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Distribution of Protists in the Deep South China Sea Revealed by High-Throughput Sequencing

  • Xinran Li
  • Alan Warren
  • Nianzhi Jiao
  • Dapeng XuEmail author
Article

Abstract

Protists (microbial eukaryotes) are indispensable members of the marine microbial food web. In recent years, organisms living in the deep sea (>1000 m water depth) have increasingly become the focus of research; however, studies on protistan assemblages are relatively scarce compared with their prokaryotic counterparts. In the present study, high-throughput sequencing of the hypervariable V9 region of the 18S rRNA gene was used to explore the community composition of protists in bathypelagic waters of the South China Sea. Based on the analysis of the alpha and beta diversities of 14 samples, we discovered: 1) members belonging to Rhizaria, Alveolata, and Excavata were the dominant groups in terms of both relative sequence abundance and operational taxonomic unit (OTU) richness in all samples, although their relative contributions differed among different samples; 2) cluster analysis showed that the distribution of protistan assemblages was related neither to the sampling location nor to the water depth, and other environmental factors might have caused the differences among the communities; 3) phototrophs, including members of the Bacillariophyta, Bolidophyceae, Dictyochophyceae, Prasinophyceae, and Prymnesiophyceae, were detected in all samples, which indicated their contributions to the downward transportation via the biological pump and the potential presence of phagotrophy of these phototrophic cells in the deep ocean.

Keywords

bathypelagic water diversity microbial eukaryotes SSU rRNA gene 

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Notes

Acknowledgements

We thank the captain and crew of the R/V Dongfang-hong-2 for successful sampling. This work was supported by the National Natural Science Foundation of China (Nos. 41876142, 91751207 and 41861144018) and the Senior User Project of RV KEXUE (No. KEXUE2019 G08) funded by the Center for Ocean Mega-Science, Chinese Academy of Sciences.

References

  1. Adl, S. M., Bass, D., Lane, C. E., Lukeš, J., Schoch, C. L., Smirnov, A., Agatha, S., Berney, C., Brown, M. W., Burki, F., Cárdenas, P., Čepička, I., Chistyakova, L., Del Campo, J., Dunthorn, M., Edvardsen, B., Eglit, Y., Guillou, L., Hampl, V., Heiss, A. A., Hoppenrath, M., James, T. Y., Karnkowska, A., Karpov, S., Kim, E., Kolisko, M., Kudryavtsev, A., Lahr, D. J. G., Lara, E., Le Gall, L., Lynn, D. H., Mann, D. G., Massana, R., Mitchell, E. A. D., Morrow, C., Park, J. S., Pawlowski, J. W., Powell, M. J., Richter, D. J., Rueckert, S., Shadwick, L., Shimano, S., Spiegel, F. W., Torruella, G., Youssef, N., Zla-togursky, V., and Zhang, Q., 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology, 66: 4–119.Google Scholar
  2. Agusti, S., Gonzalez-Gordillo, J. I., Vaque, D., Estrada, M., Cerezo, M. I., Salazar, G., Gasol, J. M., and Duarte, C. M., 2015. Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump. Nature Communications, 6: 7608.Google Scholar
  3. Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W., and Huse, S. M., 2009. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS One, 4: e6372.CrossRefGoogle Scholar
  4. Arístegui, J., Gasol, J. M., Duarte, C. M., and Herndl, G. J., 2009. Microbial oceanography of the dark ocean’s pelagic realm. Limnology and Oceanography, 54: 1501–1529.CrossRefGoogle Scholar
  5. Azam, F., Fenchel, T., Field, J. G., Gray, J. S., Meyer-Rei, L. A., and Thingstad, F., 1983. The ecological role of water-column microbes in the sea. Marine Ecology Progress Series, 10: 257–263.CrossRefGoogle Scholar
  6. Bass, D., Moreira, D., López-García, P., Polet, S., Chao, E. E., von der Heyden, S., Pawlowski, J., and Cavalier-Smith, T., 2005. Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist, 156: 149–161.CrossRefGoogle Scholar
  7. Belcher, A., Manno, C., Thorpe, S., and Tarling, G., 2018. Acantharian cysts: High flux occurrence in the bathypelagic zone of the Scotia Sea, Southern Ocean. Marine Biology, 165: 117.CrossRefGoogle Scholar
  8. Biard, T., Stemmann, L., Picheral, M., Mayot, N., Vandromme, P., Hauss, H., Gorsky, G., Guidi, L., Kiko, R., and Not, F., 2016. In situ imaging reveals the biomass of giant protists in the global ocean. Nature, 532: 504–507.CrossRefGoogle Scholar
  9. Bolger, A. M., Lohse, M., and Usadel, B., 2014. Trimmomatic: Aflexible trimmer for Illumina Sequence Data. Bioinformat-ics, 30: 2114–2120.CrossRefGoogle Scholar
  10. Cai, P., Zhao, D., Wang, L., Huang, B., and Dai, M., 2015. Role of particle stock and phytoplankton community structure in regulating particulate organic carbon export in a large marginal sea. Journal of Geophysical Research: Oceans, 120: 2063–2095.Google Scholar
  11. Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., Huttley, G. A., Kelley, S. T., Knights, D., Koenig, J. E., Ley, R. E., Lozupone, C. A., McDonald, D., Muegge, B. D., Pirrung, M., Reeder, J., Sevinsky, J. R., Turnbaugh, P. J., Walters, W. A., Widmann, J., Yatsunenko, T., Zaneveld, J., and Knight, R., 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7: 335–336.CrossRefGoogle Scholar
  12. Caron, D. A., Alexander, H., Allen, A. E., Archibald, J. M., Armbrust, E. V., Bachy, C., Bharti, A., Bell, C. J., Dyhrman, S. T., Guida, S., Heidelberg, K. B., Kaye, J. Z., Metzner, J., Smith, S. R., and Worden, A. Z., 2017. Probing the evolution, ecology and physiology of marine protists using transcrip-tomics. Nature Reviews Microbiology, 15: 6–20.CrossRefGoogle Scholar
  13. Caron, D. A., Countway, P. D., Jones, A. C., Kim, D. Y., and Schnetzer, A., 2012. Marine protistan diversity. Annual Review of Marine Science, 4: 467–493.CrossRefGoogle Scholar
  14. Caron, D. A., Worden, A. Z., Countway, P. D., Demir, E., and Heidelberg, K. B., 2009. Protists are microbes too: A perspective. The ISME Journal, 3: 4–12.CrossRefGoogle Scholar
  15. Chavez-Dozal, A., Gorman, C., Erken, M., Steinberg, P. D., McDougald, D., and Nishiguchi, M. K., 2013. From the laboratory into the field: Testing defense mechanisms of bacterial biofilms against protozoan grazing. Applied and Environmental Microbiology, 79: 553–558.CrossRefGoogle Scholar
  16. Countway, P. D., Gast, R. J., Dennett, M. R., Savai, P., Rose, J. M., and Caron, D. A., 2007. Distinct protistan assemblages characterize the euphotic zone and deep sea (2500 m) of the western North Atlantic (Sargasso Sea and Gulf Stream). Environmental Microbiology, 9: 1219–1232.CrossRefGoogle Scholar
  17. Decelle, J., Martin, P., Paborstava, K., Pond, D. W., Tarling, G., Mahé, F., de Varges, C., Lampitt, R., and Not, F., 2013. Diversity, ecology and biogeochemistry of cyst-forming Acan-tharia (Radiolaria) in the oceans. PLoS One, 8: e53598.CrossRefGoogle Scholar
  18. de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Loga-res, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Car-michael, M., Poulain, J., Romac, S., Colin, S., Aury, J. M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegon-tova, O., Guidi, L., Horák, A., Jaillon, O., Lima-Mendez, G., Lukeš, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., and Tara Oceans Coordinators, Acinas, S. G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M. E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P., and Karsenti, E., 2015. Eu-karyotic plankton diversity in the sunlit ocean. Science, 348: 1261605.CrossRefGoogle Scholar
  19. Edgar, R. C., 2013. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10: 996–998.CrossRefGoogle Scholar
  20. Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., and Knight, R., 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27: 2194–2200.CrossRefGoogle Scholar
  21. Flegontova, O., Flegontov, P., Malviya, S., Audic, S., Wincker, P., de Vargas, C., Bowler, C., Lukeš, J., and Horák, A., 2016. Extreme diversity of diplonemid eukaryotes in the ocean. Current Biology, 26: 3060–3065.CrossRefGoogle Scholar
  22. Flegontova, O., Flegontov, P., Malviya, S., Poulain, J., de Vargas, C., Bowler, C., Lukeš, J., and Horák, A., 2018. Neobodonids are dominant kinetoplastids in the global ocean. Environmental Microbiology, 20: 878–889.CrossRefGoogle Scholar
  23. Gilg, I. C., Amaral-Zettler, L. A., Countway, P. D., Moorthi, S., Schnetzer, A., and Caron, D. A., 2010. Phylogenetic affiliations of mesopelagic Acantharia and acantharian-like environmental 18S rRNA genes off the southern California coast. Protist, 161: 197–211.CrossRefGoogle Scholar
  24. Giner, C. R., Balagué, V., Pernice, M. C., Duarte, C. M., Gasol, J. M., Logares, R., and Massana, R., 2019. Marked changes in diversity and relative activity of picoeukaryotes with depth in the global ocean. BioRxiv, DOI: https://doi.org/10.1101/552604.Google Scholar
  25. Guidi, L., Chaffron, S., Bittner, L., Eveillard, D., Larhlimi, A., Roux, S., Darzi, Y., Audic, S., Berline, L., Brum, J., Coelho, L. P., Espinoza, J. C. I., Malviya, S., Sunagawa, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Poulain, J., Searson, S., Tara Oceans coordinators, Stemmann, L., Not, F., Hingamp, P., Speich, S., Follows, M., Karp-Boss, L., Boss, E., Ogata, H., Pesant, S., Weissenbach, J., Wincker, P., Acinas, S. G., Bork, P., de Vargas, C., Iudicone, D., Sullivan, M. B., Raes, J., Kar-senti, E., Bowler, C., and Gorsky, G., 2016. Plankton networks driving carbon export in the oligotrophic ocean. Nature, 532: 465–470.CrossRefGoogle Scholar
  26. Guillou, L., Viprey, M., Chambouvet, A., Welsh, R. M., Kirk-ham, A. R., Massana, R., Scanlan, D. J., and Worden, A. Z., 2008. Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environmental Microbiology, 10: 3349–3365.CrossRefGoogle Scholar
  27. Guo, R., Liang, Y., Xin, Y., Wang, L., Mou, S., Cao, C., Xie, R., Zhang, C., Tian, J., and Zhang, Y., 2018. Insight into the pico-and nano-phytoplankton communities in the deepest biosphere, the Mariana Trench. Frontiers in Microbiology, 9: 2289.Google Scholar
  28. Herndl, G. J., and Reinthaler, T., 2013. Microbial control of the dark end of the biological pump. Nature Geoscience, 6: 718–724.CrossRefGoogle Scholar
  29. Hewson, I., Steele, J. A., Capone, D. G., and Fuhrman, J. A., 2006. Remarkable heterogeneity in meso- and bathypelagic bacterioplankton assemblage composition. Limnology and Oceanography, 51: 1274–1283.CrossRefGoogle Scholar
  30. Hu, S. K., Campbell, V., Connell, P., Gellene, A. G., Liu, Z., Terrado, R., and Caron, D. A., 2016. Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific. FEMS Microbiology Ecology, 92: fiw050.Google Scholar
  31. Hu, X., Lin, X., and Song, W., 2019. Ciliates Atlas: Species Found in the South China Sea. Science Press, Beijing, 932pp.CrossRefGoogle Scholar
  32. Ishitani, Y., Ujiie, Y., de Vargas, C., Not, F., and Takahashi, K., 2012. Phylogenetic relationships and evolutionary patterns of the order Collodaria (Radiolaria). PLoS One, 7: e35775.CrossRefGoogle Scholar
  33. Jiao, N., Herndl, G. J., Hansell, D. A., Benner, R., Kattner, G., Wilhelm, S. W., Kirchman, D. L., Weinbauer, M. G., Luo, T. W., Chen, F., and Azam, F., 2010. Microbial production of recalcitrant dissolved organic matter: Long-term carbon storage in the global ocean. Nature Reviews Microbiology, 8: 593–599.CrossRefGoogle Scholar
  34. Jiao, N., Luo, T., Zhang, R., Yan, W., Lin, Y., Johnson, Z. I., Tian, J., Yuan, D., Yang, Q., Sun, J., Hu, D., and Wang, P., 2014. Presence of Prochlorococcus in the aphotic waters of the Western Pacific Ocean. Biogeosciences, 11: 2391–2400.CrossRefGoogle Scholar
  35. Li, R., Jiao, N., Warren, A., and Xu, D., 2018. Changes in community structure of active protistan assemblages from the lower Pearl River to coastal waters of the South China Sea. European Journal of Protistology, 63: 72–82.CrossRefGoogle Scholar
  36. Lozupone, C., and Knight, R., 2005. UniFrac: A new phyloge-netic method for comparing microbial communities. Applied and Environmental Microbiology, 71: 8228–8235.CrossRefGoogle Scholar
  37. Magoč, T., and Salzberg, S. L., 2011. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bio-informatics, 27: 2957–2963.Google Scholar
  38. Martín-Cuadrado, A. B., López-García, P., Alba, J. C., Moreira, D., Monticelli, L., Strittmatter, A., Gottschalk, G., and Ro-dríguez-Valera, F., 2007. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS One, 2: e914.CrossRefGoogle Scholar
  39. Moeseneder, M. M., Winter, C., and Herndl, G. J., 2001. Horizontal and vertical complexity of attached and free-living bacteria of the eastern Mediterranean Sea, determined by 16S rDNA and 16S rRNA fingerprints. Limnology and Oceanography, 46: 95–107.CrossRefGoogle Scholar
  40. Morgan-Smith, D., Herndl, G., van Aken, H., and Bochdansky, A., 2011. Abundance of eukaryotic microbes in the deep subtropical North Atlantic. Aquatic Microbial Ecology, 65: 103–115.CrossRefGoogle Scholar
  41. Morgan-Smith, D., Clouse, M. A., Herndl, G. J., and Bochdansky, A., 2013. Diversity and distribution of microbial eukaryotes in the deep tropical and subtropical North Atlantic Ocean. Deep Sea Research Part I, 78: 58–69.CrossRefGoogle Scholar
  42. Mukherjee, I., Hodoki, Y., and Nakano, S., 2015. Kinetoplastid flagellates overlooked by universal primers dominate in the oxygenated hypolimnion of Lake Biwa, Japan. FEMS Microbiology Ecology, 91: fiv083.CrossRefGoogle Scholar
  43. Nagata, T., Tamburini, C., Arístegui, J., Baltar, F., Bochdansky, A. B., Fonda-Umani, S., Fukuda, H., Gogou, A., Hansell, D. A., Hansman, R. L., Herndl, G. J., Panagiotopoulos, C., Re-inthaler, T., Sohrin, R., Verdugo, P., Yamada, N., Yamashita, Y., Yokokawa, T., and Bartlett, D. H., 2010. Emerging concepts on microbial processes in the bathypelagic ocean - Ecology, biogeochemistry, and genomics. Deep Sea Research Part II: Topical Studies in Oceanography, 57: 1519–1536.CrossRefGoogle Scholar
  44. Not, F., del Campo, J., Balagué, V., de Vargas, C., and Massana, R., 2009. New insights into the diversity of marine picoeu-karyotes. PLoS One, 4: e7143.CrossRefGoogle Scholar
  45. Not, F., Gausling, R., Azam, F., Heidelberg, J. F., and Worden, A. Z., 2007. Vertical distribution of picoeukaryotic diversity in the Sargasso Sea. Environmental Microbiology, 9: 1233–1252.CrossRefGoogle Scholar
  46. Orsi, W., Edgcomb, V., Jeon, S., Leslin, C., Bunge, J., Taylor, G. T., Varela, R., and Epstein, S., 2011. Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization. The ISME Journal, 5: 1357–1373.CrossRefGoogle Scholar
  47. Pawlowski, J., Christen, R., Lecroq, B., Bachar, D., Shahbazkia, H. R., Amaral-Zettler, L., and Guillou, L., 2011. Eukaryotic richness in the abyss: Insights from pyrotag sequencing. PLoS One, 6: e18169.CrossRefGoogle Scholar
  48. Pernice, M. C., Giner, C. R., Logares, R., Perera-Bel, J., Acinas, S. G., Duarte, C. M., Gasol, J. M., and Massana, R., 2015. Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans. The ISME Journal, 10: 945–958.CrossRefGoogle Scholar
  49. Scharek, R., Tupas, L. M., and Karl, D. M., 1999. Diatom fluxes to the deep sea in the oligotrophic North Pacific gyre at station ALOHA. Marine Ecology Progress Series, 182: 55–67.CrossRefGoogle Scholar
  50. Schlitzer, R., 2011. Ocean data view. http://odv.awi.de.Google Scholar
  51. Song, W., Warren, A., and Hu, X., 2009. Free-Living Ciliates in the Bohai and Yellow Seas, China. Science Press, Beijing, 518pp.Google Scholar
  52. Stoecker, D. K., Johnson, M. D., de Vargas, C., and Not, F., 2009. Acquired phototrophy in aquatic protists. Aquatic Microbial Ecology, 57: 279–310.CrossRefGoogle Scholar
  53. Stoecker, D. K., Hansen, P. J., Caron, D. A., and Mitra, A., 2017. Mixotrophy in the marine plankton. Annual Review of Marine Science, 9: 311–335.CrossRefGoogle Scholar
  54. Stukel, M. R., Biard, T., Krause, J., and Ohman, M. D., 2018. Large Phaeodaria in the twilight zone: Their role in the carbon cycle. Limnology and Oceanography, 63: 2579–2594.CrossRefGoogle Scholar
  55. Sun, P., Huang, L., Xu, D., Chen, N., and Warren, A., 2017. Marked seasonality and high spatial variation in estuarine ciliates are driven by exchanges between the “abundant” and “intermediate” biospheres. Scientific Reports, 7: 9494.Google Scholar
  56. Xu, D., Jiao, N., Ren, R., and Warren, A., 2017a. Distribution and diversity of microbial eukaryotes in bathypelagic waters of the South China Sea. Journal of Eukaryotic Microbiology, 64: 370–382.CrossRefGoogle Scholar
  57. Xu, D., Li, R., Hu, C., Sun, P., Jiao, N., and Warren, A., 2017b. Microbial eukaryote diversity and activity in the water column of the South China Sea based on DNA and RNA high throughput sequencing. Frontiers in Microbiology, 8: 1121.CrossRefGoogle Scholar
  58. Xu, D., Sun, P., Zhang, Y., Li, R., Huang, B., Jiao, N., Warren, A., and Wang, L., 2018. Pigmented microbial eukaryotes fuel the deep sea carbon pool in the tropical Western Pacific Ocean. Environmental Microbiology, 20: 3811–3824.CrossRefGoogle Scholar

Copyright information

© Ocean University of China, Science Press and Springer-Verlag GmbH Germany 2020

Authors and Affiliations

  • Xinran Li
    • 1
  • Alan Warren
    • 2
  • Nianzhi Jiao
    • 1
  • Dapeng Xu
    • 1
    Email author
  1. 1.State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth SciencesXiamen UniversityXiamenChina
  2. 2.Department of Life SciencesNatural History MuseumLondonUK

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