Carpenter LJ. Biogeochemical cycles | iodine. Encyclopedia of Atmospheric Sciences: Elsevier; United States; 2015. p. 205–19.
Chemburkar SR, Deming KC, Reddy RE. Chemistry of thyroxine: an historical perspective and recent progress on its synthesis. Tetrahedron. 2010;66:1955–62.
Google Scholar
Schweizer U, Steegborn C. Thyroid hormones—from crystal packing to activity to reactivity. Angew Chem. 2015;54:12856–8.
Google Scholar
Küpper FC, Feiters MC, Olofsson B, Kaiho T, Yanagida S, Zimmermann MB, et al. Commemorating two centuries of iodine research: an interdisciplinary overview of current research. Angew Chem. 2011;50:11598–620.
Google Scholar
Manley SL, Dastoor MN. Methyl iodide (CH3I) production by kelp and associated microbes. Mar Biol. 1988;98:477–82.
Google Scholar
Lebel LS, Dickson RS, Glowa GA. Radioiodine in the atmosphere after the Fukushima Dai-ichi nuclear accident. J Environ Radioact. 2016;151:82–93.
Google Scholar
Luther GW, Wu J, Cullen JB. Redox chemistry of iodine in seawater. Aquatic chemistry. Advances in chemistry. 244: American Chemical Society; Washington, DC; 1995. p. 135–55.
Gonzales J, Tymon T, Küpper FC, Edwards MS, Carrano CJ. The potential role of kelp forests on iodine speciation in coastal seawater. PloS ONE. 2017;12:e0180755.
Google Scholar
Vedamati J, Goepfert T, Moffett JW. Iron speciation in the eastern tropical South Pacific oxygen minimum zone off Peru. Limnol Oceanogr. 2014;59:1945–57.
Google Scholar
Tsunogai S, Sase T. Formation of iodide-iodine in the ocean. Deep Sea Res Oceanogr Abstr. 1969;16:489–96.
Google Scholar
Councell TB, Landa ER, Lovley DR. Microbial reduction of iodate. Water Air Soil Pollut. 1997;100:99–106.
Google Scholar
Youngblut MD, Tsai C-L, Clark IC, Carlson HK, Maglaqui AP, Gau-Pan PS, et al. Perchlorate reductase is distinguished by active site aromatic gate residues. J Biol Chem. 2016;291:9190–202.
Google Scholar
Farrenkopf AM, Dollhopf ME, Chadhain SN, Luther GW, Nealson KH. Reduction of iodate in seawater during Arabian Sea incubations and in laboratory cultures of the marine Shewanella putrefaciens strain MR-4 shipboard bacterium. Mar Chem. 1997;57:347–54.
Google Scholar
Amachi S, Kawaguchi N, Muramatsu Y, Tsuchiya S, Watanabe Y, Shinoyama H, et al. Dissimilatory iodate reduction by marine Pseudomonas sp. strain SCT. Appl Environ Microbiol. 2007;73:5725–30.
Google Scholar
Yamazaki C, Kashiwa S, Horiuchi A, Kasahara Y, Yamamura S, Amachi S. A novel dimethylsulfoxide reductase family of molybdenum enzyme, Idr, is involved in iodate respiration by Pseudomonas sp. SCT. Environ Microbiol. 2020;22:2196–212.
Google Scholar
Youngblut MD, Wang O, Barnum TP, Coates JD. (Per)chlorate in biology on earth and beyond. Annu Rev Microbiol. 2016;70:435–57.
Toporek YJ, Mok JK, Shin HD, Lee BD, Lee MH, DiChristina TJ. Metal reduction and protein secretion genes required for Iodate Reduction by Shewanella oneidensis. Appl Environ Microbiol. 2019;85:e02115–18.
Carlström CI, Lucas LN, Rohde RA, Haratian A, Engelbrektson AL, Coates JD. Characterization of an anaerobic marine microbial community exposed to combined fluxes of perchlorate and salinity. Appl Microbiol Biotechnol. 2016;100:9719–32.
Google Scholar
Yip KC-W, Gu J-D. A novel bacterium involved in the degradation of 2-methylindole isolated from sediment of Inner Deep Bay of Hong Kong. Appl Environ Biotechnol. 2015;1:52–63.
Google Scholar
Glazyrina J, Materne EM, Dreher T, Storm D, Junne S, Adams T, et al. High cell density cultivation and recombinant protein production with Escherichia coli in a rocking-motion-type bioreactor. Micro Cell Fact. 2010;9:1–11.
Google Scholar
Loferer-Krössbacher M, Klima J, Psenner R. Determination of bacterial cell dry mass by transmission electron microscopy and densitometric image analysis. Appl Environ Microbiol. 1998;64:688–94.
Google Scholar
McInerney MJ, Beaty PS. Anaerobic community structure from a nonequilibrium thermodynamic perspective. Can J Microbiol. 1988;34:487–93.
Google Scholar
Stern JH, Passchier AA. The heats of formation of triiodide and iodate ions. J Phys Chem. 1962;66:752–3.
Google Scholar
Weber KA, Achenbach LA, Coates JD. Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction. Nat Rev Microbiol. 2006;4:752–64.
Google Scholar
Leimkühler S, Iobbi-Nivol C. Bacterial molybdoenzymes: Old enzymes for new purposes. FEMS Microbiol Rev. 2016;40:1–18.
Google Scholar
McEwan AG, Ridge JP, McDevitt CA, Hugenholtz P. The DMSO reductase family of microbial molybdenum enzymes: Molecular properties and role in the dissimilatory reduction of toxic elements. Geomicrobiol J. 2002;19:3–21.
Google Scholar
Chaudhuri SK, O’Connor SM, Gustavson RL, Achenbach LA, Coates JD. Environmental factors that control microbial perchlorate reduction. Appl Environ Microbiol. 2002;68:4425–30.
Google Scholar
Snel B, Bork P, Huynen MA. Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res. 2002;12:17–25.
Google Scholar
Saunders JK, Fuchsman CA, McKay C, Rocap G. Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones. Proc Natl Acad Sci USA. 2019;116:9925–30.
Google Scholar
Dabir DV, Leverich EP, Kim SK, Tsai FD, Hirasawa M, Knaff DB, et al. A role for cytochrome c and cytochrome c peroxidase in electron shuttling from Erv1. EMBO J. 2007;26:4801–11.
Google Scholar
Martins D, Kathiresan M, English AM. Cytochrome c peroxidase is a mitochondrial heme-based H2O2 sensor that modulates antioxidant defense. Free Radic Biol Med. 2013;65:541–51.
Google Scholar
Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol. 2019;37:420–3.
Google Scholar
Berks BC. The twin-arginine protein translocation pathway. Annu Rev Biochem. 2015;84:843–64.
Google Scholar
Toporek M, Michałowska-Kaczmarczyk AM, Michałowski T. Disproportionation reactions of HIO and NaIO in static and dynamic systems. Am J Anal Chem. 2014;5:1046.
Google Scholar
Ellis KV, Van Vree HBRJ. Iodine used as a water-disinfectant in turbid waters. Water Res. 1989;23:671–6.
Google Scholar
Alternative drinking-water disinfectants: bromine, iodine and silver. Geneva: World Health Organization; 2018. Licence: CC BY-NC-SA 3.0 IGO.
Liebensteiner MG, Pinkse MWH, Schaap PJ, Stams AJM, Lomans BP. Archaeal (per)chlorate reduction at high temperature: An interplay of biotic and abiotic reactions. Science. 2013;340:85–7.
Google Scholar
Dudley M, Salamone A, Nerenberg R. Kinetics of a chlorate-accumulating, perchlorate-reducing bacterium. Water Res. 2008;42:2403–10.
Google Scholar
Melnyk RA, Youngblut MD, Clark IC, Carlson HK, Wetmore KM, Price MN, et al. Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich peptide and methionine sulfoxide reductase. MBio. 2015;6:e00233-15.
Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017;35:1026–8.
Google Scholar
Ordoñez OF, Rasuk MC, Soria MN, Contreras M, Farías ME. Haloarchaea from the Andean Puna: biological role in the energy metabolism of arsenic. Microb Ecol. 2018;76:695–705.
Google Scholar
Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 2016;7:1–11.
Google Scholar
Becraft ED, Woyke T, Jarett J, Ivanova N, Godoy-Vitorino F, Poulton N, et al. Rokubacteria: genomic giants among the uncultured bacterial phyla. Front Microbiol. 2017;8:2264.
He Z, Cai C, Wang J, Xu X, Zheng P, Jetten MSM, et al. A novel denitrifying methanotroph of the NC10 phylum and its microcolony. Sci Rep. 2016;6:1–10.
Google Scholar
Melnyk RA, Engelbrektson A, Clark IC, Carlson HK, Byrne-Bailey K, Coates JD. Identification of a perchlorate reduction genomic island with novel regulatory and metabolic genes. Appl Environ Microbiol. 2011;77:7401–4.
Google Scholar
Scornavacca C, Zickmann F, Huson DH. Tanglegrams for rooted phylogenetic trees and networks. Bioinformatics. 2011;27:i248–56.
Google Scholar
Juhas M, van der Meer JR, Gaillard M, Harding RM, Hood DW, Crook DW. Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev. 2009;33:376–93.
Google Scholar
Reiter WD, Palm P, Yeats S. Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res. 1989;17:1907–14.
Google Scholar
Larbig KD, Christmann A, Johann A, Klockgether J, Hartsch T, Merkl R, et al. Gene islands integrated into tRNAGly genes confer genome diversity on a Pseudomonas aeruginosa clone. J Bacteriol. 2002;184:6665–80.
Google Scholar
Boyd E, Barkay T. The mercury resistance operon: From an origin in a geothermal environment to an efficient detoxification machine. Front Microbiol. 2012;3:349.
Google Scholar
Besaury L, Bodilis J, Delgas F, Andrade S, De la Iglesia R, Ouddane B, et al. Abundance and diversity of copper resistance genes cusA and copA in microbial communities in relation to the impact of copper on Chilean marine sediments. Mar Pollut Bull. 2013;67:16–25.
Google Scholar
Bertelli C, Laird MR, Williams KP, Simon Fraser University Research Computing Group, Lau BY, Hoad G, et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 2017;45:W30–5.
Google Scholar
Jin HM, Lee HJ, Kim JM, Park MS, Lee K, Jeon CO. Litorimicrobium taeanense gen. nov., sp. nov., isolated from a sandy beach. Int J Syst Evol Microbiol. 2011;61:1392–6.
Google Scholar
Alex A, Antunes A. Comparative genomics reveals metabolic specificity of Endozoicomonas isolated from a marine sponge and the genomic repertoire for host-bacteria symbioses. Microorganisms. 2019;7:635.
Google Scholar
Kim Y-O, Park S, Nam B-H, Park J-M, Kim D-G, Yoon J-H. Litoreibacter ascidiaceicola sp. nov., isolated from the golden sea squirt Halocynthiaaurantium. Int J Syst Evol Microbiol. 2014;64:2545–50.
Google Scholar
Kupper FC, Carpenter LJ, McFiggans GB, Palmer CJ, Waite TJ, Boneberg EM, et al. Iodide accumulation provides kelp with an inorganic antioxidant impacting atmospheric chemistry. Proc Natl Acad Sci USA. 2008;105:6954–8.
Google Scholar
Jung HS, Jeong SE, Chun BH, Quan Z-X, Jeon CO. Rhodophyticola porphyridii gen. nov., sp. nov., isolated from a red alga, Porphyridium marinum. Int J Syst Evol Microbiol. 2019;69:1656–61.
Google Scholar
Wagner GP, Kin K, Lynch VJ. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 2012;131:281–5.
Google Scholar
Ribicic D, Netzer R, Hazen TC, Techtmann SM, Drabløs F, Brakstad OG. Microbial community and metagenome dynamics during biodegradation of dispersed oil reveals potential key-players in cold Norwegian seawater. Mar Pollut Bull. 2018;129:370–8.
Google Scholar
Lachkar Z, Lévy M, Smith KS. Strong intensification of the Arabian Sea oxygen minimum zone in response to Arabian Gulf warming. Geophys Res Lett. 2019;46:5420–9.
Google Scholar
Farrenkopf AM, Luther GW. Iodine chemistry reflects productivity and denitrification in the Arabian Sea: evidence for flux of dissolved species from sediments of western India into the OMZ. Deep-Sea Res Pt II. 2002;49:2303–18.
Google Scholar
Bertagnolli AD, Stewart FJ. Microbial niches in marine oxygen minimum zones. Nat Rev Microbiol. 2018;16:723–9.
Google Scholar
Cutter GA, Moffett JW, Nielsdóttir MC, Sanial V. Multiple oxidation state trace elements in suboxic waters off Peru: In situ redox processes and advective/diffusive horizontal transport. Mar Chem. 2018;201:77–89.
Google Scholar
Karstensen J, Stramma L, Visbeck M. Oxygen minimum zones in the eastern tropical Atlantic and Pacific oceans. Prog Oceanogr. 2008;77:331–50.
Google Scholar
Farrenkopf AM, Luther GW, Truesdale VW, Van Der Weijden CH. Sub-surface iodide maxima: evidence for biologically catalyzed redox cycling in Arabian Sea OMZ during the SW intermonsoon. Deep Sea Res Pt II. 1997;44:1391–409.
Google Scholar
Kalvelage T, Lavik G, Jensen MM, Revsbech NP, Löscher C, Schunck H, et al. Aerobic microbial respiration in oceanic oxygen minimum zones. PLoS ONE. 2015;10:e0133526.
Google Scholar
Howarth RW. Nutrient limitation of net primary production in marine ecosystems. Annu Rev Ecol Syst. 1988;19:89–110.
Google Scholar
Shalel Levanon S, San K-Y, Bennett GN. Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses. Biotechnol Bioeng. 2005;89:556–64.
Google Scholar
Wright JJ, Konwar KM, Hallam SJ. Microbial ecology of expanding oxygen minimum zones. Nat Rev Microbiol. 2012;10:381–94.
Google Scholar
Hardisty DS, Horner TJ, Evans N, Moriyasu R, Babbin AR, Wankel SD, et al. Limited iodate reduction in shipboard seawater incubations from the Eastern Tropical North Pacific oxygen deficient zone. Earth Planet Sci Lett. 2021;554:116676.
Google Scholar
Li H-P, Yeager CM, Brinkmeyer R, Zhang S, Ho Y-F, Xu C, et al. Bacterial production of organic acids enhances H2O2-dependent iodide oxidation. Environ Sci Technol. 2012;46:4837–44.
Google Scholar
Shiroyama K, Kawasaki Y, Unno Y, Amachi S. A putative multicopper oxidase, IoxA, is involved in iodide oxidation by Roseovarius sp. strain A-2. Biosci Biotechnol Biochem. 2015;79:1898–905.
Google Scholar
Lavik G, Stührmann T, Brüchert V, Van der Plas A, Mohrholz V, Lam P, et al. Detoxification of sulphidic African shelf waters by blooming chemolithotrophs. Nature. 2009;457:581–4.
Google Scholar
Wadley MR, Stevens DP, Jickells T, Hughes C, Chance R, Hepach H, et al. Modelling iodine in the ocean. Earth Space Sci Open Access Arch. 2020:46. https://doi.org/10.1002/essoar.10502078.1.
Waite TJ, Truesdale VW. Iodate reduction by Isochrysis galbana is relatively insensitive to de-activation of nitrate reductase activity—are phytoplankton really responsible for iodate reduction in seawater? Mar Chem. 2003;81:137–48.
Google Scholar
Coates JD, Achenbach LA. Microbial perchlorate reduction: rocket-fuelled metabolism. Nat Rev Microbiol. 2004;2:569–80.
Google Scholar
Jones DS, Bailey JV, Flood BE. Sedimenticola thiotaurini sp. nov., a sulfur-oxidizing bacterium isolated from salt marsh sediments, and emended descriptions of the genus Sedimenticola and Sedimenticola selenatireducens. Int J Syst Evol Microbiol. 2015;65:2522–30.
Google Scholar
Kanehisa M, Sato Y. KEGG Mapper for inferring cellular functions from protein sequences. Protein Sci. 2020;29:28–35.
Google Scholar
Boden R, Hutt LP, Rae AW. Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the ‘Proteobacteria’, and four new families within the orders Nitrosomonadales and Rhodocyclales. Int J Syst Evol Microbiol. 2017;67:1191–205.
Google Scholar
Brinkmann T, Specht CH, Frimmel FH. Non-linear calibration functions in ion chromatography with suppressed conductivity detection using hydroxide eluents. J Chromatogr. 2002;957:99–109.
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
Google Scholar
Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 2015;31:3350–2.
Google Scholar
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
Google Scholar
Edgar RC. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Google Scholar
Finn RD, Clements J, Eddy SR. HMMER web server: Interactive sequence similarity searching. Nucleic Acids Res. 2011;39:W29–37.
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490.
Google Scholar
Huerta-Cepas J, Serra F, Bork P. ETE 3: Reconstruction, analysis, and visualization of phylogenomic data. Mol Biol Evol. 2016;33:1635–8.
Google Scholar
Méheust R, Burstein D, Castelle CJ, Banfield JF. The distinction of CPR bacteria from other bacteria based on protein family content. Nat Commun. 2019;10:4173.
Google Scholar
Barnum TP, Figueroa IA, Carlström CI, Lucas LN, Engelbrektson AL, Coates JD. Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities. ISME J. 2018;12:1568–81.
Google Scholar
Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, et al. Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25:1422–3.
Google Scholar
Karsenti E. The making of Tara Oceans: Funding blue skies research for our Blue Planet. Mol Syst Biol. 2015;11:811.
Google Scholar
Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N, Gorsky G, et al. Open science resources for the discovery and analysis of Tara Oceans data. Sci Data. 2015;2:1–16.
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357.
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Google Scholar
Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, et al. Scikit-learn: Machine learning in Python. J Mac Learn Res. 2011;12:2825–30.
Azur MJ, Stuart EA, Frangakis C, Leaf PJ. Multiple imputation by chained equations: what is it and how does it work? Int J methods Psychiatr Res. 2011;20:40–9.
Google Scholar
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