Azam, F. et al. The ecological role of water-column microbes in the sea. Mar. Ecol. Prog. Ser. 10, 257–263 (1983).
Google Scholar
Seymour, J. R., Amin, S. A., Raina, J.-B. & Stocker, R. Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships. Nat. Microbiol. 2, 17065 (2017).
Google Scholar
Worden, A. Z. et al. Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes. Science 347, 1257594 (2015).
Google Scholar
Andersson, A. F., Riemann, L. & Bertilsson, S. Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities. ISME J. 4, 171–181 (2010).
Google Scholar
Chen, T., Liu, Y., Song, S. & Li, C. Characterization of the parasitic dinoflagellate Amoebophrya sp. infecting akashiwo sanguinea in coastal waters of China. J. Eukaryotic Microbiol. 65, 448–457 (2018).
Google Scholar
Azam, F. & Malfatti, F. Microbial structuring of marine ecosystems. Nat. Rev. Microbiol. 5, 782–791 (2007).
Google Scholar
Yang, C. et al. Bacterial community dynamics during a bloom caused by Akashiwo sanguinea in the Xiamen sea area, China. Harmful algae 20, 132–141 (2012).
Google Scholar
Yang, C. et al. A comprehensive insight into functional profiles of free-living microbial community responses to a toxic Akashiwo sanguinea bloom. Sci. Rep. 6, 34645 (2016).
Google Scholar
Kang, et al. Zooming on dynamics of marine microbial communities in the phycosphere of Akashiwo sanguinea (Dinophyta) blooms. Mol. Ecol. 30, 207–221 (2021).
Google Scholar
Kim, H. J. et al. Effects of temperature and nutrients on changes in genetic diversity of bacterioplankton communities in a semi-closed bay, South Korea. Mar. Pollut. Bull. 106, 139–148 (2016).
Google Scholar
Flaviani, F. et al. A pelagic microbiome (viruses to protists) from a small cup of seawater. Viruses 9, 47 (2017).
Google Scholar
Jung, S. W. et al. Can the algicidal material Ca-aminoclay be harmful when applied to a natural ecosystem? An assessment using microcosms. J. Hazard. Mater. 298, 178–187 (2015).
Google Scholar
Jung, S. W., Noh, S. Y., Kang, D. & Lee, T.-K. Comparison of bacterioplankton communities between before and after inoculation with an algicidal material, Ca-aminoclay, to mitigate Cochlodinium polykrikoides blooms: assessment using microcosm experiments. J. Appl. Phycol. 29, 1343–1354 (2017).
Google Scholar
Jung, S. W., Kim, B. H., Katano, T., Kong, D. S. & Han, M. S. Pseudomonas fluorescens HYK0210-SK09 offers species-specific biological control of winter algal blooms caused by freshwater diatom Stephanodiscus hantzschii. J. Appl. Microbiol. 105, 186–195 (2008).
Google Scholar
Jung, S. W. et al. Testing addition of Pseudomonas fluorescens HYK0210-SK09 to mitigate blooms of the diatom Stephanodiscus hantzschii in small- and large-scale mesocosms. J. Appl. Phycol. 22, 409–419 (2010).
Google Scholar
Anderson, D. M. Turning back the harmful red tide. Nature 388, 513–514 (1997).
Google Scholar
Du, X., Peterson, W., McCulloch, A. & Liu, G. An unusual bloom of the dinoflagellate Akashiwo sanguinea off the central Oregon, USA, coast in autumn 2009. Harmful Algae 10, 784–793 (2011).
Google Scholar
Lee, C.-K., Lee, O.-H. & Lee, S.-G. Impacts of temperature, salinity and irradiance on the growth of ten harmful algal bloom-forming microalgae isolated in Korean coastal waters. The Sea (J Korean Soc Oceanogr) 10, 79–91 (2005).
Luo, Z. et al. Cryptic diversity within the harmful dinoflagellate Akashiwo sanguinea in coastal Chinese waters is related to differentiated ecological niches. Harmful Algae 66, 88–96 (2017).
Google Scholar
Chen, T. et al. The effects of major environmental factors and nutrient limitation on growth and encystment of planktonic dinoflagellate Akashiwo sanguinea. Harmful Algae 46, 62–70 (2015).
Google Scholar
Matsubara, T. et al. Effects of temperature, salinity, and irradiance on the growth of the dinoflagellate Akashiwo sanguinea. J. Exp. Mar. Biol. Ecol. 342, 226–230 (2007).
Google Scholar
Teeling, H. et al. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336, 608–611 (2012).
Google Scholar
Buchan, A., LeCleir, G. R., Gulvik, C. A. & González, J. M. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat. Rev. Microbiol. 12, 686–698 (2014).
Google Scholar
Riemann, L., Steward, G. F. & Azam, F. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl. Environ. Microbiol. 66, 578–587 (2000).
Google Scholar
Jones, K. L., Mikulski, C. M., Barnhorst, A. & Doucette, G. J. Comparative analysis of bacterioplankton assemblages from Karenia brevis bloom and nonbloom water on the west Florida shelf (Gulf of Mexico, USA) using 16S rRNA gene clone libraries. FEMS Microbiol. Ecol. 73, 468–485 (2010).
Google Scholar
Theroux, S., Huang, Y. & Amaral-Zettler, L. Comparative molecular microbial ecology of the spring haptophyte bloom in a Greenland arctic oligosaline lake. Front. Microbiol. 3, 415 (2012).
Google Scholar
Amin, S. et al. Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature 522, 98–101 (2015).
Google Scholar
Mayali, X. & Azam, F. Algicidal bacteria in the sea and their impact on algal blooms. J. Eukaryot. Microbiol. 51, 139–144 (2004).
Google Scholar
Tan, S. et al. An association network analysis among microeukaryotes and bacterioplankton reveals algal bloom dynamics. J. Phycol. 51, 120–132 (2015).
Google Scholar
Cruz-López, R., Maske, H., Yarimizu, K. & Holland, N. A. The B-vitamin mutualism between the dinoflagellate Lingulodinium polyedrum and the bacterium Dinoroseobacter shibae. Front. Mar. Sci. 5, 274 (2018).
Google Scholar
Park, B. S., Joo, J.-H., Baek, K.-D. & Han, M.-S. A mutualistic interaction between the bacterium Pseudomonas asplenii and the harmful algal species Chattonella marina (Raphidophyceae). Harmful Algae 56, 29–36 (2016).
Google Scholar
Needham, D. M., Sachdeva, R. & Fuhrman, J. A. Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters. ISME J. 11, 1614–1629 (2017).
Google Scholar
Bloem, J., Starink, M., Bär-Gilissen, M.-J.B. & Cappenberg, T. E. Protozoan grazing, bacterial activity, and mineralization in two-stage continuous cultures. Appl. Environ. Microbiol. 54, 3113–3121 (1988).
Google Scholar
Gao, X., Olapade, O. A. & Leff, L. G. Comparison of benthic bacterial community composition in nine streams. Aquat. Microb. Ecol. 40, 51–60 (2005).
Google Scholar
González, J. M., Kiene, R. P. & Moran, M. A. Transformation of sulfur compounds by an abundant lineage of marine bacteria in the α-subclass of the class Proteobacteria. Appl. Environ. Microbiol. 65, 3810–3819 (1999).
Google Scholar
Cui, Y. et al. The water depth-dependent co-occurrence patterns of marine bacteria in shallow and dynamic Southern Coast, Korea. Sci. Rep. 9, 9176 (2019).
Google Scholar
Huang, X. et al. Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach. Microbiol. Res. 217, 1–13 (2018).
Google Scholar
Orsi, W. D. et al. Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter. ISME J. 9, 1747–1763 (2015).
Google Scholar
Salter, I. et al. Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea. ISME J. 9, 347–360 (2015).
Google Scholar
Berdjeb, L., Parada, A., Needham, D. M. & Fuhrman, J. A. Short-term dynamics and interactions of marine protist communities during the spring–summer transition. ISME J. 12, 1907–1917 (2018).
Google Scholar
Chow, C.-E.T., Kim, D. Y., Sachdeva, R., Caron, D. A. & Fuhrman, J. A. Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists. ISME J. 8, 816–829 (2014).
Google Scholar
Louca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the globalocean microbiome. Science 353, 1272–1277 (2016).
Google Scholar
Rivett, D. W. & Bell, T. Abundance determines the functional role of bacterial phylotypes in complex communities. Nat. Microbiol. 3, 767–772 (2018).
Google Scholar
Amblard, C., Rachiq, S. & Bourdier, G. Photolithotrophy, photoheterotrophy and chemoheterotrophy during spring phytoplankton development (Lake Pavin). Microb. Ecol. 24, 109–123 (1992).
Google Scholar
Chun, S.-J. et al. Characterization of distinct cyanoHABs-related modules in microbial recurrent association network. Front. Microbiol. 10, 1637 (2019).
Google Scholar
He, T., Xie, D., Ni, J., Li, Z. & Li, Z. Nitrous oxide produced directly from ammonium, nitrate and nitrite during nitrification and denitrification. J. Hazard. Mater. 388, 122114 (2020).
Google Scholar
Leahy, J. G. & Colwell, R. R. Microbial degradation of hydrocarbons in the environment. Microbiol. Rev. 54, 305–315 (1990).
Google Scholar
Porter, K. G. & Feig, Y. S. The use of DAPI for identifying and counting aquatic microflora 1. Limnol. Oceanogr. 25, 943–948 (1980).
Google Scholar
Andrew, S. A quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. (2010)
Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Google Scholar
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
Google Scholar
Li, R. W. et al. Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools. Environ. Microbiol. 14, 129–139 (2012).
Google Scholar
Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).
Google Scholar
Oksanen, J. et al. Package ‘vegan’. Community ecology package. https://github.com/vegandevs/vegan (2019).
Paradis, E. et al. Package ‘ape’. Analyses of phylogenetics and evolution. http://ape-package.ird.fr/. (2019).
Wickham, H. et al. ggplot2: Create elegant data visualisations using the grammar of graphics. https://github.com/tidyverse/ggplot2 (2020).
Walker, I. R., Levesque, A. J., Cwynar, L. C. & Lotter, A. F. An expanded surface-water palaeotemperature inference model for use with fossil midges from eastern Canada. J. Paleolimnol. 18, 165–178 (1997).
Google Scholar
Clarke, K. R. Non-parametric multivariate analyses of changes in community structure. Aust. J. Ecol. 18, 117–143 (1993).
Google Scholar
Ter Braak, C. J. Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis. Ecology 67, 1167–1179 (1986).
Google Scholar
Ter Braak, C.J.F. & Šmilauer, P. CANOCO Reference Manual and CanoDraw for Windows User’s Guide: Software for Canonical Community Ordination, version 4.5. Ithaca, NY, USA: Microcomputer Power. (2002).
Xia, L. C. et al. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Syst. Biol. 5, S15 (2011).
Google Scholar
Xia, L. C., Ai, D., Cram, J., Fuhrman, J. A. & Sun, F. Efficient statistical significance approximation for local similarity analysis of high-throughput time series data. Bioinformatics 29, 230–237 (2013).
Google Scholar
Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
Google Scholar
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