Investigation of microbial communities of subsurface sediment layers of the shelf and deep-sea zones of the Black Sea using Oxford Nanopore sequencing
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Abstract
Bacterial communities occurring in subsurface bottom sediment layers from the deep basin and shelf zone of the Black Sea were analyzed. The aim was to show that these sediments, formed under different bottom-water conditions (reduced environment characterized by hydrogen sulfide at a depth of 2,030 m vs. oxidized environment with oxygenated seawater at 49 m), serve as habitats for distinct microbial communities. DNA was extracted from various sediment layers; the procedure was followed by PCR amplification and Oxford Nanopore sequencing. The analysis revealed a total of 28 classified bacterial phylotypes: 24 recorded in both zones, and 1 being specific to the deep sediment of the hydrogen sulfide zone. In total, 335 representatives were identified from 171 families. Among those, 37 families were found to be specific to the shelf sediment of the oxygen zone of the Black Sea, while 46 families were exclusive to the deep sediment of the hydrogen sulfide zone. Moreover, 88 families were identified as overlapping between two zones. These findings indicate that the two zones of the Black Sea indeed harbor unique microbial communities, with greater diversity observed on the shelf. The results also highlight the potential for research on roles of these communities in biogeochemical cycles.
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References
Babraham Bioinformatics. FastQC : A quality control tool for high throughput sequence data : [site]. Babraham, 2019. URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ [accessed: 05.03.2026].
Badmadashiev D. V., Stroeva A. R., Klyukina A. A., Poludetkina E. N., Bonch-Osmolovskaya E. A. Phylogenetic diversity of prokaryotic communities of the upper sediment layers of the Kandalaksha Bay, White Sea. Microbiology, 2023, vol. 92, no. 6, pp. 581–594. (in Russ.). https://doi.org/10.31857/s0026365623600244
Benson D. A., Cavanaugh M., Clark K., Karsch-Mizrachi I., Ostell J., Pruitt K. D., Sayers E. W. GenBank. Nucleic Acids Research, 2013, vol. 41, iss. D1, pp. D36–D42. https://doi.org/10.1093/nar/gks1195
Bertagnolli A. D., Padilla C. C., Glass J. B., Thamdrup B., Stewart F. J. Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column. Environmental Microbiology, 2017, vol. 19, iss. 11, pp. 4392–4416. https://doi.org/10.1111/1462-2920.13879
Cabello-Yeves P. J., Callieri C., Picazo A., Mehrshad M., Haro-Moreno J. M., Roda-Garcia J. J., Dzhembekova N., Slabakova V., Slabakova N., Moncheva S., Rodriguez-Valera F. The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics. Environmental Microbiome, 2021, vol. 16, art. 5 (15 p.). https://doi.org/10.1186/s40793-021-00374-1
Coolen M. J. L., Saenz J. P., Giosan L., Trowbridge N. Y., Dimitrov P., Dimitrov D., Eglinton T. I. DNA and lipid molecular stratigraphic records of haptophyte succession in the Black Sea during the Holocene. Earth and Planetary Science Letters, 2009, vol. 284, iss. 3–4, pp. 610–621. https://doi.org/10.1016/j.epsl.2009.05.029
Coolen M. J. L. 7000 years of Emiliania huxleyi viruses in the Black Sea. Science, 2011, vol. 333, iss. 6041, pp. 451–452. https://doi.org/10.1126/science.1200072
Coolen M. J. L., Orsi W. D., Balkema C., Quince C., Harris K., Sylva S. P., Filipova-Marinova M., Giosan L. Evolution of the plankton paleome in the Black Sea from the Deglacial to Anthropocene. Proceedings of National Academy of Science of USA, 2013, vol. 110, no. 21, pp. 8609–8614. https://doi.org/10.1073/pnas.1219283110
DerrickWood/kraken 2 : [site]. [2023]. URL: https://github.com/derrickwood/kraken2 [accessed: 01.03.2026].
Durisch-Kaiser E., Klauser L., Wehrli B., Schubert C. Evidence of intense archaeal and bacterial methanotrophic activity in the Black Sea water column. Applied Environmental Microbiology, 2005, vol. 71, no. 12, pp. 8099–8106. https://doi.org/10.1128/aem.71.12.8099-8106.2005
Egorov V. N., Gulin S. B., Popovichev V. N., Mirzoeva N. Yu., Tereshchenko N. N., Lazorenko G. E., Malakhova L. V., Plotitsina O. V., Malakhova T. V., Proskurnin V. Yu., Sidorov I. G., Gulina L. V., Stetsyk A. P., Marchenko Yu. G. Biogeochemical mechanisms of formation of critical zones concerning to pollutants in the Black Sea. Morskoj ekologicheskij zhurnal, 2013, vol. 12, no. 4, pp. 5–26. (in Russ.). https://repository.marine-research.ru/handle/299011/1305
EPI2ME – Data Analysis for All Levels of Expertise. Nanopore Technologies : [site]. 2008–2024. URL: https://nanoporetech.com/products/analyse/epi2me [accessed: 01.02.2026].
Ghate S. D., Shastry R. P., Arun A. B., Rekha P. D. Unraveling the bacterial community composition across aquatic sediments in the southwestern coast of India by employing high-throughput 16S rRNA gene sequencing. Regional Studies in Marine Science, 2021, vol. 46, art. 101890 (9 p.). https://doi.org/10.1016/j.rsma.2021.101890
Hawley A. K., Nobu M. K., Wright J. J., Durno W. E., Morgan-Lang C., Sage B., Schwientek P., Swan B. K., Rinke C., Torres-Beltrán M., Mewis K., Liu W.-T., Stepanauskas R., Woyke T., Hallam S. J. Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. Nature Community, 2017, vol. 8, art. 1507 (10 p.). https://doi.org/10.1038/s41467-017-01376-9
Jessen G. L., Lichtschlag A., Ramette A., Pantoja S., Rossel P. E., Schubert C. J., Struck U., Boetius A. Hypoxia causes preservation of labile organic matter and changes seafloor microbial community composition (Black Sea). Science Advances, 2017, vol. 3, iss. 2, art. e1601897 (14 p.). https://doi.org/10.1126/sciadv.1601897
Klatt J. M., Al-Najjar M. A. A., Yilmaz P., Lavik G., de Beer D., Polerecky L. Anoxygenic photosynthesis controls oxygenic photosynthesis in a cyanobacterium from a sulfidic spring. Applied and Environmental Microbiology, 2015, vol. 81, no. 6, pp. 2025–2031. https://doi.org/10.1128/aem.03579-14
Kondratev S. I., Vidnichuk A. V. Features of the oxygen and sulfide vertical distribution in the Black Sea based on the expedition data obtained by Marine Hydrophysical Institute in 1995–2015. Physical Oceanography, 2018, vol. 25, no. 5, pp. 390–400. https://elibrary.ru/ryjllq
Kondratev S. I., Vidnichuk A. V. Vertical distribution of oxygen and hydrogen sulphide in the Black Sea in 2016. Vestnik Moskovskogo universiteta. Seriya 5: Geografiya, 2020, no. 3, pp. 91–99. (in Russ.). https://elibrary.ru/hacwmh
Leloup J., Loy A., Knab N. J., Borowski C., Wagner M., Jørgensen B. B. Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment, Black Sea. Environmental Microbiology, 2007, vol. 9, iss. 1, pp. 131–142. https://doi.org/10.1111/j.1462-2920.2006.01122.x
Merkel A. Y., Pimenov N. V., Rusanov I. I., Slobodkin A. I., Slobodkina G. B., Tarnovetckii I. Yu., Frolov E. N., Dubin A. V., Perevalova A. A., Bonch-Osmolovskaya E. A. Microbial diversity and autotrophic activity in Kamchatka hot springs. Extremophiles, 2017, vol. 21, iss. 2, pp. 307–317. https://doi.org/10.1007/s00792-016-0903-1
More K. D., Giosan L., Grice K., Coolen M. J. L. Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea. Geobiology, 2019, vol. 17, iss. 4, pp. 436–448. https://doi.org/10.1111/gbi.12338
Nunoura T., Hirai M., Miyazaki M., Kazama H., Makita H., Hirayama H., Furushima Y., Yamamoto H., Imachi H., Takai K. Isolation and characterization of a thermophilic, obligately anaerobic and heterotrophic marine Chloroflexi bacterium from a Chloroflexi-dominated microbial community associated with a Japanese shallow hydrothermal system, and proposal for Thermomarinilinea lacunofontalis gen. nov., sp. nov. Microbes and Environment, 2013, vol. 28, iss. 2, pp. 228–235. https://doi.org/10.1264/jsme2.me12193
Oxford Nanopore Technology : [site]. 2008–2024. URL: https://nanoporetech.com/ [accessed: 01.03.2026].
Roussel E. G., Cambon Bonavita M.-A., Querellou J., Cragg B. A., Webster G., Prieur D., Parkes R. J. Extending the sub-sea-floor biosphere. Science, 2008, vol. 320, no. 5879, art. 1046 (1 p.). https://doi.org/10.1126/science.1154545. Supporting online material: https://www.sciencemag.org/cgi/content/full/320/5879/1046/dc1
Schippers A., Kock D., Höft G., Köweker G., Siegert M. Quantification of microbial communities in subsurface marine sediments of the Black Sea and off Namibia. Frontiers in Microbiology, 2012, vol. 3, art. 16 (11 p.). https://doi.org/10.3389/fmicb.2012.00016
Shah V., Zhao X., Lundeen R. A., Ingalls A. E., Nicastro D., Morris R. M. Morphological plasticity in a sulfur-oxidizing marine bacterium from the SUP05 clade enhances dark carbon fixation. mBio, 2019, vol. 10, no. 3, art. e00216-19 (11 p.). https://doi.org/10.1128/mbio.00216-19
Stroeva A. R., Melnik A. D., Klyukina A. A., Pirogova A. S., Vidishcheva O. N., Poludetkina E. N., Akhmanov G. G., Bonch-Osmolovskaya E. A., Merkel A. Yu. Microbial community structure in the bottom sediments of the Barents and Kara seas and their relation to methane discharge. Microbiology, 2023, vol. 92, suppl. 1, pp. S63–S68. https://doi.org/10.1134/s0026261723603639
Suominen S., Dombrowski N., Sinninghe Damsté J. S., Villanueva L. A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone. Environmental Microbiology, 2021, vol. 23, iss. 6, pp. 2709–2728. https://doi.org/10.1111/1462-2920.14902
Tereshchenko N. N., Parkhomenko A. V. Features of formation of the sedimentation and mass accumulation rate in western Black Sea bottom sediments. Oceanology, 2021, vol. 61, iss. 4, pp. 499–510. https://doi.org/10.1134/s0001437021040147
Tereshchenko N. N., Gulin S. B., Proskurnin V. Yu., Paraskiv A. A. Geochronological reconstruction of sedimentary flows of technogenic plutonium based on radioisotope determination of the rate of sedimentation of suspended matter in sediments on a half-century scale. In: The Black Sea System / A. P. Lisitzin (Ed). Moscow : Nauchnyi mir, 2018, pp. 641–659. (in Russ.). https://elibrary.ru/oyzzik
Trimmomatic : [site]. [2021]. URL: https://github.com/usadellab/trimmomatic [accessed: 14.02.2026].
Webster G., Newberry C. J., Fry J. C., Weightman A. J. Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: A cautionary tale. Journal of Microbiological Methods, 2003, vol. 55, iss. 1, pp. 155–164. https://doi.org/10.1016/s0167-7012(03)00140-4
Wood D. E., Lu J., Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biology, 2019, vol. 20, iss. 1, art. 257 (13 p.). https://doi.org/10.1186/s13059-019-1891-0
Yesin N. V., Kos’yan R. D. Field study of sedimentation and radionuclide pollution of the Black Sea. In: Isotopes in Environmental Studies – Aquatic Forum 2004 : proceedings of International Conference, Monte-Carlo, Monaco, 25–29 October, 2004. Vienna : IAEA, 2006, pp. 277–278.
Zaitsev Yu. P., Polikarpov G. G., Egorov V. N., Gulin S. B., Kopitina N. I., Kurilov A. V., Nesterova D. A., Nidzvetskaya L. M., Nikonova S. E., Polikarpov I. G., Stokozov N. A., Teplinskaya N. G., Terenko L. M. Biological diversity of oxybionts (in the form of viable spores) and anaerobes in the bottom sediments of the hydrogen sulfide bathyal of the Black Sea. Dopovidi NAN Ukrainy, 2008, no. 5, pp. 168–173. (in Russ.). https://repository.marine-research.ru/handle/299011/10466
Zinger L. A., Amaral-Zettler J. A., Fuhrman M., Horner-Devine M. C., Huse S. M., Welch D. B. M., Martiny J. B. H., Sogin M., Boetius A., Ramette A. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE, 2011, vol. 6, no. 9, art. e24570 (11 p.). https://doi.org/10.1371/journal.pone.0024570
