High-throughput sequencing of 16S rRNA gene reveals substantial bacterial diversity on the municipal dumpsite
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Date
2016
Journal Title
Journal ISSN
Volume Title
Publisher
Microbiology
Abstract
Multiple types of solid waste in developing countries is disposed of together in dumpsites where
there is interaction between humans, animals and the bacteria in the waste. To study the bacteria at the dumpsite
and the associated risks, previous studies have focused on culturable, leaving behind a great number of unculturable
bacteria. This study focuses on a more comprehensive approach to study bacteria at the dumpsite. Since the site
comprised of unsorted wastes, a qualitative survey was first performed to identify the variety of solid waste as this has
influence on the microbial composition. Thus, domestic (Dom), biomedical (Biom), river sludge (Riv), and fecal material
of pigs scavenging on the dumpsite (FecD) were sampled. Total DNA was extracted from 78 samples and the v4-16S
rRNA amplicons was characterized using an Illumina MiSeq platform.
Results: A total of 8,469,294 sequences passed quality control. Catchall analysis predicted a mean of 8243 species per
sample. Diversity was high with an average InvSimpson index of 44.21 ± 1.44. A total of 35 phyla were detected and
the predominant were Firmicutes (38 %), Proteobacteria (35 %), Bacteroidetes (13 %) and Actinobacteria (3 %). Overall
76,862 OTUs were detected, however, only 20 % were found more than 10 times. The predominant OTUs were
Acinetobacter (12.1 %), Clostridium sensu stricto (4.8 %), Proteinclasticum and Lactobacillus both at (3.4 %),
Enterococcus (2.9 %) and Escherichia/Shigella (1.7 %). Indicator analysis (P ≤ 0.05, indicator value ≥ 70) shows that
Halomonas, Idiomarina, Tisierella and Proteiniclasticum were associated with Biom; Enterococcus, Bifidobacteria, and
Clostridium sensu stricto with FecD and Flavobacteria, Lysobacter and Commamonas to Riv. Acinetobacter and
Clostridium sensu stricto were found in 62 % and 49 % of all samples, respectively, at the relative abundance of
1 %. None of OTUs was found across all samples.
Conclusions: This study provides a comprehensive report on the abundance and diversity bacteria in municipal
dumpsite. The species richness reported here shows the complexity of this man-made ecosystem and calls for
further research to assess for a link between human diseases and the dumpsite. This would provide insight into
proper disposal of the waste, as well as, limit the risks to human health associated with the dumpsite.
Description
Journal Article
Keywords
Municipal dumpsite, Solid waste, Molecular diversity, 16S rRNA, Illumina MiSeq