Acta Oceanologica Sinica

, Volume 37, Issue 12, pp 118–128 | Cite as

Variation of bacterial community associated with Phaeodactylum tricornutum in response to different inorganic nitrogen concentrations

  • Feng Shi
  • Xiaoxue Wei
  • Jianfeng FengEmail author
  • Yingxue Sun
  • Lin ZhuEmail author


Specific bacterial communities interact with phytoplankton in laboratory algal cultures. These communities influence phytoplankton physiology and metabolism by transforming and exchanging phytoplankton-derived organic matter. Functional bacterial groups may participate in various critical nutrients fluxes within these associations, including nitrogen (N) metabolism. However, it is unclear how bacterial communities and the associated algae respond to changes of phycosphere N conditions. This response may have far-reaching implications for global nutrient cycling, algal bloom formation, and ecosystem function. Here, we identified changes in the bacterial communities associated with Phaeodactylum tricornutum when co-cultured with different forms and concentrations of N based on the Illumina HiSeq sequencing of 16S rRNA amplicons. Phylogenetic analysis identified Proteobacteria and Bacteroidetes as the dominant phyla, accounting for 99.5% of all sequences. Importantly, bacterial abundance and community structure were more affected by algal abundance than by the form or concentration of inorganic N. The relative abundance of three gammaproteobacterial genera (Marinobacter, Algiphilus and Methylophaga) markedly increased in N-deficient cultures. Thus, some bacterial groups may play a role in the regulation of N metabolism when co-cultured with P. tricornutum.

Key words

Phaeodactylum tricornutum nitrogen concentrations nitrogen forms bacterial diversity community structure Gammaproteobacteria 


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  1. Alavi M, Miller T, Erlandson K, et al. 2001. Bacterial community associated with Pfiesteria-like dinoflagellate cultures. Environmental Microbiology, 3(6): 380–396Google Scholar
  2. Amin S A, Green D H, Hart M C, et al. 2009. Photolysis of iron-siderophore chelates promotes bacterial-algal mutualism. Proceedings of the National Academy of Sciences of the United States of America, 106(40): 17071–17076Google Scholar
  3. Amin S A, Hmelo L R, Van Tol H M, et al. 2015. Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature, 522(7554): 98–101Google Scholar
  4. Amin S A, Parker M S, Armbrust E V. 2012. Interactions between diatoms and bacteria. Microbiology and Molecular Biology Reviews, 76(3): 667–684Google Scholar
  5. Balvanera P, Pfisterer A B, Buchmann N, et al. 2006. Quantifying the evidence for biodiversity effects on ecosystem functioning and services. Ecology Letters, 9(10): 1146–1156Google Scholar
  6. Behringer G, Ochsenkühn M A, Fei Cong, et al. 2018. Bacterial communities of diatoms display strong conservation across strains and time. Frontiers in Microbiology, 9: 659Google Scholar
  7. Bell W, Mitchell R. 1972. Chemotactic and growth responses of marine bacteria to algal extracellular products. The Biological Bulletin, 143(2): 265–277Google Scholar
  8. Bell W H. 1984. Bacterial adaptation to low-nutrient conditions as studied with algal extracellular products. Microbial Ecology, 10(3): 217–230Google Scholar
  9. Bolch C J S, Bejoy T A, Green D H. 2017. Bacterial associates modify growth dynamics of the dinoflagellate Gymnodinium catenatum. Frontiers in Microbiology, 8: 670Google Scholar
  10. Borcard D, Gillet F, Legendre P. 2011. Numerical Ecology with R. New York: Springer, 115–151Google Scholar
  11. Bowler C, Allen A E, Badger J H, et al. 2008. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature, 456(7219): 239–244Google Scholar
  12. Buchan A, Collier L S, Neidle E L, et al. 2000. Key aromatic-ringcleaving enzyme, protocatechuate 3,4-Dioxygenase, in the ecologically important marine Roseobacter Lineage. Applied and Environmental Microbiology, 66(11): 4662–4672Google Scholar
  13. Buchan A, LeCleir G R, Gulvik C A, et al. 2014. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nature Reviews Microbiology, 12(10): 686–698Google Scholar
  14. Capone D G, Bronk D A, Mulholland M R, et al. 2008. Nitrogen in the Marine Environment. 2nd ed. San Diego: Academic Press, 757Google Scholar
  15. Caporaso J G, Kuczynski J, Stombaugh J, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5): 335–336Google Scholar
  16. Caporaso J G, Lauber C L, Walters W A, et al. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences of the United States of America, 108(Suppl 1): 4516–4522Google Scholar
  17. Casciotti K L. 2016. Nitrogen and oxygen isotopic studies of the marine nitrogen cycle. Annual Review of Marine Science, 8: 379–407Google Scholar
  18. Chapin III F S I, Zavaleta E S, Eviner V T, et al. 2000. Consequences of changing biodiversity. Nature, 405(6783): 234–242Google Scholar
  19. Chiu H C, Levy R, Borenstein E. 2014. Emergent biosynthetic capacity in simple microbial communities. PLoS Computational Biology, 10(7): e1003695Google Scholar
  20. Croft M T, Lawrence A D, Raux-Deery E, et al. 2005. Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature, 438(7064): 90–93Google Scholar
  21. de-Bashan L E, Antoun H, Bashan Y. 2008. Involvement of indole-3-acetic acid produced by the growth-promoting bacterium Azospirillum spp. in promoting growth of Chlorella vulgaris. Journal of Phycology, 44(4): 938–947Google Scholar
  22. De La Haba R R, Sánchez-Porro C, Marquez M C, et al. 2011. Taxonomy of halophiles. In: Horikoshi K, ed. Extremophiles Handbook. Tokyo: Springer, 255–265Google Scholar
  23. De Martino A, Bartual A, Willis A, et al. 2011. Physiological and molecular evidence that environmental changes elicit morphological interconversion in the model diatom Phaeodactylum tricornutum. Protist, 162(3): 462–481Google Scholar
  24. Donald D B, Bogard M J, Finlay K, et al. 2011. Comparative effects of urea, ammonium, and nitrate on phytoplankton abundance, community composition, and toxicity in hypereutrophic freshwaters. Limnology and Oceanography, 56(6): 2161–2175Google Scholar
  25. Edgar R C. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10(10): 996–998Google Scholar
  26. Edgar R C, Haas B J, Clemente J C, et al. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16): 2194–2200Google Scholar
  27. Foster R A, Kuypers M M M, Vagner T, et al. 2011. Nitrogen fixation and transfer in open ocean diatom-cyanobacterial symbioses. ISME Journal, 5(9): 1484–1493Google Scholar
  28. Fowler D, Coyle M, Skiba U, et al. 2013. The global nitrogen cycle in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences, 368(1621): 20130164Google Scholar
  29. Gauthier M J, Lafay B, Christen R, et al. 1992. Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium. International Journal of Systematic and Evolutionary Microbiology, 42(4): 568–576Google Scholar
  30. González J M, Kiene R P, Moran M A. 1999. Transformation of sulfur compounds by an abundant lineage of marine bacteria in the α-subclass of the class Proteobacteria. Applied and Environmental Microbiology, 65(9): 3810–3819Google Scholar
  31. Green D H, Echavarri-Bravo V, Brennan D, et al. 2015. Bacterial diversity associated with the coccolithophorid algae Emiliania huxleyi and Coccolithus pelagicus f. braarudii. BioMed Research International, 2015: 194540Google Scholar
  32. Green D H, Hart M C, Blackburn S I, et al. 2010. Bacterial diversity of Gymnodinium catenatum and its relationship to dinoflagellate toxicity. Aquatic Microbial Ecology, 61(1): 73–87Google Scholar
  33. Green D H, Llewellyn L E, Negri A P, et al. 2004. Phylogenetic and functional diversity of the cultivable bacterial community associated with the paralytic shellfish poisoning dinoflagellate Gymnodinium catenatum. FEMS Microbiology Ecology, 47(3): 345–357Google Scholar
  34. Grossart H P, Levold F, Allgaier M, et al. 2010. Marine diatom species harbour distinct bacterial communities. Environmental Microbiology, 7(6): 860–873Google Scholar
  35. Guillard R R L. 1975. Culture of phytoplankton for feeding marine invertebrates. In: Smith W L, Chanley M H, ed. Culture of Marine Invertebrate Animals. Boston, MA: Springer, 29–60Google Scholar
  36. Guillard R R L, Ryther J H. 1962. Studies of marine planktonic diatoms: I. Cyclotella nana Hustedt, and Detonula confervacea (cleve) Gran. Canadian Journal of Microbiology, 8(2): 229–239Google Scholar
  37. Gutierrez T, Green D H, Whitman W B, et al. 2012. Algiphilus aromaticivorans gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from a culture of the marine dinoflagellate Lingulodinium polyedrum, and proposal of Algiphilaceae fam. nov.. International Journal of Systematic and Evolutionary Microbiology, 62(11): 2743–2749Google Scholar
  38. Haas B J, Gevers D, Earl A M, et al. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research, 21(3): 494–504Google Scholar
  39. Haines K C, Guillard R R L. 1974. Growth of vitamin B12-requiring marine diatoms in mixed laboratory cultures with vitamin B12-producing marine bacteria. Journal of Phycology, 10(3): 245–252Google Scholar
  40. Hatton A D, Shenoy D M, Hart M C, et al. 2012. Metabolism of DMSP, DMS and DMSO by the cultivable bacterial community associated with the DMSP-producing dinoflagellate Scrippsiella trochoidea. Biogeochemistry, 110(1–3): 131–146Google Scholar
  41. Jasti S, Sieracki M E, Poulton N J, et al. 2005. Phylogenetic diversity and specificity of bacteria closely associated with Alexandrium spp. and other phytoplankton. Applied and Environmental Microbiology, 71(7): 3483–3494Google Scholar
  42. Kaczmarska I, Ehrman J M, Bates E S S, et al. 2005. Diversity and distribution of epibiotic bacteria on Pseudo-nitzschia multiseries (Bacillariophyceae) in culture, and comparison with those on diatoms in native seawater. Harmful Algae, 4(4): 725–741Google Scholar
  43. Kuo R C, Lin Senjie. 2013. Ectobiotic and endobiotic bacteria associated with Eutreptiella sp. isolated from Long Island Sound. Protist, 164(1): 60–74Google Scholar
  44. Langille M G I, Zaneveld J, Caporaso J G, et al. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology, 31(9): 814–821Google Scholar
  45. Li Yang, Wang Zhen, Lin Xuezheng. 2016. Microbial community structure of Arctic seawater as revealed by pyrosequencing. Acta Oceanologica Sinica, 35(6): 78–84Google Scholar
  46. Little A E F, Robinson C J, Peterson S B, et al. 2008. Rules of engagement: interspecies interactions that regulate microbial communities. Annual Review of Microbiology, 62: 375–401Google Scholar
  47. Liu Lemian, Yang Jun, Lv Hong, et al. 2015. Phytoplankton communities exhibit a stronger response to environmental changes than bacterioplankton in three subtropical reservoirs. Environmental Science & Technology, 49(18): 10850–10858Google Scholar
  48. Løvdal T, Eichner C, Grossart H P, et al. 2008. Competition for inorganic and organic forms of nitrogen and phosphorous between phytoplankton and bacteria during an Emiliania huxleyi spring bloom. Biogeosciences, 5(2): 371–383Google Scholar
  49. Lupette J, Lami R, Krasovec M, et al. 2016. Marinobacter dominates the bacterial community of the Ostreococcus tauri phycosphere in culture. Frontiers in Microbiology, 7: 1414Google Scholar
  50. Ma Yuexin, Tao Wei, Liu Changfa, et al. 2017. Response of microbial biomass and bacterial community composition to fertilization in a salt marsh in China. Acta Oceanologica Sinica, 36(6): 80–88Google Scholar
  51. Magoč T, Salzberg S L. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27(21): 2957–2963Google Scholar
  52. Maheswari U, Jabbari K, Petit J L, et al. 2010. Digital expression profiling of novel diatom transcripts provides insight into their biological functions. Genome Biology, 11(8): R85Google Scholar
  53. Martens-Habbena W, Berube P M, Urakawa H, et al. 2009. Ammonia oxidation kinetics determine niche separation of nitrifying archaea and bacteria. Nature, 461(7266): 976–979Google Scholar
  54. Maruyama A, Maeda M, Simidu U. 1986. Occurrence of plant hormone (cytokinin)-producing bacteria in the sea. Journal of Applied Bacteriology, 61(6): 569–574Google Scholar
  55. Mayali X, Azam F. 2004. Algicidal bacteria in the sea and their impact on algal blooms. Journal of Eukaryotic Microbiology, 51(2): 139–144Google Scholar
  56. Miller T R, Belas R. 2004. Dimethylsulfoniopropionate metabolism by Pfiesteria-associated Roseobacter spp.. Applied and Environmental Microbiology, 70(6): 3383–3391Google Scholar
  57. Paerl H W, Dyble J, Moisander P H, et al. 2003. Microbial indicators of aquatic ecosystem change: current applications to eutrophication studies. FEMS Microbiology Ecology, 46(3): 233–246Google Scholar
  58. Quast C, Pruesse E, Yilmaz P, et al. 2013. The SILVA ribosomal RNA gene database project: improved data processing and webbased tools. Nucleic Acids Research, 41(D1): D590–D596Google Scholar
  59. Ramanan R, Kim B H, Cho D H, et al. 2016. Algae-bacteria interactions: Evolution, ecology and emerging applications. Biotechnology Advances, 34(1): 14–29Google Scholar
  60. Ramirez K S, Lauber C L, Knight R, et al. 2010. Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology, 91(12): 3463–3470Google Scholar
  61. Risgaard-Petersen N, Nicolaisen M H, Revsbech N P, et al. 2004. Competition between ammonia-oxidizing bacteria and benthic microalgae. Applied and Environmental Microbiology, 70(9): 5528–5537Google Scholar
  62. Rooney-Varga J N, Giewat M W, Savin M C, et al. 2005. Links between phytoplankton and bacterial community dynamics in a coastal marine environment. Microbial Ecology, 49(1): 163–175Google Scholar
  63. Sapp M, Wichels A, Wiltshire K H, et al. 2007. Bacterial community dynamics during the winter-spring transition in the North Sea. FEMS Microbiology Ecology, 59(3): 622–637Google Scholar
  64. Sasaki K, Ikeda S, Ohkubo T, et al. 2013. Effects of plant genotype and nitrogen level on bacterial communities in rice shoots and roots. Microbes and Environments, 28(3): 391–395Google Scholar
  65. Schäfer H, Abbas B, Witte H, et al. 2002. Genetic diversity of ‘satellite’ bacteria present in cultures of marine diatoms. FEMS Microbiology Ecology, 42(1): 25–35Google Scholar
  66. Segata N, Izard J, Waldron L, et al. 2011. Metagenomic biomarker discovery and explanation. Genome Biology, 12(6): R60Google Scholar
  67. Seymour J R, Amin S A, Raina J B, et al. 2017. Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships. Nature Microbiology, 2: 17065Google Scholar
  68. Seibold A, Wichels A, Schütt C. 2001. Diversity of endocytic bacteria in the dinoflagellate Noctiluca scintillans. Aquatic Microbial Ecology, 25(3): 229–235Google Scholar
  69. Villeneuve C, Martineau C, Mauffrey F, et al. 2013. Methylophaga nitratireducenticrescens sp. nov. and Methylophaga frappieri sp. nov., isolated from the biofilm of the methanol-fed denitrification system treating the seawater at the Montreal Biodome. International Journal of Systematic and Evolutionary Microbiology, 63(6): 2216–2222Google Scholar
  70. Wang Qiong, Garrity G M, Tiedje J M, et al. 2007. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73(16): 5261–5267Google Scholar
  71. Wang Xin, Li Zhijiang, Su Jianqiang, et al. 2010. Lysis of a red-tide causing alga, Alexandrium tamarense, caused by bacteria from its phycosphere. Biological Control, 52(2): 123–130Google Scholar
  72. Wemheuer B, Güllert S, Billerbeck S, et al. 2014. Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches. FEMS Microbiology Ecology, 87(2): 378–389Google Scholar
  73. Yang Caiyun, Li Yi, Zhou B, et al. 2015. Illumina sequencing-based analysis of free-living bacterial community dynamics during an Akashiwo sanguine bloom in Xiamen sea, China. Scientific Reports, 5: 8476Google Scholar
  74. Zehr J P, Kudela R M. 2010. Nitrogen cycle of the open ocean: from genes to ecosystems. Annual Review of Marine Science, 3: 197–225Google Scholar
  75. Zehr J P, Ward B B. 2002. Nitrogen cycling in the ocean: new perspectives on processes and paradigms. Applied and Environmental Microbiology, 68(3): 1015–1024Google Scholar

Copyright information

© The Chinese Society of Oceanography and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Key Laboratory of Pollution Process and Environmental Criteria of Ministry of Education and Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and EngineeringNankai UniversityTianjinChina

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