Metagenomic analysis of the microbial community in Çal Cave soil to elucidate biotechnological potential

Year 2020, Volume: 21 Issue: 3, 254 - 259, 30.09.2020

Hasan Demirci , Emel Ordu

https://doi.org/10.18182/tjf.658468

Cited By: 3

Abstract

Turkey has a great number of karstic caves which are unexplored and have unknown microbial diversity. The biodiversity characterisation of these caves has not yet been systematically studied from the molecular point of view. Çal Cave in Trabzon, Turkey is one of the important karstic caves. In the present study, a metagenomic approach was used to explore the microbial diversity of Çal Cave for the first time to assess the potential of gene sources. Detailed taxonomic profiling was defined by sequencing all environmental genomes instead of a specific marker gene such as 16S rRNA which only targets prokaryotes. Taxonomic analysis revealed that the Çal Cave soil sample was represented as 98% Bacteria, 2% Eukaryota, 0.3% Archaea, and 0.01% Virus. Results showed that, the 31 distinct bacterial phyla represented in the Çal Cave soil sample were dominated by Actinobacteria (65%) and Proteobacteria (31%). The most dominant bacterial genus was Streptomyces. Among the 2% Eukaryotic population, the largest phylum was Ascomycota and it was mostly represented as Sordariomycetes. It was determined that 77% of Archaea was Halobacteria. The most abundant class of viruses dwelling in Çal Cave was Caudovirales. 91.61% of total readings could not be classified into any specific kingdom. Overall, classified and unclassified data verify that there exists vast microbial biodiversity in Çal Cave which could not be identified with classical microbiology techniques, and this microbial diversity provides a promising gene source for novel enzyme and bioactive compounds to be used in biotechnological applications.

Keywords

Actinobacteria, Cave soil, Metagenomics, Proteobacteria, Taxonomic profiling

Supporting Institution

the Yildiz Technical University.

Project Number

FDK-2019-3586 ".

Thanks

This study was performed with the permission of Ministry of Forest and Water Affairs of Turkey

Çal Mağarası toprak mikrobiyal çeşitliliğindeki biyoteknolojik potansiyelin metagenomik analizi

Abstract

Türkiye henüz araştırılmamış ve mikrobiyal çeşitliliği belirlenmemiş çok sayıda karstik mağaraya sahiptir. Bu mağaraların biyoçeşitlilik karakterizasyonu henüz moleküler bakış açısıyla ele alınarak sistematik bir şekilde incelenmemiştir. Trabzon’da yer alan Çal Mağarası önemli karstik mağaralardan biridir. Bu çalışmada Çal Mağarası’nın gen kaynaklarının biyoteknolojik potansiyelini değerlendirmek amacıyla, mağaranın mikrobiyal çeşitliliği ilk kez metagenomik yaklaşım ile araştırılmıştır. Detaylı taksonomik sınıflandırma 16S rRNA gibi sadece prokaryotları hedef alan spesifik bir markör gen yerine tüm çevresel genomların dizilenmesi ile gerçekleştirilmiştir. Taksonomik analize göre Çal Mağarası toprağındaki mikrobiyal çeşitliliğin %98’ni bakteriler, %2’sini ökaryotlar, %0.3’ünü arkealar ve %0.01’ini virüsler temsil etmektedir. Sonuçlar, Çal Mağarası toprak örneğinde temsil edilen 31 farklı bakteri filumunun %65’inin Actinobacteria ve %31’inin Proteobacteria olduğunu göstermektedir. Bunlar arasında en baskın bakteri cinsi Streptomyces olarak tespit edilmiştir. %2’lik ökaryotik popülasyon arasında en geniş filum Ascomycota’dır ve bu filumun toprak örneği içindeki en yaygın temsilcisinin Sordariomycetes olduğu görülmüştür. Arkeaların %77’sinin Halobacteria olduğu belirlenmiştir. Çal Mağarası toprağında yaşayan en yaygın virüs sınıfının Caudovirales olduğu ortaya çıkmıştır. Toplam okumaların %91.61’i için ise herhangi bir spesifik sınıflandırma yapılamamıştır. Sınıflandırılmış ve sınıflandırılmamış tüm verilere bakıldığında Çal Mağarası’nda klasik mikrobiyoloji teknikleriyle tanımlanamayacak olan çok büyük bir mikrobiyal biyoçeşitliliğin olduğunu ve bu mikrobiyal çeşitliliğin biyoteknolojik uygulamalarda kullanılacak yeni enzim ve biyoaktif bileşenlerin keşfi için umut verici bir gen kaynağı sağladığı doğrulanmaktadır.

Keywords

Aktinobakteriler, Mağara Toprağı, Metagenomik, Proteobakteriler, Taksonomik sınıflandırma

Project Number

FDK-2019-3586 ".

References

• Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., 1990. Basic local alignment search tool. Journal of Molecular Biology, 215(3): 403-410.
• Cheeptham, N., 2012. Cave Microbiomes: A Novel Resource for Drug Discovery. 1st ed. Springer Science & Business Media. New York, NY, USA.
• Davison A.J., Eberle R., Ehlers, B., Hayward, G.S., McGeoch, D.J., Minson, A.J., Pellett, P.E., Roizman, B., Kovler , M.B., Studdert, M.J., 2009. The Order Herpesvirales. Archives of Virology, 154(1): 171–177.
• D’Auria, G., Artacho, A., Rojas, R.A., Bautista, J.S., Méndez, R., Gamboa, M.T., Gómez-Cruz, R., 2018. Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs. Genes, 9(1): 55-68.
• De Mandal, S., Chatterjee, R., Kumar, N.S., 2017. Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle. BMC Microbiology, 17(1): 90-99.
• Ghosh, S., Kuisiene, N., Cheeptham, N., 2017. The cave microbiome as a source for drug discovery: Reality or pipe dream? Biochemical Pharmacology, 134:18-34.
• Grothet, I., Vettermann, R., Schuetze, B., Schumann, P., Sáiz-Jiménez, C., 1999. Actinomycetes in karstic caves of northern Spain (Altamira and Tito Bustillo). Journal of Microbiological Methods, 36 (1-2): 115-122.
• Inglis, D.O., Binkley, J., Skrzypek, M.S., Arnaud, M.B., Cerqueira, G.C., Shah, P., Sherlock, G., 2013. Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae. BMC Microbiology, 13(1): 91-114.
• Jones, D.S., Schaperdoth, I., Macalady, J.L., 2016. Biogeography of sulfur-oxidizing Acidithiobacillus populations in extremely acidic cave biofilms. The ISME Journal, 10(12): 2879-2891.
• Kalenov, S.V., Gordienko, M.G., Murzina, E.D., Poberezhniy, D.Y., Baurin, D.V., Suzina, N.E., Yarovaya, O.V., 2018. Halobacterium salinarum storage and rehydration after spray drying and optimization of the processes for preservation of carotenoids. Extremophiles, 22(3): 511-523.
• Katz, M., Hover, B.M., Brady, S.F., 2016. Culture-independent discovery of natural products from soil metagenomes. Journal of Industrial Microbiology & Biotechnology, 43(2-3): 129-141.
• King, A.M., Lefkowitz, E., Adams, M.J., Carstens, E.B., 2011. Virus taxonomy: Ninth report of the International Committee on Taxonomy of Viruses. 1st ed. Elsevier, San Diego, CA, USA.
• Mendoza, M.L.Z., Lundberg, J., Ivarsson, M., Campos, P., Nylander, J.A.A., Sallstedt, T., Dalen, L., 2016. Metagenomic analysis from the interior of a speleothem in Tjuv-Ante's Cave, Northern Sweden. PLoS One, 11(3): e0151577.
• Morin-Adeline, V., Vogelnest, L., Dhand, N.K., Shiels, M., Angus, W., Šlapeta, J., 2011. Afternoon shedding of a new species of Isospora (Apicomplexa) in the endangered Regent Honeyeater (Xanthomyza phrygia). Parasitology, 138(6):713-724.
• Oliveira, C., Gunderman. L., Coles, C.A., Lochmann, J., Parks, M., Ballard, E., Thomas, D.J., 2017. 16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria. Diversity, 9(3): 31-47.
• Ondov, B.D., Bergman, N.H., Phillippy, A.M., 2011. Interactive metagenomic visualization in a web browser. BMC Bioinformatics, 12(1): 385-394.
• Ramakrishnan, D., Tiwari, M.K., Manoharan, G., Sairam, T., Thangamani, R., Lee, J.K., Marimuthu, J., 2018. Molecular characterization of two alkylresorcylic acid synthases from Sordariomycetes fungi. Enzyme and Microbial Technology, 115:16-22.
• Rastogi, G., Sani, R.K., 2011. Molecular techniques to assess microbial community structure, function, and dynamics in the environment. In Microbes and Microbial Technology, Springer, New York, NY, pp. 29-57.
• Riquelme, C., Dapkevicius, M.D.L.E., Miller, A.Z., Charlop-Powers, Z., Brady, S., Mason, C., Cheeptham, N., 2017. Biotechnological potential of Actinobacteria from Canadian and Azorean volcanic caves. Applied Microbiology and Biotechnology, 101(2): 843-857.
• Rusznyák, A., Akob, D.M., Nietzsche, S., Eusterhues, K., Totsche, K.U., Neu, T.R., Katzschmann, L., 2011. Calcite biomineralization by bacterial isolates from the recently discovered pristine karstic Herrenberg cave. Applied and Environmental Microbiology, 78(4): 1157-1167.
• Schabereiter-Gurtner, C., Lubitz, W., Rölleke, S., 2003. Application of broad-range 16S rRNA PCR amplification and DGGE fingerprinting for detection of tick-infecting bacteria. Journal of Microbiological Methods, 52(2): 251-260.
• Sorokin, D.Y., Khijniak, T.V., Kostrikina, N.A., Elcheninov, A.G., Toshchakov, S.V., Bale, N.J., Kublanov, I.V., 2018. Natronobiforma cellulositropha gen. nov., sp. nov., a novel haloalkaliphilic member of the family Natrialbaceae (class Halobacteria) from hypersaline alkaline lakes. Systematic and Applied Microbiology, 41(4): 355-362.
• Wiseschart, A., Mhuanthong, W., Thongkam, P., Tangphatsornruang, S., Chantasingh, D., Pootanakit, K., 2018. Bacterial Diversity and Phylogenetic Analysis of Type II Polyketide Synthase Gene from Manao-Pee Cave, Thailand. Geomicrobiology Journal, 35(6): 518-527.
• Wood, D.E., Salzberg, S.L., 2014. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology, 15(3): R46.
• Yücel, S., Yamaç, M., 2010. Selection of Streptomyces isolates from Turkish karstic caves against antibiotic resistant microorganisms. Pakistan Journal of Pharmaceutical Science, 23 (1): 1-6.
• Zaman, M., Şahin, İ.F., Birinci, S., 2011. The Importance of Çal Cave (Düzköy-Trabzon) and its Surroundings as Regards Ecotourism Potential. Doğu Coğrafya Dergisi, 16(26): 24-47.
• Zhang, J., Kobert, K., Flouri, T., Stamatakis, A., 2014. PEAR: A fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics, 30(5): 614-620.
• Zhou, J., Gu, Y., Zou, C., Mo, M., 2007. Phylogenetic diversity of bacteria in an earth-cave in Guizhou Province, Southwest of China. The Journal of Microbiology, 45(2): 105-112.