jzs-10627

Exploring Fungal Diversity and distribution in Dukan Freshwater Lake Using ITS rDNA-based PCR Cloning/ Sequencing

Ibrahim Sulaiman Hamad1, Huner Hiwa Arif2, Harem Sabr Muhamad Amin2, Kamal Ahmad Khidir3

1 Charmo Research Center, University of Charmo, Kurdistan Region, Iraq

2 Department of Biology, College of Science, University of Sulaimani, Kurdistan Region, Iraq

3 Department of Biology, Faculty of Science, University of Raparin, Kurdistan Region, Iraq

Doi Link/ https://doi.org/10.17656/jzs.10627

Original: 5 Augest 2017, Revised: 5 October 2017, Accepted: 22 November 2017,  Published online: 20 December 2017

Abstarct

Fungi represent important trophic inhabitants in aquatic ecosystems, they have crucial roles in nutrient cycling in freshwater ecosystems. In the present study, Internal Transcribed Spacer ITS rDNA-based investigations of fungal communities in Dukan Lake were conducted from two collection sites using large-scale clonal Sanger sequencing. Herein we report for the first time, the composition of fungal communities in water samples of Dukan Lake through cloning/sequencing method. A total of 576 clones were obtained from ITS gene library and resulted in retrieving of 33 fungal

operational taxonomic units (OTUs). The majority of clone sequences belonged to Ascomycota while members of other fungal phyla were recovered at much lower frequencies. Molecular diversity analysis in Dukan Lake revealed the existence of fungi belonged to Pleosporales, Hypocreales, Helotiales, Mortierellales, Eurotiales, whereas Capnodiales, Onygenales, Pezizales, and Xylariales were detected in relatively minor abundances in the Dukan Lake ecosystem. In conclusion, molecular techniques using ITS rDNA-based PCR cloning/ sequencing is currently used as an effective tool to investigate the complex fungal communities in the aquatic systems however additional studies using next generation sequencing are needed for descriptive details regarding the occurrence and abundance of fungi in aquatic environments.

Keywords: Aquatic fungi, Clone, Detection, Metagenomics,Taxonomy

References:

[1] Wong MKM, Goh T-K, Hodgkiss IJ, Hyde KD, Ranghoo VM, Tsui CKM, et al. “Role of fungi in freshwater ecosystems” Biodiversity & Conservation. Vol. 7, No. 9, pp.1187-1206. (1998).

[2] Chamier A-C. “Cell-wall-degrading enzymes of aquatic hyphomycetes: a review”, Botanical Journal of the Linnean Society. Vol. 91, No. 1-2, pp. 67-81. (1985).

[3] Cuadros-Orellana S, Leite LR, Smith A, Medeiros JD, Badotti F, Fonseca PL, et al. “Assessment of fungal diversity in the environment using metagenomics: a decade in review”, Fungal Genomics & Biology. Vol. 3, No. 2, pp. 1. (2013).

[4] Kossuga MH, Romminger S, Xavier C, Milanetto MC, Valle MZd, Pimenta EF, et al. “Evaluating methods for the isolation of marine-derived fungal strains and production of bioactive secondary metabolites”, Revista Brasileira de Farmacognosia. Vol. 22, No. 2, pp. 257-267. (2012).

[5] Kiziewicz B. “Aquatic fungi growing on seeds of plants in various types of water bodies of Podlasie Province”, Polish Journal of Environmental Studies. Vol. 14, No. 1, pp. 49. (2005).

[6] Richards TA, Jones MD, Leonard G, Bass D. “Marine fungi: their ecology and molecular diversity”, Annual review of marine science. Vol. 4, pp. 495-522. (2012).

[7] Richards TA, Leonard G, Mahé F, del Campo J, Romac S, Jones MD, et al., editors. “Molecular diversity and distribution of marine fungi across 130 European environmental samples”, Proc R Soc B. The Royal Society, Vol. 282, Issue 18-19. (2015).

[8] Neelakanta G, Sultana H. “The use of metagenomic approaches to analyze changes in microbial communities” Microbiology insights, Vol. 6, pp. 37-48. (2013).

[9] Valderrama B, Paredes-Valdez G, Rodríguez R, Romero-Guido C, Martínez F, Martínez-Romero J, et al. “Assessment of non-cultured aquatic fungal diversity from different habitats in Mexico”, Revista Mexicana de Biodiversidad. Vol. 87, No. 1, pp. 18-28. (2016).

[10] Andreakis N, Høj L, Kearns P, Hall MR, Ericson G, Cobb RE, et al. “Diversity of marine-derived fungal cultures exposed by DNA barcodes: The algorithm matters”, PloS one. Vol. 10, No. 8, :e0136130. (2015).

[11] Monchy S, Sanciu G, Jobard M, Rasconi S, Gerphagnon M, Chabé M, et al. “Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing”, Environmental Microbiology, Vol. 13, No. 6, pp. 1433-1453. (2011).

[12] Bruns TD, White TJ, Taylor JW. “Fungal Molecular Systematics”, Annual Review of Ecology and Systematics, Vol. 22, pp. 525-564 (1991).

[13] Panzer K, Yilmaz P, Weiß M, Reich L, Richter M, Wiese J, et al. “Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data”, PloS one. Vol. 10, No. 7. e0134377. (2015).

[14] White TJ, Bruns TD, Lee S TJ. “Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics”, PCR protocols: a guide and applications. New York: Academic Press, Harcourt Brace Jovanovich. pp. 315-22 (1990).

[15] Dentinger BT, Didukh MY, Moncalvo JM. “Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina)”, PloS one. Vol. 6, No. 9. e25081. (2011).

[16] Ararat KA, N. Abdul Rahman, S. “Key Biodiversity Areas Survey of Kurdistan, Northern Iraq 2009 Site Review”, Sulaimani: Nature Iraq; (2009).

[17] Hamad I, Sokhna C, Raoult D, Bittar F. “Molecular detection of eukaryotes in a single human stool sample from Senegal”, PloS one. Vol. 7, No. 7. e40888. (2012).

[18] Gardes M, Bruns TD. “ITS primers with enhanced specificity for basidiomycetes--application to the identification of mycorrhizae and rusts”, MolEcol. Vol. 2, No. 2, pp. 113-118. (1993).

[19] Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. “MEGA6: Molecular Evolutionary Genetics Analysis version 6.0” Mol Biol Evol. Vol. 30, No. 12, pp. 2725-2729. (2013).

[20] Fakruddin M, Mannan K. “Methods for analyzing diversity of microbial communities in natural environments”, Ceylon Journal of Science (Biological Sciences). Vol.42, No. 1, pp. 19-33. (2013).

[21] O'Brien HE, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R. “Fungal community analysis by large- scale sequencing of environmental samples”, ApplEnvironMicrobiol. Vol. 71, No. 9, pp. 5544-5550.(2005).

[22] Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H. “ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases”, BMC microbiology. Vol. 10, pp. 189. (2010).

[23] Gouba N, Raoult D, Drancourt M. “Eukaryote culturomics of the gut reveals new species”, PloS one. Vol. 9, No. 9. e106994. (2014).

[24] Hamad I, Keita MB, Peeters M, Delaporte E, Raoult D, Bittar F. “Pathogenic eukaryotes in gut microbiota of western lowland gorillas as revealed by molecular survey” Scientific reports. Vol. 4. No. 6417. (2014).

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