Falkowski PG, Fenchel T, Delong EF. The microbial engines that drive Earth’s biogeochemical cycles. Science. 2008;320:1034–9.
Google Scholar
Arnosti C. Microbial extracellular enzymes and the marine carbon cycle. Ann Rev Mar Sci. 2011;3:401–25.
Google Scholar
Arnosti C, Bell C, Moorhead DL, Sinsabaugh RL, Steen AD, Stromberger M, et al. Extracellular enzymes in terrestrial, freshwater, and marine environments: perspectives on system variability and common research needs. Biogeochemistry. 2013;117:5–21.
Google Scholar
Moorhead DL, Rinkes ZL, Sinsabaugh RL, Weintraub MN. Dynamic relationships between microbial biomass, respiration, inorganic nutrients and enzyme activities: informing enzyme-based decomposition models. Front Microbiol. 2013;4:223.
Google Scholar
Li M, Gao Y, Qian W-J, Shi L, Liu Y, Nelson WC, et al. Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes. Environ Microbiol Rep. 2017;9:512–21.
Google Scholar
Song H-S, Thomas DG, Stegen JC, Li M, Liu C, Song X, et al. Regulation-structured dynamic metabolic model provides a potential mechanism for delayed enzyme response in denitrification process. Front Microbiol. 2017;8:1866.
Google Scholar
Khersonsky O, Tawfik DS. Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem. 2010;79:471–505.
Google Scholar
Baier F, Copp JN, Tokuriki N. Evolution of enzyme superfamilies: comprehensive exploration of sequence-function relationships. Biochemistry. 2016;55:6375–88.
Google Scholar
Sebastián M, Niell FX. Alkaline phosphatase activity in marine oligotrophic environments: implications of single-substrate addition assays for potential activity estimations. Mar Ecol Prog Ser. 2004;277:285–90.
Google Scholar
Catrina I, O’Brien PJ, Purcell J, Nikolic-Hughes I, Zalatan JG, et al. Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction. J Am Chem Soc. 2007;129:5760–5.
Google Scholar
Sunden F, AlSadhan I, Lyubimov AY, Ressl S, Wiersma-Koch H, Borland J, et al. Mechanistic and evolutionary insights from comparative enzymology of phosphomonoesterases and phosphodiesterases across the alkaline phosphatase superfamily. J Am Chem Soc. 2016;138:14273–87.
Google Scholar
Yang K, Metcalf WW. A new activity for an old enzyme: Escherichia coli bacterial alkaline phosphatase is a phosphite-dependent hydrogenase. Proc Natl Acad Sci USA. 2004;101:7919–24.
Google Scholar
Copley SD. Shining a light on enzyme promiscuity. Curr Opin Struct Biol. 2017;47:167–75.
Google Scholar
Steen AD, Vazin JP, Hagen SM, Mulligan KH, Wilhelm SW. Substrate specificity of aquatic extracellular peptidases assessed by competitive inhibition assays using synthetic substrates. Aquat Micro Ecol. 2015;75:271–81.
Google Scholar
Ivars-Martínez E, D’Auria G, RodrÍGuez-Valera F, SÁNchez-Porro C, Ventosa A, et al. Biogeography of the ubiquitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysis. Mol Ecol. 2008;17:4092–106.
Google Scholar
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
Schubert M, Lindgreen S, Orlando L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. 2016;9:88.
Google Scholar
Li D, Liu C, Luo R, Sadakane K, Lam T. 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 Bioinforma. 2010;11:119.
Google Scholar
Bushnell B. “BBMap: a fast, accurate, splice-aware aligner,” in Proceedings of the 9th Annual Genomics of Energy & Environment Meeting. Walnut Creek, CA, USA; 2014.
Scholz J, Besir H, Strasser C, Suppmann S. A new method to customize protein expression vectors for fast, efficient and background free parallel cloning. BMC Biotechnol. 2013;13:12.
Google Scholar
McLoughlin SY, Jackson C, Liu JW, Ollis DL. Growth of Escherichia coli coexpressing phosphotriesterase and glycerophosphodiester phosphodiesterase, using paraoxon as the sole phosphorus source. Appl Environ Microbiol. 2004;70:404–12.
Google Scholar
Britton J, Dyer RP, Majumdar S, Raston CL, Weiss GA. Ten-minute protein purification and surface tethering for continuous-flow biocatalysis. Angew Chem Int Ed Engl. 2017;56:2296–301.
Google Scholar
Ortiz-Tena JG, Rühmann B, Sieber V. Colorimetric determination of sulfate via an enzyme cascade for high-throughput detection of sulfatase activity. Anal Chem. 2018;90:2526–33.
Google Scholar
Huitema C, Horsman G. Analyzing enzyme kinetic data using the powerful statistical capabilities of R. 2018. http://biorxiv.org/content/10.1101/316588v1.
Rainer SF. Soft-bottom benthic communities in Otago Harbour and Blueskin Bay, New Zealand. New Zealand Oceanographic Institute Memoir 80; 1981.
Grove SL, Probert PK. Sediment macrobenthos of upper Otago Harbour, New Zealand. New Zeal J Mar Fresh. 1999;33:469–80.
Hoppe HG. Significance of exoenzymatic activities in the ecology of brackish water: measurements by means of methylumbelliferyl-substrates. Mar Ecol Prog Ser. 1983;11:299–308.
Google Scholar
Yamaguchi T, Sato M, Hashihama F, Ehama M, Shiozaki T, Takahashi K, et al. Basin‐scale variations in labile dissolved phosphoric monoesters and diesters in the central North Pacific Ocean. J Geophys Res Oceans. 2019;124:3058–72.
Google Scholar
Baltar F, Lundin D, Palovaara J, Lekunberri I, Reinthaler T, Herndl GJ, et al. Prokaryotic responses to ammonium and organic carbon reveal alternative CO2 fixation pathways and importance of alkaline phosphatase in the mesopelagic North Atlantic. Front Microbiol. 2016;7:1670.
Google Scholar
Yamaguchi H, Arisaka H, Seki M, Adachi M, Kimura K, Tomaru Y. Phosphotriesterase activity in marine bacteria of the genera Phaeobacter, Ruegeria, and Thalassospira. Int Biodeter Biodegr. 2016;115:186–91.
Google Scholar
Davidi D, Noor E, Liebermeister W, Bar-Even A, Flamholz A, Tummler K, et al. Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements. Proc Natl Acad Sci USA. 2016;113:3401–6.
Google Scholar
Paytan A, Cade-Menum BJ, McLaughlin K, Faul KL. Selective phosphorus regeneration of sinking marine particles: evidence from 31P-NMR. Mar Chem. 2003;82:55–70.
Google Scholar
Wu J, Wang P, Wang Y. Cytotoxic and mutagenic properties of alkyl phosphotriester lesions in Escherichia coli cells. Nucleic Acids Res. 2018;46:4013–21.
Google Scholar
McCarthy JG, Edington BV, Schendel PF. Inducible repair of phosphotriesters in Escherichia coli. Proc Natl Acad Sci USA. 1983;80:7380–4.
Google Scholar
Helbert W. Marine polysaccharide sulfatases. Front Mar Sci. 2017;4:6.
Google Scholar
Wegner CE, Richter-Heitmann T, Klindworth A, Klockow C, Richter M, Achstetter T, et al. Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula. Mar Genomics. 2013;9:51–61.
Google Scholar
Canfield DE, Farquhar J. Animal evolution, bioturbation, and the sulfate concentration of the oceans. Proc Natl Acad Sci USA. 2009;106:8123–7.
Google Scholar
Luo HW, Benner R, Long RA, Hu JJ. Subcellular localization of marine bacterial alkaline phosphatases. Proc Nat Acad Sci USA. 2009;106:21219–23.
Google Scholar
Wu J-R, Shien J-H, Shieh HK, Hu C-C, Gong S-R, Chen L-Y, et al. Cloning of the gene and characterization of the enzymatic properties of the monomeric alkaline phosphatase (PhoX) from Pasteurella multocida strain X-73. FEMS Microbiol Lett. 2007;267:113–20.
Google Scholar
Kageyama H, Tripathi K, Rai AK, Cha-um S, Waditee-Sirisattha R, Takabe T. An alkaline phosphatase/phosphodiesterase, PhoD, induced by salt stress and secreted out of the cells of Aphanothece halophytica, a halotolerant cyanobacterium. Appl Environ Micro. 2011;77:5178–83.
Google Scholar
Rodriguez F, Lillington J, Johnson S, Timmel CR, Lea SM, Berks BC. Crystal structure of the Bacillus subtilis phosphodiesterase PhoD reveals an iron and calcium-containing active site. J Biol Chem. 2014;289:30889–99.
Google Scholar
Noskova Y, Likhatskaya G, Terentieva N, Son O, Tekutyeva L, Balabanova L. A novel alkaline phosphatase/phosphodiesterase, CamPhoD, from marine bacterium Cobetia amphilecti KMM 296. Mar Drugs. 2019;17:657.
Google Scholar
Dyhrman ST, Ammerman JW, Van, Mooy BAS. Microbes and the marine phosphorus cycle. Oceanography. 2007;20:110–6.
Google Scholar
Larson TJ, Ehrmann M, Boos W. Periplasmic glycerophosphodiester phosphodiesterase of Escherichia coli, a new enzyme of the glp regulon. J Biol Chem. 1983;258:5428–32.
Google Scholar
van Veen HW. Phosphate transport in prokaryotes: molecules, mediators and mechanisms. Antonie Van Leeuwenhoek. 1997;72:299–315.
Google Scholar
Parthasarathy S, Parapatla H, Nandavaram A, Palmer T, Siddavattam D. Organophosphate hydrolase is a lipoprotein and interacts with Pi-specific transport system to facilitate growth of Brevundimonas diminuta using op insecticide as source of phosphate. J Biol Chem. 2016;291:7774–85.
Google Scholar
Hong T, Kong A, Lam J, Young L. Periplasmic alkaline phosphatase activity and abundance in Escherichia coli B23 and C29 during exponential and stationary phase. J Exp Microbiol Immunol. 2007;11:8–13.
Baltar F, Arístegui J, Gasol J, Yokokawa T, Herndl GJ. Bacterial versus archaeal origin of extracellular enzymatic activity in the Northeast Atlantic deep waters. Micro Ecol. 2013;65:277–88.
Google Scholar
Thomson B, Wenley J, Currie K, Hepburn C, Herndl GJ, Baltar F. Resolving the paradox: continuous cell-free alkaline phosphatase activity despite high phosphate concentrations. Mar Chem. 2019;214:103671.
Google Scholar
Lei L, Cherukuri KP, Alcolombri U, Meltzer D, Tawfik DS. The dimethylsulfoniopropionate (DMSP) lyase and lyase-like cupin family consists of bona fide DMSP lyases as well as other enzymes with unknown function. Biochemistry. 2018;57:3364–77.
Google Scholar
Ferla MP, Brewster JL, Hall KR, Evans GB, Patrick WM. Primordial‐like enzymes from bacteria with reduced genomes. Primordial-like enzymes from bacteria with reduced genomes. Mol Microbiol. 2017;105:508–24.
Google Scholar
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