Research Article
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Bor maden göletleri: bakteriyel çeşitliliğe metagenomik bakış

Year 2021, Volume 14, Issue 2, 229 - 235, 15.08.2021
https://doi.org/10.46309/biodicon.2021.902221

Abstract

Biyolojik potansiyeli olan yeni mikroorganizmaların kaynağı olabileceği için, bor içeriği yüksek ortamlarda bulunan mikroorganizmaların belirlenmesi ekolojik ve biyoteknolojik uygulama potansiyelleri açısından önemlidir. Bu bağlamda, bor madenciliği faaliyetlerinin gerçekleştirildiği çevrelerdeki birikinti suları boronofilik / boronotolerant mikroorganizmalar için önemli habitatlardır. Bu çalışmada, Balıkesir-Bigadiç ve Eskişehir-Kırka Bor Maden İşletmeleri atık madenciliği havuzlarındaki bakteri topluluğu, 16S rDNA gen hedefli Illumina MiSeq dizilimi kullanılarak incelenmiştir. Yüksek verimli dizilerin büyük kısımları Proteobacteria, Planctomycetes, Bacteriodetes, Verrucomicrobia ve Actinobacteria filumları ile ilişkili bulunmuştur. Cyanobacteria ve Parcubacteria, düşük miktara sahip diğer önemli gruplar arasındadır. Blastopirellula, Luteolibacter, Porhyrobacter ve Hydrogenophaga'ya ait cinsler tüm örneklerde en çok bulunan taksonlardır. Ekim örneklerinde Sandarakinorhabdus, Pseudoanabena, Roseinatronobacter ve Pontimonas cinsine bağlı okumalar da tespit edilmiştir. Mikrobiyal popülasyonların türü ve sayısı açısından örnekler arasında çarpıcı mevsimsel farklılıklar tespit edilmiştir.

References

  • Böcük, H., Yakar, A. & Türker, O. C. (2013). Assessment of Lemna gibba L. (duckweed) as a potential ecological indicator for contaminated aquatic ecosystem by boron mine effluent. Ecological Indicators, 29, 538–548. https://doi.org/10.1016/j.ecolind.2013.01.029
  • Kabu M., Kabu, M., Uyarlar, C., Zarczynska, K., Milewska, W. & Sobiech, P. (2015). The role of boron in animal health. Journal of Elementology, 20(2), 535–541. https://doi.org/10.5601/jelem.2014.19.3.706
  • Poyraz, N. & Mutlu, M. B. (2017). Alkaliphilic bacterial diversity of Lake Van/Turkey. Biological Diversity and Conservation, 10(1), 92-103.
  • Gürsu, B. Y., Aytar, P., İlhan, S., Kocabıyık, Y. E., Gedıkli, S. & Çabuk, A. (2017). Diversity of microfungi in acid mine drainages. Biological Diversity and Conservation, 10(3), 190-198.
  • Nural Yaman, B., Deniz Sonmez, G., Aytar Celik, P., Korkmaz, F., Mutlu, M. B. & Cabuk, A. (2019). Culture‐dependent diversity of boron‐tolerant bacteria from boron mine tailings pond and solid wastes. Water and Environment Journal, 33(4), 574–581. https://doi.org/10.1111/wej.12429
  • Miwa, H. & Fujiwara, T. (2009). Isolation and identification of boron-accumulating bacteria from contaminated soils and active sludge. Soil Science and Plant Nutrition, 55(5), 643–646. https://doi.org/10.1111/j.1747-0765.2009.00402.x
  • Ahmed, I., Yokota, A. & Fujiwara, T. (2007a). Chimaereicella boritolerans sp. Nov., a boron-tolerant and alkaliphilic bacterium of the family Flavobacteriaceae isolated from soil. International Journal of Systematic and Evolutionary Microbiology, 57(5), 986–992. https://doi.org/10.1099/ijs.0.64728-0
  • Ahmed, I., Yokota, A. & Fujiwara, T. (2007b). Gracilibacillus boraciitolerans sp. Nov., a highly boron-tolerant and moderately halotolerant bacterium isolated from soil. International Journal of Systematic and Evolutionary Microbiology, 57(4), 796–802. https://doi.org/10.1099/ijs.0.64284-0
  • Aytar, P., Kay, C. M., Mutlu, M. B., Çabuk, A. & Johnson, D. B. (2015). Diversity of acidophilic prokaryotes at two acid mine drainage sites in Turkey. Environmental Science and Pollution Research, 22(8), 5995–6003. https://doi.org/10.1007/s11356-014-3789-4
  • Çınar, S. & Mutlu, M. B. (2016). Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey). Extremophiles, 20(5), 589–601. https://doi.org/10.1007/s00792-016-0845-7.
  • Mutlu, M. B., Martínez-García, M., Santos, F., Peña, A., Guven, K. & Antón, J. (2008). Prokaryotic diversity in Tuz Lake, a hypersaline environment in Inland Turkey: Prokaryotic diversity in an inland Turkish salt lake. FEMS Microbiology Ecology, 65(3), 474–483. https://doi.org/10.1111/j.1574-6941.2008.00510.x
  • Çınar, S. & Mutlu, M. B. (2020). Prokaryotic Community Compositions of the Hypersaline Sediments of Tuz Lake Demonstrated by Cloning and High-Throughput Sequencing. Microbiology, 89(6), 756–768. https://doi.org/10.1134/S0026261720060028
  • Nural Yaman, B., Aytar Çelik, P., Mutlu, M. B. & Çabuk, A. (2020). A Combinational Analysis of Acidophilic Bacterial Diversity of an Iron-Rich Environment. Geomicrobiology Journal, 37(10), 877–889. https://doi.org/10.1080/01490451.2020.1795320
  • Nural Yaman, B., Mutlu, M. B., Aytar Celik, P. & Çabuk, A. (2020). Metagenomics (16S Amplicon Sequencing) and DGGE Analysis of Bacterial Diversity of Acid Mine Drainage. Journal of Microbiology, Biotechnology and Food Sciences, 9(5), 932–936. https://doi.org/10.15414/jmbfs.2020.9.5.932-936
  • Orphan, V. J., Hinrichs, K.-U., Ussler, W., Paull, C. K., Taylor, L. T., Sylva, S. P., Hayes, J. M. & Delong, E. F. (2001). Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments. Applied and Environmental Microbiology, 67(4), 1922–1934. https://doi.org/10.1128/AEM.67.4.1922-1934.2001
  • Watanabe, K., Watanabe, K., Kodama, Y., Syutsubo, K. & Harayama, S. (2000). Molecular Characterization of Bacterial Populations in Petroleum-Contaminated Groundwater Discharged from Underground Crude Oil Storage Cavities. Applied and Environmental Microbiology, 66(11), 4803–4809. https://doi.org/10.1128/AEM.66.11.4803-4809.2000
  • Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J. & Goodman, R. M. (1998). Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chemistry & Biology, 5(10), R245–R249. https://doi.org/10.1016/S1074-5521(98)90108-9
  • Oulas, A., Pavloudi, C., Polymenakou, P., Pavlopoulos, G. A., Papanikolaou, N., Kotoulas, G., Arvanitidis, C. & Iliopoulos, l. (2015). Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies. Bioinformatics and Biology Insights, 9, BBI.S12462. https://doi.org/10.4137/BBI.S12462
  • Nural Yaman, B., Mutlu, M. B., Aytar Çelik, P. & Çabuk, A. (2021). Prokaryotic Community Determination of Metal-Rich Acidic Environment by Comparative Methods, Geomicrobiology Journal, 38(6), 504-514. https://doi.org/10.1080/01490451.2021.1897713
  • Helvaci, C. (2003). Türkiye Borat Yatakları Jeolojik Konumu, Ekonomik Önemi ve Bor Politikası. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 5(1).
  • Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. & Schloss, P. D. (2013). Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform. Applied and Environmental Microbiology, 79(17), 5112–5120. https://doi.org/10.1128/AEM.01043-13
  • Yoon, S. H., Ha, S. M., Kwon, S., Lim, J., Kim, Y., Seo, H. & Chun, J. (2017). Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. International Journal of Systematic and Evolutionary Microbiology, 67(5), 1613–1617. https://doi.org/10.1099/ijsem.0.001755
  • Yarza, P., Yilmaz, P., Pruesse, E., Glöckner, F. O., Ludwig, W., Schleifer, K. H., Whitman, W. B., Euzéby, J., Amann, R. & Rosselló-Móra, R. (2014). Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Reviews Microbiology, 12(9), 635–645. https://doi.org/10.1038/nrmicro333
  • Sonthiphand, P., Hall, M. W. & Neufeld, J. D. (2014). Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria. Frontiers in Microbiology, 5. https://doi.org/10.3389/fmicb.2014.00399
  • Trzcińska, M. & Pawlik-Skowrońska, B. (2008). Soil algal communities inhabiting zinc and lead mine spoils. Journal of Applied Phycology, 20(4), 341–348. https://doi.org/10.1007/s10811-007-9259-3
  • Kersters, K., De Vos, P., Gillis, M., Swings, J., Vandamme, P. & Stackebrandt, E. (2006). Introduction to the Proteobacteria. In M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, & E. Stackebrandt (Eds.), The Prokaryotes (pp. 3–37). Springer New York. https://doi.org/10.1007/0-387-30745-1
  • Stevens, H., Stübner, M., Simon, M. & Brinkhoff, T. (2005). Phylogeny of Proteobacteria and Bacteroidetes from oxic habitats of a tidal flat ecosystem. FEMS Microbiology Ecology, 54(3), 351–365. https://doi.org/10.1016/j.femsec.2005.04.008

Boron mine ponds: metagenomic insight to bacterial diversity

Year 2021, Volume 14, Issue 2, 229 - 235, 15.08.2021
https://doi.org/10.46309/biodicon.2021.902221

Abstract

Since it can be a source of new microorganisms with biological potential, it is important to identify the microorganisms found in environments with high boron content in terms of ecological and biotechnological application potentials. In this context, deposit waters in environments where boron mining activities perform are important habitats for boronophilic/boronotolerant microorganisms. In this study, bacterial community in the waste mining ponds of Balıkesir-Bigadiç and Eskişehir-Kırka Boron Mining Operations were investigated by using 16S rDNA gene-targeted Illumina MiSeq sequencing. The greater parts of high-throughput sequences were related to Proteobacteria, Planctomycetes, Bacteriodetes, Verrucomicrobia and Actinobacteria phyla. Cyanobacteria and Parcubacteria were other notable groups with low abundance. Genera belonged to Blastopirellula, Luteolibacter, Porhyrobacter and Hydrogenophaga were the most abundant taxa for all the samples. Sandarakinorhabdus, Pseudoanabena, Roseinatronobacter and Pontimonas genera-affiliated reads were also detected at in the October samples. Striking seasonal variations were detected between samples in terms of the type and number of microbial populations.

References

  • Böcük, H., Yakar, A. & Türker, O. C. (2013). Assessment of Lemna gibba L. (duckweed) as a potential ecological indicator for contaminated aquatic ecosystem by boron mine effluent. Ecological Indicators, 29, 538–548. https://doi.org/10.1016/j.ecolind.2013.01.029
  • Kabu M., Kabu, M., Uyarlar, C., Zarczynska, K., Milewska, W. & Sobiech, P. (2015). The role of boron in animal health. Journal of Elementology, 20(2), 535–541. https://doi.org/10.5601/jelem.2014.19.3.706
  • Poyraz, N. & Mutlu, M. B. (2017). Alkaliphilic bacterial diversity of Lake Van/Turkey. Biological Diversity and Conservation, 10(1), 92-103.
  • Gürsu, B. Y., Aytar, P., İlhan, S., Kocabıyık, Y. E., Gedıkli, S. & Çabuk, A. (2017). Diversity of microfungi in acid mine drainages. Biological Diversity and Conservation, 10(3), 190-198.
  • Nural Yaman, B., Deniz Sonmez, G., Aytar Celik, P., Korkmaz, F., Mutlu, M. B. & Cabuk, A. (2019). Culture‐dependent diversity of boron‐tolerant bacteria from boron mine tailings pond and solid wastes. Water and Environment Journal, 33(4), 574–581. https://doi.org/10.1111/wej.12429
  • Miwa, H. & Fujiwara, T. (2009). Isolation and identification of boron-accumulating bacteria from contaminated soils and active sludge. Soil Science and Plant Nutrition, 55(5), 643–646. https://doi.org/10.1111/j.1747-0765.2009.00402.x
  • Ahmed, I., Yokota, A. & Fujiwara, T. (2007a). Chimaereicella boritolerans sp. Nov., a boron-tolerant and alkaliphilic bacterium of the family Flavobacteriaceae isolated from soil. International Journal of Systematic and Evolutionary Microbiology, 57(5), 986–992. https://doi.org/10.1099/ijs.0.64728-0
  • Ahmed, I., Yokota, A. & Fujiwara, T. (2007b). Gracilibacillus boraciitolerans sp. Nov., a highly boron-tolerant and moderately halotolerant bacterium isolated from soil. International Journal of Systematic and Evolutionary Microbiology, 57(4), 796–802. https://doi.org/10.1099/ijs.0.64284-0
  • Aytar, P., Kay, C. M., Mutlu, M. B., Çabuk, A. & Johnson, D. B. (2015). Diversity of acidophilic prokaryotes at two acid mine drainage sites in Turkey. Environmental Science and Pollution Research, 22(8), 5995–6003. https://doi.org/10.1007/s11356-014-3789-4
  • Çınar, S. & Mutlu, M. B. (2016). Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey). Extremophiles, 20(5), 589–601. https://doi.org/10.1007/s00792-016-0845-7.
  • Mutlu, M. B., Martínez-García, M., Santos, F., Peña, A., Guven, K. & Antón, J. (2008). Prokaryotic diversity in Tuz Lake, a hypersaline environment in Inland Turkey: Prokaryotic diversity in an inland Turkish salt lake. FEMS Microbiology Ecology, 65(3), 474–483. https://doi.org/10.1111/j.1574-6941.2008.00510.x
  • Çınar, S. & Mutlu, M. B. (2020). Prokaryotic Community Compositions of the Hypersaline Sediments of Tuz Lake Demonstrated by Cloning and High-Throughput Sequencing. Microbiology, 89(6), 756–768. https://doi.org/10.1134/S0026261720060028
  • Nural Yaman, B., Aytar Çelik, P., Mutlu, M. B. & Çabuk, A. (2020). A Combinational Analysis of Acidophilic Bacterial Diversity of an Iron-Rich Environment. Geomicrobiology Journal, 37(10), 877–889. https://doi.org/10.1080/01490451.2020.1795320
  • Nural Yaman, B., Mutlu, M. B., Aytar Celik, P. & Çabuk, A. (2020). Metagenomics (16S Amplicon Sequencing) and DGGE Analysis of Bacterial Diversity of Acid Mine Drainage. Journal of Microbiology, Biotechnology and Food Sciences, 9(5), 932–936. https://doi.org/10.15414/jmbfs.2020.9.5.932-936
  • Orphan, V. J., Hinrichs, K.-U., Ussler, W., Paull, C. K., Taylor, L. T., Sylva, S. P., Hayes, J. M. & Delong, E. F. (2001). Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments. Applied and Environmental Microbiology, 67(4), 1922–1934. https://doi.org/10.1128/AEM.67.4.1922-1934.2001
  • Watanabe, K., Watanabe, K., Kodama, Y., Syutsubo, K. & Harayama, S. (2000). Molecular Characterization of Bacterial Populations in Petroleum-Contaminated Groundwater Discharged from Underground Crude Oil Storage Cavities. Applied and Environmental Microbiology, 66(11), 4803–4809. https://doi.org/10.1128/AEM.66.11.4803-4809.2000
  • Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J. & Goodman, R. M. (1998). Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chemistry & Biology, 5(10), R245–R249. https://doi.org/10.1016/S1074-5521(98)90108-9
  • Oulas, A., Pavloudi, C., Polymenakou, P., Pavlopoulos, G. A., Papanikolaou, N., Kotoulas, G., Arvanitidis, C. & Iliopoulos, l. (2015). Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies. Bioinformatics and Biology Insights, 9, BBI.S12462. https://doi.org/10.4137/BBI.S12462
  • Nural Yaman, B., Mutlu, M. B., Aytar Çelik, P. & Çabuk, A. (2021). Prokaryotic Community Determination of Metal-Rich Acidic Environment by Comparative Methods, Geomicrobiology Journal, 38(6), 504-514. https://doi.org/10.1080/01490451.2021.1897713
  • Helvaci, C. (2003). Türkiye Borat Yatakları Jeolojik Konumu, Ekonomik Önemi ve Bor Politikası. Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 5(1).
  • Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. & Schloss, P. D. (2013). Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform. Applied and Environmental Microbiology, 79(17), 5112–5120. https://doi.org/10.1128/AEM.01043-13
  • Yoon, S. H., Ha, S. M., Kwon, S., Lim, J., Kim, Y., Seo, H. & Chun, J. (2017). Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. International Journal of Systematic and Evolutionary Microbiology, 67(5), 1613–1617. https://doi.org/10.1099/ijsem.0.001755
  • Yarza, P., Yilmaz, P., Pruesse, E., Glöckner, F. O., Ludwig, W., Schleifer, K. H., Whitman, W. B., Euzéby, J., Amann, R. & Rosselló-Móra, R. (2014). Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Reviews Microbiology, 12(9), 635–645. https://doi.org/10.1038/nrmicro333
  • Sonthiphand, P., Hall, M. W. & Neufeld, J. D. (2014). Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria. Frontiers in Microbiology, 5. https://doi.org/10.3389/fmicb.2014.00399
  • Trzcińska, M. & Pawlik-Skowrońska, B. (2008). Soil algal communities inhabiting zinc and lead mine spoils. Journal of Applied Phycology, 20(4), 341–348. https://doi.org/10.1007/s10811-007-9259-3
  • Kersters, K., De Vos, P., Gillis, M., Swings, J., Vandamme, P. & Stackebrandt, E. (2006). Introduction to the Proteobacteria. In M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, & E. Stackebrandt (Eds.), The Prokaryotes (pp. 3–37). Springer New York. https://doi.org/10.1007/0-387-30745-1
  • Stevens, H., Stübner, M., Simon, M. & Brinkhoff, T. (2005). Phylogeny of Proteobacteria and Bacteroidetes from oxic habitats of a tidal flat ecosystem. FEMS Microbiology Ecology, 54(3), 351–365. https://doi.org/10.1016/j.femsec.2005.04.008

Details

Primary Language English
Subjects Biodiversity Conservation
Journal Section Research Article
Authors

Pınar AYTAR ÇELİK
ESKİŞEHİR OSMANGAZİ ÜNİVERSİTESİ, ESKİŞEHİR MESLEK YÜKSEKOKULU
0000-0002-9447-1668
Türkiye


Mehmet Burçin MUTLU
ESKİŞEHİR TEKNİK ÜNİVERSİTESİ, FEN FAKÜLTESİ, BİYOLOJİ BÖLÜMÜ
0000-0002-9404-6389
Türkiye


Ferhan KORKMAZ
ESKİŞEHİR OSMANGAZİ ÜNİVERSİTESİ, FEN-EDEBİYAT FAKÜLTESİ
0000-0002-3797-842X
Türkiye


Belma NURAL YAMAN (Primary Author)
ESKİŞEHİR OSMANGAZİ ÜNİVERSİTESİ, MÜHENDİSLİK-MİMARLIK FAKÜLTESİ
0000-0003-2576-1300
Türkiye


Serap GEDİKLİ
ESKİŞEHİR OSMANGAZİ ÜNİVERSİTESİ, FEN-EDEBİYAT FAKÜLTESİ
0000-0001-5632-6585
Türkiye


Doç. Dr. Ahmet ÇABUK
ESKİŞEHİR OSMANGAZİ ÜNİVERSİTESİ, FEN-EDEBİYAT FAKÜLTESİ
0000-0002-4619-6948
Türkiye

Supporting Institution Eskişehir Osmangazi University Scientific Research Project Committee
Project Number 201838064
Publication Date August 15, 2021
Application Date March 24, 2021
Acceptance Date June 30, 2021
Published in Issue Year 2021, Volume 14, Issue 2

Cite

APA Aytar Çelik, P. , Mutlu, M. B. , Korkmaz, F. , Nural Yaman, B. , Gedikli, S. & Çabuk, D. D. A. (2021). Boron mine ponds: metagenomic insight to bacterial diversity . Biyolojik Çeşitlilik ve Koruma , 14 (2) , 229-235 . DOI: 10.46309/biodicon.2021.902221

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