Luo H, Moran MA. Evolutionary ecology of the marine Roseobacter clade. Microbiol Mol Biol Rev. 2014;78:573–87.
Google Scholar
Wietz M, Gram L, Jørgensen B, Schramm A. Latitudinal patterns in the abundance of major marine bacterioplankton groups. Aquat Microbial Ecol. 2010;61:179–89.
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, et al. Structure and function of the global ocean microbiome. Science. 2015;348:1261359.
Google Scholar
González JM, Simó R, Massana R, Covert JS, Casamayor EO, Pedrós-Alió C, et al. Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appli Environ Microbiol. 2000;66:4237–46.
González JM, Moran MA. Numerical dominance of a group of marine bacteria in the alpha-subclass of the class Proteobacteria in coastal seawater. Appl Environ Microbiol. 1997;63:4237–42.
Google Scholar
Grossart HP, Levold F, Allgaier M, Simon M, Brinkhoff T. Marine diatom species harbour distinct bacterial communities. Environ Microbiol. 2005;7:860–73.
Google Scholar
Amin SA, Parker MS, Armbrust EV. Interactions between diatoms and bacteria. Microbiol Mol Biol Rev. 2012;76:667–84.
Google Scholar
Alavi M, Miller T, Erlandson K, Schneider R, Belas R. Bacterial community associated with Pfiesteria‐like dinoflagellate cultures. Environ Microbiol. 2001;3:380–96.
Google Scholar
Jasti S, Sieracki ME, Poulton NJ, Giewat MW, Rooney-Varga JN. Phylogenetic diversity and specificity of bacteria closely associated with Alexandrium spp. and other phytoplankton. Appl Environ Microbiol. 2005;71:3483–94.
Google Scholar
Zubkov MV, Fuchs BM, Archer SD, Kiene RP, Amann R, Burkill PH. Rapid turnover of dissolved DMS and DMSP by defined bacterioplankton communities in the stratified euphotic zone of the North Sea. Deep Sea Res Top Stud Oceanogr. 2002;49:3017–38.
Google Scholar
Zubkov MV, Fuchs BM, Archer SD, Kiene RP, Amann R, Burkill PH. Linking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulphoniopropionate in an algal bloom in the North Sea. Environ Microbiol. 2001;3:304–11.
Google Scholar
Teeling H, Fuchs BM, Becher D, Klockow C, Gardebrecht A, Bennke CM, et al. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science. 2012;336:608–11.
Google Scholar
Voget S, Wemheuer B, Brinkhoff T, Vollmers J, Dietrich S, Giebel H-A, et al. Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses. ISME J. 2015;9:371–84.
Google Scholar
Billerbeck S, Wemheuer B, Voget S, Poehlein A, Giebel H-A, Brinkhoff T, et al. Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage. Nat Microbiol. 2016;1:16063.
Google Scholar
Buchan A, LeCleir GR, Gulvik CA, González JM. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat Rev Microbiol. 2014;12:686–98.
Google Scholar
Amin S, Hmelo L, van Tol H, Durham B, Carlson L, Heal K, et al. Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature. 2015;522:98–101.
Google Scholar
Landa M, Burns AS, Durham BP, Esson K, Nowinski B, Sharma S, et al. Sulfur metabolites that facilitate oceanic phytoplankton–bacteria carbon flux. ISME J. 2019;13:2536–50.
Google Scholar
Durham BP, Boysen AK, Carlson LT, Groussman RD, Heal KR, Cain KR, et al. Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean. Nat Microbiol. 2019;4:1706–15.
Google Scholar
Howard EC, Henriksen JR, Buchan A, Reisch CR, Bürgmann H, Welsh R, et al. Bacterial taxa that limit sulfur flux from the ocean. Science. 2006;314:649–52.
Google Scholar
Levine NM, Toole DA, Neeley A, Bates NR, Doney SC, Dacey JW. Revising upper-ocean sulfur dynamics near Bermuda: new lessons from 3 years of concentration and rate measurements. Environ Chem. 2016;13:302–13.
Google Scholar
Kiene RP. Turnover of dissolved DMSP in estuarine and shelf waters of the northern Gulf of Mexico. In Biological and environmental chemistry of DMSP and related sulfonium compounds. Boston, MA: Springer; 1996. pp. 337–49.
Kiene RP, Linn LJ. Distribution and turnover of dissolved DMSP and its relationship with bacterial production and dimethylsulfide in the Gulf of Mexico. Limnol Oceanogr. 2000;45:849–61.
Google Scholar
Curson AR, Todd JD, Sullivan MJ, Johnston AW. Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes. Nat Rev Microbiol. 2011;9:849–59.
Google Scholar
Simó R. Production of atmospheric sulfur by oceanic plankton: biogeochemical, ecological and evolutionary links. Trends Ecol Evol. 2001;16:287–94.
Google Scholar
Charlson RJ, Lovelock JE, Andreae MO, Warren SG. Oceanic phytoplankton, atmospheric sulphur, cloud albedo and climate. Nature. 1987;326:655–61.
Google Scholar
Reisch CR, Moran MA, Whitman WB. Bacterial catabolism of dimethylsulfoniopropionate (DMSP). Front Microbiol. 2011;2:172.
Google Scholar
Varaljay VA, Howard EC, Sun S, Moran MA. Deep sequencing of a dimethylsulfoniopropionate-degrading gene (dmdA) by using PCR primer pairs designed on the basis of marine metagenomic data. Appl Environ Microbiol. 2010;76:609–17.
Google Scholar
Varaljay VA, Robidart J, Preston CM, Gifford SM, Durham BP, Burns AS, et al. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate. ISME J. 2015;9:1677.
Google Scholar
Ledyard KM, DeLong EF, Dacey JW. Characterization of a DMSP-degrading bacterial isolate from the Sargasso Sea. Arch Microbiol. 1993;160:312–8.
Google Scholar
Todd JD, Kirkwood M, Newton-Payne S, Johnston AW. DddW, a third DMSP lyase in a model Roseobacter marine bacterium, Ruegeria pomeroyi DSS-3. ISME J. 2012;6:223–6.
Google Scholar
Todd JD, Curson AR, Kirkwood M, Sullivan MJ, Green RT, Johnston AW. DddQ, a novel, cupin‐containing, dimethylsulfoniopropionate lyase in marine roseobacters and in uncultured marine bacteria. Environ Microbiol. 2011;13:427–38.
Google Scholar
Todd J, Curson A, Dupont C, Nicholson P, Johnston A. The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi. Environ Microbiol. 2009;11:1376–85.
Google Scholar
Todd JD, Curson AR, Nikolaidou‐Katsaraidou N, Brearley CA, Watmough NJ, Chan Y, et al. Molecular dissection of bacterial acrylate catabolism–unexpected links with dimethylsulfoniopropionate catabolism and dimethyl sulfide production. Environ Microbiol. 2010;12:327–43.
Google Scholar
Curson A, Rogers R, Todd J, Brearley C, Johnston A. Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate‐changing gas dimethylsulfide in several marine α‐proteobacteria and Rhodobacter sphaeroides. Environ Microbiol. 2008;10:757–67.
Google Scholar
Delmont TO, Hammar KM, Ducklow HW, Yager PL, Post AF. Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya. Front Microbiol. 2014;5:646.
Google Scholar
Stoica E, Herndl GJ. Bacterioplankton community composition in nearshore waters of the NW Black Sea during consecutive diatom and coccolithophorid blooms. Aquat Sci. 2007;69:413–8.
Google Scholar
Giebel HA, Brinkhoff T, Zwisler W, Selje N, Simon M. Distribution of Roseobacter RCA and SAR11 lineages and distinct bacterial communities from the subtropics to the Southern Ocean. Environ Microbiol. 2009;11:2164–78.
Google Scholar
Landa M, Blain S, Christaki U, Monchy S, Obernosterer I. Shifts in bacterial community composition associated with increased carbon cycling in a mosaic of phytoplankton blooms. ISME J. 2016;10:39–50.
Google Scholar
Wemheuer B, Güllert S, Billerbeck S, Giebel H-A, Voget S, Simon M, et al. Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches. FEMS Microbiol Ecol. 2014;87:378–89.
Google Scholar
Alonso-Gutiérrez J, Lekunberri I, Teira E, Gasol JM, Figueras A, Novoa B. Bacterioplankton composition of the coastal upwelling system of ‘Ría de Vigo’, NW Spain. FEMS Microbiol Ecol. 2009;70:493–505.
Google Scholar
Brown MV, Van De Kamp J, Ostrowski M, Seymour JR, Ingleton T, Messer LF, et al. Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative. Sci Data. 2018;5:180130.
Google Scholar
Ajani P, Hallegraeff G, Allen D, Coughlan A, Richardson A, Armand L, et al. Establishing baselines: a review of eighty years of phytoplankton diversity and biomass in southeastern Australia. Oceanogr Mar Biol. 2016;54:387–412.
Matear R, Chamberlain M, Sun C, Feng M. Climate change projection of the Tasman Sea from an eddy‐resolving ocean model. J Geophys Res Oceans. 2013;118:2961–76.
Ostrowski M, Seymour J, Messer L, Varkey D, Goosen K, Smith M, et al. Status of Australian marine microbial assemblages. In State and Trends of Australia’s Ocean Report, Integrated Marine Observing System (IMOS). 2020. https://doi.org/10.26198/5e16aa3e49e7f.
Lynch TP, Morello EB, Evans K, Richardson AJ, Rochester W, Steinberg CR, et al. IMOS National Reference Stations: a continental-wide physical, chemical and biological coastal observing system. PloS ONE. 2014;9:e113652.
Google Scholar
Lynch T, Roughan M, Mclaughlan D, Hughes D, Cherry D, Critchley G, et al. A national reference station infrastructure for Australia – Using telemetry and central processing to report multi-disciplinary data streams for monitoring marine ecosystem response to climate change. In: OCEANS 2008. 2008. https://doi.org/10.1109/OCEANS.2008.5151856.
Appleyard SA, Abell G, Watson R. Tackling microbial related issues in cultured shellfish via integrated molecular and water chemistry approaches. Clayton: CSIRO Marine and Atmospheric Research; 2013.
Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 2016;18:1403–14.
Google Scholar
Duarte CM. Seafaring in the 21st century: the Malaspina 2010 circumnavigation expedition. Limnol Oceanogr Bull. 2015;24:11–4.
Biller SJ, Berube PM, Dooley K, Williams M, Satinsky BM, Hackl T, et al. Marine microbial metagenomes sampled across space and time. Sci Data. 2018;5:1–7.
Logares R, Sunagawa S, Salazar G, Cornejo‐Castillo FM, Ferrera I, Sarmento H, et al. Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environm Microbiol. 2014;16:2659–71.
Google Scholar
Dadon-Pilosof A, Conley KR, Jacobi Y, Haber M, Lombard F, Sutherland KR, et al. Surface properties of SAR11 bacteria facilitate grazing avoidance. Nat Microbiol. 2017;2:1608–15.
Google Scholar
Lane D. 16S/23S rRNA sequencing. In: Nucleic acid techniques in bacterial systematics. New York: John Wiley & Sons; 1991, pp. 115–75.
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci. 1985;82:6955–9.
Google Scholar
Piredda R, Tomasino M, D’erchia A, Manzari C, Pesole G, Montresor M, et al. Diversity and temporal patterns of planktonic protist assemblages at a Mediterranean Long Term Ecological Research site. FEMS Microbiol Ecol. 2017;93.
Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW, et al. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol. 2010;19:21–31.
Google Scholar
Andrews S. FastQC: a quality control tool for high throughput sequence data. Cambridge, United Kingdom: Babraham Bioinformatics, Babraham Institute; 2010.
Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;27:2957–63.
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Google Scholar
Gordon A, Hannon G. Fastx-toolkit. FASTQ/A short-reads preprocessing tools. 2010;5. http://hannonlab.cshl.edu/fastx_toolkit/.
Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, et al. The SILVA and “all-species living tree project (LTP)” taxonomic frameworks. Nucl Acids Res. 2014;42:D643–8.
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261–7.
Google Scholar
Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucl Acids Res. 2012;41:D597–604.
Google Scholar
Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, et al. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME J. 2017;11:1483–99.
Google Scholar
Brinkhoff T, Giebel H-A, Simon M. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol. 2008;189:531–9.
Google Scholar
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.
Google Scholar
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res. 2004;32:1792–7.
Google Scholar
Felsenstein J. Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution. 1981:1229–42.
Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993;10:512–26.
Google Scholar
emcparland. emcparland/dmspOTUs: first release. 2021. https://doi.org/10.5281/zenodo.5090864.
Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, et al. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 2014;12:e1001889.
Google Scholar
Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013;29:2933–5.
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Google Scholar
Matsen FA, Kodner RB, Armbrust EV. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinform. 2010;11:538.
McParland EL, Levine NM. The role of differential DMSP production and community composition in predicting variability of global surface DMSP concentrations. Limnol Oceanogr. 2019;64:757–73.
Google Scholar
Reshef DN, Reshef YA, Sabeti PC, Mitzenmacher M. An empirical study of the maximal and total information coefficients and leading measures of dependence. Ann Appl Stat. 2018;12:123–55.
Hammer Ø, Harper DA, Ryan PD. PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron. 2001;4:9.
Buchan A, González JM, Moran MA. Overview of the marine Roseobacter lineage. Appl Environ Microbiol. 2005;71:5665–77.
Google Scholar
Moran MA, González JM, Kiene RP. Linking a bacterial taxon to sulfur cycling in the sea: studies of the marine Roseobacter group. Geomicrobiol J. 2003;20:375–88.
Google Scholar
Harris G, Nilsson C, Clementson L, Thomas D. The water masses of the east coast of Tasmania: seasonal and interannual variability and the influence on phytoplankton biomass and productivity. Mar Freshw Res. 1987;38:569–90.
Google Scholar
Kiene RP, Linn LJ, González J, Moran MA, Bruton JA. Dimethylsulfoniopropionate and methanethiol are important precursors of methionine and protein-sulfur in marine bacterioplankton. Appl Environ Microbiol. 1999;65:4549–58.
Google Scholar
Raina J-B, Tapiolas D, Willis BL, Bourne DG. Coral-associated bacteria and their role in the biogeochemical cycling of sulfur. Appl Environ Microbiol. 2009;75:3492–501.
Google Scholar
Brinkmeyer R, Rappé M, Gallacher S, Medlin L. Development of clade-(Roseobacter and Alteromonas) and taxon-specific oligonucleotide probes to study interactions between toxic dinoflagellates and their associated bacteria. Eur J Phycol. 2000;35:315–29.
Töpel M, Pinder MI, Johansson ON, Kourtchenko O, Clarke AK, Godhe A. Complete genome sequence of novel Sulfitobacter pseudonitzschiae Strain SMR1, isolated from a culture of the marine diatom Skeletonema marinoi. J Genomics. 2019;7:7.
Google Scholar
Hong Z, Lai Q, Luo Q, Jiang S, Zhu R, Liang J, et al. Sulfitobacter pseudonitzschiae sp. nov., isolated from the toxic marine diatom Pseudo-nitzschia multiseries. Int J Syst Evol Microbiol. 2015;65:95–100.
Google Scholar
Yang Q, Ge Y-M, Iqbal NM, Yang X, Zhang X-l. Sulfitobacter alexandrii sp. nov., a new microalgae growth-promoting bacterium with exopolysaccharides bioflocculanting potential isolated from marine phycosphere. Antonie Van Leeuwenhoek. 2021;114:1091–106.
Google Scholar
Ankrah NY, Lane T, Budinoff CR, Hadden MK, Buchan A. Draft genome sequence of Sulfitobacter sp. CB2047, a member of the Roseobacter clade of marine bacteria, isolated from an emiliania huxleyi bloom. Genome Announc. 2014;2:e01125–14.
Google Scholar
Kwak M-J, Lee J-S, Lee KC, Kim KK, Eom MK, Kim BK, et al. Sulfitobacter geojensis sp. nov., Sulfitobacter noctilucae sp. nov., and Sulfitobacternoctilucicola sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol. 2014;64:3760–7.
Google Scholar
Zhang F, Fan Y, Zhang D, Chen S, Bai X, Ma X, et al. Effect and mechanism of the algicidal bacterium Sulfitobacter porphyrae ZFX1 on the mitigation of harmful algal blooms caused by Prorocentrum donghaiense. Environ Pollut. 2020;263:114475.
Google Scholar
Keller MD. Dimethyl sulfide production and marine phytoplankton: the importance of species composition and cell size. Biol Oceanogr. 1989;6:375–82.
McParland EL, Lee MD, Webb EA, Alexander H, Levine NM. DMSP synthesis genes distinguish two types of DMSP producer phenotypes. Environ Microbiol. 2021;23:1656–69.
Google Scholar
Galí M, Simó R. A meta‐analysis of oceanic DMS and DMSP cycling processes: disentangling the summer paradox. Glob Biogeochem Cycles. 2015;29:496–515.
Carr A, Diener C, Baliga NS, Gibbons SM. Use and abuse of correlation analyses in microbial ecology. ISME J. 2019;13:2647–55.
Google Scholar
Amin S, Hmelo L, Van Tol H, Durham B, Carlson L, Heal K, et al. Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature. 2015;522:98.
Google Scholar
Miller TR, Hnilicka K, Dziedzic A, Desplats P, Belas R. Chemotaxis of Silicibacter sp. strain TM1040 toward dinoflagellate products. Appl Environ Microbiol. 2004;70:4692–701.
Google Scholar
Seymour JR, Simó R, Ahmed T, Stocker R. Chemoattraction to dimethylsulfoniopropionate throughout the marine microbial food web. Science. 2010;329:342–5.
Google Scholar
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