ISSN: 2155-6199
Journal of Bioremediation & Biodegradation
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Research Article Open Access
Pahbase, a Freely Available Functional Database of Polycyclic Aromatic Hydrocarbons (Pahs) Degrading Bacteria
| Jaimin J. Surani, Viral G. Akbari, Megha K. Purohit and Satya P. Singh* | |
| Department of Biosciences, Saurashtra University, Rajkot, Gujarat, India-360 005 | |
| Corresponding Author : | Dr. Satya P. Singh Department of Biosciences Saurashtra University Rajkot, Gujarat, India-360 005 E-mail: satyapsingh@yahoo.com satyapsingh125@gmail.com |
| Received December 22, 2011; Accepted January 30, 2011; Published February 02, 2011 | |
| Citation: Surani JJ, Akbari VG, Purohit MK, Singh SP (2011) Pahbase, a Freely Available Functional Database of Polycyclic Aromatic Hydrocarbons (Pahs) Degrading Bacteria. J Bioremed Biodegrad 2:116. doi:10.4172/2155-6199.1000116 | |
| Copyright: © 2011 Surani JJ, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. | |
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Abstract
PAHbase is a freely available functional database of Polycyclic Aromatic Hydrocarbons (PAHs) degrading bacteria. The database consists of relevant information obtained from scientific literature and databases. The database provides a comprehensible representation of PAH degrading bacteria with reference to its occurrence, phylogeny, and stress adaptation, potential to withstand extreme conditions, biodegradative ability, metabolic pathways and genetic basis of the degradation. The narrow search and limit options of the constructed database provide comparable information from the relevant PAH degrading candidates. The user friendly approach of PHP front end facilitates to add sequences of reported entries leading to scientific information for the specific purpose. The functional PAH database available freely on internet under URL: www.pahbase.in .
| Keywords |
| PAHs; Biodegradation; Database; PAHbase |
| Introduction |
| Microbial population is a highly diverse and a ubiquitous group among the living world. One of the novel features of the microbes relates to their versatility in utilizing a large numbers of natural and manmade compounds. This property proves highly valuable in bioremediation for the complete destruction and removal of pollutants [1]. Contamination of soils and sediments by Polycyclic Aromatic Hydrocarbons (PAHs) is widespread, which raises enormous environmental concerns. It has been observed that PAH degradation in soil is dominated by bacterial strains belonging to a very limited number of taxonomic groups such as Sphingomonads, Burkholderia, Pseudomonas, Bacillus, Micrococcus and Mycobacterium [2-9] Members of these genera are specialized in the degradation of aromatic chemicals [10,11]. As such, bioremediation may provide relatively low-cost and less intensified technology with high public acceptance. |
| Bioinformatics based analysis and prediction is playing a pivotal role in understanding and capturing the in-depth knowledge of biological molecules particularly with reference to proteomics and genomics. Although with this advancement, there have been only limited efforts on the collection of all relevant information for a specific field of interest. With this realization, present study focuses on the wide spread data and information related to the occurrence and potential of PAH degrading bacteria. The information and detailed account on these bacteria are quite limited and scattered in scientific journals. Therefore, details from the research papers were extracted, analyzed and presented in form of a precise informative database: PAHbase reflecting the diversity and functional analysis of PAHs degrading bacteria. |
| Methodology |
| PAHbase contains information regarding PAHs degrading bacteria with respect to morphology, Gram reaction, degradation potential, metabolic pathways and genetic basis. Backhand database of PAHbase was created in MS Access and front end was done by PHP: Hypertext Preprocessor which provided the easy web access to database for data entry, retrieval and analysis. Data was collected and extracted from original research publications and public databases, i.e. NCBI, DDBJ and EMBL. |
| Data input |
| In PAHbase, we selected 45 PAHs degrading bacteria and integrated detailed information comprising multiple fields of interest; such as name of the organism, habitat, site of isolation, Gram's reaction, activity, country, extremophilic nature (Halophilic/Thermophilic/Mesophilic), taxonomy and phylogenetic relatedness with nearby species, preferred PAH source of utilization as carbon source, media used in laboratory to access its potential for respective PAH, physical, chemical and environmental conditions provided for degradation, degradation potential, enzymes involved in degradation, gene/s involved and gene location, metabolic pathway,16S ribosomal gene sequence and references. |
| Data retrieval |
| PAHbase is a freely accessed web database constructed using PHP on windows platform. "PAHbase" is the database which gives user friendly search criteria and also provides easy access, retrieval and manipulation with secure administrator and users. |
| Results and Discussion |
| PAHbase creation |
| The PAHbase database was constructed primarily in Access 2007 as back hand and exported to PHP as front hand with MySQL for the easy access and portability. Considerable efforts have added to the field of environmental biotechnology with reference to PAHs degrading bacteria. Over the years our group has focused on capturing diversity and degradation aspects of PAHs degrading bacteria and as an extension of our current research work, we constructed a web driven database system for PAHs degraders to focus on their different aspects. This data base would be of immense help for scientific fraternity conducting their research on PAHs degrading bacteria. |
| 'PAHbase' provides platform for the easy access and retrieval of data from the database (Figure 1). To the best of our knowledge, this would be the first report on the submission of specialized database for PAHs degrading organisms. The functionality to add and edit data to the database through a user friendly web based portal facilitates to update and maintain database system. All information required by the researchers for the study of PAHs degrading bacteria including basic microbiological features, ecological aspects, PAHs substrate specificity and molecular biological studies relevant to the source organisms were thrust area for database construction. Retrieval and analyzing all important parameters under a single system assures wide applicability of constructed PAHbase. |
| Acknowledgement |
| We gratefully acknowledge the financial and other logistics support from Saurashtra University, Rajkot, India. |
References
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Figures at a glance
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