Metagenomic Analysis of Bacterial Communities in Drinking Water Distribution Systems in Mombasa County (Kenya)
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Date
2016
Authors
Jeophita, Mwajuma June
Journal Title
Journal ISSN
Volume Title
Publisher
Kenyatta University
Abstract
Hygienic problems in drinking water distribution systems may originate from
contamination by external microorganisms or growth of indigenous biomass. Among all
water related disease outbreaks, 33% waterborne diseases were caused by-contaminated
source water, 39% by inadequate or interrupted treatment processes and 18% by
distribution systems and premise --plumbing deficiencies (Craun et 'al., 2010). The
Mombasa County water distribution systems have since inception undergone a sanitary
survey and there has been no information on the bacterial community composition
therein . .The primary focus of this study therefore was to generate detailed information
on the genome information stored within the water distribution system, microbiome.
This was achieved through an analysis of the 16S rRNA phylotypes of the microbes
present within the microbial community of21 water and biofilm samples collected from
Mzima and Baricho water lines, which have been operational for more than 50 years,
making them excellent sources of mature distribution system biofilms. Physicochemical
characteristics of the water were determined by a portable Palin Photometer
and Atomic Absorption Spectrophotometer; while bacterial taxonomic affiliations were
analyzed using 16S rRNA based 454-FLX Titanium pyrosequencing. Water from both
water lines registered pH, nitrates, phosphates and residual chlorine levels that were
within the limits stipulated for drinking water by the Kenya Bureau of Standards
(KEBS). All Baricho line samples had iron and lead levels way above the maximum
allowable limit of 0.05 mg L-1• Nitrates, iron and temperature correlated positively with
bacterial community composition and diversity in all samples as shown by Canonical
correspondence analysis (Mantel test: r = 0.27, P = 0.001). Pyrosequencing yielded
27,937 sequences, which were denovo clustered into 2,294 unique operational
taxonomic units (OTUs) based on their sequence similarity (3%). A total of 20 bacterial
phyla and 6 candidate phyla were identified from pooled samples and were dominated
by the Proteobacteria (73.2%), Firmicutes (13.4%), Bacteriodetes (5.9%) and
Candidate divisions at 0.9% of the total phylotypes. Renyi diversity profiles
t' demonstrated that all sampled sites regardless of source or type have larger species
richness, but lower species evenness. Shannon-Wiener diversity (H) index of each
sampling site ranged from 0.00 to 1.725. The highest bacterial diversity was found in
Baricho water (1.725) and Mzima biofilms (1.391). Biofilms featured characteristically
higher bacterial diversity, richness and abundance than bulk water. Bulk water was
predominated by Nitrospirae (20.2%), Betaproteobacteria (15.9%) and
Alphaproteobacteria (6.4%), while Favobacteria (8.6%), Deltaproteobcteria (3.2%),
bacteria NP L. UPA2 and Candidate division OD! were characteristic of biofilms.
Redundancy analysis indicated substantial comparative differences in water and
biofilms bacterial community composition among the two water lines. Nitrospirae,
Elusimicrobia, Cyanobacteria, Gemmatimonadetes, NP-UPA2, and Candidate
Divisions TM7, OP11 and OD1 were present only at source but not at endpoints.
Differences in community structure and abundance were noted between Baricho water
line source and endpoint water and biofilms bacterial composition (p= 0.013). A total of
140 phylotypes of potentially pathogenic species including; Pseudomonas, Escherichia,
Shigella, Aeromonas, Enterobacter and Bdelovibrio were identified. Metagenome
analyses also confirmed the ubiquity of mycobacteria in drinking water distribution
systems. Maintainance of the integrity of water systems, periodic monitoring and
effective treatment techniques should take precedence in water delivery services to
reduce the risk of contaminating the drinking water with pathogenic microorganisms.
Description
A research thesis submitted in fulfillment of the requirements for the award of Doctor of Philosophy Degree (Microbiology) in the School of Pure and Applied Sciences of Kenyatta University