Hansell DA. Recalcitrant dissolved organic carbon fractions. Ann Rev Mar Sci. 2013;5:421–45.
Azam F. Microbial control of oceanic carbon flux: the plot thickens. Science. 1998;280:694–6.
Simon M, Rosenstock B. Different coupling of dissolved amino acid, protein, and carbohydrate turnover to heterotrophic picoplankton production in the Southern Ocean in austral summer and fall. Limnol Oceanogr. 2007;52:85–95.
Suttle CA, Chan AM, Fuhrman JA. Dissolved free amino acids in the Sargasso Sea: uptake and respiration rates, turnover times, and concentrations. Mar Ecol Prog Ser. 1991;70:189–99.
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 II Top Stud Oceanogr. 2002;49:3017–38.
Hertkorn N, Benner R, Frommberger M, Schmitt-Kopplin P, Witt M, Kaiser K, et al. Characterization of a major refractory component of marine dissolved organic matter. Geochim Cosmochim Acta. 2006;70:2990–3010.
Koch H, Duerwald A, Schweder T, Noriega-Ortega B, Vidal-Melgosa S, Hehemann J-H, et al. Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. ISME J. 2019;13:92.
Ferguson RL, Sunda WG. Utilization of amino acids by planktonic marine bacteria: importance of clean technique and low substrate additions 1, 2. Limnol Oceanogr. 1984;29:258–74.
Fuhrman JA, Ferguson RL. Nanomolar concentrations and rapid turnover of dissolved free amino acids in seawater: agreement between chemical and microbiological measurements. Mar Ecol Prog Ser. 1986;33:237–42.
Hodson R, Azam F, Carlucci A, Fuhrman J, Karl D, Holm-Hansen O. Microbial uptake of dissolved organic matter in McMurdo Sound, Antarctica. Mar Biol. 1981;61:89–94.
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.
Thornton DC. Dissolved organic matter (DOM) release by phytoplankton in the contemporary and future ocean. Eur J Phycol. 2014;49:20–46.
Fogg GE. The ecological significance of extracellular products of phytoplankton photosynthesis. Bot Mar. 1983;26:3–14.
Mühlenbruch M, Grossart HP, Eigemann F, Voss M. Mini‐review: phytoplankton‐derived polysaccharides in the marine environment and their interactions with heterotrophic bacteria. Environ Microbiol. 2018;20:2671–85.
Obernosterer I, Herndl GJ. Phytoplankton extracellular release and bacterial growth: dependence on the inorganic N:P ratio. Mar Ecol Progr Ser. 1995;116:247–57.
Flynn KJ, Clark DR, Xue Y. Modeling the release of dissolved organic matter by phytoplankton 1. J Phycol. 2008;44:1171–87.
Seymour JR, Simó R, Ahmed T, Stocker R. Chemoattraction to dimethylsulfoniopropionate throughout the marine microbial food web. Science. 2010;329:342–5.
Strom S, Wolfe G, Slajer A, Lambert S, Clough J. Chemical defense in the microplankton II: Inhibition of protist feeding by β‐dimethylsulfoniopropionate (DMSP). Limnol Oceanogr. 2003;48:230–7.
Wolfe GV, Steinke M, Kirst GO. Grazing-activated chemical defence in a unicellular marine alga. Nature. 1997;387:894.
Bidle KD. The molecular ecophysiology of programmed cell death in marine phytoplankton. Ann Rev Mar Sci. 2015;7:341–75.
Caron DA, Hutchins DA. The effects of changing climate on microzooplankton grazing and community structure: drivers, predictions and knowledge gaps. J Plank Res. 2013;35:235–52.
Fuhrman JA. Marine viruses and their biogeochemical and ecological effects. Nature. 1999;399:541–8.
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.
Sapp M, Schwaderer AS, Wiltshire KH, Hoppe H-G, Gerdts G, Wichels A. Species-specific bacterial communities in the phycosphere of microalgae? Micro Ecol. 2007;53:683–99.
Amin SA, Parker MS, Armbrust EV. Interactions between diatoms and bacteria. Microbiol Mol Biol Rev. 2012;76:667–84.
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.
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.
Avcı B, Krüger K, Fuchs BM, Teeling H, Amann RI. Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms. ISME J. 2020;14:1369–83.
Kirchman DL. The ecology of Cytophaga–Flavobacteria in aquatic environments. FEMS Microbiol Ecol. 2002;39:91–100.
Pedler BE, Aluwihare LI, Azam F. Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean. Proc Nat Acad Sci. 2014;111:7202–7.
Tang K, Jiao N, Liu K, Zhang Y, Li S. Distribution and functions of TonB-dependent transporters in marine bacteria and environments: implications for dissolved organic matter utilization. PloS ONE. 2012;7:e41204.
Nelson DM, Tréguer P, Brzezinski MA, Leynaert A, Quéguiner B. Production and dissolution of biogenic silica in the ocean: revised global estimates, comparison with regional data and relationship to biogenic sedimentation. Glob Biogeochem Cycles. 1995;9:359–72.
Alavi M, Miller T, Erlandson K, Schneider R, Belas R. Bacterial community associated with Pfiesteria‐like dinoflagellate cultures. Environ Microbiol. 2001;3:380–96.
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.
Behringer G, Ochsenkühn MA, Fei C, Fanning J, Koester JA, Amin SA. Bacterial communities of diatoms display strong conservation across strains and time. Front Microbiol. 2018;9:659.
Green DH, Llewellyn LE, Negri AP, Blackburn SI, Bolch CJ. Phylogenetic and functional diversity of the cultivable bacterial community associated with the paralytic shellfish poisoning dinoflagellate Gymnodinium catenatum. FEMS Microbiol Ecol. 2004;47:345–57.
Hold GL, Smith EA, Rappë MS, Maas EW, Moore ER, Stroempl C, et al. Characterisation of bacterial communities associated with toxic and non-toxic dinoflagellates: Alexandrium spp. and Scrippsiella trochoidea. FEMS Microbiol Ecol. 2001;37:161–73.
Guillard R, Hargraves P. Stichochrysis immobilis is a diatom, not a chrysophyte. Phycologia. 1993;32:234–6.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
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.
Widner B, Kido Soule MCK, Ferrer-González FX, Moran MA, Kujawinski EB. Superior and novel detection of small, polar metabolites in saline samples using pre-extraction benzoyl chloride derivatization and Ultra-High Performance Liquid Chromatography Tandem Mass Spectrometry (UHPLC MS/MS). chemRXiv. 2020. https://doi.org/10.26434/chemrxiv.12915488.v1.
Oehlke J, Brudel M, Blasig IE. Benzoylation of sugars, polyols and amino acids in biological fluids for high-performance liquid chromatographic analysis. J Chromatogr B Biomed Sci Appl. 1994;655:105–11.
Wong J-MT, Malec PA, Mabrouk OS, Ro J, Dus M, Kennedy RT. Benzoyl chloride derivatization with liquid chromatography–mass spectrometry for targeted metabolomics of neurochemicals in biological samples. J Chromatogr A. 2016;1446:78–90.
Kido Soule MC, Longnecker K, Johnson WM, Kujawinski EB. Environmental metabolomics: analytical strategies. Mar Chem. 2015;177:374–87.
Pino LK, Searle BC, Bollinger JG, Nunn B, MacLean B, MacCoss MJ. The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. Mass Spectrom Rev. 2017;39:229–44.
Henderson CM, Shulman NJ, MacLean B, MacCoss MJ, Hoofnagle AN. Skyline performs as well as vendor software in the quantitative analysis of serum 25-hydroxy vitamin D and vitamin D binding globulin. Clin Chem. 2018;64:408–10.
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.
Todd JD, Curson AR, Sullivan MJ, Kirkwood M, Johnston AW. The Ruegeria pomeroyi acuI gene has a role in DMSP catabolism and resembles yhdH of E. coli and other bacteria in conferring resistance to acrylate. PloS ONE. 2012;7:e35947.
Grondin JM, Tamura K, Déjean G, Abbott DW, Brumer H. Polysaccharide utilization loci: fueling microbial communities. J Bacteriol. 2017;199:e00860–16.
Boulanger A, Déjean G, Lautier M, Glories M, Zischek C, Arlat M, et al. Identification and regulation of the N-acetylglucosamine utilization pathway of the plant pathogenic bacterium Xanthomonas campestris pv. campestris. J Bacteriol. 2010;192:1487–97.
Eisenbeis S, Lohmiller S, Valdebenito M, Leicht S, Braun V. NagA-dependent uptake of N-acetyl-glucosamine and N-acetyl-chitin oligosaccharides across the outer membrane of Caulobacter crescentus. J Bacteriol. 2008;190:5230–8.
Brinkkötter A, Shakeri-Garakani A, Lengeler JW. Two class II D-tagatose-bisphosphate aldolases from enteric bacteria. Arch Microbiol. 2002;177:410–9.
Leyn SA, Gao F, Yang C, Rodionov DA. N-Acetylgalactosamine utilization pathway and regulon in Proteobacteria, genomic reconstruction and experimental characterization in Shewanella. J Biol Chem. 2012;287:28047–56.
Rodionov DA, Yang C, Li X, Rodionova IA, Wang Y, Obraztsova AY, et al. Genomic encyclopedia of sugar utilization pathways in the Shewanella genus. BMC Genomics. 2010;11:494.
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2013;42:D490–5.
Beattie A, Hirst E, Percival E. Studies on the metabolism of the Chrysophyceae. Comparative structural investigations on leucosin (chrysolaminarin) separated from diatoms and laminarin from the brown algae. Biochem J. 1961;79:531.
Størseth TR, Hansen K, Reitan KI, Skjermo J. Structural characterization of β-D-(1→ 3)-glucans from different growth phases of the marine diatoms Chaetoceros mülleri and Thalassiosira weissflogii. Carbohydr Res. 2005;340:1159–64.
Becker S, Tebben J, Coffinet S, Wiltshire K, Iversen MH, Harder T, et al. Laminarin is a major molecule in the marine carbon cycle. Proc Nat Acad Sci. 2020;117:6599–607.
Unfried F, Becker S, Robb CS, Hehemann J-H, Markert S, Heiden SE, et al. Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms. ISME J. 2018;12:2894.
Martens EC, Lowe EC, Chiang H, Pudlo NA, Wu M, McNulty NP, et al. Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 2011;9:e1001221.
Gügi B, Le Costaouec T, Burel C, Lerouge P, Helbert W, Bardor M. Diatom-specific oligosaccharide and polysaccharide structures help to unravel biosynthetic capabilities in diatoms. Mar Drugs. 2015;13:5993–6018.
Barbeyron T, Thomas F, Barbe V, Teeling H, Schenowitz C, Dossat C, et al. Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae‐associated bacterium Zobellia galactanivorans DsijT. Environ Microbiol. 2016;18:4610–27.
Kabisch A, Otto A, König S, Becher D, Albrecht D, Schüler M, et al. Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii’ KT0803. ISME J. 2014;8:1492.
Mann AJ, Hahnke RL, Huang S, Werner J, Xing P, Barbeyron T, et al. The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides. Appl Environ Microbiol. 2013;79:6813–22.
Datta MS, Sliwerska E, Gore J, Polz MF, Cordero OX. Microbial interactions lead to rapid micro-scale successions on model marine particles. Nat Commun. 2016;7:11965.
Goldford JE, Lu N, Bajić D, Estrela S, Tikhonov M, Sanchez-Gorostiaga A, et al. Emergent simplicity in microbial community assembly. Science. 2018;361:469–74.
Azam F, Fenchel T, Field J, Grey J, Meyer-Reil L, Thingstad F. The ecological role of water-column microbes in the sea. Mar Ecol Prog Ser. 1983;10:257–63.
Cole JJ, Findlay S, Pace ML. Bacterial production in fresh and saltwater ecosystems: a cross-system overview. Mar Ecol Progr Ser. 1988;43:1–10.
Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, Buchan A, et al. Deciphering ocean carbon in a changing world. Proc Nat Acad Sci. 2016;113:3143–51.
Kujawinski EB. The impact of microbial metabolism on marine dissolved organic matter. Ann Rev Mar Sci. 2011;3:567–99.
Larsbrink J, Zhu Y, Kharade SS, Kwiatkowski KJ, Eijsink VG, Koropatkin NM, et al. A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin. Biotechnol Biofuels. 2016;9:260.
Mathieu S, Touvrey-Loiodice M, Poulet L, Drouillard S, Vincentelli R, Henrissat B, et al. Ancient acquisition of “alginate utilization loci” by human gut microbiota. Sci Rep. 2018;8:8075.
Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, et al. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science. 2004;306:79–86.
Azizan A, Ahamad Bustamam MS, Maulidiani M, Shaari K, Ismail IS, Nagao N, et al. Metabolite profiling of the microalgal diatom Chaetoceros calcitrans and correlation with antioxidant and nitric oxide inhibitory activities via 1H NMR-based metabolomics. Mar Drugs. 2018;16:154.
Hellebust JA. Excretion of some organic compounds by marine phytoplankton 1. Limnol Oceanogr. 1965;10:192–206.
Boroujerdi AF, Lee PA, DiTullio GR, Janech MG, Vied SB, Bearden DW. Identification of isethionic acid and other small molecule metabolites of Fragilariopsis cylindrus with nuclear magnetic resonance. Anal Bioanal Chem. 2012;404:777–84.
Iglesias MJ, Soengas R, Probert I, Guilloud E, Gourvil P, Mehiri M, et al. NMR characterization and evaluation of antibacterial and antiobiofilm activity of organic extracts from stationary phase batch cultures of five marine microalgae (Dunaliella sp., D. salina, Chaetoceros calcitrans, C. gracilis and Tisochrysis lutea). Phytochemistry. 2019;164:192–205.
Jeong K-S, Jeong K-Y, Hong Y-S, Kim D-K, Oh H-J, Chang K-H. Application of nuclear magnetic resonance for analyzing metabolic characteristics of winter diatom blooms. J Plank Res. 2020;42:31–9.
Scholz B, Liebezeit G. Compatible solutes in three marine intertidal microphytobenthic Wadden Sea diatoms exposed to different salinities. Eur J Phycol. 2012;47:393–407.
Bell W, Mitchell R. Chemotactic and growth responses of marine bacteria to algal extracellular products. Biol Bull. 1972;143:265–77.
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.
Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature. 2003;424:1042–7.
Basan M, Hui S, Okano H, Zhang Z, Shen Y, Williamson JR, et al. Overflow metabolism in Escherichia coli results from efficient proteome allocation. Nature. 2015;528:99–104.
Kinkel LL, Schlatter DC, Xiao K, Baines AD. Sympatric inhibition and niche differentiation suggest alternative coevolutionary trajectories among Streptomycetes. ISME J. 2014;8:249–56.
Kirchman DL. Phytoplankton death in the sea. Nature. 1999;398:293–4.
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.
Enke TN, Datta MS, Schwartzman J, Cermak N, Schmitz D, Barrere J, et al. Modular assembly of polysaccharide-degrading marine microbial communities. Curr Biol. 2019;29:1528–35.
Ferraris RP, Diamond JM. Specific regulation of intestinal nutrient transporters by their dietary substrates. Ann Rev Physiol. 1989;51:125–41.
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 Nat Acad Sci. 2010;107:16420–7.
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.
Salzberg SL. Next-generation genome annotation: we still struggle to get it right. Genome Biol. 2019;20:92.
Freilich S, Zarecki R, Eilam O, Segal ES, Henry CS, Kupiec M, et al. Competitive and cooperative metabolic interactions in bacterial communities. Nat Commun. 2011;2:589.
Fu H, Uchimiya M, Gore J, Moran MA. Ecological drivers of bacterial community assembly in synthetic phycospheres. Proc Nat Acad Sci. 2020;117:3656–62.
Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proc Nat Acad Sci. 2015;112:6449–54.
Benson A, Lee R. The sulphoglycolytic pathway in plants. Biochem J. 1972;128:29P.
Busby WF. Sulfoporpanedial and cysteinolic acid in the diatom. Biochim Biophys Acta. 1966;121:160–1.
Durham BP, Sharma S, Luo H, Smith CB, Amin SA, Bender SJ, et al. Cryptic carbon and sulfur cycling between surface ocean plankton. Proc Nat Acad Sci. 2015;112:453–7.
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.
Denger K, Lehmann S, Cook AM. Molecular genetics and biochemistry of N-acetyltaurine degradation by Cupriavidus necator H16. Microbiology. 2011;157:2983–91.
Mayer J, Huhn T, Habeck M, Denger K, Hollemeyer K, Cook AM. 2, 3-Dihydroxypropane-1-sulfonate degraded by Cupriavidus pinatubonensis JMP134: purification of dihydroxypropanesulfonate 3-dehydrogenase. Microbiology. 2010;156:1556–64.
Source: Ecology - nature.com