Gattuso JP, Frankignoulle M, Wollast R. Carbon and carbonate metabolism in coastal aquatic ecosystems. Annu Rev Ecol Syst. 1998;29:405–34.
Google Scholar
Arnosti C, Wietz M, Brinkhoff T, Hehemann JH, Probandt D, Zeugner L, et al. The biogeochemistry of marine polysaccharides: sources, inventories, and bacterial drivers of the carbohydrate cycle. Ann Rev Mar Sci. 2021;13:81–108.
Google Scholar
Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, Buchan A, et al. Deciphering ocean carbon in a changing world. Proc Natl Acad Sci USA. 2016;113:3143–51.
Google Scholar
Poretsky RS, Sun S, Mou X, Moran MA. Transporter genes expressed by coastal bacterioplankton in response to dissolved organic carbon. Environ Microbiol. 2010;12:616–27.
Google Scholar
Azam F. Microbial control of oceanic carbon flux: The plot thickens. Science.1998;280:694–96.
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
Bunse C, Bertos-Fortis M, Sassenhagen I, Sildever S, Sjoqvist C, Godhe A, et al. Spatio-temporal interdependence of bacteria and phytoplankton during a baltic sea spring bloom. Front Microbiol. 2016;7:517.
Google Scholar
Cram JA, Chow CE, Sachdeva R, Needham DM, Parada AE, Steele JA, et al. Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. ISME J. 2015;9:563–80.
Google Scholar
Seymour JR, Amin SA, Raina JB, Stocker R. Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships. Nat Microbiol. 2017;2:17065.
Google Scholar
Taylor JD, Cottingham SD, Billinge J, Cunliffe M. Seasonal microbial community dynamics correlate with phytoplankton-derived polysaccharides in surface coastal waters. ISME J. 2014;8:245–8.
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
Hernando-Morales V, Varela MM, Needham DM, Cram J, Fuhrman JA, Teira E. Vertical and seasonal patterns control bacterioplankton communities at two horizontally coherent coastal upwelling sites off galicia (NW Spain). Microb Ecol. 2018;76:866–84.
Needham DM, Fuhrman JA. Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nat Microbiol. 2016;1:16005.
Tada Y, Taniguchi A, Nagao I, Miki T, Uematsu M, Tsuda A, et al. Differing growth responses of major phylogenetic groups of marine bacteria to natural phytoplankton blooms in the western North Pacific Ocean. Appl Environ Microbiol. 2011;77:4055–65.
Google Scholar
Williams TJ, Wilkins D, Long E, Evans F, DeMaere MZ, Raftery MJ, et al. The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics. Environ Microbiol. 2013;15:1302–17.
Google Scholar
Ottesen EA, Young CR, Eppley JM, Ryan JP, Chavez FP, Scholin CA, et al. Pattern and synchrony of gene expression among sympatric marine microbial populations. Proc Natl Acad Sci USA. 2013;110:E488–97.
Google Scholar
Ottesen EA, Young CR, Gifford SM, Eppley JM, Marin R 3rd, Schuster SC, et al. Ocean microbes. Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science. 2014;345:207–12.
Google Scholar
Beier S, Rivers AR, Moran MA, Obernosterer I. The transcriptional response of prokaryotes to phytoplankton-derived dissolved organic matter in seawater. Environ Microbiol. 2015;17:3466–80.
Google Scholar
Sarmento H, Gasol JM. Use of phytoplankton-derived dissolved organic carbon by different types of bacterioplankton. Environ Microbiol. 2012;14:2348–60.
Google Scholar
Shi Y, McCarren J, DeLong EF. Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment. Environ Microbiol. 2012;14:191–206.
Google Scholar
Vorobev A, Sharma S, Yu M, Lee J, Washington BJ, Whitman WB, et al. Identifying labile DOM components in a coastal ocean through depleted bacterial transcripts and chemical signals. Environ Microbiol. 2018;20:3012–30.
Google Scholar
Moran MA, Belas R, Schell MA, González JM, Sun F, Sun S, et al. Ecological genomics of marine Roseobacters. Appl Environ Microbiol. 2007;73:4559–69.
Google Scholar
Nowinski B, Moran MA. Niche dimensions of a marine bacterium are identified using invasion studies in coastal seawater. Nat Microbiol. 2021;6:524–32.
Google Scholar
Rinta-Kanto JM, Sun S, Sharma S, Kiene RP, Moran MA. Bacterial community transcription patterns during a marine phytoplankton bloom. Environ Microbiol. 2012;14:228–39.
Google Scholar
Sharma AK, Becker JW, Ottesen EA, Bryant JA, Duhamel S, Karl DM, et al. Distinct dissolved organic matter sources induce rapid transcriptional responses in coexisting populations of Prochlorococcus, Pelagibacter and the OM60 clade. Environ Microbiol. 2013;16:2815–30.
Google Scholar
Kieft B, Li Z, Bryson S, Hettich RL, Pan C, Mayali X, et al. Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits. Proc Natl Acad Sci USA. 2021;118:e2101178118.
McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom RR, et al. Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci USA. 2010;107:16420–7.
Google Scholar
Sosa OA, Gifford SM, Repeta DJ, DeLong EF. High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures. ISME J. 2015;9:2725–39.
Google Scholar
Pontiller B, Martínez-García S, Lundin D, Pinhassi J. Labile dissolved organic matter compound characteristics select for divergence in marine bacterial activity and transcription. Front Microbiol. 2020;11:588778.
Google Scholar
Bryson S, Li Z, Chavez F, Weber PK, Pett-Ridge J, Hettich RL, et al. Phylogenetically conserved resource partitioning in the coastal microbial loop. ISME J. 2017;11:2781–92.
Google Scholar
Joglar V, Prieto A, Barber-Lluch E, Hernández-Ruiz M, Fernández E, Teira E. Spatial and temporal variability in the response of phytoplankton and prokaryotes to B-vitamin amendments in an upwelling system. Biogeosciences.2020;17:2807–23.
Google Scholar
Martínez-García S, Fernández E, Álvarez-Salgado XA, González J, Lønborg C, Marañón E, et al. Differential responses of phytoplankton and heterotrophic bacteria to organic and inorganic nutrient additions in coastal waters off the NW Iberian Peninsula. Mar Ecol Prog Ser. 2010;416:17–33.
Google Scholar
Welschmeyer NA. Fluorometric analysis of chlorophyll a in the presence of chlorophyll b and pheopigments. Limnol Oceanogr. 1994;39:1985–92.
Google Scholar
Parsons TR, Maita Y, Lalli CM. Fluorometric determination of chlorophylls. A manual of chemical & biological methods for seawater analysis: Oxford, UK: Pergamon Press; 1984. p. 107–09.
Hansen H, Grasshoff K. Automated chemical analysis. Methods of seawater analysis. 2nd ed: Verlag Chemie, Weinheim; 1983. p. 347–95.
Álvarez-Salgado XA, Miller AEJ. Simultaneous determination of dissolved organic carbon and total dissolved nitrogen in seawater by high temperature catalytic oxidation: conditions for precise shipboard measurements. Mar Chem. 1998;62:325–33.
Google Scholar
Calvo-Díaz A, Morán XAG. Seasonal dynamics of picoplankton in shelf waters of the southern Bay of Biscay. Aquat Micro Ecol. 2006;42:159–74.
Google Scholar
Smith DC, Farooq A. A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine. Mar Micro Food Webs. 1992;6:107–14.
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
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. Environ Microbiol. 2014;16:2659–71.
Google Scholar
Straub D, Blackwell N, Langarica-Fuentes A, Peltzer A, Nahnsen S, Kleindienst S. Interpretations of environmental microbial community studies are biased by the selected 16S rRNA (Gene) amplicon sequencing pipeline. Front Microbiol. 2020;11:1–18.
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
Google Scholar
Poretsky RS, Gifford S, Rinta-Kanto J, Vila-Costa M, Moran MA. Analyzing gene expression from marine microbial communities using environmental transcriptomics. J Vis Exp. 2009;24:1–6.
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. 2011;17:10–12.
Google Scholar
Joshi NA, Fass JN. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files. 2011. https://github.com/najoshi/sickle.
Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM. An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One. 2013;8:1–13.
Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics.2015;31:1674–6.
Google Scholar
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010;11:119.
Google Scholar
Rognes T, Flouri T, Nichols B, Quince C, Mahe F. VSEARCH: a versatile open source tool for metagenomics. PeerJ.2016;4:e2584.
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.
Google Scholar
Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, et al. MEGAN community edition – interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput Biol. 2016;12:1–12.
Google Scholar
Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, et al. dbCAN2: A meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018;46:W95–101.
Google Scholar
Gloor GB, Wu JR, Pawlowsky-Glahn V, Egozcue JJ. It’s all relative: analyzing microbiome data as compositions. Ann Epidemiol. 2016;26:322–9.
Google Scholar
R Core Team. R: A language and environment for statistical computing. 4.1.0 ed. Vienna, Austria: R Foundation for Statistical Computing; 2021.
Cottrell MT, Kirchman DL. Transcriptional control in marine copiotrophic and oligotrophic bacteria with streamlined genomes. Appl Environ Microbiol. 2016;82:6010–18.
Google Scholar
Giovannoni SJ. SAR11 bacteria: The most abundant plankton in the oceans. Ann Rev Mar Sci. 2017;9:231–55.
Google Scholar
Newton RJ, Griffin LE, Bowles KM, Meile C, Gifford S, Givens CE, et al. Genome characteristics of a generalist marine bacterial lineage. ISME J. 2010;4:784–98.
Google Scholar
Allers E, Gomez-Consarnau L, Pinhassi J, Gasol JM, Simek K, Pernthaler J. Response of Alteromonadaceae and Rhodobacteriaceae to glucose and phosphorus manipulation in marine mesocosms. Environ Microbiol. 2007;9:2417–29.
Google Scholar
Alonso C, Pernthaler J. Roseobacter and SAR11 dominate microbial glucose uptake in coastal North Sea waters. Environ Microbiol. 2006;8:2022–30.
Google Scholar
Noell SE, Giovannoni SJ. SAR11 bacteria have a high affinity and multifunctional glycine betaine transporter. Environ Microbiol. 2019;21:2559–75.
Google Scholar
Sowell SM, Wilhelm LJ, Norbeck AD, Lipton MS, Nicora CD, Barofsky DF, et al. Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J. 2009;3:93–105.
Google Scholar
Chenard C, Wijaya W, Vaulot D, Lopes Dos Santos A, Martin P, Kaur A, et al. Temporal and spatial dynamics of bacteria, archaea and protists in equatorial coastal waters. Sci Rep. 2019;9:16390.
Google Scholar
Pajares S, Varona-Cordero F, Hernández-Becerril DU. Spatial distribution patterns of bacterioplankton in the oxygen minimum zone of the tropical mexican pacific. Micro Ecol. 2020;80:519–36.
Google Scholar
Signori CN, Pellizari VH, Enrich-Prast A, Sievert SM. Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula. Deep-Sea Res Pt Ii. 2018;149:150–60.
Google Scholar
Ling SK, Xia J, Liu Y, Chen GJ, Du ZJ. Agarilytica rhodophyticola gen. nov., sp. nov., isolated from Gracilaria blodgettii. Int J Syst Evol Microbiol. 2017;67:3778–83.
Google Scholar
Cheng H, Zhang S, Huo YY, Jiang XW, Zhang XQ, Pan J, et al. Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus. Int J Syst Evol Microbiol. 2015;65:562–69.
Google Scholar
Malmstrom RR, Kiene RP, Cottrell MT, Kirchman DL. Contribution of SAR11 bacteria to dissolved dimethylsulfoniopropionate and amino acid uptake in the North Atlantic ocean. Appl Environ Microbiol. 2004;70:4129–35.
Google Scholar
Kirchman DL. Growth rates of microbes in the oceans. Ann Rev Mar Sci. 2016;8:285–309.
Google Scholar
Durham BP, Dearth SP, Sharma S, Amin SA, Smith CB, Campagna SR, et al. Recognition cascade and metabolite transfer in a marine bacteria-phytoplankton model system. Environ Microbiol. 2017;19:3500–13.
Google Scholar
Ferrer-González FX, Widner B, Holderman NR, Glushka J, Edison AS, Kujawinski EB, et al. Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy. ISME J. 2021;15:762–73.
Google Scholar
Landa M, Burns AS, Roth SJ, Moran MA. Bacterial transcriptome remodeling during sequential co-culture with a marine dinoflagellate and diatom. ISME J. 2017;11:2677–90.
Google Scholar
Pedler BE, Aluwihare LI, Azam F. Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean. Proc Natl Acad Sci USA. 2014;111:7202–7.
Google Scholar
Koch H, Dürwald A, Schweder T, Noriega-Ortega B, Vidal-Melgosa S, Hehemann JH, et al. Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. ISME J. 2019;13:92–103.
Google Scholar
López-Pérez M, Gonzaga A, Martin-Cuadrado AB, Onyshchenko O, Ghavidel A, Ghai R, et al. Genomes of surface isolates of Alteromonas macleodii: the life of a widespread marine opportunistic copiotroph. Sci Rep. 2012;2:696.
Google Scholar
Bergauer K, Fernandez-Guerra A, Garcia JAL, Sprenger RR, Stepanauskas R, Pachiadaki MG, et al. Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics. Proc Natl Acad Sci USA. 2018;115:E400–8.
Google Scholar
Hou S, López-Pérez M, Pfreundt U, Belkin N, Stüber K, Huettel B, et al. Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise. ISME J. 2018;12:981–96.
Google Scholar
Pinhassi J, Sala MM, Havskum H, Peters F, Guadayol O, Malits A, et al. Changes in bacterioplankton composition under different phytoplankton regimens. Appl Environ Microbiol. 2004;70:6753–66.
Google Scholar
Riemann L, Steward GF, Azam F. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl Environ Microbiol. 2000;66:578–87.
Google Scholar
Cottrell MT, Kirchman DL. Natural assemblages of marine Proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl Environ Microbiol. 2000;66:1692–7.
Google Scholar
Krüger K, Chafee M, Ben Francis T, Glavina Del Rio T, Becher D, Schweder T, et al. In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes. ISME J. 2019;13:2800–16.
Google Scholar
Ben Hania W, Joseph M, Bunk B, Spröer C, Klenk HP, Fardeau ML, et al. Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria. Environ Microbiol. 2017;19:1134–48.
Google Scholar
Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG, González JM, et al. Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J. 2013;7:1026–37.
Google Scholar
Orsi WD, Smith JM, Liu S, Liu Z, Sakamoto CM, Wilken S, et al. Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean. ISME J. 2016;10:2158–73.
Google Scholar
Xing P, Hahnke RL, Unfried F, Markert S, Huang S, Barbeyron T, et al. Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom. ISME J. 2015;9:1410–22.
Google Scholar
Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, et al. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol. 2020;5:1026–39.
Ivanova AA, Naumoff DG, Miroshnikov KK, Liesack W, Dedysh SN. Comparative genomics of four Isosphaeraceae Planctomycetes: a common pool of plasmids and glycoside hydrolase genes shared by Paludisphaera borealis PX4(T), Isosphaera pallida IS1B(T), Singulisphaera acidiphila DSM 18658(T), and Strain SH-PL62. Front Microbiol. 2017;8:412.
Google Scholar
Vidal-Melgosa S, Sichert A, Francis TB, Bartosik D, Niggemann J, Wichels A, et al. Diatom fucan polysaccharide precipitates carbon during algal blooms. Nat Commun. 2021;12:1150.
Google Scholar
Le Costaouëc T, Unamunzaga C, Mantecon L, Helbert W. New structural insights into the cell-wall polysaccharide of the diatom Phaeodactylum tricornutum. Algal Res. 2017;26:172–9.
Google Scholar
Francis TB, Bartosik D, Sura T, Sichert A, Hehemann JH, Markert S, et al. Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom. ISME J. 2021;15:2336–50.
Bode A, Estévez MG, Varela M, Vilar JA. Annual trend patterns of phytoplankton species abundance belie homogeneous taxonomical group responses to climate in the NE Atlantic upwelling. Mar Environ Res. 2015;110:81–91.
Google Scholar
Cermeño P, Marañón E, Pérez V, Serret P, Fernández E, Castro CG. Phytoplankton size structure and primary production in a highly dynamic coastal ecosystem (Ría de Vigo, NW-Spain): Seasonal and short-time scale variability. Estuar Coast Shelf Sci. 2006;67:251–66.
Google Scholar
Nogueira E, Pérez FF, Rı́os AF. Modelling thermohaline properties in an estuarine upwelling ecosystem (Rı́a de Vigo: NW Spain) using box-jenkins transfer function models. Estuar Coast Shelf Sci. 1997;44:685–702.
Google Scholar
Broullón E, López-Mozos M, Reguera B, Chouciño P, Doval MD, Fernández-Castro B, et al. Thin layers of phytoplankton and harmful algae events in a coastal upwelling system. Prog Oceanogr. 2020;189:102449.
Fraga F. Upwelling off the Galician Coast, Northwest Spain. In: Richards FA, editor. Coastal Upwelling. Washington: American Geophysical Union; 1981. p. 176–82.
Nogueira E, Figueiras FG. The microplankton succession in the Ría de Vigo revisited: species assemblages and the role of weather-induced, hydrodynamic variability. J Mar Syst. 2005;54:139–55.
Google Scholar
Pitcher GC, Walker DR, Mitchellinnes BA, Moloney CL. Short-term variability during an anchor station study in the southern Benguela Upwelling System – phytoplankton dynamics. Prog Oceanogr. 1991;28:39–64.
Google Scholar
Smayda TJ, Trainer VL. Dinoflagellate blooms in upwelling systems: Seeding, variability, and contrasts with diatom bloom behaviour. Prog Oceanogr. 2010;85:92–107.
Google Scholar
Wilkerson FP, Lassiter AM, Dugdale RC, Marchi A, Hogue VE. The phytoplankton bloom response to wind events and upwelled nutrients during the CoOP WEST study. Deep-Sea Res Pt Ii. 2006;53:3023–48.
Google Scholar
Reintjes G, Arnosti C, Fuchs B, Amann R. Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation. ISME J. 2019;13:1119–32.
Google Scholar
Mayali X, Weber PK, Pett-Ridge J. Taxon-specific C/N relative use efficiency for amino acids in an estuarine community. FEMS Microbiol Ecol. 2013;83:402–12.
Google Scholar
Source: Ecology - nature.com
