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Influences of Diurnal Sampling Bias on Fixed-Point Monitoring of Plankton Biodiversity Determined Using a Massively Parallel Sequencing-Based Technique

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Abstract

In this study, we investigated the influence of diurnal sampling bias on the community structure of plankton by comparing the biodiversity among seawater samples (n = 9) obtained every 3 h for 24 h by using massively parallel sequencing (MPS)-based plankton monitoring at a fixed point conducted at Himedo seaport in Yatsushiro Sea, Japan. During seawater sampling, the semidiurnal tidal current having an amplitude of 0.3 m s−1 was dominant, and the westward residual current driven by the northeasterly wind was continuously observed during the 24-h monitoring. Therefore, the relative abundance of plankton species apparently fluctuated among the samples, but no significant difference was noted according to G-test (p > 0.05). Significant differences were observed between the samples obtained from a different locality and at different dates, suggesting that the influence of diurnal sampling bias on plankton diversity is acceptable and data taken at a certain time in a day can be used as the representative one.

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Abbreviations

MPS:

 Massively parallel sequencing

NMDS:

 Non-metric multidimensional scaling

OTUs:

 Operational taxonomy units

References

  • Adl SM, Simpson AG, Farmer MA, Andersen RA, Anderson OR, Barta JR et al (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Euk Microbiol 52:399–451

    PubMed  Google Scholar 

  • Amaral-Zettler L, McCliment E, Ducklow H, Huse S (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

    PubMed  PubMed Central  Google Scholar 

  • Anderson DM, Stolzenbach KD (1985) Selective retention of two dinoflagellates in a wall-mixed estuarine embayment: the important of diel vertical migration and surface avoidance. Mar Ecol Prog Ser 25:39–50

    Google Scholar 

  • Aoki K, Goh O, Shimizu M, Kuoda H, Matsuyama Y et al (2012) Factors controlling the spatio-temporal distribution of the 2009 Chattonella antiqua bloom in the Yatsushiro Sea, Japan. Est Coast Shelf Sci 114:148–155

    Google Scholar 

  • Archibald JM (2009) The puzzle of plastid evolution. Curr Biol 19:R81–R88

    CAS  PubMed  Google Scholar 

  • Ault TR (2000) Vertical migration by the marine dinoflagellate Prorocentrum triestinum maximises photosynthetic yield. Oecol 125:466–475

    CAS  Google Scholar 

  • Blauw AN, Benincà E, Laane RWPM, Greenwood N, Huisman J (2012) Dancing with the tides: fluctuations of coastal phytoplankton orchestrated by different oscillatory modes of the tidal cycle. PLoS One 7:e49319

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brunet C, Lizon F (2003) Tidal and diel periodicities of size-fractionated phytoplankton pigment signatures at an offshore station in the southeastern English Channel. Est Coast Shelf Sci 56:833–843

    Google Scholar 

  • Burki F, Shalchian-Tabrizi K, Minge M, Skjæveland Å, Nikolaev SI et al (2007) Phylogenomics reshuffles the eukaryotic supergroups. PLoS One 2:e790

    PubMed  PubMed Central  Google Scholar 

  • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al (2009) BLAST+: architecture and applications. BMC Bioinformatics 10:421

    PubMed  PubMed Central  Google Scholar 

  • Chen Z, Hu C, Muller-Karger FE, Luther ME (2010) Short-term variability of suspended sediment and phytoplankton in Tampa Bay, Florida: observations from a coastal oceanographic tower and ocean color satellites. Est Coast Shelf Sci 89:62–72

    CAS  Google Scholar 

  • Cheung M, Au C, Chu K, Kwan H, Wong C (2010) Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing. ISME J 4:1053–1059

    PubMed  Google Scholar 

  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eppley RW, Holm-Hansen O, Strickland JDH (1968) Some observation on the vertical migration of dinoflagellates. J Phycol 4:330–340

    Google Scholar 

  • Fauchot J, Levasseur M, Roy S (2005) Daytime and nighttime vertical migrations of Alexandrium tamarense in the St. Lawrence estuary (Canada). Mar Ecol Prog Ser 296:241–250

    CAS  Google Scholar 

  • Fisheries Agency (2010) Information on the occurrence of red tide in Kyushu area. Kyushu Fisheries Coordination Office, Annual Report 2009 p. 95. (in Japanese)

    Google Scholar 

  • Fisheries Agency (2011). Information on the occurrence of red tide in Kyushu area. Kyushu Fisheries Coordination Office, Annual Report 2010 pp. 102–103. (in Japanese)

    Google Scholar 

  • Frommolt R, Werner S, Paulsen H, Goss R, Wilhelm C et al (2008) Ancient recruitment by chromists of green algal genes encoding enzymes for carotenoid biosynthesis. Mol Biol Evol 25:2653–2667

    CAS  PubMed  Google Scholar 

  • Gallienne CP, Robins DB (2001) Is Oithona the most important copepod in the world’s oceans? J Plankton Res 23:1421–1432

    Google Scholar 

  • Hampl V, Hug L, Leigh JW, Dacks JB, Fanz-Lang B et al (2009) Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”. Proc Natl Acad Sci U S A 106:3859–3864

    CAS  PubMed  PubMed Central  Google Scholar 

  • Heaney SI, Eppley RW (1981) Light, temperature and nitrogen as interacting factors affecting diel vertical migrations of dinoflagellates in culture. J Plankton Res 3:331–344

    Google Scholar 

  • Huse SM, Welch DM, Morrison HG, Sogin ML (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12:1889–1898

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kemp WM, Mitsch WJ (1979) Turbulence and phytoplankton diversity: a general model of the “paradox of plankton”. Ecol Model 7:201–222

    Google Scholar 

  • Maestrini S, Bonin D (1981) Allelopathic relationships between phytoplankton species. Can Bull Fish Aquat Sci 210:323–338

    Google Scholar 

  • Manabe T, Tanda M, Hori Y, Nagai S, Nakamura Y (1994) Changes in eutrophication and phytoplankton in Harima-Nada—results of environmental monitoring for 20 years. Bull Coast Oceanogr 31:169–181. (in Japanese with English abstract)

    Google Scholar 

  • Margalef R (1967) Some concepts relative to the organization of plankton. Oceanogr Mar Biol Annu Rev 5:257–289

    Google Scholar 

  • Margalef R (1978) Life-forms of phytoplankton as survival alternatives in an unstable environment. Oceanologia 1:493–509

    Google Scholar 

  • Minowa M, Kobari T, Akamatsu H, Ichikawa T, Fukuda R et al (2011) Seasonal changes in abundance, biomass and depth distribution of mesozooplankton community in Kagoshima Bay. Bull Japan Soc Fish Oceanogr 75:71–81

    Google Scholar 

  • Monchy S, Grattepanche JD, Breton E, Meloni D, Sanciu G et al (2012) Microplanktonic community structure in a coastal system relative to a Phaeocystis bloom inferred from morphological and tag pyrosequencing methods. PLoS One 7:e39924

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nagai S, Yamamoto K, Hata N, Itakura S (2012) Study of DNA extraction methods for use in loop-mediated isothermal amplification detection of single resting cysts in the toxic dinoflagellates Alexandrium tamarense and A. catenella. Mar Genomics 7:51–56

    PubMed  Google Scholar 

  • Nishikawa T, Hori Y, Nagai S, Miyahara K, Nakamura Y et al (2010) Nutrient and phytoplankton dynamics in Harima-Nada, eastern Seto Inland Sea, Japan during a 35-year period from 1973 to 2007. Estuar Coast 33:417–427

    CAS  Google Scholar 

  • Nishitani G, Nagai S, Hayakawa S, Kosaka Y, Sakurada K et al (2012) Multiple plastids collected by the dinoflagellate Dinophysis mitra through kleptoplastidy. App Environ Microbiol 78:813–821

    CAS  Google Scholar 

  • Nolte V, Pandey RV, Jost S (2010) Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Mol Ecol 19:2908–2915

    CAS  PubMed  PubMed Central  Google Scholar 

  • Okamoto N, Chantangsi C, Horak A, Leander BS, Keeling PJ (2009) Molecular phylogeny and description of the novel katablepharid Roombia truncata gen. Et sp. nov., and establishment of the Hacrobia taxon nov. PLoS One 4:e7080

    PubMed  PubMed Central  Google Scholar 

  • Onitsuka G, Aoki K, Shimizu M, Matsuyama Y, Kimoto K et al (2011) Short-term dynamics of a Chattonella antiqua bloom in the Yatsushiro Sea, Japan, in summer 2010: characteristics of its appearance in the southern area. Bull Japan Soc Fish Oceanogr 75:143–153. (in Japanese with English abstract)

    Google Scholar 

  • Pawlowski J, Christen R, Lecroq B, Bachar D, Shahbazkia HR et al (2011) Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS One 6:e18169

    CAS  PubMed  PubMed Central  Google Scholar 

  • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl Acids Res 41:590–596

    Google Scholar 

  • R Development Core Team (2014) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org

  • Sakurada K, Yamagata S, Oyama N, Itoyama R (2008) The prediction of harmful blooms Chattonella antiqua in Yatsushiro Sea. Report of Kumamoto Prefecture Fish Res Center 8:35–45. (in Japanese)

    Google Scholar 

  • Schloss PD, Gevers D, Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 6:e27310

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shikata T, Skamoto S, Onitsuka G, Aoki K, Yamaguchi M (2014) Effects of salinity on diel vertical migration behavior in two red-tide algae, Chattonella antiqua and Karenia mikimotoi. Plank Benth Res 9:42–50

    Google Scholar 

  • Shikata T, Sakurada K, Jomoto Y, Oyama N, Onji M et al (2011) Growth dynamics of Chattonella antiqua in relation to nutrients in the Yatsushiro Sea. Nippon Suisan Gakkaishi 77:40–52. in Japanese with English abstract

    CAS  Google Scholar 

  • Sharples J (2008) Potential impacts of the spring-neap tidal cycle on shelf sea primary production. J Plankton Res 30:183–197

    CAS  Google Scholar 

  • Smayda TJ (1973) The growth of Skeletonema costatum during a winter-spring bloom in Narragansett Bay, Rhode Island. Nor J Bot 20:219–247

    Google Scholar 

  • Smayda TJ (1980) Phytoplankton species succession. In: Morris I (ed) The physiological ecology of phytoplankton. Blackwell Scientific Publication, Oxford, UK, pp 493–570

    Google Scholar 

  • Smayda TJ (1998) Patterns of variability characterizing marine phytoplankton, with examples from Narragansett Bay. ICES J Mar Sci 55:562–573

    Google Scholar 

  • Stomp M, van Dijk MA, van Overzee HMJ, Wortel M, Sigon C et al (2008) The timescale of phenotypic plasticity and its impact on competition in fluctuating environments. Am Nat 172:169–185

    PubMed  Google Scholar 

  • Takeuchi T (1988) Diel vertical migration of Protogonyaulax catenella (dinophyceae). Bull Plank Soc Japan 35:149–157. (in Japanese with English abstract)

    Google Scholar 

  • Tanabe AS (2012a) Claident v0.1.2013.07.23. software distributed by the author at http://www.claident.org/

  • Tanabe AS (2012b) Assams v0.1.2013.07.19. software distributed by the author at http://www.fifthdimension.jp/

  • Watanabe M, Kohata K, Kimura T (1991) Diel vertical migration and nocturnal uptake of nutrients by Chattonella antiqua under stable stratification. Limnol Oceanogr 36:593–602

    Google Scholar 

  • Yamamoto K, Matsuyama Y, Ohmi H, Ariyama H (2010) Diel vertical migration of the toxic dinoflagellate Alexandrium tamarense, temporal changes of associated environmental factors and cell toxin content during the course of a large-scale bloom. Nippon Suisan Gakkaishi 75:877–885. in Japanese with English abstract

    Google Scholar 

  • Yoshida Y, Numata K (1982) Accumulation and movement of Chattonella sp. in Kagoshima Bay and Suho Nada. Bull Japan Soc Sci Fish 48:1401–1405. (in Japanese with English abstract)

    Google Scholar 

  • Zhang Y, Shi K, Liu X, Zhou Y, Qin B (2014) Lake topography and wind waves determining seasonal-spatial dynamics of Total suspended matter in turbid Lake Taihu, China: assessment using long-term high-resolution MERIS data. PLoS One 9:e98055

    PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This study was supported by a Grant-in-Aid (Marine Metagenomics for Monitoring the Coastal Microbiota) from the Ministry of Agriculture, Forestry and Fisheries of Japan.

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Authors and Affiliations

  1. National Research Institute of Fisheries Science, Yokohama, Kanagawa, Japan

    Satoshi Nagai, Motoshige Yasuike, Yoji Nakamura, Atushi Fujiwara & Takanori Kobayashi

  2. AXIOHELIX Co. Ltd., Tokyo, Japan

    Noriko Nishi & Shingo Urushizaki

  3. National Research Institute of Fisheries and Environment of Inland Sea, Hiroshima, Japan

    Goh Onitsuka

  4. Kumamoto Prefectural Fisheries Research Center, Kumamoto, Japan

    Seisuke Tajimi

  5. Center for Information Biology, National Institute of Genetics, Shizuoka, Japan

    Takashi Gojobori

  6. National Research Institute of Aquaculture, Minami-ise, Mie, Japan

    Mitsuru Ototake

Authors
  1. Satoshi Nagai
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Corresponding author

Correspondence to Satoshi Nagai .

Editor information

Editors and Affiliations

  1. Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia

    Takashi Gojobori

  2. Japan Fisheries Research and Education Agency (Retired), Yokohama, Japan

    Tokio Wada

  3. Kitasato University School of Marine Biosciences, Sagamihara, Japan

    Takanori Kobayashi

  4. Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia

    Katsuhiko Mineta

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Nagai, S. et al. (2019). Influences of Diurnal Sampling Bias on Fixed-Point Monitoring of Plankton Biodiversity Determined Using a Massively Parallel Sequencing-Based Technique. In: Gojobori, T., Wada, T., Kobayashi, T., Mineta, K. (eds) Marine Metagenomics. Springer, Singapore. https://doi.org/10.1007/978-981-13-8134-8_14

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