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http://dx.doi.org/10.1080/12298093.2022.2028436

Genetic Diversity of Amylomyces rouxii from Ragi tapai in Java Island Based on Ribosomal Regions ITS1/ITS2 and D1/D2  

Delva, Ega (Laboratory of Microbiology, Faculty of Biology, Universitas Gadjah Mada)
Arisuryanti, Tuty (Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada)
Ilmi, Miftahul (Laboratory of Microbiology, Faculty of Biology, Universitas Gadjah Mada)
Publication Information
Mycobiology / v.50, no.2, 2022 , pp. 132-141 More about this Journal
Abstract
Amylomyces rouxii is commonly found as amylolytic fungi in tapai fermentation. However, its diversity is rarely reported despite being often used for food production in Southeast Asia. This research aims to analyze the genetic diversity and the distribution pattern of A. rouxii from Ragi tapai in Java Island, Indonesia. We isolated the fungus from samples obtained from Ragi tapai producing centers in Bandung, Sumedang, Muntilan, Blora, Yogyakarta, and Bondowoso. The obtained isolates were molecularly identified based on the ribosomal regions ITS1/ITS2 and D1/D2, then analyzed for phylogenetic tree reconstruction, genetic distance, genetic variation, and haplotype networking. Six isolates showed specific morphological traits of A. rouxii. However, phylogenetic tree reconstruction on the ribosomal genes showed that the isolates were grouped into two different clades related to two species. Clade A included BDG, SMD, and MTL isolates related to A. rouxii, whereas clade B included YOG, BLR, and BDS isolates related to Mucor indicus. The genetic distances between clades for ITS1/ITS2 and D1/D2 were 0.6145 and 0.1556, respectively. In conclusion, we confirmed the genetic diversity of molds from Ragi tapai in Java Island and showed that the isolates are not only related to A. rouxii as reported before.
Keywords
Distribution pattern; DNA sequence analysis; fermentation inoculum; fungi; taxonomic status;
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1 Fajarningsih ND. Internal transcribed spacer (ITS) as dna barcoding to identify fungal species: a review. Squalen Bull Marine Fisheries Postharvest Biotech. 2016;11(2):37.   DOI
2 Nucleotide [Internet]. Bethesda (MD): National Library of Medicine, National Center for Biotechnology Information; [1988]. Accession No. AY238888, Amylomyces rouxii 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence; [cited 2020 Nov 11]. Available from: https://www.ncbi.nlm.nih.gov/nuccore/29692017/
3 Maddison WP, Maddison DR. 2019. Mesquite: a modular system for' 'evolutionary analysis (3.61). 2019. Available from: http://www.mesquiteproject.org.
4 Ko SD. Tape fermentation. Appl Microbiol. 1972; 23(5):976-978.,   DOI
5 Saono S. 1982. Microflora of ragi: its composition and as source of industrial yeast. In Proceedings of a technical seminar. Jakarta: Indonesia: the Indonesian Institute of Science (LIPI); pp. 241-249.
6 Ellis JJ, Rhodes LJ, Hesseltine CW. The genus Amylomyces. Mycologia. 1976;68(1):131-143.   DOI
7 White TJ, Tom DB, Lee SB, et al. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Gurr SJ, editor. PCR protocols, a guide to methods and applications. London: Academic Press. p. 315-322.
8 Lv X-C, Huang Z-Q, Zhang W, et al. Identification and characterization of filamentous fungi isolated from fermentation starters for Hong Qu glutinous rice wine brewing. J Gen Appl Microbiol. 2012;58(1):33-42.   DOI
9 Raja HA, Miller AN, Pearce CJ, et al. Fungal identification using molecular tools: a primer for the natural products research community. J Nat Prod. 2017;80(3):756-770.   DOI
10 Nucleotide [Internet]. Bethesda (MD): National Library of Medicine, National Center for Biotechnology Information; [1988]. Accession No. AB181331, Amylomyces rouxii genes for 18S rRNA, ITS1, 5.8S rRNA, ITS2, 28S rRNA, partial and complete sequence, strain: ATCC 22962; [cited 2020 Nov 11]. Available from: https://www.ncbi.nlm.nih.gov/nuccore/AB181331.1/
11 O'Donnell K, Lutzoni FM, Ward TJ, et al. Evolutionary relationships among mucoralean fungi (Zygomycota): evidence for family polyphyly on a large scale. Mycologia. 2001;93(2):286.   DOI
12 Rahayu ES, Indrati R, Utami T, et al. 1993. Bahan pangan hasil fermentasi. Yogyakarta: PAU Pangan dan Gizi. Universitas Gadjah Mada.
13 Dung NTP, Rombouts FM, Nout MJR. Functionality of selected strains of moulds and yeasts from Vietnamese rice wine starters. Food Microbiol. 2006;23(4):331-340.   DOI
14 Pino-Bodas R, Martin MP, Burgaz AR, et al. Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy. Mol Ecol Resour. 2013;13(6):1058-1068.   DOI
15 Karimi K, Zamani A. Mucor indicus: biology and industrial application perspectives: a review. Biotechnol Adv. 2013;31(4):466-481.   DOI
16 Sharifyazd S, Karimi K. Effects of fermentation conditions on valuable products of ethanolic fungus Mucor indicus. Electron J Biotechnol. 2017;30: 77-82.   DOI
17 de Souza CF, Lima D, de Oliveira RV, et al. Mucor indicus isolated from the semiarid region of Brazil: a first record for South America. Mycotaxon. 2016; 131(4):897-906.   DOI
18 Kasmidjo RB. 1983. Mikrobiologi ragi. Yogyakarta: PAU Pangan dan Gizi Universitas Gadjah Mada.
19 Siebenhandl S, Lestario LN, Trimmel D, et al. Studies on tape Ketan-an Indonesian fermented rice food. Int J Food Sci Nutr. 2001;52(4):347-357.   DOI
20 Kito Hideki Abe A, Sujaya I-N, Oda Y, et al. Molecular characterization of the relationships among Amylomyces rouxii, Rhizopus oryzae, and rhizopus delemar. Biosci Biotechnol Biochem. 2009;73(4):861-864.   DOI
21 Abe A, Sone T, Sujaya IN, et al. rDNA ITS sequence of Rhizopus oryzae: its application to classification and identification of lactic acid producers. Biosci Biotechnol Biochem. 2003;67(8): 1725-1731.   DOI
22 Djien KS. Tape fermentation. Appl Microbiol. 1972;23:976-978.   DOI
23 Ardhana MM, Fleet GH. The microbial ecology of tape ketan fermentation. Int J Food Microbiol. 1989;9(3):157-165.   DOI
24 Zheng R, Chen G, Huang H, et al. A monograph of Rhizopus. Sydowia. 2007;59(2):273-372.
25 Gandjar I. 2003. Tapai from Cassava and Cereals (pp. 13-17). Presented at the the First International Symposium and Workshop on Insight into the World of Indigenous Fermented Foods for Technology Development and Food Safety, the First International Symposium and Workshop on Insight into the World of Indigenous Fermented Foods for Technology Development and Food Safety: Kasetsart University.
26 Cronk TC, Steinkraus KH, Hackler LR, et al. Indonesian Tape Ketan fermentation. Appl Environ Microbiol. 1977;33(5):1067-1073.   DOI
27 Steinkraus K. Handbook of indigenous fermented foods. New York: CRC Press; 1995.
28 Komagata K, Rahayu E, Uchimura T. 1988. Identification of lactic acid bacteria isolated from a Chinese starter, ragi, in Indonesia. LIPI.
29 Azmi AS, Ngoh GC, Mel M, et al. Ragi tapai and Saccharomyces cerevisiae as potential culture in viscous fermentation medium for ethanol production. Afr J Biotechnol. 2010;9(42):7122-7127.
30 Saono S, Basuki T, Sastraatmadja S. 1978. Indonesia ragi. Symposium on indigenous foods. Bangkok, Thailand: Presented at the Symposium on Indigenous Foods.
31 Dijksterhuis J, Samson RA. 2007. Food mycology: a multifaceted approach to fungi and food. (1st ed.). Boca Raton: CRC Press; p. 428.
32 Kartika AN. 2012. Isolasi amylomyces dari berbagai jenis ragi untuk pembuatan tape rendah alkohol. Yogyakarta: Tekhnologi Pangan dan Hasil Pertanian. Universitas Gadjah Mada.
33 Hebert PDN, Cywinska A, Ball SL, et al. Biological identifications through DNA barcodes. Proc R Soc Lond B. 2003;270(1512):313-321.   DOI
34 Zein M, Prawiradalaga D. 2013. DNA barcode fauna Indonesia. Jakarta: Prenadamedia Group.
35 Kwiatkowski NP, Babiker WM, Merz WG, et al. Evaluation of nucleic acid sequencing of the D1/D2 region of the large subunit of the 28S rDNA and the internal transcribed spacer region using SmartGene IDNS [corrected] software for identification of filamentous fungi in a clinical laboratory. J Mol Diagn. 2012;14(4):393-401.   DOI
36 Nucleotide [Internet]. Bethesda (MD): National Library of Medicine, National Center for Biotechnology Information; [1988]. Accession No. EF583634, Rhizomucor sp. Rm-33 small subunit ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence; [cited 2020 Nov 11]. Available from: https://www.ncbi.nlm.nih.gov/nuccore/EF583634
37 Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009;25(11):1451-1452.   DOI
38 Peakall R, Smouse PE. GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research-an update. Bioinformatics. 2012;28(19):2537-2539.   DOI
39 Vu D, Groenewald M, de Vries M, et al. Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation. Stud Mycol. 2019;92: 135-154.   DOI
40 Ying L. 2012. Identification of mold isolated from Rice Wine Start (Master thesis).
41 Vitale RG, de Hoog GS, Schwarz P, et al. Antifungal susceptibility and phylogeny of opportunistic members of the order Mucorales. J Clin Microbiol. 2012;50(1):66-75.   DOI
42 Anupma A. Filamentous moulds associated with some traditionally prepared mixed starter cultures of North East India. Microbiology. 2019;11(905): 1-16.
43 Abe A, Oda Y, Asano K, et al. The molecular phylogeny of the genus Rhizopus based on rDNA sequences. Biosci Biotechnol Biochem. 2006;70(10): 2387-2393.   DOI
44 TajAldeen SJ, Boekhour T, Theelen B. 2015. Mucor indicus from Qatar. CBS-KNAW Fungal Biodiversity Centre (CBS).
45 Schoch CL, Seifert KA, Huhndorf S, et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci. 2012;109(16):6241-6246.   DOI