The microbial community structure of the Dupnisa cave in Kırklareli, Turkey

  • Nihal Doğruöz-Güngör istanbul university
Keywords: cave microbiology, bacterial diversity, archaeal diversity, next generation metagenomic sequencing


Cave ecosystems count to be extreme environments due to their stable temperature, darkness, high humidity rates, and limited organic materials. In this context, these ecosystems represent invaluable laboratories for microbiological studies. Although there are common features between the microorganism groups obtained from the culture-based microbiological studies conducted in the caves and the groups highlighted through molecular methods, the microorganism groups determined through this last method are richer. The detected microorganisms are variable depending on the characteristics of each cave. The aim of this study is to determine the microbial diversity in samples taken from 5 different regions (including regions visited by tourists) of Dupnisa Cave and to reveal the differences between these regions. This is the first microbiological study running in cave sediments of Dupnisa Cave System situated in the north-western of Turkey. In this study, using the Illumina MiSeq next-generation sequencing approach for analyses of Dupnisa Cave samples, 14 phyla and 298 genera as well as 2 phyla and 20 genera can be attributed to bacterial and archaea OTUs, respectively. Moreover, the bacterial community is dominated by the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi and Acidobacteria distributed with 1 % and above. Archaeal community is represented by Thaumarchaeota and Euryarchaeota phyla. Proteobacteria is the most dominant bacterial phylum and Thaumarchaeota dominates the archaeal phyla. The highest number of types of bacteria according to Chao 1 richness estimation index were found at point AF (cave entrance / sediment), and that of types of archaea were found at point F2 (touristic area 2 / cave sediment). F2 was determined as the sampling point with the highest diversity of archaeal and bacterial genera according to Shannon-Wiener diversity index.


Download data is not yet available.


Anda, D., Krett, G., Makk, J., Márialigeti, K., Mádl-Szőnyi, J. & A.K. Borsodi, 2017: Comparison of Bacterial and Archaeal communities from different habitats of the hypogenic Molnár János Cave of the Buda Thermal Karst System (Hungary).- Journal of Cave and Karst Studies, 79, 113-121.

Bai, R., Wang J.T., Deng, Y., He, J.Z., Feng, K. & L.M. Zhang, 2017: Microbial community and functional structure significantly varied among distinct types of paddy soils but responded differently along gradients of soil depth layers.- Frontiers in microbiology, 8, 945.
Barton, H.A., Taylor, M.R. & N.R. Pace, 2004: Molecular phylogenetic analysis of a bacterial community in an oligotrophic cave environment.- Geomicrobiology Journal, 21, 11-20.
Barton, H.A., 2006: Introduction to cave microbiology: a review for the non-specialist.- Journal of Cave and Karst Studies, 68, 43–54.

Barton, H.A. & V. Jurado, 2007: What’s up down there? Microbial diversity in caves.- Microbe, 2, 132–138.

Barton, H.A., Taylor, N.M., Kreate, M.P., Springer, A.C., Oehrle, S.A. & J.L. Bertog, 2007: The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments.- International Journal of Speleology, 36, 93-104.

Barton, H.A., 2015: Starving artists: Bacterial oligotrophic heterotrophy in caves. -In: Engel A. & de Gruyter W. (eds.), In Life in Extreme Environments: Microbial Life of Cave Systems. New York, NY. pp. 350.

Bartossek, R., Spang, A., Weidler, G., Lanzen, A. & C. Schleper, 2012: Metagenomic analysis of ammonia-oxidizing archaea affiliated with the soil group.- Frontiers in microbiology, 3, 208.

Baskar, S., Chalia, S. & R. Baskar, 2018: Calcite precipitation by Rhodococcus sp. isolated from Kotumsar cave, Chhattisgarh, India.- Current Science, 114,1063-1074.

Bastian, F. & C. Alabouvette, 2009: Lights and shadows on the conservation of a rock art cave: the case of Lascaux Cave.- International Journal of Speleology, 38, 55-60.

Bates, S.T., Berg-Lyons, D., Caporaso J.G., Walters, W.A., Knight, R. & N. Fierer, 2011: Examining the global distribution of dominant archaeal populations in soil. -The ISME journal, 5, 908-917.

Carmichael, M.J., Carmichael, S.K., Santelli, C.M., Strom, A. & S.L. Bräuer, 2013: Mn (II)-oxidizing bacteria are abundant and environmentally relevant members of ferromanganese deposits in caves of the upper Tennessee River Basin.- Geomicrobiology Journal, 30, 779-800.

Chelius, M.K. & J.C. Moore, 2004: Molecular phylogenetic analysis of Archaea and Bacteria in Wind Cave, South Dakota. -Geomicrobiology Journal, 21, 123-134.

Chelius, M.K., Beresford, G., Horton, H., Quirk, M., Selby, G., Simpson, R.T., Horrocks, R. & J.C. Moore, 2009: Impacts of alterations of organic inputs on the bacterial community within the sediments of Wind Cave, South Dakota, USA.- International Journal of Speleology, 38, 1-10.

Chen, Y., Wu, L., Boden, R., Hillebrand, A., Kumaresan, D., Moussard, H., Baciu, M., Lu, Y. & J. Colin Murrell, 2009: Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave. -The ISME Journal, 3,1093-1104.

Chroňáková, A., Horák, A., Elhottová, D. & V. Krištůfek, 2009: Diverse archaeal community of a bat guano pile in Domica Cave (Slovak Karst, Slovakia). -Folia microbiologica, 54, 436-446.

Ciais, P., Sabine, C., Bala, G., Bopp, L., Brovkin, V., Canadell, J., ... & C. Jones, 2014: Carbon and other biogeochemical cycles.- In Climate change 2013: the physical science basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, p. 465-570

Cuezva, S., Fernandez-Cortes, A., Porca, E., Pašić, L., Jurado, V., Hernandez-Marine, M., ... & C. Saiz-Jimenez, 2012: The biogeochemical role of actinobacteria in Altamira cave, Spain.- FEMS microbiology ecology, 81, 281-290.

De Mandal, S., Panda, A.K., Bisht, S.S. & N.S. Kumar, 2015: First report of bacterial community from a bat guano using Illumina next-generation sequencing.- Genomics Data, 4, 99-101.

De Leon, M.P., Montecillo, A.D., Pinili, D.S., Siringan, M.A.T. & D.S. Park, 2018: Bacterial diversity of bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines: A first report on the metagenome of Philippine bat guano.- PloS one, 13, e0200095.

Dworkin, M., 2002: The Prokaryotes: An evolving electronic resource for the microbiological community. Springer-Verlag, New York.

Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C. & R. Knight, 2011: UCHIME improves sensitivity and speed of chimera detection.- Bioinformatics, 27, 2194-2200.

Engel, A.S., 2010: Microbial diversity of cave ecosystem. -In: Loy A., Mandl M. & Barton L.L. (eds.) Geomicrobiology: Molecular and environmental perspective. Springer Science and Business Media B.V., pp. 219-238.

Engel, A.S., Meisinger, D.B., Porter, M.L., Payn, R.A., Schmid, M., Stern, L.A., ... & N.M. Lee, 2010, Linking phylogenetic and functional diversity to nutrient spiraling in microbial mats from Lower Kane Cave (USA).- The ISME journal, 4, 98-110.

Fong, D.W., 2011: Management of subterranean fauna in karst.- In Karst management Springer, Dordrecht. p. 201-224.

Griffin, D.W., Gray, M.A., Lyles, M.B. & D.E. Northup, 2014: The transport of nonindigenous microorganisms into caves by human visitation: a case study at Carlsbad Caverns National Park.- Geomicrobiology Journal, 31, 175-185.

Groth, I. & C. Saiz-Jiménez, 1999: Actinomycetes in hypogean environments.- Geomicrobiology Journal, 16, 1-8.

Groth, I., Vettermann, R., Schuetze, B., Schumann, P. & C. Saiz-Jiménez, 1999: Actinomycetes in karstic caves of Northern Spain (Altamira and Tito Bustillo).- Journal of Microbiological Methods, 36, 115-122.

Gulecal-Pektas, Y., 2016: Bacterial diversity and composition in oylat cave (Turkey) with combined sanger/pyrosequencing approach.- Polish Journal of Microbiology, 65, 69-75.

Gulecal-Pektas, Y. & M. Temel, 2017: A Window to the Subsurface: Microbial Diversity in Hot Springs of a Sulfidic Cave (Kaklik, Turkey).- Geomicrobiology Journal, 34, 374-384.

Hathaway, J.J.M., Garcia, M.G., Balasch, M.M., Spilde, M.N., Stone, F.D., Dapkevicius, M.D.L. N., ... & D.E. Northup, 2014: Comparison of bacterial diversity in Azorean and Hawai'ian lava cave microbial mats.- Geomicrobiology journal, 31, 205-220.

Hoyos, M., Soler, V., Cañaveras, J.C., Sánchez-Moral, S. & E. Sanz-Rubio, 1998, Microclimatic characterization of a karstic cave: human impact on microenvironmental parameters of a prehistoric rock art cave (Candamo Cave, northern Spain).- Environmental Geology, 33, 231-242.

Huttenhower, C., Gevers, D., Knight, R., Abubucker, S., Badger, J.H., Chinwalla, A.T., ... & M.G. Giglio, 2012: Structure, function and diversity of the healthy human microbiome.- Nature, 486, 207-214.

Ikner, L.A., Toomey, R.S., Nolan, G., Neilson, J.W., Pryor, B.M. & R.M. Maier, 2007: Culturable microbial diversity and the impact of tourism in Kartchner Caverns, Arizona.- Microbial Ecology, 53, 30-42.

Iţcuş, C., Pascu, M.D., Brad, T., Perşoiu, A., & C. Purcarea, 2016: Diversity of cultured bacteria from the perennial ice block of Scarisoara Ice Cave, Romania.- International Journal of Speleology, 45, 89-100.

Jones, D.S., Tobler, D.J., Schaperdoth, I., Mainiero, M. & J.L. Macalady, 2010: Community structure of subsurface biofilms in the thermal sulfidic caves of Acquasanta Terme, Italy. -Applied and Environmental Microbiology, 76, 5902-5910.

Jones, D.S., Albrecht, H.L., Dawson, K.S., Schaperdoth, I., Freeman, K.H., Pi Y., & et al., 2012: Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm.- The ISME Journal, 6, 158-170.

Jones, A.A. & P.C. Bennett 2014: Mineral microniches control the diversity of subsurface microbial populations. -Geomicrobiology Journal, 31, 246-261.

Jurado, V., Laiz, L., Rodriguez-Nava, V., Boiron, P., Hermosin, H., Sanchez-Moral, S. & C., Saiz-Jimenez, 2010: Pathogenic and opportunistic microorganisms in caves.- International Journal of Speleology, 39, 15-24.

Kalyuzhnaya, M.G., Lidstrom, M.E. & L. Chistoserdova, 2008: Real-time detection of actively metabolizing microbes by redox sensing as applied to methylotroph populations in Lake Washington.- The ISME journal, 2, 696-706.

Kieraite-Aleksandrova, I., Aleksandrovas, V. & N. Kuisiene, 2016: Down into the Earth: microbial diversity of the deepest cave of the world.- Biologia, 70, 989-1002.

Kimble, J.C., 2017: Comparison of Bacterial and Archaeal Communities in the Subsurface versus Surface: Implications for Nitrogen Cycling. University of New Mexico.

Lavoie, K.H., Winter, A.S., Read, K.J., Hughes, E.M., Spilde, M.N. & D.E. Northup, 2017: Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA. -PloS one, 12, e0169339.

Lee, I.T., Liu, J.Y., Lin, C.H., Oyama, K.-I., Chen, C.Y., & C.H. Chen, 2012: Ionospheric plasma caves under the equatorial ionization anomaly.- Journal of Geophysical Research, 117, A11309,

Macalady, J.L., Lyon, E.H., Koffman, B., Albertson, L.K., Meyer, K., Galdenzi, S. & S. Mariani, 2006: Dominant microbial populations in limestone-corroding stream biofilms, Frasassi cave system, Italy.- Applied and Environmental Microbiology, 72, 5596-5609.

Martens-Habbena, W., Berube, P.M., Urakawa, H., José, R. & D.A. Stahl, 2009: Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria.- Nature, 461, 976-979.

Mulec J. & G. Kosi, 2009: Lampenflora algae and methods of growth control. -Journal of cave and karst studies, 71, 109-115.

Nazik, L., Törk K., Özel, E., Mengi, H., Aksoy, B. & C. Acar, 1998: Kuzey ve Kuzeydoğu Trakya’nın (Kırklareli-Tekirdağ) Doğal Mağaraları. Dosya No: 43584. Ankara: Maden Tetkik ve Arama Genel Müdürlüğü, Jeoloji Etütleri Dairesi Başkanlığı.

Northup D.E. & K.H. Lavoie, 2001: Geomicrobiology of caves: a review.- Geomicrobiology Journal, 18: 199-222.

Northup, D.E., Barns, S.M., Yu, L.E., Spilde, M.N., Schelble, R.T., Dano, K.E., ... & C. N. Dahm, 2003: Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves.- Environmental Microbiology, 5, 1071-1086.

Oliveira, C., Gunderman, L., Coles, C.A., Lochmann, J., Parks, M., Ballard, E., ... & D.J. Thomas, 2017: 16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria.- Diversity. 9, 31.

Ortiz, M., Neilson, J.W., Nelson, W.M., Legatzki, A., Byrne, A., Yu, Y., Wing, R.A., Soderlund, C.A., Pryor, B.M., Pierson, L.S. & R.M. Maier, 2013: Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZ.- Microbial ecology, 65, 371-383.

Ortiz, M., Legatzki, A., Neilson, J.W., Fryslie, B., Nelson, W.M., Wing, R.A., ... & R.M. Maier, 2014: Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave.- The ISME journal, 8, 478-491.

Palmer A.N., 1991: Origin and morphology of limestone caves.- Geological Society of America Bulletin, 103, 1–21.<0001:OAMOLC>2.3.CO;2

Paksuz, S., Özkan, B., & T. Postawa, 2007: Seasonal changes of cave-dwelling bat fauna, and their relationship with microclimate in Dupnisa Cave System (Turkish Thrace).- Acta Zoologica Cracoviensia-Series A: Vertebrata, 50, 57-66.

Paksuz, S., 2017: Important Caves in Turkish Thrace for Bats: Dupnisa Cave System and Koyunbaba Cave. In Cave Investigation.- IntechOpen, 77-93.

Pašić, L., Kovče, B., Sket, B., & B. Herzog-Velikonja, 2010: Diversity of microbial communities colonizing the walls of a Karstic cave in Slovenia.- FEMS Microbiology Ecology, 71, 50-60.

Pester, M., Schleper, C., & M. Wagner, 2011: The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology.- Current opinion in microbiology, 14, 300-306.

Porter, M.L., Engel, A.S., Kane, T.C. & B.K. Kinkle, 2009: Productivity-diversity relationships from chemolithoautotrophically based sulfidic karst systems.- International Journal of Speleology, 38, 27-40.

Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J. & F.O. Glöckner, 2007: SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.- Nucleic Acids Research, 35, 7188-7196.

Reitschuler, C., Lins, P., Wagner, A. O. & P. Illmer, 2014: Cultivation of moonmilk-born non-extremophilic Thaum and Euryarchaeota in mixed culture.- Anaerobe, 29, 73-79.

Reitschuler, C., Lins, P., Schwarzenauer, T., Spötl, C., Wagner, A.O. & P. Illmer, 2015: New undescribed lineages of non-extremophilic archaea form a homogeneous and dominant element within alpine moonmilk microbiomes.- Geomicrobiology Journal, 32, 890-902.

Reitschuler, C., Spötl, C., Hofmann, K., Wagner, A.O. & P. Illmer, 2016: Archaeal distribution in moonmilk deposits from Alpine caves and their ecophysiological potential.- Microbial ecology, 71, 686-699.

Rusznyák, A., Akob, D.M., Nietzsche, S., Eusterhues, K., Totsche, K.U., Neu, T.R., ... & L. Katzschmann, 2012: Calcite biomineralization by bacterial isolates from the recently discovered pristine karstic Herrenberg cave.- Applied and Environmental Microbiology, 78, 1157-1167.

Sarmiento, F.B., Leigh, J.A., & W.B. Whitman, 2011: Genetic systems for hydrogenotrophic methanogens. In Methods in enzymology.- Academic Press, 494, 43-73.

Schabereiter-Gurtner, C., Saiz-Jimenez, C., Piñar, G., Lubitz, W. & S. Rölleke, 2002: Altamira cave Paleolithic paintings harbor partly unknown bacterial communities.- FEMS Microbiology Letters, 211, 7-11.

Shapiro J. & A. Pringle, 2010: Anthropogenic influences on the diversity of fungi isolated from caves in Kentucky and Tennessee.- The American Midland Naturalist, 163, 76-87.

Stahl, D.A. & J.R. de la Torre, 2012: Physiology and diversity of ammonia-oxidizing archaea. Annual review of microbiology, 66, 83-101.

Tetu, S.G., Breakwell, K., Elbourne, L.D., Holmes, A.J., Gillings, M.R. & I.T. Paulsen, 2013: Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism.- The ISME journal, 7, 1227-1236.

Tomczyk-Żak, K. & U. Zielenkiewicz, 2016, Microbial diversity in caves.- Geomicrobiology Journal, 33, 20-38.

Torsvik, V. & L. Øvreås, 2002: Microbial diversity and function in soil: from genes to ecosystems.- Current Opinion in Microbiology, 5, 240-245.

Van Dijk, E.L., Auger, H., Jaszczyszyn, Y. & C. Thermes, 2014: Ten years of next-generation sequencing technology.- Trends in genetics, 30, 418-426.

Wiseschart, A., Mhuanthong, W., Thongkam, P., Tangphatsornruang, S., Chantasingh, D. & K. Pootanakit, 2018: Bacterial Diversity and Phylogenetic Analysis of Type II Polyketide Synthase Gene from Manao-Pee Cave, Thailand.- Geomicrobiology Journal, 35, 518-527.

Wu, J.H., Chen, W.Y., Kuo, H.C. & Y.M. Li, 2019: Redox fluctuations shape the soil microbiome in the hypoxic bioremediation of octachlorinated dibenzodioxin-and dibenzofuran-contaminated soil.- Environmental Pollution, 248, 506-515.

Yan, Y., Fu, D. & J. Shi, 2019: Screening and Immobilizing the Denitrifying Microbes in Sediment for Bioremediation.- Water, 11, 614.
Yasir, M., 2018: Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota.- Brazilian Journal of Microbiology, 49, 248-257.

Zhou, J., Gu, Y., Zou, C. & M. Mo, 2007: Phylogenetic diversity of bacteria in an earth-cave in Guizhou Province, Southwest of China.- Journal of Microbiology, 45, 105-112.

Zhao, R., Wang, H., Yang, H., Yun, Y. & H.A. Barton, 2017: Ammonia-oxidizing Archaea dominate ammonia-oxidizing communities within alkaline cave sediments.- Geomicrobiology journal, 34, 511-523.
How to Cite
Doğruöz-GüngörN. The microbial community structure of the Dupnisa cave in Kırklareli, Turkey. AC [Internet]. 2020Dec.16 [cited 2022Jan.24];49(2-3). Available from:
Original papers