• Warqaa Yehia Al-Meshhdany Institute of Genetic Engineering and Biotechnology for Postgraduate Studies, University of Baghdad, Baghdad, Iraq.
  • Fikrat M. Hassan Department of Biology, College of Science for Women University of Baghdad, Baghdad, Iraq.
Keywords: Algae, Diatoms, Edema, Freshwater, NGS, Tigris River.


   Molecular barcoding was widely recognized as a powerful tool for the identification of organisms during the past decade; the aim of this study is to use the molecular approach to identify the diatoms by using the environmental DNA. The diatom specimens were taken from Tigris River. The environmental DNA(e DNA) extraction and analysis of sequences using the Next Generation Sequencing (NGS) method showed the highest percentage of epipelic diatom genera including Achnanthidium minutissimum (Kützing) Czarnecki, 1994 (21.1%), Cocconeis placentula Ehrenberg, 1838 (21.3%) and Nitzschia palea (Kützing) W. Smith, 1856 (16.3%).

   Five species of diatoms: Achnanthidium minutissimum; Fistulifera saprophila (Lange-Bertalot & Bonik) Lange-Bertalot, 1997; Gomphonema pumilum (Grunow) E. Reichardt & Lange-Bertalot, 1991; Navicula veneta Kützing, 1844 and Thalassiosira pseudonana Hasle Heimdal, 1970 were registered in NCBI under the accession numbers as follows: MN749640.1, MN749641.1, MN749642.1, MN749643.1 and MN749646.1 for the first time; while the two algae Fistulifera saprophila and Thalassiosira pseudonana are regarded as a new record to algal flora in Iraq.

   The environmental DNA study will be a catalyst for new studies of biodiversity and environmental studies in Iraq and the region.


Download data is not yet available.


Abed, I. J., Abdulhasan, G. A. and Najem, A. M. 2018. Genotype versus phenotype to determine the definitive identification of the genera Chlorella Berjrinck, 1890 (Chlorophyceae) and Coelastrella Chodat, 1922 (Scenedesmaceae). Bulletin of Iraq Natural History Museum, 15 (1):101-111.

Adebayo, O. O., Sangodoyin, A.Y., Ogedengbe, K., and Taiwo, O. 2013. Mapping of river water quality using inverse distance weighted interpolation in Ogun-Osun river basin, Nigeria. Acta Geographica Debrecina Landscape and Environment, 7 (2): 48-62.

Al-Hussieny, A. A., Hussein, H. T. and Hmood, A. H. 2014. Propagation of algae farms using several methods by different farming media. Journal of the College of Basic Education, 20 (84/Scientific): 121-142.

Al-Rawi, A., Alwash, B. M. J., Al-Essa, N. E. and Hassan, F. M. 2018. A new record of Coelastrella terrestris (Reisigle) Hegewald & N. Hangata, 2002 (Sphaeropleales, Scenedesmaceae) in Iraq. Bulletin of Iraq Natural History Museum, 15 (2): 153-161.

Amend, A. S., Seifert, K. A., Bruns, T. D. 2010. Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Molecular ecology, 19(24): 5555-6565.

Aydın, G. Ș. and Büyükıșık, B. 2014. Effects on the species-specific variables nutrient pulses: Thalassiosira allenii (Takano). Journal of Tekirdag Agricultural Faculty, 11(3): 82-90.

Baird, D. J. and Hajibabaei, M. 2012. Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Molecular Ecology, 21(8): 2039-2044.

Berthold, M., Karsten, U., von Weber, M., Bachor, A. and Schumann, R. 2018. Phytoplankton can bypass nutrient reductions in eutrophic coastal water bodies. Ambio, 47(1): 146-158.

Campbell, B. M., Beare, D.J., Bennett, E. M., Hall-Spencer, J. M., Ingram, J. S., Jaramillo, F., Ortiz, R., Ramankutty, N., Sayer, J. A. and Shindell, D. 2017. Agriculture production as a major driver of the Earth system exceeding planetary boundaries. Ecology and Society, 22(4): 1-8.

Chang, H. 2008. Spatial analysis of water quality trends in the Han River basin, South Korea. Water Research, 42 (13): 3285-3304.

Çiçek, A., Bakiş, R., Uğurluoğlu, A., Köse, E. and Tokatli, C. 2013. The effects of large borate deposits on ground water quality. Polish Journal of Environmental Studies, 22(4): 1031- 1037.

Ewing, B. and Green, P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research, 8(3):186-194.

Gao, Z., Wang, X., Wei, X., Liu, Y. and Han, J. 2019. DNA Mini-Barcoding: A Derived Barcoding Method for Herbal Molecular Identification. Frontiers in plant science, 10: 987.

Gibson, J., Shokralla, S., Porter, T. M., King, I., van Konynenburg, S., Janzen, D. H., Hallwachs, W. and Hajibabaei, M.2014. Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. Proceedings of the National Academy of Sciences, 111(22): 8007-8012.

Godhe, A. and Härnström, K. 2010. Linking the planktonic and benthic habitat: genetic structure of the marine diatom Skeletonema marinoi. Molecular Ecology, 19(20): 4478-4490.

Guillard, R. R. 1975. Culture of phytoplankton for feeding marine invertebrates. In: Smith, W. L., Chanley, M. H. (eds), Culture of marine invertebrate animals (pp. 29-60). Springer, Boston, MA.

Gurbuz, H. and Kivrak, E. 2002. Use of epilithic diatoms to evaluate water quality in the Karasu River of Turkey. Journal of Environmental Biology, 23(3): 239-246.

Hamsher, S. E., Evans, K .M., Mann, D. G., Poulíčková, A. and Saunders, G. W. 2011. Barcoding diatoms: exploring alternatives to COI-5P. Protist, 162 (3): 405-422.

Heyse, G., Jönsson, F., Chang, W.J. and Lipps, H.J. 2010. RNA-dependent control of gene amplification. Proceedings of the National Academy of Sciences, 107(51): 22134-22139.

Kiss, K. T. 1984. Occurrence of Thalassiosira pseudonana Hasle et Heimdal (Bacillariophyceae) in some rivers of Hungary. Act Botiunica Hungarica, 30 (3-4): 277-287.

Luddington, I.A., Kaczmarska, I. and Lovejoy, C. 2012. Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae). PLoS ONE, 7 (9): e45664.

Moniz, M. B. and Kaczmarska, I. 2010. Barcoding of diatoms: nuclear encoded ITS revisited. Protist, 161(1): 7-34.

Novais, M. H., Juettner, I., Van de Vijver, B., Morais, M. M., Hoffmann, L. and Ector, L. 2015. Morphological variability within the Achnanthidium minutissimum species complex (Bacillariophyta): comparison between the type material of Achnanthes minutissima and related taxa, and new freshwater Achnanthidium species from Portugal. Phytotaxa, 224 (2): 101-139.

Passy, S. I., Bode, R. W., Carlson, D. M. and Novak, M. A. 2004. Comparative environmental assessment in the studies of benthic diatom, macroinvertebrate, and fish communities. International Review of Hydrobiology: A Journal Covering all Aspects of Limnology and Marine Biology, 89 (2): 121-138.

Pawlowski, J., Lejzerowicz, F. and Esling, P. 2014. Next-generation environmental diversity surveys of foraminifera: preparing the future. The Biological Bulletin, 227(2): 93-106.

Prokopowich, C. D., Gregory, T. R. and Crease, T. J. 2003. The correlation between rDNA copy number and genome size in eukaryotes. Genome, 46(1): 48-50.

Reichardit, E. 1997. Taxonomic revision of species complex of Gomophonema pumilum (Bacillariophyceae). Nova Hedwigia, 65:99-130.

Round, F. E., Crawford, R. M. and Mann, D. G. 1990. The Diatoms. Morphology and biology of the genera. Cambridge University Press, Cambridge, UK, ix+747 pp.‏

Salman, J. M., Hassan, F. M. and Baiee, M. A. 2017. Practical methods in environmental and pollution laboratory. Issued by Environmental Research Center, University of Babylon. ISBN2463.

Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C. and Willerslev, E. 2012. Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular ecology, 21(8): 2045-2050.

Tan, X., Zhang, Q., Burford, M. A., Sheldon, F. and Bunn, S. E. 2017. Benthic diatom based indices for water quality assessment in two subtropical streams. Frontiers in microbiology, 8: 601.

Thomsen, P.F. and Willerslev, E. 2015. Environmental DNA–An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation, 183: 4-18.

Tokatlı, C. and Dayıoğlu, H. 2011. Use of epilithic diatoms to evaluate water quality of Murat Stream (Sakarya River Basin, Kütahya): different saprobity levels and pH status. Journal of Applied Biological Sciences, 5(2): 55-60.

Vasselon, V., Domaizon, I., Rimet, F., Kahlert, M. and Bouchez, A. 2017. Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?. Freshwater Science, 36(1): 162-177.

Visco, J. A., Apothéloz-Perret-Gentil, L., Cordonier, A., Esling, P., Pillet, L. and Pawlowski, J. 2015. Environmental monitoring: inferring the diatom index from next-generation sequencing data. Environmental Science and Technology, 49 (13): 7597-7605.

Weber, A. A. and Pawlowski, J. 2013. Can abundance of protists be inferred from sequence data: a case study of Foraminifera. PloS ONE, 8 (2): e56739.

Wojtal, A. 2003. Diatoms of the genus Gomphonema Ehr. [Bacillariophyceae] from a karstic stream in the Krakowsko-Czestochowska Upland. Acta Societatis Bot Anicorum Poloniae, 72 (3): 213- 220.

Yu, L., Zhang, W., Liu, L. and Yang, J. 2015. Determining microeukaryotic plankton community around Xiamen Island, southeast China, using Illumina MiSeq and PCR-DGGE techniques. PLoS ONE, 10(5): e0127721

Zimmerman, J., Glöckner, G., Jahn, R., Enke, N. and Gemeinholzer, B. 2015.. Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies. Molecular Ecology Resources, 15(3):526-42.