Isolation and Characterization of Polycyclic Aromatic Hydrocarbons-degrading Bacteria from Mangrove Habitat’s Sediments in Makupa Creek, Mombasa County, Kenya
Loading...
Date
2025-06
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Kenyatta University
Abstract
In humans and animals, polycyclic aromatic hydrocarbons (PAHs) have a long and notorious history of being recognized as potent endocrine system disruptors, cancers, and mutagens. Their lipophilic nature and the unique chemical structure of fused aromatic rings allow them to disseminate swiftly throughout the environment. The biological degradation of PAHs is the natural ecosystem primary remediation mechanism, where microorganisms are essential to PAH metabolism. The objective of the study was to isolate, characterize and identify bacteria capable of degrading PAHs from sediment samples collected in a mangrove habitat. Twelve sediment samples were collected from various sections within the mangrove region of Makupa Creek, Mombasa, County. Anthracene and Naphthalene-supplemented marine agar were used to isolate the bacteria that broke down PAHs. Biochemical assays were conducted to assess the activities of amylase, oxidase, and catalase. Molecular methods to identify the isolated bacterium were achieved by amplifying the 16S rRNA followed by sequencing using dye terminator technique. BLAST and the RDP's SeqMatch technique were used to search the NCBI database using sequence data. ClustalW 1.6 program was then used to align the 16S rRNA gene sequence. Determination of isolates' evolutionary connection was achieved using a maximum likelihood algorithm on MEGA 6 software. Twenty-one of the 44 bacterial samples isolated from the sediments were viable. The isolates had anthracene and naphthalene degradation efficiencies ranging from 93.8% to 99.5% and 79.1% to 99.39%, respectively. Biochemical tests showed that all isolates were positive for the catalase test, while 90% and 95% had oxidase and amylase activity, respectively. The genomic DNA from each bacterial isolate was extracted. The bacterial universal primers 27F and 1492R were then used to amplify the 16S rRNA gene, yielding an amplicon of about 1500 bp. Compared to the other isolates, S3B01, S2A01 A, and S1A01 produced less DNA. Blast searches indicated that the isolates shared a sequence similarity index of between 81% - 100% with those of other existing taxon, 60% of which were Pseudomonas and the rest were Bacillus, Ralstonia, Enterobacter, and Exiguobacterium. Ten isolates had a similarity score of less than 97% with other species, indicating that they are novel strains. The prominence of Pseudomonas reinforces its significance in PAH degradation. Furthermore, the emergence of unclassified isolates suggests the exciting possibility of novel bacterial strains that can be targeted for developing anti-pollution agents. In conclusion Mangrove sediments from Makupa Creek, Mombasa County, harbor diverse bacteria capable of degrading PAHs, particularly naphthalene and anthracene. The enzymatic; catalase, amylase, oxidase activity of these isolates supported microbial degradation. The 16S rRNA analysis identified Pseudomonas, Bacillus, Ralstonia, Enterobacter, and Exiguobacterium spp as the key hydrocarbon-degrading genera. The presence of other genera undocumented isolates suggested the presence of potentially novel strains. There is need therefore, to develop the bacterial consortia from Makupa Creek sediments for hydrocarbon bioremediation.
Description
A Thesis Submitted in Partial Fulfillment for the Award of the Degree of Master of Science (Biotechnology) of the School of Pure and Applied Sciences of Kenyatta University, June 2025.
Supervisors
1. David Mburu
2. Joseph Mwafaida
3. Mathew Ngugi