Snow AJD, Burchill L, Sharma M, Davies GJ, Williams SJ. Sulfoglycolysis: Catabolic pathways for metabolism of sulfoquinovose. Chem Soc Rev. 2021;50:13628–45.
Google Scholar
Van Mooy BAS, Rocap G, Fredricks HF, Evans CT, Devol AH. Sulfolipids dramatically decrease phosphorus demand by picocyanobacteria in oligotrophic marine environments. Proc Natl Acad Sci USA 2006;103:8607–12.
Google Scholar
Wu J, Sunda W, Boyle EA, Karl DM. Phosphate depletion in the western North Atlantic. Ocean Sci 2000;289:759–62.
Google Scholar
Goddard-Borger ED, Williams SJ. Sulfoquinovose in the biosphere: occurrence, metabolism and functions. Biochem J. 2017;474:827–49.
Google Scholar
Harwood JL, Nicholls RG. The plant sulpholipid- a major component of the sulphur cycle. Biochem Soc Trans. 1979;7:440–7.
Google Scholar
Moran MA, Durham BP. Sulfur metabolites in the pelagic ocean. Nat Rev Microbiol. 2019;17:665–78.
Google Scholar
Tang K. Chemical diversity and biochemical transformation of biogenic organic sulfur in the ocean. Front Mar Sci. 2020;7:68.
Google Scholar
Denger K, Weiss M, Felux AK, Schneider A, Mayer C, Spiteller D, et al. Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle. Nature 2014;507:114–7.
Google Scholar
Hanson BT, Kits KD, Loffler J, Burrichter AG, Fiedler A, Denger K, et al. Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut. ISME J. 2021;15:2779–91.
Google Scholar
Strickland TC, Fitzgerald JW. Mineralization of sulfur in sulfoquinovose by forest soils. Soil Biol Biochem. 1983;15:347–9.
Google Scholar
Felux AK, Spiteller D, Klebensberger J, Schleheck D. Entner-Doudoroff pathway for sulfoquinovose degradation in Pseudomonas putida SQ1. Proc Natl Acad Sci USA 2015;112:E4298–E305.
Google Scholar
Frommeyer B, Fiedler AW, Oehler SR, Hanson BT, Loy A, Franchini P, et al. Environmental and intestinal phylum Firmicutes bacteria metabolize the plant sugar sulfoquinovose via a 6-deoxy-6-sulfofructose transaldolase pathway. Iscience. 2020;23:101510.
Google Scholar
Roy AB, Hewlins MJE, Ellis AJ, Harwood JL, White GF. Glycolytic breakdown of sulfoquinovose in bacteria: A missing link in the sulfur cycle. Appl Environ Microbiol. 2003;69:6434–41.
Google Scholar
Liu J, Wei Y, Ma K, An J, Liu X, Liu Y, et al. Mechanistically diverse pathways for sulfoquinovose degradation in bacteria. ACS Catal. 2021;11:14740–50.
Google Scholar
Zhang S, Li Z, Yan Y, Zhang C, Li J, Zhao B. Bacillus urumqiensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a salt lake. Int J Syst Evol Microbiol. 2016;66:2305–12.
Google Scholar
Durham BP, Sharma S, Luo H, Smith CB, Amin SA, Bender SJ, et al. Cryptic carbon and sulfur cycling between surface ocean plankton. Proc Natl Acad Sci USA 2015;112:453–7.
Google Scholar
Chen X, Liu L, Gao X, Dai X, Han Y, Chen Q, et al. Metabolism of chiral sulfonate compound 2,3-dihydroxypropane-1-sulfo-nate (DHPS) by Roseobacter bacteria in marine environment. Environ Int. 2021;157:106829.
Google Scholar
Liu J, Wei Y, Lin L, Teng L, Yin J, Lu Q, et al. Two Radical-dependent mechanisms for anaerobic degradation of the globally abundant Organosulfur Compound Dihydroxypropanesulfonate. Proc Natl Acad Sci USA 2020;117:15599.
Google Scholar
Xing M, Wei Y, Zhou Y, Zhang J, Lin L, Hu Y, et al. Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria. Nat Commun. 2019;10:1609.
Google Scholar
Sharma M, Lingford JP, Petricevic M, Snow AJD, Zhang Y, Jarva MA, et al. Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria. Proc Natl Acad Sci USA 2022;119:e2116022119.
Google Scholar
Scholz SS, Serif M, Schleheck D, Sayer MDJ, Cook AM, Kupper FC. Sulfoquinovose metabolism in marine algae. Bot Mar. 2021;64:301–12.
Google Scholar
Abayakoon P, Epa R, Petricevic M, Bengt C, Mui JWY, van der Peet PL, et al. Comprehensive synthesis of substrates, intermediates, and products of the sulfoglycolytic Embden-Meyerhoff-Parnas pathway. J Org Chem. 2019;84:2901–10.
Google Scholar
Denger K, Smits THM, Cook AM. L-Cysteate sulpho-lyase, a widespread pyridoxal 5 ‘-phosphate-coupled desulphonative enzyme purified from Silicibacter pomeroyi DSS-3. Biochem J. 2006;394:657–64.
Google Scholar
Guillard RRL. Culture of Phytoplankton for Feeding Marine Invertebrates. Smith WL, Chanley MH, (eds): Springer US; 1975. Boston, MA. pp 29–60.
Moore LR, Coe A, Zinser ER, Saito MA, Sullivan MB, Lindell D, et al. Culturing the marine cyanobacterium Prochlorococcus. Limnol Oceanogr Methods. 2007;5:353–62.
Google Scholar
Waterbury J, Watson S, Valois F, Franks D. Biological and ecological characterization of the marine unicellular cyanobacterium Synechococcus. Platt T, Li WKW, (eds). Department of Fisheries and Oceans, Ottawa 1986. pp 71–120.
Olenina I, Hajdu S, Edler L, Andersson A, Wasmund N, Busch S, et al. Biovolumes and size-classes of phytoplankton in the Baltic Sea. HELCOM Balt Sea Environ Proc. 2006;106:144.
Zheng Q, Wang Y, Lu J, Lin W, Chen F, Jiao N. Metagenomic and metaproteomic insights into photoautotrophic and heterotrophic interactions in a Synechococcus culture. mbio 2020;11:e03261–19.
Google Scholar
Partensky F, Hess WR, Vaulot D. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol Mol Biol Rev. 1999;63:106–27.
Google Scholar
Han Y, Zhang M, Chen X, Zhai W, Tan E, Tang K. Transcriptomic evidences for microbial carbon and nitrogen cycles in the deoxygenated seawaters of Bohai Sea. Environ Int. 2022;158:106889.
Google Scholar
Li WKW. Primary production of prochlorophytes, cyanobacteria, and eukaryotic ultraphytoplankton – measurements from flow cytometric sorting. Limnol Oceanogr. 1994;39:169–75.
Google Scholar
Denger K, Ruff A, Rein U, Cook AM. Sulphoacetaldehyde sulpho-lyase (EC 4.4.1.12) from Desulfonispora thiosulfatigenes: purification, properties and primary sequence. Biochem J. 2001;357:581–6.
Google Scholar
Ismail R, Lee HY, Mahyudin NA, Abu, Bakar F. Linearity study on detection and quantification limits for the determination of avermectins using linear regression. J Food Drug Anal. 2014;22:407–12.
Google Scholar
Klemetsen T, Raknes IA, Fu J, Agafonov A, Balasundaram SV, Tartari G, et al. The MAR databases: development and implementation of databases specific for marine metagenomics. Nucleic Acids Res. 2018;46:D692–D9.
Google Scholar
Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 2007;23:1282–8.
Google Scholar
Rozewicki J, Li S, Amada KM, Standley DM, Katoh K. MAFFT-DASH: Integrated protein sequence and structural alignment. Nucleic Acids Res. 2019;47:W5–W10.
Google Scholar
Schuller DJ, Reisch CR, Moran MA, Whitman WB, Lanzilotta WN. Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique. Protein Sci. 2012;21:289–98.
Google Scholar
Bharath SR, Bisht S, Harijan RK, Savithri HS, Murthy MR. Structural and mutational studies on substrate specificity and catalysis of Salmonella typhimurium D-cysteine desulfhydrase. PLoS One. 2012;7:e36267.
Google Scholar
Chartron J, Carroll KS, Shiau C, Gao H, Leary JA, Bertozzi CR, et al. Substrate Recognition, Protein Dynamics, and Iron-Sulfur Cluster in Pseudomonas aeruginosa Adenosine 5′-Phosphosulfate Reductase. J Mol Biol. 2006;364:152–69.
Google Scholar
Davis KM, Altmyer M, Martinie RJ, Schaperdoth I, Krebs C, Bollinger JM Jr, et al. Structure of a Ferryl Mimic in the Archetypal Iron(II)- and 2-(Oxo)-glutarate-Dependent Dioxygenase, TauD. Biochemistry 2019;58:4218–23.
Google Scholar
Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: Making protein folding accessible to all. Nat Methods. 2022;19:679–82.
Google Scholar
Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al. Highly accurate protein structure prediction with AlphaFold. Nature 2021;596:583–9.
Google Scholar
Zhang C, Shine M, Pyle AM, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nat Methods. 2022;19:1109–15.
Google Scholar
Xu J, Zhang Y. How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 2010;26:889–95.
Google Scholar
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2014;32:268–74.
Google Scholar
Villar E, Vannier T, Vernette C, Lescot M, Cuenca M, Alexandre A, et al. The Ocean Gene Atlas: exploring the biogeography of plankton genes online. Nucleic Acids Res. 2018;46:W289–W95.
Google Scholar
Vernette C, Henry N, Lecubin J, de Vargas C, Hingamp P, Lescot M. The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms. Mol Ecol Resour. 2021;21:1347–58.
Google Scholar
Paoli L, Ruscheweyh H-J, Forneris CC, Hubrich F, Kautsar S, Bhushan A, et al. Biosynthetic potential of the global ocean microbiome. Nature 2022;607:111–8.
Google Scholar
Sunagawa S, Acinas SG, Bork P, Bowler C, Acinas SG, Babin M, et al. Tara Oceans: towards global ocean ecosystems biology. Nat Rev Microbiol. 2020;18:428–45.
Google Scholar
Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, et al. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Commun Biol. 2021;4:604.
Google Scholar
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;5:180176.
Google Scholar
Pachiadaki MG, Brown JM, Brown J, Bezuidt O, Berube PM, Biller SJ, et al. Charting the Complexity of the Marine Microbiome through Single-Cell Genomics. Cell 2019;179:1623–35.
Google Scholar
Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee STM, Rappé MS, et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018;3:804–13.
Google Scholar
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.
Google Scholar
Subramanian B, Gao S, Lercher MJ, Hu S, Chen W-H. Evolview v3: A webserver for visualization, annotation, and management of phylogenetic trees. Nucleic Acids Res. 2019;47:W270–W5.
Google Scholar
Xing M, Wei Y, Zhou Y, Zhang J, Lin L, Hu Y, et al. Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria. Nat Commun. 2019;10:1609.
Google Scholar
Biebl H, Allgaier M, Tindall BJ, Koblizek M, Lunsdorf H, Pukall R, et al. Dinoroseobacter shibae gen. nov., sp nov., a new aerobic phototrophic bacterium isolated from dinoflagellates. Int J Syst Evol Microbiol. 2005;55:1089–96.
Google Scholar
Fu H, Uchimiya M, Gore J, Moran MA. Ecological drivers of bacterial community assembly in synthetic phycospheres. Proc Natl Acad Sci USA 2020;117:3656–62.
Google Scholar
Chen I-MA, Chu K, Palaniappan K, Ratner A, Huang J, Huntemann M, et al. The IMG/M data management and analysis system v.7: content updates and new features. Nucleic Acids Res. 2022. https://doi.org/10.1093/nar/gkac976.
Shiba T. Roseobacter litoralis gen. nov., sp. nov., and Roseobacter denitrificans sp. nov., aerobic pink-pigmented bacteria which contain bacteriochlorophyll a. Syst Appl Microbiol. 1991;14:140–5.
Google Scholar
Kopriva S, Calderwood A, Weckopp SC, Koprivova A. Plant sulfur and big data. Plant Sci. 2015;241:1–10.
Google Scholar
Simon J, Kroneck PMH. Microbial sulfite respiration. Adv Micro Physiol. 2013;62:45–117.
Google Scholar
Gonzalez JM, Covert JS, Whitman WB, Henriksen JR, Mayer F, Scharf B, et al. Silicibacter pomeroyi sp nov and Roseovarius nubinhibens sp nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int J Syst Evol Microbiol. 2003;53:1261–9.
Google Scholar
Liang KYH, Orata FD, Boucher YF, Case RJ. Roseobacters in a sea of poly- and paraphyly: whole genome-based taxonomy of the family Rhodobacteraceae and the proposal for the split of the “Roseobacter clade” into a novel family, Roseobacteraceae fam. nov. Front Microbiol. 2021;12:683109.
Google Scholar
Howard EC, Sun S, Biers EJ, Moran MA. Abundant and diverse bacteria involved in DMSP degradation in marine surface waters. Environ Microbiol. 2008;10:2397–410.
Google Scholar
Howard EC, Henriksen JR, Buchan A, Reisch CR, Buergmann H, Welsh R, et al. Bacterial taxa that limit sulfur flux from the ocean. Science. 2006;314:649–52.
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
Smetacek V. Diatoms and the ocean carbon cycle. Protist 1999;150:25–32.
Google Scholar
Stoecker DK, Lavrentyev PJ. Mixotrophic plankton in the polar seas: A pan-Arctic review. Front Mar Sci. 2018;5:292.
Google Scholar
Turner SM, Malin G, Liss PS, Harbour DS, Holligan PM. The seasonal-variation of dimethyl sulfide and dimethylsulfoniopropionate concentrations in nearshore waters. Limnol Oceanogr. 1988;33:364–75.
Google Scholar
Belviso S, Kim S-K, Rassoulzadegan F, Krajka B, Nguyen BC, Mihalopoulos N, et al. Production of dimethylsulfonium propionate (DMSP) and dimethylsulfide (DMS) by a microbial food web. Limnol Oceanogr. 1990;35:1810–21.
Google Scholar
Simo R, Pedros-Alio C, Malin G, Grimalt JO. Biological turnover of DMS, DMSP and DMSO in contrasting open-sea waters. Mar Ecol Prog Ser. 2000;203:1–11.
Google Scholar
Flombaum P, Gallegos JL, Gordillo RA, Rincon J, Zabala LL, Jiao N, et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci USA 2013;110:9824–9.
Google Scholar
Gasparovic B, Penezic A, Frka S, Kazazic S, Lampitt RS, Holguin FO, et al. Particulate sulfur-containing lipids: Production and cycling from the epipelagic to the abyssopelagic zone. Deep Sea Res Part I Oceanogr Res Pap. 2018;134:12–22.
Google Scholar
Zhan P, Tang K, Chen X, Yu L. Complete genome sequence of Maribacter sp T28, a polysaccharide-degrading marine flavobacteria. J Biotechnol. 2017;259:1–5.
Google Scholar
Van Mooy BAS, Fredricks HF. Bacterial and eukaryotic intact polar lipids in the eastern subtropical South Pacific: Water-column distribution, planktonic sources, and fatty acid composition. Geochim Cosmochim Acta. 2010;74:6499–516.
Google Scholar
Popendorf KJ, Tanaka T, Pujo-Pay M, Lagaria A, Courties C, Conan P, et al. Gradients in intact polar diacylglycerolipids across the Mediterranean Sea are related to phosphate availability. Biogeosciences 2011;8:3733–45.
Google Scholar
Source: Ecology - nature.com
