Cultivable Sponge-Associated Actinobacteria from Coastal Area of Eastern Mediterranean Sea
Author(s)
Özlem Öner,
Güner Ekiz,
E. Esin Hameş*,
Volkan Demir,
Özkan Gübe,
F. Can Özkaya,
M. Baki Yokeş,
Ataç Uzel,
Erdal Bedir*
Affiliation(s)
Department of Biotechnology, Graduate School of Natural and Applied Sciences, Ege University, Bornova, Izmir, Turkey. Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey. Institute of Marine Sciences and Management, Istanbul University, Vefa, Istanbul, Turkey. Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Halic University, Siracevizler Cd. No: 29 Bomonti, Sisli, Istanbul, Turkey. Department of Biology, Faculty of Science, Ege University, Bornova, Izmir, Turkey.
Department of Biotechnology, Graduate School of Natural and Applied Sciences, Ege University, Bornova, Izmir, Turkey. Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey. Institute of Marine Sciences and Management, Istanbul University, Vefa, Istanbul, Turkey. Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Halic University, Siracevizler Cd. No: 29 Bomonti, Sisli, Istanbul, Turkey. Department of Biology, Faculty of Science, Ege University, Bornova, Izmir, Turkey.
ABSTRACT
In this study, 16 marine sponge samples collected from Eastern Mediterranean Sea were used for the isolation of sponge-associated Actinobacteria. Different media and pre-treatment methods were applied for the isolation experiments. In total, 7578 actinomycetes colonies were observed on the primary isolation plates, and 20 representative isolates were selected for further studies based on their morphologies and chemical profiles. These isolates were investigated for their antimicrobial activities, seawater requirements and 16S rRNA gene sequences. The phylogenetic analysis revealed that 80% of the isolated Actinobacteria was a member of the Streptomyces genus. All the isolates showed no absolute requirement for seawater. Fifteen of the selected isolates exhibited antimicrobial activity against methicillin resistant Staphylococcus aureus and vancomycin resistant Enterococcus faecium, whereas 3 isolates were active against Candida albicans.
Cite this paper
Öner, Ö. , Ekiz, G. , Hameş, E. , Demir, V. , Gübe, Ö. , Özkaya, F. , Yokeş, M. , Uzel, A. and Bedir, E. (2014) Cultivable Sponge-Associated Actinobacteria from Coastal Area of Eastern Mediterranean Sea. Advances in Microbiology, 4, 306-316. doi: 10.4236/aim.2014.46037.
Öner, Ö. , Ekiz, G. , Hameş, E. , Demir, V. , Gübe, Ö. , Özkaya, F. , Yokeş, M. , Uzel, A. and Bedir, E. (2014) Cultivable Sponge-Associated Actinobacteria from Coastal Area of Eastern Mediterranean Sea. Advances in Microbiology, 4, 306-316. doi: 10.4236/aim.2014.46037.
References
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http://dx.doi.org/10.1038/ismej.2009.143 [13] Webster, N.S., Taylor, M.W., Behnam, F., Lücker, S., Rattei, T., Whalan, S., Horn, M. and Wagner, M. (2010) Deep Sequencing Reveals Exceptional Diversity and Modes of Transmission for Bacterial Sponge Symbionts. Environmental Microbiology, 2, 2070-2082. [14] Myadoh, S. (1993) Research on Antibiotic Screening in Japan over the Last Decade: A Producing Microorganism Approach. Actinomycetologica, 7, 100-106.
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http://dx.doi.org/10.1128/AEM.68.10.5005-5011.2002 [18] Kim, T.K., Garson, M.J. and Fuerst, J.A. (2005) Marine Actinomycetes Related to the “Salinispora” Group from the Great Barrier Reef Sponge Pseudoceratina clavata. Environmental Microbiology, 7, 509-518.
http://dx.doi.org/10.1111/j.1462-2920.2005.00716.x [19] Li, Z.Y. and Liu, Y. (2006) Marine Sponge Craniella austrialiensis-Associated Bacterial Diversity Revelation Based on 16S rDNA Library and Biologically Active Actinomycetes Screening, Phylogenetic Analysis. Letters in Applied Microbiology, 43, 410-416.
http://dx.doi.org/10.1111/j.1472-765X.2006.01976.x [20] Jiang, S., Sun, W., Chen, M., Dai, S., Zhang, L., Liu, Y., Lee, K.J. and Li, X. (2007) Diversity of Culturable Actinobacteria Isolated from Marine Sponge Haliclona sp. Antonie van Leeuwenhoek, 92, 405-416.
http://dx.doi.org/10.1007/s10482-007-9169-z [21] Jiang, S., Li, X., Zhang, L., Sun, W., Dai, S., Xie, L., Liu, Y. and Lee, K.J. (2008) Culturable Actinobacteria Isolated from Marine Sponge Iotrochota sp. Marine Biology, 153, 945-952.
http://dx.doi.org/10.1007/s00227-007-0866-y [22] Schneemann, I., Ohlendorf, B., Zinecker, H., Nagel, K., Wiese, J. and Imhoff, J.F. (2010) Nocapyrones A-D, Gamma-Pyrones from a Nocardiopsis Strain Isolated from the Marine Sponge Halichondria panicea. Journal of Natural Products, 73, 1444-1447.
http://dx.doi.org/10.1021/np100312f [23] Zhang, H., Zhang, W., Jin, Y., Jin, M. and Yu, X. (2008) A Comparative Study on the Phylogenetic Diversity of Culturable Actinobacteria Isolated from Five Marine Sponge Species. Antonie van Leeuwenhoek, 93, 241-248.
http://dx.doi.org/10.1007/s10482-007-9196-9 [24] Selvin, J., Shanmughapriya, S., Gandhimathi, R., Kiran, G.S., Ravji, T.R., Natarajaseenivasan, K. and Hema, T.A. (2009) Optimization and Production of Novel Antimicrobial Agents from Sponge Associated Marine Actinomycetes Nocardiopsis dassonvillei MAD08. Applied Microbiology and Biotechnology, 83, 435-445.
http://dx.doi.org/10.1007/s00253-009-1878-y [25] Abdelmohsen, U.R., Pimente-Elardo, S.M., Hanora, A., Radwan, M., Abou-El-Ela, S.H., Ahmed, S. and Hentschel, U. (2010) Isolation, Phylogenetic Analysis and Anti-Infective Activity Screening of Marine Sponge-Associated Actinomycetes. Marine Drugs, 8, 399-412.
http://dx.doi.org/10.3390/md8030399 [26] Jensen, P.R., Gontang, E., Mafnas, C., Mincer, T.J. and Fenical, W. (2005) Culturable Marine Actinomycete Diversity from Tropical Pacific Ocean Sediments. Environmental Microbiology, 7, 1039-1048.
http://dx.doi.org/10.1111/j.1462-2920.2005.00785.x [27] Connon, S.A. and Giovannoni, S.J. (2002) High-Throughput Methods for Culturing Microorganisms in Very-Low-Nutrient Media Yield Diverse New Marine Isolates. Applied and Environmental Microbiology, 68, 3878-3885.
http://dx.doi.org/10.1128/AEM.68.8.3878-3885.2002 [28] CLSI (Clinical and Laboratory Standards) (2007) Performance Standards for Antimicrobial Susceptibility Testing, 17th Informational Supplement. M100-S17, Vol. 27, CLSI. [29] Liu, D., Coloe, S., Baird, R. and Pedersen, J. (2000) Rapid Mini-Preparation of Fungal DNA for PCR. Journal of Clinical Microbiology, 38, 471. [30] Hames-Kocabas, E.E. and Uzel, A. (2012) Isolation Strategies of Marine-Derived Actinomycetes from Sponge and Sediment Samples. Journal of Microbiological Methods, 88, 342-347.
http://dx.doi.org/10.1016/j.mimet.2012.01.010 [31] Jensen, P.R., Dwight, R. and Fenical. W. (1991) Distribution of Actinomycetes in Near-Shore Tropical Marine Sediments. Applied and Environmental Microbiology, 57, 1102-1108. [32] Kroppenstedt, R.M. and Evtushenko, L.I. (2006) The Family Nocardiopsaceae. In: Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.H. and Stackebrandt, E., Eds, The Prokaryotes, 3rd Edition, Springer Science+Business Media, LLC, New York, 754-795. [33] Maldonado, L.A., Stach, J.E.M., Pathom-aree, W., Ward, A.C., Bull, A.T. and Goodfellow, M. (2005) Diversity of Cultivable Actinobacteria in Geographically Widespread Marine Sediments. Antonie van Leeuwenhoek, 87, 11-18.
http://dx.doi.org/10.1007/s10482-004-6525-0 [34] Khan, S.T., Komaki, H., Motohashi, K., Kozone, I., Mukai, A., Takagi, M, and Shin-ya, K. (2011) Streptomyces Associated with a Marine Sponge Haliclona sp.; Biosynthetic Genes for Secondary Metabolites and Products. Environmental Microbiology, 13, 391-403.
http://dx.doi.org/10.1111/j.1462-2920.2010.02337.x [35] Sun, W., Dai, S., Jiang, S., Wang, G., Liu, G., Wu, H. and Li, X. (2010) Culture-Dependent and Culture-Independent Diversity of Actinobacteria Associated with the Marine Sponge Hymeniacidon perleve from the South China Sea. Antonie van Leeuwenhoek, 98, 65-75.
http://dx.doi.org/10.1007/s10482-010-9430-8 [36] Hentschel, U., Schmid, M., Wagner, M., Fieseler, L., Gernert, C. and Hacker, J. (2001) Isolation and Phylogenetic Analysis of Bacteria with Antimicrobial Activities from the Mediterranean Sponges Aplysina aerophoba and Aplysina cavernicola. FEMS Microbiology Ecology, 35, 305-312.
http://dx.doi.org/10.1111/j.1574-6941.2001.tb00816.x [37] Muscholl-Silberhorn, A., Thiel, V. and Imhoff, J.F. (2007) Abundance and Bioactivity of Cultured Sponge-Associated Bacteria from the Mediterranean Sea. Microbial Ecology, 55, 94-106.
http://dx.doi.org/10.1007/s00248-007-9255-9 [38] Ozcan, K., Aksoy, S.C., Kalkan, O., Uzel, A., Hames-Kocabas, E.E. and Bedir, E. (2013) Diversity and Antibiotic Producing Potentials of Cultivable Marine-Derived Actinomycetes from Coastal Sediments of Turkey. Journal of Soils and Sediments, 13, 1493-1501.
http://dx.doi.org/10.1007/s00248-007-9255-9 [39] Bredholt, H., Fjærvik, E., Johnsen, G. and Zotchev, S.B. (2008) Actinomycetes from Sediments in the Trondheim Fjord, Norway: Diversity and Biological Activity. Marine Drugs, 6, 12-24.
http://dx.doi.org/10.3390/md6010012 [40] Gontang, E.A., Fenical, W. and Jensen, P.R. (2007) Phylogenetic Diversity of Gram-Positive Bacteria Cultured from Marine Sediments. Applied and Environmental Microbiology, 73, 3272-3282.
http://dx.doi.org/10.1128/AEM.02811-06 [41] Imada, C., Masuda, S., Kobayashi, T., Hamada-Sato, N. and Nakashima, T. (2010) Isolation and Characterization of Marine and Terrestrial Actinomycetes Using a Medium Supplemented with NaCl. Actinomycetologica, 24, 12-17.
http://dx.doi.org/10.3209/saj.SAJ240104
[1] Fieseler, L., Horn, M., Wagner, M. and Hentschel, U. (2004) Discovery of the Novel Candidate Phylum “Poribacteria” in Marine Sponges. Applied and Environmental Microbiology, 70, 3724-3732.
http://dx.doi.org/10.1128/AEM.70.6.3724-3732.2004 [2] Taylor, M.W., Radax, R., Steger, D. and Wagner, M. (2007) Sponge-Associated Microorganisms: Evolution, Ecology, and Biotechnological Potential. Microbiology and Molecular Biology Reviews, 71, 295-347.
http://dx.doi.org/10.1128/MMBR.00040-06 [3] Zhang, H., Lee, Y.K., Zhang, W. and Lee, H.K. (2006) Culturable Actinobacteria from the Marine Sponge Hymeniacidonperleve: Isolation and Phylogenetic Diversity by 16S rRNA Gene-RFLP Analysis. Antonie van Leeuwenhoek, 90, 159-169.
http://dx.doi.org/10.1007/s10482-006-9070-1 [4] Proksch, P. (1994) Defensive Roles for Secondary Metabolites from Marine Sponges and Sponge-Feeding Nudibranchs. Toxicon, 32, 639-655.
http://dx.doi.org/10.1016/0041-0101(94)90334-4 [5] Thakur, N.L. and Müller, W.E.G. (2004) Biotechnological Potential of Marine Sponges. Current Science, 86, 1506-1512. [6] Oclarit, J.M., Okada, H., Ohta, S., Kaminura, K., Yamaoka, Y., Iizuka, T., Miyashiro, S. and Ikegami, S. (1994) Anti-Bacillus Substance in the Marine Sponge, Hyatella Species, Produced by an Associated Vibrio Species Bacterium. Microbios, 78, 7-16. [7] Jayatilake, G.S., Thornton, M.P., Leonard, A.C., Grimwade, J.E. and Baker, B.J. (1996) Metabolites from an Antarctic Sponge Associated Bacterium, Pseudomonas aeruginosa. Journal of Natural Products, 59, 293-296.
http://dx.doi.org/10.1021/np960095b [8] Piel, J., Hui, D., Wen, G., Butzke, D., Platzer, M., Fusetani, N. and Matsunaga, S. (2004) Antitumor Polyketide Biosynthesis by an Uncultivated Bacterial Symbiont of the Marine Sponge Theonellaswinhoei. Proceedings of the National Academy of Sciences, 101, 16222-16227.
http://dx.doi.org/10.1073/pnas.0405976101 [9] Montalvo, N.F., Mohamed, N.M., Enticknap, J.J. and Hill, R.T. (2005) Novel Actinobacteria from Marine Sponges. Antonie van Leeuwenhoek, 87, 29-36.
http://dx.doi.org/10.1007/s10482-004-6536-x [10] Webster, N.S., Wilson, K.J., Blackall, L.L. and Hill, R.T. (2001) Phylogenetic Diversity of Bacteria Associated with the Marine Sponge Rhopaloeidesodorabile. Applied and Environmental Microbiology, 67, 434-444.
http://dx.doi.org/10.1128/AEM.67.1.434-444.2001 [11] Hentschel, U., Hopke, J., Horn, M., Friedrich, A.B., Wagner, M., Hacker, J. and Moore, B.S. (2002) Molecular Evidence for a Uniform Microbial Community in Sponges from Different Oceans. Applied and Environmental Microbiology, 68, 4431-4440.
http://dx.doi.org/10.1128/AEM.68.9.4431-4440.2002 [12] Kamke, J., Taylor, M.W. and Schmitt, S. (2010) Activity Profiles for Marine Sponge-Associated Bacteria Obtained by 16S rRNA vs 16S rRNA Gene Comparisons. The ISME Journal, 4, 498-508.
http://dx.doi.org/10.1038/ismej.2009.143 [13] Webster, N.S., Taylor, M.W., Behnam, F., Lücker, S., Rattei, T., Whalan, S., Horn, M. and Wagner, M. (2010) Deep Sequencing Reveals Exceptional Diversity and Modes of Transmission for Bacterial Sponge Symbionts. Environmental Microbiology, 2, 2070-2082. [14] Myadoh, S. (1993) Research on Antibiotic Screening in Japan over the Last Decade: A Producing Microorganism Approach. Actinomycetologica, 7, 100-106.
http://dx.doi.org/10.3209/saj.7_100 [15] Kampfer, P. (2006) The Family Streptomycetaceae, Part I: Taxonomy. In: Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H. and Stackebrandt, E., Eds., The Prokaryotes, 3rd Edition, Springer Science + Business Media, LLC, New York, 538-604. [16] Moran, M.A., Rutherford, L.T. and Hodson, R.E. (1995) Evidence for Indigenous Streptomyces Populations in a Marine Environment Determined with a 16S rRNA Probe. Applied and Environmental Microbiology, 61, 3695-3700. [17] Mincer, T.J., Jensen, P.R., Kauffman, C.A. and Fenical, W. (2002) Widespread and Persistent Populations of a Major New Marine Actinomycete Taxon in Ocean Sediments. Applied and Environmental Microbiology, 68, 5005-5011.
http://dx.doi.org/10.1128/AEM.68.10.5005-5011.2002 [18] Kim, T.K., Garson, M.J. and Fuerst, J.A. (2005) Marine Actinomycetes Related to the “Salinispora” Group from the Great Barrier Reef Sponge Pseudoceratina clavata. Environmental Microbiology, 7, 509-518.
http://dx.doi.org/10.1111/j.1462-2920.2005.00716.x [19] Li, Z.Y. and Liu, Y. (2006) Marine Sponge Craniella austrialiensis-Associated Bacterial Diversity Revelation Based on 16S rDNA Library and Biologically Active Actinomycetes Screening, Phylogenetic Analysis. Letters in Applied Microbiology, 43, 410-416.
http://dx.doi.org/10.1111/j.1472-765X.2006.01976.x [20] Jiang, S., Sun, W., Chen, M., Dai, S., Zhang, L., Liu, Y., Lee, K.J. and Li, X. (2007) Diversity of Culturable Actinobacteria Isolated from Marine Sponge Haliclona sp. Antonie van Leeuwenhoek, 92, 405-416.
http://dx.doi.org/10.1007/s10482-007-9169-z [21] Jiang, S., Li, X., Zhang, L., Sun, W., Dai, S., Xie, L., Liu, Y. and Lee, K.J. (2008) Culturable Actinobacteria Isolated from Marine Sponge Iotrochota sp. Marine Biology, 153, 945-952.
http://dx.doi.org/10.1007/s00227-007-0866-y [22] Schneemann, I., Ohlendorf, B., Zinecker, H., Nagel, K., Wiese, J. and Imhoff, J.F. (2010) Nocapyrones A-D, Gamma-Pyrones from a Nocardiopsis Strain Isolated from the Marine Sponge Halichondria panicea. Journal of Natural Products, 73, 1444-1447.
http://dx.doi.org/10.1021/np100312f [23] Zhang, H., Zhang, W., Jin, Y., Jin, M. and Yu, X. (2008) A Comparative Study on the Phylogenetic Diversity of Culturable Actinobacteria Isolated from Five Marine Sponge Species. Antonie van Leeuwenhoek, 93, 241-248.
http://dx.doi.org/10.1007/s10482-007-9196-9 [24] Selvin, J., Shanmughapriya, S., Gandhimathi, R., Kiran, G.S., Ravji, T.R., Natarajaseenivasan, K. and Hema, T.A. (2009) Optimization and Production of Novel Antimicrobial Agents from Sponge Associated Marine Actinomycetes Nocardiopsis dassonvillei MAD08. Applied Microbiology and Biotechnology, 83, 435-445.
http://dx.doi.org/10.1007/s00253-009-1878-y [25] Abdelmohsen, U.R., Pimente-Elardo, S.M., Hanora, A., Radwan, M., Abou-El-Ela, S.H., Ahmed, S. and Hentschel, U. (2010) Isolation, Phylogenetic Analysis and Anti-Infective Activity Screening of Marine Sponge-Associated Actinomycetes. Marine Drugs, 8, 399-412.
http://dx.doi.org/10.3390/md8030399 [26] Jensen, P.R., Gontang, E., Mafnas, C., Mincer, T.J. and Fenical, W. (2005) Culturable Marine Actinomycete Diversity from Tropical Pacific Ocean Sediments. Environmental Microbiology, 7, 1039-1048.
http://dx.doi.org/10.1111/j.1462-2920.2005.00785.x [27] Connon, S.A. and Giovannoni, S.J. (2002) High-Throughput Methods for Culturing Microorganisms in Very-Low-Nutrient Media Yield Diverse New Marine Isolates. Applied and Environmental Microbiology, 68, 3878-3885.
http://dx.doi.org/10.1128/AEM.68.8.3878-3885.2002 [28] CLSI (Clinical and Laboratory Standards) (2007) Performance Standards for Antimicrobial Susceptibility Testing, 17th Informational Supplement. M100-S17, Vol. 27, CLSI. [29] Liu, D., Coloe, S., Baird, R. and Pedersen, J. (2000) Rapid Mini-Preparation of Fungal DNA for PCR. Journal of Clinical Microbiology, 38, 471. [30] Hames-Kocabas, E.E. and Uzel, A. (2012) Isolation Strategies of Marine-Derived Actinomycetes from Sponge and Sediment Samples. Journal of Microbiological Methods, 88, 342-347.
http://dx.doi.org/10.1016/j.mimet.2012.01.010 [31] Jensen, P.R., Dwight, R. and Fenical. W. (1991) Distribution of Actinomycetes in Near-Shore Tropical Marine Sediments. Applied and Environmental Microbiology, 57, 1102-1108. [32] Kroppenstedt, R.M. and Evtushenko, L.I. (2006) The Family Nocardiopsaceae. In: Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.H. and Stackebrandt, E., Eds, The Prokaryotes, 3rd Edition, Springer Science+Business Media, LLC, New York, 754-795. [33] Maldonado, L.A., Stach, J.E.M., Pathom-aree, W., Ward, A.C., Bull, A.T. and Goodfellow, M. (2005) Diversity of Cultivable Actinobacteria in Geographically Widespread Marine Sediments. Antonie van Leeuwenhoek, 87, 11-18.
http://dx.doi.org/10.1007/s10482-004-6525-0 [34] Khan, S.T., Komaki, H., Motohashi, K., Kozone, I., Mukai, A., Takagi, M, and Shin-ya, K. (2011) Streptomyces Associated with a Marine Sponge Haliclona sp.; Biosynthetic Genes for Secondary Metabolites and Products. Environmental Microbiology, 13, 391-403.
http://dx.doi.org/10.1111/j.1462-2920.2010.02337.x [35] Sun, W., Dai, S., Jiang, S., Wang, G., Liu, G., Wu, H. and Li, X. (2010) Culture-Dependent and Culture-Independent Diversity of Actinobacteria Associated with the Marine Sponge Hymeniacidon perleve from the South China Sea. Antonie van Leeuwenhoek, 98, 65-75.
http://dx.doi.org/10.1007/s10482-010-9430-8 [36] Hentschel, U., Schmid, M., Wagner, M., Fieseler, L., Gernert, C. and Hacker, J. (2001) Isolation and Phylogenetic Analysis of Bacteria with Antimicrobial Activities from the Mediterranean Sponges Aplysina aerophoba and Aplysina cavernicola. FEMS Microbiology Ecology, 35, 305-312.
http://dx.doi.org/10.1111/j.1574-6941.2001.tb00816.x [37] Muscholl-Silberhorn, A., Thiel, V. and Imhoff, J.F. (2007) Abundance and Bioactivity of Cultured Sponge-Associated Bacteria from the Mediterranean Sea. Microbial Ecology, 55, 94-106.
http://dx.doi.org/10.1007/s00248-007-9255-9 [38] Ozcan, K., Aksoy, S.C., Kalkan, O., Uzel, A., Hames-Kocabas, E.E. and Bedir, E. (2013) Diversity and Antibiotic Producing Potentials of Cultivable Marine-Derived Actinomycetes from Coastal Sediments of Turkey. Journal of Soils and Sediments, 13, 1493-1501.
http://dx.doi.org/10.1007/s00248-007-9255-9 [39] Bredholt, H., Fjærvik, E., Johnsen, G. and Zotchev, S.B. (2008) Actinomycetes from Sediments in the Trondheim Fjord, Norway: Diversity and Biological Activity. Marine Drugs, 6, 12-24.
http://dx.doi.org/10.3390/md6010012 [40] Gontang, E.A., Fenical, W. and Jensen, P.R. (2007) Phylogenetic Diversity of Gram-Positive Bacteria Cultured from Marine Sediments. Applied and Environmental Microbiology, 73, 3272-3282.
http://dx.doi.org/10.1128/AEM.02811-06 [41] Imada, C., Masuda, S., Kobayashi, T., Hamada-Sato, N. and Nakashima, T. (2010) Isolation and Characterization of Marine and Terrestrial Actinomycetes Using a Medium Supplemented with NaCl. Actinomycetologica, 24, 12-17.
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