The importance of eDNA as a bioindicator for bacterial biodiversity in Baghdad river

YOne of the most critical problems of the 21st century is the
continuous ongoing decrease in Earth’s biodiversity. Worldwide,
wild flora and fauna populations are depleted owing
to anthropogenic disturbances and species extinction levels
exceed those of pre-human periods which have a significant
impact on our planet’s human health and sustainability. We
focus on Tigris river in Baghdad, Iraq, the second longest river
in Western Asia, a length 1,800 km2 , originates in Armenian
Highlands in Turkey, source of water for supplies drinking water,
agriculture, industry, domestic water supply and for disposal
of sewage. Water samples were collected from gradient
area of pollution from November 2018-July 2019. Populations
and communities information by collecting DNA from environmental
samples (eDNA), defining it as a “complex mixture
of genomic DNA from many different organisms found in an
environmental sample.” This method includes the metabarcoding
of the mixed DNA samples of any source, followed by
the next-generation high performance sequencing (NGS), using
universal polymerase chain reaction (PCR) to determine
the species composition of the sample .In Sample Preparation
DNA/RNA is extracted from a sample; qualified samples proceed
to library construction. The sequencing library is prepared
by random fragmentation of the DNA or cDNA sample,
followed by 5’ and 3’ adapter ligation, then PCR amplified,
gel purified and Sequencing. In Generation of Raw Data the
Illumina sequencer generates raw images utilizing sequencing
control software for system control and base calling through
integrated primary analysis software called RTA (Real Time
Analysis). 12 phylum of bacteria in result of taxonomy abundance
ratio with lest in Chloroflexi and Synergistetes (0.01%)
with abundance count (3) and highest ratio in Proteobacteria
(57.27 %) with abundance count (22,068). In Result of Assembly
Total bases (bp) for water sample (by FLASH) was recorded
85,413,665. With Read Count, Total number of reads, for Illumina
paired-end sequencing, this value refers to the sum of
read 1 and read 2 N (%) , GC content ( GC %) , ratio of bases
that have phred quality score of over 20(Q20 %) , Ratio of bases
that have phred quality score of over 30 (Q30 %) , 186,224 ,
0.0002 , 51.21 , 97.45 , 91.97 respectively.

Author(s): Warqaa Y. Al Meshhdany, Halah H Al- Haideri, Fikrat M. Hassan

Abstract | PDF

Share This Article