Screening of bacteria in Yarık Sinkhole, Antalya, Turkey for carbonate dissolution, biomineralization and biotechnological potentials


  • Elif Özlem Arslan- Aydoğdu Istanbul University, Faculty of Science, Department of Biology
  • Yağmur Avci Istanbul University, Institute of Graduate Studies in Sciences
  • Nahdhoit Ahamada Rachid Istanbul University, Institute of Graduate Studies in Sciences
  • Batu Çolak Istanbul University, Institute of Graduate Studies in Sciences
  • Nihal Doğruöz-Güngör Istanbul University, Faculty of Science, Department of Biology



cave bacteria, non-ureolytic bacteria, carbonate dissolution, carbonate precipitation, polyketide synthase, nonribosomal pšeštide synthetase


Abiotic and biotic factors, especially microorganisms, play a role in the development of cave formations and the existence of unique characteristics of each cave. Due to the ecological conditions that characterize the cave environments, highly specialized microorganisms that are the main source of diverse bioactive compounds, inhabit these environments. The aim of this study is to determine the role and biotechnological potential of the bacteria isolated from Yarık Sinkhole located in Antalya (Turkey) by screening their ability to induce the CaCO3 precipitation, to hydrolyze urea, to induce calcite dissolution, and screening their possession of NRPS/PKS gene clusters. The most prevalent phylum is the Bacillota (synonym Firmicutes) (75.7 %), while the dominant species is Bacillus pumilus (33 %). All the isolates showed crystal formation on B4 agar medium, and the Energy dispersive X-Ray spectroscopy (EDS) analyses showed that the crystals are predominately composed of calcium, carbon and oxygen. Ninety-six (96 %) of our isolates have negative ureolytic activity. According to this result and having the ability to induce the CaCO3 precipitation, bac­teria in this environment use other biosynthesis pathways than urea hydrolysis. MgCO3 and CaCO3 were dissolved by 61 % and 59 % of the isolates, respectively. In addition, 5.9 % and 53.7 % of the isolates showed the possession of PKS and NRPS genes, respectively. This result reveals that our isolates have high in­dustrial and biotechnological potential. They may constitute good candidates for further biotechnological applications such as construction of bio-concretes, bioremediation, soil fertility, and production of biologically active secondary metabolites.


Download data is not yet available.


Aleti, G., Sessitsch, A., & G. Brader, 2015: Genome mining: prediction of lipopeptides and polyketides from Bacillus and related Firmicutes.- Computational and Structural Biotechnology Journal, 13, 192-203.

Amos, G. C., Borsetto, C., Laskaris, P., Krsek, M., Berry, A. E., Newsham, K. K., Calvo-Bado, L., Pearce, D.A., Vallin, C. & E.M. Wellington, 2015: Designing and implementing an assay for the detection of rare and Divergent NRPS and PKS Clones in European, Antarctic and Cuban soils.- PloS one, 10, 9, e0138327.

Banks, E.D., Nicholas, M.T., Gulley, J., Lubbers, B.R., Giarrizo, J.G., Bullen, H.A., Hoehler, T.M. & A.B. Hazel, 2010: Bacterial calcium carbonate precipitation in cave environments: A function of calcium homeostasis.- Geomicrobiology Journal, 646, 27, 5, 444-454.

Bansal, R., Dhami, N. K., Mukherjee, A. & M.S. Reddy, 2016: Biocalcification by halophilic bacteria for remediation of concrete structures in marine environment.- Journal of Industrial Microbiology and Biotechnology, 43, 11, 1497-1505.

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

Baskar, S., Baskar, R., Lee, N. & P.K. Theophilus, 2009: Speleothems from Mawsmai and Krem Phyllut caves, Meghalaya, India: some evidences on biogenic activities.- Environmental Geology, 57, 5, 1169-1186.

Bauer, M.A., Kainz, K., Carmona-Gutierrez, D. & F. Madeo, 2018: Microbial wars: competition in ecological niches and within the microbiome.- Microbial Cell, 5, 215–219.

https://doi: 10.15698/mic2018.05.628

Boquet, E., Boronate, A. & A. Ramos-Cormenzana, 1973: Production of calcite (calcium carbonate) crystals by soil bacteria is a general phenomenon.- Nature, 246,527–529.

Bukelskis, D., Dabkeviciene, D., Lukoseviciute, L., Bucelis, A., Kriaučiūnas, I., Lebedeva, J. & N. Kuisiene, 2019: Screening and transcriptional analysis of polyketide synthases and non-ribosomal peptide synthetases in bacterial strains from Krubera–Voronja Cave.- Frontiers in Microbiology, 10, 2149.

Cacchio, P. & M. Del Gallo, 2019: A novel approach to isolation and screening of calcifying bacteria for biotechnological applications.- Geosciences, 9, 11, 479.

Cacchio, P., Contento, R., Ercole, C., Cappuccio, G., Martinez, M. P. & A. Lepidi, 2004: Involvement of microorganisms in the formation of carbonate speleothems in the Cervo Cave (L'Aquila-Italy).- Geomicrobiology Journal, 21, 8, 497-509.

Cacchio, P., Ercole, C., Cappuccio, G. & A. Lepidi, 2003: Calcium carbonate precipitation by bacterial strains isolated from a limestone cave and from a loamy soil.- Geomicrobiology Journal, 20, 2, 85-98.

Canaveras, J.C., Sanchez-Moral, S., Soler, V. & C. Saiz-Jimenez, 2001: Microorganisms and microbially induced fabrics in cave walls.- Geomicrobiology Journal, v.18, p. 223–240.

Carrow, R.N., 2019: Best management practices for saline and sodic turfgrass soils: assessment and reclamation.- CRC Press.

Cheeptham, N., 2013: Advances and challenges in studying cave microbial diversity.- In Cave Microbiomes: A Novel Resource for Drug Discovery, pp. 1-34, Springer, New York, NY.

Choi, S., Park, S., Park, M., Kim, Y., Lee, K.M., Lee, O.M. & H.J. Son, 2021: Characterization of a novel CaCO3-forming alkali-tolerant Rhodococcus erythreus S26 as a filling agent for repairing concrete cracks.- Molecules, 26, 10, 2967.

Çandiroğlu, B. & N.D. Güngör, 2020: The biotechnological potentials of bacteria isolated from Parsık Cave, Turkey: Measuring the enzyme profiles, antibiotic resistance and antimicrobial activity in bacteria.- Johnson Matthey Technology Review, 64, 4, 466-479.

De los Ríos, A., Bustillo, M. A., Ascaso, C. & M.D.R. Carvalho, 2011: Bioconstructions in ochreous speleothems from lava tubes on Terceira Island (Azores).- Sedimentary Geology, 236, 1-2, 117-128.

Dhami, N.K., Reddy, M.S. & A. Mukherjee, 2013: Biomineralization of calcium carbonate polymorphs by the bacterial strains isolated from calcareous sites.- Journal of Microbiology and Biotechnology, 23, 5, 707-714.

Dupraz, C., Visscher, P.T., Baumgartner, L.K. & R.P Reid, 2004: Microbe-mineral interactions: early carbonate precipitation in a hypersaline lake (Eleuthera Island, Bahamas).- Sedimentology, 51, 745–765.

Ercole, C., Bozzelli, P., Altieri, F., Cacchio, P. & M. Del Gallo, 2012: Calcium carbonate mineralization: involvement of extracellular polymeric materials isolated from calcifying bacteria.- Microscopy and Microanalysis, 18, 4, 829-839. DOI:

Ercole, C., Cacchio, P., Botta, A.L., Centi, V. & A. Lepidi, 2007: Bacterially induced mineralization of calcium carbonate: the role of exopolysaccharides and capsular polysaccharides.- Microscopy and Microanalysis, 13, 1, 42-50.

Farhadi, S. & S. Ziadloo, 2020: Self-Healing Microbial Concrete-A Review.- Materials Science Forum, Vol. 990, pp. 8-12, Trans Tech Publications Ltd.

Fujita, Y., Ferris, F.G., Lawson, R.D., Colwell, F.S. & R.W. Smith, 2000: Subscribed content calcium carbonate precipitation by ureolytic subsurface bacteria.- Geomicrobiology Journal, 17, 305–318.

Ganendra, G., De Muynck, W., Ho, A., Arvaniti, E.C., Hosseinkhani, B., Ramos, J. A., Rahier, H. & N. Boon, 2014: Formate oxidation-driven calcium carbonate precipitation by Methylocystis parvus OBBP.-Applied and Environmental Microbiology, 80, 15, 4659-4667.

Hamedi, J., Kafshnouchi, M. & M. Ranjbaran, 2019: A study on actinobacterial diversity of Hampoeil cave and screening of their biological activities.- Saudi Journal of Biological Sciences, 26, 7, 1587-1595.

Hammes, F., Seka, A., de Knijf, S. & W. Verstraete, 2003: A novel approach to calcium removal from calcium-rich industrial wastewater.- Water Research, 37, 3, 699-704.

Jones, B., 2001: Microbial activity in caves — a geological perspective.- Geomicrobiology Journal, v. 18, p. 345–358.

Kenawy, A., Dailin, D.J., Abo-Zaid, G.A., Abd Malek, R., Ambehabati, K.K., Zakaria, K.H.N., Sayyed, R.Z. & H.A. El Enshasy, 2019: Biosynthesis of antibiotics by PGPR and their roles in biocontrol of plant diseases.- In Plant Growth Promoting Rhizobacteria for Sustainable Stress Management, pp. 1-35, Springer, Singapore.

Lee, Y.S., Kim, H.J. & W. Park, 2017: Non-ureolytic calcium carbonate precipitation by Lysinibacillus sp. YS11 isolated from the rhizosphere of Miscanthus sacchariflorus.- Journal of Microbiology, 55, 6, 440-447.

Li, W., Rokni-Zadeh, H., De Vleeschouwer, M., Ghequire, M G., Sinnaeve, D., Xie, G. L., Rozenski J., Madder, A., Martins J.C., & R. De Mot, 2013: The antimicrobial compound xantholysin defines a new group of Pseudomonas cyclic lipopeptides.- PloS one, 8, 5, e62946.

Lukoseviciute, L., Lebedeva, J., & N. Kuisiene, 2021: Diversity of polyketide synthases and nonribosomal peptide synthetases revealed through metagenomic analysis of a deep oligotrophic cave.- Microbial Ecology, 81, 1, 110-121.

Marvasi, M., Gallagher, K.L., Martinez, L.C., Molina Pagan W.C., Rodríguez Santiago, R.E., Castilloveitía Vega, G. & P.T. Visscher, 2012: Importance of B4 medium in determining organomineralization potential of bacterial environmental isolates.- Geomicrobiology Journal, 29, 10, 916-924.

Meier, A., Kastner, A., Harries, D., Wierzbicka-Wieczorek, M., Majzlan, J., Büchel, G. & E. Kothe, 2017: Calcium carbonates: induced biomineralization with controlled micromorphology.-Biogeosciences. 14, 21, 4867-4878.

Miller, A.Z., Garcia-Sanchez, A.M., Martin-Sanchez, P.M., Pereira, M.F.C., Spangenberg, J.E., Jurado, V., Dionisio, A., Afonso, M.J., Chaminé, H.I., Hermosin, B. & C. Saiz-Jimenez, 2018: Origin of abundant moonmilk deposits in a subsurface granitic environment.- Sedimentology, 65, 1482-1503.

Northup, E., Kathleen, H. & D. Lavoie, 2001: Geomicrobiology of caves: a review.- Geomicrobiology Journal, 18, 3, 199-222.

Olishevska, S., Nickzad, A. & E. Déziel, 2019: Bacillus and Paenibacillus secreted polyketides and peptides involved in controlling human and plant pathogens.- Applied Microbiology and Biotechnology, 103, 3, 1189-1215.

Omoregie, A.I, Ong D.E.L. & P.M. Nissom, 2018: Assessing ureolytic bacteria with calcifying abilities isolated from limestone caves for biocalcification.- Letters in Applied Microbiology, 68, 2, 173-181.

Orhan, F., Demirci, A. & D. Yanmis, 2017: CaCO3 and MgCO3 dissolving halophilic bacteria.- Geomicrobiology Journal, 34, 9, 804-810.

Ortega-Villamagua, E., Gudiño-Gomezjurado, M. & A. Palma-Cando, 2020: Microbiologically induced carbonate precipitation in the restoration and conservation of cultural heritage materials.- Molecules, 25, 23, 5499.

Parida, A. K. & A.B. Das, 2005: Salt tolerance and salinity effects on plants: a review.- Ecotoxicology and Environmental Safety, 60, 3, 324-349.

Qian, C. X., Wang, R. X., Cheng, L. & J.Y. Wang, 2010: Theory of microbial carbonate precipitation and its application in restoration of cement-based materials defects.- Chinese Journal of Chemistry, 28, 5, 847–857.

Raaijmakers, J.M., De Bruijn, I., Nybroe, O. & M. Ongena, 2010: Natural functions of lipopeptides from Bacillus and Pseudomonas: more than surfactants and antibiotics.- FEMS Microbiology Reviews, 34, 6, 1037-1062.

Rajasekar, A., Wilkinson, S. & C.K. Moy, 2021: MICP as a potential sustainable technique to treat or entrap contaminants in the natural environment: A review.- Environmental Science and Ecotechnology, 100096.

Reddy, P.Y., Ramesh, B. & L.P. Kumar, 2020: Influence of bacteria in self healing of concrete-a review.- Materials Today: Proceedings, 33, 4212-4218.

Reeburgh, W., 2007: Oceanic methane biogeochemistry.- Chemical Reviews, 107, 2, 486-513.

Saravanan, A., Kumar, P.S., Vardhan, K.H., Jeevanantham, S., Karishma, S.B., Yaashikaa, P.R. & P. Vellaichamy, 2020: A review on systematic approach for microbial enhanced oil recovery technologies: Opportunities and challenges.- Journal of Cleaner Production, 258, 120777.

Sarda, D., Choonia, H.S., Sarode, D.D. & S.S Lele, 2009: Biocalcification by Bacillus pasteurii urease: a novel application.- Journal of Industrial Microbiology and Biotechnology, 36, 8, 1111-1115.

Seifan, M., Samani A.K. & A. Berenjian, 2016: Induced calcium carbonate precipitation using Bacillus species.- Applied Microbiology and Biotechnology, 100, 23, 9895-9906.

Seifan, M., Sarabadani, Z. & A. Berenjian, 2020: Microbially induced calcium carbonate precipitation to design a new type of bio self-healing dental composite.- Applied Microbiology and Biotechnology, 104, 5, 2029-2037.

Su F. & Y.Y. Yang, 2020: Microbially induced carbonate precipitation via methanogenesis pathway by a microbial consortium enriched from activated anaerobic sludge.- Journal of Applied Microbiology, 131, 1, 236-256.

Su, Y., Qian, C., Rui, Y., & J. Feng, 2021: Exploring the coupled mechanism of fibers and bacteria on self-healing concrete from bacterial extracellular polymeric substances (EPS).- Cement and Concrete Composites, 116, 103896.

Sukhanova, E., Zimens, E., Kaluzhnaya, O., Parfenova, V. & O. Belykh, 2018: Epilithic biofilms in Lake Baikal: screening and diversity of PKS and NRPS genes in the genomes of heterotrophic bacteria.- Polish Journal of Microbiology, 67, 4, 501.

Tambadou, F., Lanneluc, I., Sablé, S., Klein, G. L., Doghri, I., Sopéna, V., Didelot, S., Barthélémy, C., Thiéry, V. & R. Chevrot, 2014: Novel nonribosomal peptide synthetase (NRPS) genes sequenced from intertidal mudflat bacteria.- FEMS Microbiology Letters, 357, 2, 123-130.

Teodosiu, G. & M. Enache, 2019: Biotechnological potential of halophilic archaea isolated from Romanian extreme habitats.- Studia Universitatis Babes-Bolyai, Biologia, 64, 1.

Tourney, J. & B.T. Ngwenya, 2009: Bacterial extracellular polymeric substances (EPS) mediate CaCO3 morphology and polymorph.- Chemical Geology, 262, 138-146.

Turchyn, A.V., Bradbury, H.J., Walker, K. & X. Sun, 2021: Controls on the precipitation of carbonate minerals within marine sediments.- Frontiers in Earth Science, 9, 57.

Tyagi, B., Gupta, B. & I.S. Thakur, 2020: Biosorption of Cr (VI) from aqueous solution by extracellular polymeric substances (EPS) produced by Parapedobacter sp. ISTM3 strain isolated from Mawsmai cave, Meghalaya, India.- Environmental Research, 191, 110064.

Van Paassen, L.A., Daza, C.M., Staal, M., Sorokin, D.Y., Van Der Zon, W. & M.C. Van Loosdrecht, 2010: Potential soil reinforcement by biological denitrification.- Ecological Engineering, 36, 168–175.




How to Cite

Arslan- Aydoğdu, E. Özlem, Avci, Y., Ahamada Rachid, N. ., Çolak, B. ., & Doğruöz-Güngör, N. (2023). Screening of bacteria in Yarık Sinkhole, Antalya, Turkey for carbonate dissolution, biomineralization and biotechnological potentials. Acta Carsologica, 52(1).



Original papers