Seasonal Gene Profiling in Tuz Lake with Regard to Biogeochemical Cycling

Suzan Sahin Dogan; Aytaç Kocabaş

doi:10.18016/ksutarimdoga.vi.1212062

EN TR

Seasonal Gene Profiling in Tuz Lake with Regard to Biogeochemical Cycling

Abstract

Tuz Lake, a thalassohaline lake with a salt rate of 32%, is a unique habitat for a halophilic microbiome. Culture-dependent and independent methods have been applied to identify prokaryotic microbial diversity in Tuz Lake. However, the key processes and genes involved in biogeochemical cycles in Tuz Lake have not been investigated seasonally. The aim of the study is to investigate seasonal gene profiling in Tuz Lake associated with biogeochemical cycling and thereby reveal more about the ecosystem dynamics of this extreme environment. Therefore, the PICRUSt2 tool was applied to analyze the metabolic function of archaeal and bacterial diversity in Tuz Lake. As a result of metabolic functions based on 16S rDNA amplicon sequencing data, it was observed that methane production by H2 and CO2 by anaerobic archaea in Tuz Lake was the predominant methanogenesis pathway. It was determined that sulfur oxidation was the dominant sulfur metabolism, while the reductive citric acid cycle was the dominant carbon fixation pathway.

Keywords

Supporting Institution

TUBITAK (Turkish Scientific and Technical Research Council)

Project Number

117z966

References

Akyol, İ., Yıldız, M.A., & Tutar, E. (2017). Yeni Nesil Nükleotid Dizileme Metotlarının Biyokimyasal Temelleri. KSU Doğa Bilimleri Dergisi, 20(1), 1–15.
Alfreider, A., Baumer, A., Bogensperger, T., Posch, T., Salcher, M.M., & Summerer, M (2017). CO 2 assimilation strategies in stratified lakes: Diversity and distribution patterns of chemolithoautotrophs. Environmental Microbiology, 19(7), 2754–2768. https://doi.org/10.1111/1462-2920.13786
Alfreider, A. & Tartarotti, B. (2019). Spatiotemporal dynamics of different CO2 fixation strategies used by prokaryotes in a dimictic lake. Scientific Reports, 9(1), 15068. https://doi.org/10.1038/s41598-019-51584-0
Başkaya, Y. & Kocabaş, A. (2016). Topraktan İzole Edilen Mikroorganizmaların Antimikrobiyal Madde Üretim Potansiyellerinin Belirlenmesi. KSU Doğa Bilimleri Dergisi, 19(4), 393–398.
Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., … Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8), 852–857. https://doi.org/10.1038/s41587-019-0209-9
Check Hayden, E. (2014). Technology: The $1,000 genome. Nature, 507(7492), 294–295. https:// doi.org/10.1038/507294a
Doğan, S. Ş. & Kocabaş, A. (2021). Metagenomic Assessment of Prokaryotic Diversity within Hypersaline Tuz Lake, Turkey. Microbiology, 90(5), 647–655. https://doi.org/10.1134/S00262617210 50118
Douglas, G. M., Maffei, V. J., Zaneveld, J. R., Yurgel, S. N., Brown, J. R., Taylor, C. M., Huttenhower, C. & Langille, M. G. I. (2020). PICRUSt2 for prediction of metagenome functions. Nature Biotechnology, 38(6), 685–688. https://doi.org/10.1038/s41587-020-0548-6

Feng, H., Sun, Y., Zhi, Y., Wei, X., Luo, Y., Mao, L. & Zhou, P. (2014). Identification and characterization of the nitrate assimilation genes in the isolate of Streptomyces griseorubens JSD-1. Microbial Cell Factories, 13(1), 174. https://doi.org/10.1186/ s12934-014-0174-4
Fernández, A. B., Ghai, R., Martin-Cuadrado, A.-B., Sánchez-Porro, C., Rodriguez-Valera, F. & Ventosa, A. (2014). Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics. FEMS Microbiology Ecology, 88(3), 623–635. https://doi.org/10.1111/1574-6941.12329
Ferrer, M., Werner, J., Chernikova, T. N., Bargiela, R., Fernández, L., La Cono, V., Waldmann, J., Teeling, H., Golyshina, O. V., Glöckner, F. O., Yakimov, M. M. & Golyshin, P. N. (2012). Unveiling microbial life in the new deep-sea hypersaline Lake Thetis. Part II: a metagenomic study. Environmental Microbiology, 14(1), 268–281. https://doi.org/ 10.1111/j.1462-2920.2011.02634.x
Goyal, N., Zhou, Z. & Karimi, I. A. (2016). Metabolic processes of Methanococcus maripaludis and potential applications. Microbial Cell Factories, 15(1), 107. https://doi.org/10.1186/s12934-016-0500-0
Hu, B. -l., Shen, L. -d., Lian, X., Zhu, Q., Liu, S., Huang, Q., He, Z. -f., Geng, S., Cheng, D. -q., Lou, L. -p., Xu, X. -y., Zheng, P. & He, Y. -f. (2014). Evidence for nitrite-dependent anaerobic methane oxidation as a previously overlooked microbial methane sink in wetlands. Proceedings of the National Academy of Sciences, 111(12), 4495–4500. https://doi.org/ 10.1073/pnas.1318393111
Isaji, Y., Kawahata, H., Ogawa, N. O., Kuroda, J., Yoshimura, T., Jiménez-Espejo, F. J., Makabe, A., Shibuya, T., Lugli, S., Santulli, A., Manzi, V., Roveri, M. & Ohkouchi, N. (2019). Efficient recycling of nutrients in modern and past hypersaline environments. Scientific Reports, 9(1), 3718. https://doi.org/10.1038/s41598-019-40174-9
Kırkağaç, M., Gümüş, E. & Yokuş, G. (2017). Tuz Gölü’nde Çevresel Faktörlerin Artemia Populasyonu’na Etkisi. Iğdır Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 7(2), 303–312.
Kuypers, M. M. M., Marchant, H. K. & Kartal, B. (2018). The microbial nitrogen-cycling network. Nature Reviews Microbiology, 16(5), 263–276. https://doi.org/10.1038/nrmicro.2018.9
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., Beiko, R. G. & Huttenhower, C. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology, 31(9), 814–821. https://doi.org/10.1038/nbt.2676
Lopes, L. D., Pereira e Silva, M. de C. & Andreote, F. D. (2016). Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization. Frontiers in Microbiology, 7. https://doi.org/10.3389/ fmicb.2016. 01341
Maier, R. M. (2015). Biogeochemical Cycling. In Environmental Microbiology (pp. 339–373). Elsevier. https://doi.org/10.1016/B978-0-12-394626-3.00016-8
McGonigle, J. M., Bernau, J. A., Bowen, B. B. & Brazelton, W. J. (2021). Metabolic Potential of Microbial Communities in the Hypersaline Sediments of the Bonneville Salt Flats. BioRxiv, 2021.10.18.464844. https://doi.org/10.1101/ 2021. 10.18.464844
Michoud, G., Ngugi, D. K., Barozzi, A., Merlino, G., Calleja, M. L., Delgado-Huertas, A., Morán, X. A. G. & Daffonchio, D. (2021). Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline. The ISME Journal, 15(8), 2351–2365. https://doi.org/10.1038/s41396-021-00931-z
Parks, D. H., Tyson, G. W., Hugenholtz, P. & Beiko, R. G. (2014). STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics, 30(21), 3123–3124. https://doi.org/10.1093/ bioinformatics/ btu494
Robertson, G. P. & Groffman, P. M. (2015). Nitrogen Transformations. In Soil Microbiology, Ecology and Biochemistry (pp. 421–446). Elsevier. https ://doi.org/10.1016/B978-0-12-415955-6.00014-1
Shapleigh, J. P. (2009). Dissimilatory and Assimilatory Nitrate Reduction in the Purple Photosynthetic Bacteria (pp. 623–642). https://doi.org/10.1007/978-1-4020-8815-5_31
Shi, W., Tang, S., Huang, W., Zhang, S. & Li, Z. (2021). Distribution Characteristics of C–N–S Microorganism Genes in Different Hydraulic Zones of High-Rank Coal Reservoirs in Southern Qinshui Basin. ACS Omega, 6(33), 21395–21409. https://doi.org/10.1021/acsomega.1c02169
Song, Y., Lee, J. S., Shin, J., Lee, G. M., Jin, S., Kang, S., Lee, J.-K., Kim, D. R., Lee, E. Y., Kim, S. C., Cho, S., Kim, D. & Cho, B.-K. (2020). Functional cooperation of the glycine synthase-reductase and Wood–Ljungdahl pathways for autotrophic growth of Clostridium drakei. Proceedings of the National Academy of Sciences, 117(13), 7516–7523. https://doi.org/10.1073/pnas.1912289117
Sorokin, D. Y., Berben, T., Melton, E. D., Overmars, L., Vavourakis, C. D. & Muyzer, G. (2014). Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles, 18(5), 791–809. https://doi.org/ 10.1007/s00792-014-0670-9
Sternai, P., Caricchi, L., Garcia-Castellanos, D., Jolivet, L., Sheldrake, T. E. & Castelltort, S. (2017). Magmatic pulse driven by sea-level changes associated with the Messinian salinity crisis. Nature Geoscience, 10(10), 783–787. https:// doi.org/10.1038/ngeo3032
Vavourakis, C. D., Andrei, A.-S., Mehrshad, M., Ghai, R., Sorokin, D. Y. & Muyzer, G. (2018). A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. Microbiome, 6(1), 168. https://doi.org/10.1186/ s40168-018-0548-7
Ventosa, A. (2006). Unusual micro-organisms from unusual habitats: Hypersaline environments. In Prokaryotic Diversity: Mechanisms and Significance: Published for the Society for General Microbiology (pp. 223–254). Cambridge University Press. https://doi.org/10.1017/CBO9780511754913.015
Wasmund, K., Mußmann, M. & Loy, A. (2017). The life sulfuric: microbial ecology of sulfur cycling in marine sediments. Environmental Microbiology Reports, 9(4), 323–344. https://doi.org/10.1111/ 1758-2229.12538
Youssef, N. H., Farag, I. F., Rudy, S., Mulliner, A., Walker, K., Caldwell, F., Miller, M., Hoff, W. & Elshahed, M. (2019). The Wood–Ljungdahl pathway as a key component of metabolic versatility in candidate phylum Bipolaricaulota (Acetothermia, OP1). Environmental Microbiology Reports, 11(4), 538–547. https://doi.org/ 10.1111/1758-2229.12753
Yuan, Z., Druzhinina, I. S., Labbé, J., Redman, R., Qin, Y., Rodriguez, R., Zhang, C., Tuskan, G. A. & Lin, F. (2016). Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity. Scientific Reports, 6(1), 32467. https://doi.org/10.1038/srep32467
Zeng, B., Han, S., Wang, P., Wen, B., Jian, W., Guo, W., Yu, Z., Du, D., Fu, X., Kong, F., Yang, M., Si, X., Zhao, J. & Li, Y. (2015). The bacterial communities associated with fecal types and body weight of rex rabbits. Scientific Reports, 5(1), 9342. https://doi.org/10.1038/srep09342
Zhu, D., Han, R., Long, Q., Gao, X., Xing, J., Shen, G., Li, Y. & Wang, R. (2020). An evaluation of the core bacterial communities associated with hypersaline environments in the Qaidam Basin, China. Archives of Microbiology, 202(8), 2093–2103. https://doi.org/10.1007/s00203-020-01927-7

Details

Primary Language

English

Subjects

Structural Biology

Journal Section

Research Article

Authors

Suzan Sahin Dogan ^*
0000-0002-1554-0080
Türkiye

Aytaç Kocabaş
0000-0001-7622-1932
Türkiye

Early Pub Date

January 21, 2024

Publication Date

April 1, 2024

Submission Date

November 30, 2022

Acceptance Date

June 1, 2023

Published in Issue

Year 1970 Volume: 27 Number: 2

DOI

https://doi.org/10.18016/ksutarimdoga.vi.1212062

IZ

https://izlik.org/JA77GJ29AC

Cite

RIS / Bibtex

APA

Sahin Dogan, S., & Kocabaş, A. (2024). Seasonal Gene Profiling in Tuz Lake with Regard to Biogeochemical Cycling. Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi, 27(2), 273-284. https://doi.org/10.18016/ksutarimdoga.vi.1212062

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https://doi.org/10.53447/communc.1206230

Uncovering High-Yield Ectoine Producers from Extreme Environments: Insights from Tuz Lake

Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi

https://doi.org/10.18016/ksutarimdoga.vi.1653239

Seasonal Gene Profiling in Tuz Lake with Regard to Biogeochemical Cycling

Seasonal Gene Profiling in Tuz Lake with Regard to Biogeochemical Cycling

Abstract

Keywords

Biyojeokimyasal Döngüyle İlişkili Tuz Gölü'ndeki Mevsimsel Gen Profili

Öz

Anahtar Kelimeler

Supporting Institution

Project Number

References

Details

Primary Language

Subjects

Journal Section

Authors

Early Pub Date

Publication Date

Submission Date

Acceptance Date

Published in Issue

DOI

IZ

Cite

Cited By

Profiling the genes associated with osmoadaptation and their variation by seasonally in Tuz Lake

Uncovering High-Yield Ectoine Producers from Extreme Environments: Insights from Tuz Lake