic DNA in recombinant clones from the two libraries. Although, the primer pair 515F & 1492R could amplify both bacterial and archaeal 16S rRNA gene sequences, we did not get any archaeal sequence in our library (D16S_pMOS). This was probably because of the limitation in our total DNA extraction protocol and low primer specificities towards the archaeal 16S rRNA gene sequences. Our phylogenetic analysis revealed that 130 bacterial clones (50 clones from D16S_pMOS library and 80 clones from DUni_pMOS library) fell into 8 major phyla of the bacterial domain: Proteobacteria (Alpha-, Beta-, Gamma-, and Delta-), the Cytophaga-Flexibacter-Bacteroides (CFB) group, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, Acidobacteria group, and Planctomycetes (Table 1).


Culture independent molecular analysis of bacterial communities in the mangrove sediment of Sundarban, India.

Ghosh A, Dey N, Bera A, Tiwari A, Sathyaniranjan K, Chakrabarti K, Chattopadhyay D - Saline Syst. (2010)

16S rRNA gene tree showing positions of proteobacterial sequences in D16S_pMOS library including the reference sequences retrieved from GenBank. 16S rRNA gene sequence of Bacillus subtilis 168 is used to assign an out-group species.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2837041&req=5

Figure 1: 16S rRNA gene tree showing positions of proteobacterial sequences in D16S_pMOS library including the reference sequences retrieved from GenBank. 16S rRNA gene sequence of Bacillus subtilis 168 is used to assign an out-group species.
Mentions: The total DNA was extracted from the sediment of Netidhopani, Sundarban, using modified CTAB-SDS based DNA isolation technique. Two partial 16S rRNA gene clone libraries were established from the PCR amplified partial 16S rRNA gene sequences using 515F/1492R and uni-for/uni-rev primer sets, respectively. The recombinant clones in the libraries were selected based on α-complementation (blue-white screening) technique and also confirmed by the re-PCR analysis and restriction enzyme digestion. Our sequencing analysis included 85 clones from D16S_pMOS library and 110 clones from DUni_pMOS library. All the sequenced clones were screened for sequences that repeat more than once in the library. Our final analysis included 50 clones from D16S_pMOS library and 80 clones from DUni_pMOS library, respectively (Table1) (Figures 1, 2, 3 and 4). Methylophaga spp. was found to be abundant in both the libraries. We also found four non bacterial chloroplastic DNA in recombinant clones from the two libraries. Although, the primer pair 515F & 1492R could amplify both bacterial and archaeal 16S rRNA gene sequences, we did not get any archaeal sequence in our library (D16S_pMOS). This was probably because of the limitation in our total DNA extraction protocol and low primer specificities towards the archaeal 16S rRNA gene sequences. Our phylogenetic analysis revealed that 130 bacterial clones (50 clones from D16S_pMOS library and 80 clones from DUni_pMOS library) fell into 8 major phyla of the bacterial domain: Proteobacteria (Alpha-, Beta-, Gamma-, and Delta-), the Cytophaga-Flexibacter-Bacteroides (CFB) group, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, Acidobacteria group, and Planctomycetes (Table 1).

Bottom Line: The gammaproteobacteria were found to be the most abundant bacterial group in Sundarban sediment.The present study indicates a probable hydrocarbon and oil contamination in this sediment.In the present study, a number of clones were identified that have shown similarity with bacterial clones or isolates responsible for the maintenance of the S-cycle in the saline environment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Department of Biotechnology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata- 700019, West Bengal, India. dhrubajyotic@gmail.com.

ABSTRACT

Background: Sundarban is the world's largest coastal sediment comprising of mangrove forest which covers about one million hectares in the south-eastern parts of India and southern parts of Bangladesh. The microbial diversity in this sediment is largely unknown till date. In the present study an attempt has been made to understand the microbial diversity in this sediment using a cultivation-independent molecular approach.

Results: Two 16 S rRNA gene libraries were constructed and partial sequencing of the selected clones was carried out to identify bacterial strains present in the sediment. Phylogenetic analysis of partially sequenced 16 S rRNA gene sequences revealed the diversity of bacterial strains in the Sundarban sediment. At least 8 different bacterial phyla were detected. The major divisions of detected bacterial phyla were Proteobacteria (alpha, beta, gamma, and delta), Flexibacteria (CFB group), Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, Planctomycetes and Gammatimonadates.

Conclusion: The gammaproteobacteria were found to be the most abundant bacterial group in Sundarban sediment. Many clones showed similarity with previously reported bacterial lineages recovered from various marine sediments. The present study indicates a probable hydrocarbon and oil contamination in this sediment. In the present study, a number of clones were identified that have shown similarity with bacterial clones or isolates responsible for the maintenance of the S-cycle in the saline environment.

No MeSH data available.