Citation: | SHI Feng, WEI Xiaoxue, FENG Jianfeng, SUN Yingxue, ZHU Lin. Variation of bacterial community associated with Phaeodactylum tricornutum in response to different inorganic nitrogen concentrations[J]. Acta Oceanologica Sinica, 2018, 37(12): 118-128. doi: 10.1007/s13131-018-1272-7 |
Alavi M, Miller T, Erlandson K, et al. 2001. Bacterial community associated with Pfiesteria-like dinoflagellate cultures. Environmental Microbiology, 3(6): 380-396
|
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): 17071-17076
|
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): 98-101
|
Amin S A, Parker M S, Armbrust E V. 2012. Interactions between diatoms and bacteria. Microbiology and Molecular Biology Reviews, 76(3): 667-684
|
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): 1146-1156
|
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: 659
|
Bell W, Mitchell R. 1972. Chemotactic and growth responses of marine bacteria to algal extracellular products. The Biological Bulletin, 143(2): 265-277
|
Bell W H. 1984. Bacterial adaptation to low-nutrient conditions as studied with algal extracellular products. Microbial Ecology, 10(3): 217-230
|
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: 670
|
Borcard D, Gillet F, Legendre P. 2011. Numerical Ecology with R. New York: Springer, 115-151
|
Bowler C, Allen A E, Badger J H, et al. 2008. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature, 456(7219): 239-244
|
Buchan A, Collier L S, Neidle E L, et al. 2000. Key aromatic-ring-cleaving enzyme, protocatechuate 3,4-Dioxygenase, in the ecologically important marine Roseobacter Lineage. Applied and Environmental Microbiology, 66(11): 4662-4672
|
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): 686-698
|
Capone D G, Bronk D A, Mulholland M R, et al. 2008. Nitrogen in the Marine Environment. 2nd ed. San Diego: Academic Press, 757
|
Caporaso J G, Kuczynski J, Stombaugh J, et al. 2010. QⅡME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5): 335-336
|
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): 4516-4522
|
Casciotti K L. 2016. Nitrogen and oxygen isotopic studies of the marine nitrogen cycle. Annual Review of Marine Science, 8: 379-407
|
Chapin Ⅲ F S I, Zavaleta E S, Eviner V T, et al. 2000. Consequences of changing biodiversity. Nature, 405(6783): 234-242
|
Chiu H C, Levy R, Borenstein E. 2014. Emergent biosynthetic capacity in simple microbial communities. PLoS Computational Biology, 10(7): e1003695
|
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): 90-93
|
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): 938-947
|
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, 255-265
|
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): 462-481
|
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): 2161-2175
|
Edgar R C. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10(10): 996-998
|
Edgar R C, Haas B J, Clemente J C, et al. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16): 2194-2200
|
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): 1484-1493
|
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): 20130164
|
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): 568-576
|
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): 3810-3819
|
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: 194540
|
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): 73-87
|
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): 345-357
|
Grossart H P, Levold F, Allgaier M, et al. 2010. Marine diatom species harbour distinct bacterial communities. Environmental Microbiology, 7(6): 860-873
|
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, 29-60
|
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): 229-239
|
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): 2743-2749
|
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): 494-504
|
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): 245-252
|
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): 131-146
|
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): 3483-3494
|
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): 725-741
|
Kuo R C, Lin Senjie. 2013. Ectobiotic and endobiotic bacteria associated with Eutreptiella sp. isolated from Long Island Sound. Protist, 164(1): 60-74
|
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): 814-821
|
Li Yang, Wang Zhen, Lin Xuezheng. 2016. Microbial community structure of Arctic seawater as revealed by pyrosequencing. Acta Oceanologica Sinica, 35(6): 78-84
|
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: 375-401
|
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): 10850-10858
|
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): 371-383
|
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: 1414
|
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): 80-88
|
Magoč T, Salzberg S L. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27(21): 2957-2963
|
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): R85
|
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): 976-979
|
Maruyama A, Maeda M, Simidu U. 1986. Occurrence of plant hormone (cytokinin)-producing bacteria in the sea. Journal of Applied Bacteriology, 61(6): 569-574
|
Mayali X, Azam F. 2004. Algicidal bacteria in the sea and their impact on algal blooms. Journal of Eukaryotic Microbiology, 51(2): 139-144
|
Miller T R, Belas R. 2004. Dimethylsulfoniopropionate metabolism by Pfiesteria-associated Roseobacter spp. Applied and Environmental Microbiology, 70(6): 3383-3391
|
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): 233-246
|
Quast C, Pruesse E, Yilmaz P, et al. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41(D1): D590-D596
|
Ramanan R, Kim B H, Cho D H, et al. 2016. Algae-bacteria interactions: Evolution, ecology and emerging applications. Biotechnology Advances, 34(1): 14-29
|
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): 3463-3470
|
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): 5528-5537
|
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): 163-175
|
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): 622-637
|
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): 391-395
|
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): 25-35
|
Segata N, Izard J, Waldron L, et al. 2011. Metagenomic biomarker discovery and explanation. Genome Biology, 12(6): R60
|
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: 17065
|
Seibold A, Wichels A, Schütt C. 2001. Diversity of endocytic bacteria in the dinoflagellate Noctiluca scintillans. Aquatic Microbial Ecology, 25(3): 229-235
|
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): 2216-2222
|
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): 5261-5267
|
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): 123-130
|
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): 378-389
|
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: 8476
|
Zehr J P, Kudela R M. 2010. Nitrogen cycle of the open ocean: from genes to ecosystems. Annual Review of Marine Science, 3: 197-225
|
Zehr J P, Ward B B. 2002. Nitrogen cycling in the ocean: new perspectives on processes and paradigms. Applied and Environmental Microbiology, 68(3): 1015-1024
|