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A Preliminary Metabarcoding Study of Prokaryotes in Gökçeada Salt Lake Lagoon, Turkey

Year 2021, Volume: 80 Issue: 1, 69 - 74, 15.06.2021

Abstract

Objective: Microorganisms play an important role in all ecosystem processes and a growing body of molecular and ecological evidence has shown that microbial biodiversity is much more diverse and complex than previously anticipated. This study aimed to determine the prokaryotic microorganisms present in Gökçeada Salt Lake Lagoon.

Materials and Methods: We used the metabarcoding approach to determine the microbial diversity in Gökçeada Salt Lake Lagoon.

Results: 16S rDNA targeted sequencing contained 5 Archaea and 31 Bacteria species and Archaea represented 63.2%. The most frequent Archaea genus was Halorubrum, which belongs to the Euryarchaeota phylum, and the dominant species of Bacteria was Halomonas sulfidaeris (Proteobacteria phylum).

Conclusion: This work will contribute to our understanding of the microbial community structure and composition however further surveys will improve our knowledge on microbiota in Gökçeada Salt Lake Lagoon.

Supporting Institution

There are no funders to report for this submission.

References

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  • Elevi Bardavid R, Ionescu D, Oren A, Rainey FA, Hollen BJ, Bagaley DR, Small AM, McKay C. Selective enrichment, isolation and molecular detection of Salinibacter and related extremely halophilic Bacteria from hypersaline environments. Hydrobiologica 2007; 576: 3-13.
  • Fernandez AB, Ghai R, Martin-Cuadrado AB, Sanchez-Porro C, Rodriguez-Valera F, Ventosa A. Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics. FEMS Microbiol Ecol 2014; 88: 623–635.
  • Fouts DE, Szpakowski S, Purushe J, Torralba M, Waterman RC, et al. Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PLoS One 2012; 7: e48289.
  • Ghai R, Pašić L, Fernández AB, Martin-Cuadrado AB, Mizuno CM, McMahon KD, Papke RT, Stepanauskas R, Rodriguez-Brito B, Rohwer F, Sánchez-Porro C, Ventosa A, Rodríguez-Valera F. New abundant microbial groups in aquatic hypersaline environments. Sci Rep 2011; 1: 135.
  • Leininger S, Urich T, Schloter M, Schwark L, Qi JW, Nicol G, Prosse JI, Schuster SC, Schleper C. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 2006; 442: 806-809.
  • Mutlu MB, Martinez-Garcia M, Santos F, Pena A, Guven K and Anton J. Prokaryotic diversity in Tuz Lake, a hypersaline environment in inland Turkey. FEMS Microbiol Ecol 2008; 65: 474-483.
  • Mutlu MB and Guven K. Bacterial diversity in Çamaltı Saltern, Turkey. Pol J Microbiol 2015; 64: 37-45.
  • Ondov BD, Bergman NH and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinform 2011; 12: 385.
  • Oren A. Life at high salt concentrations. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, editors. The prokaryotes. A handbook on the biology of bacteria: ecophysiology and biochemistry, vol 2. New York: Springer; 2011. p. 263–282.
  • Pavan-Kumar A, Gireesh-Babu P and Lakra WS. DNA Metabarcoding: A new approach for rapid biodiversity assessment. J Cell Sci Mol Biol 2015; 2: 111.
  • Simachew A, Lanzén A, Gessesse A, Øvreås L. Prokaryotic community diversity along an increasing salt gradient in a soda ash concentration pond. Microb Ecol 2016; 71: 326-338.
  • Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM and Herndl GJ. Microbial diversity in the deep sea and the underexplored “rare biosphere”. PNAS 2006; 103: 12115-12120.
  • Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol 2012; 21: 2045-2050.
  • Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A and Knight R. Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems 2016; 1: e00009–15.
  • Wardle DA. Communities and ecosystems: Linking the above‐ground and below‐ground components. Princeton, NJ: Princeton University Press; 2002.
  • Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res 2014; 42: 643–648.
Year 2021, Volume: 80 Issue: 1, 69 - 74, 15.06.2021

Abstract

References

  • Abdelfattah A, Malacrinò A, Wisniewski M, Cacciola SO and Schena L. Metabarcoding: a powerful tool to investigate microbial communities and shape future plant protection strategies. Biol Control 2017; 120: 1–10.
  • Amaral-Zettler LA, McCliment EA, Ducklow HW, and Huse SM. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA Genes. PLoS ONE 2009; 4: e6372.
  • Anton J, Pena A, Santos F, Martinez-Garcia M, Schmitt-Kopplin P and Rossello-Mora R. Distribution, abundance and diversity of the extremely halophilic bacterium Salinibacter ruber. Saline Systems 2008; 4: 15.
  • Aslan H, Gonulal O, Can-Yilmaz E, Elipek B, Baytut O, Tosunoglu M, Karabacak E, Kurt Y. Species diversity in lentic, lotic, marine and terrestrial biotopes of Gokceada Salt Lake Wetland (Canakkale, Turkey). Fresenius Environ Bull 2018; 5: 2853-2866.
  • Bassler-Veit B, Barut IF, Merc E, Avsar N, Nazik A, Kapan-Yesilyurt S, Yildiz A. Distribution of microflora, meiofauna, and macrofauna assemblages in the hypersaline environment of northeastern Aegean Sea coasts. J Coast Res 2013; 29: 883-898.
  • Bolyen E, Rideout JR, Dillon MR et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 2019; 37: 852-857.
  • Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes S. DADA2: High resolution sample inference from Illumina amplicon data. Nat Methods 2016; 13: 581-583.
  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. QIIME allows analysis of high throughput community sequencing data. Nat Methods 2010; 7: 335-336.
  • Caporaso JG, Lauber C L, Walters W A, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, & Knight R. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 2012; 6: 1621–1624.
  • Edgar RC. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nature Methods 2013; 10: 996–998.
  • Elevi Bardavid R, Ionescu D, Oren A, Rainey FA, Hollen BJ, Bagaley DR, Small AM, McKay C. Selective enrichment, isolation and molecular detection of Salinibacter and related extremely halophilic Bacteria from hypersaline environments. Hydrobiologica 2007; 576: 3-13.
  • Fernandez AB, Ghai R, Martin-Cuadrado AB, Sanchez-Porro C, Rodriguez-Valera F, Ventosa A. Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics. FEMS Microbiol Ecol 2014; 88: 623–635.
  • Fouts DE, Szpakowski S, Purushe J, Torralba M, Waterman RC, et al. Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PLoS One 2012; 7: e48289.
  • Ghai R, Pašić L, Fernández AB, Martin-Cuadrado AB, Mizuno CM, McMahon KD, Papke RT, Stepanauskas R, Rodriguez-Brito B, Rohwer F, Sánchez-Porro C, Ventosa A, Rodríguez-Valera F. New abundant microbial groups in aquatic hypersaline environments. Sci Rep 2011; 1: 135.
  • Leininger S, Urich T, Schloter M, Schwark L, Qi JW, Nicol G, Prosse JI, Schuster SC, Schleper C. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 2006; 442: 806-809.
  • Mutlu MB, Martinez-Garcia M, Santos F, Pena A, Guven K and Anton J. Prokaryotic diversity in Tuz Lake, a hypersaline environment in inland Turkey. FEMS Microbiol Ecol 2008; 65: 474-483.
  • Mutlu MB and Guven K. Bacterial diversity in Çamaltı Saltern, Turkey. Pol J Microbiol 2015; 64: 37-45.
  • Ondov BD, Bergman NH and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinform 2011; 12: 385.
  • Oren A. Life at high salt concentrations. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, editors. The prokaryotes. A handbook on the biology of bacteria: ecophysiology and biochemistry, vol 2. New York: Springer; 2011. p. 263–282.
  • Pavan-Kumar A, Gireesh-Babu P and Lakra WS. DNA Metabarcoding: A new approach for rapid biodiversity assessment. J Cell Sci Mol Biol 2015; 2: 111.
  • Simachew A, Lanzén A, Gessesse A, Øvreås L. Prokaryotic community diversity along an increasing salt gradient in a soda ash concentration pond. Microb Ecol 2016; 71: 326-338.
  • Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM and Herndl GJ. Microbial diversity in the deep sea and the underexplored “rare biosphere”. PNAS 2006; 103: 12115-12120.
  • Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol Ecol 2012; 21: 2045-2050.
  • Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A and Knight R. Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems 2016; 1: e00009–15.
  • Wardle DA. Communities and ecosystems: Linking the above‐ground and below‐ground components. Princeton, NJ: Princeton University Press; 2002.
  • Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res 2014; 42: 643–648.
There are 26 citations in total.

Details

Primary Language English
Journal Section Short Communication
Authors

Sibel Kucukyildirim Celik This is me 0000-0003-2241-3060

Publication Date June 15, 2021
Submission Date October 10, 2020
Published in Issue Year 2021 Volume: 80 Issue: 1

Cite

AMA Kucukyildirim Celik S. A Preliminary Metabarcoding Study of Prokaryotes in Gökçeada Salt Lake Lagoon, Turkey. Eur J Biol. June 2021;80(1):69-74.