Atashgahi S, Liebensteiner MG, Janssen DB, Smidt H, Stams AJM, Sipkema D. Microbial synthesis and transformation of inorganic and organic chlorine compounds. Front Microbiol. 2018;9:1–22.
Liebensteiner MG, Oosterkamp MJ, Stams AJM. Microbial respiration with chlorine oxyanions: diversity and physiological and biochemical properties of chlorate- and perchlorate-reducing microorganisms. Ann NY Acad Sci. 2016;1365:59–72.
Palmisano A, Hazen T. Bioremediation of metals and radionuclides: what it is and how it works, 2 edn. United States: N. 2003. p. 2003.
Winterbourn CC. Reconciling the chemistry and biology of reactive oxygen species. Nat Chem Biol. 2008;4:278–86.
Youngblut MD, Wang O, Barnum TP, Coates JD. (Per)chlorate in biology on earth and beyond. Annu Rev Microbiol. 2016;70:435–459.
Gray MJ, Wholey W-Y, Jakob U. Bacterial responses to reactive chlorine species. Annu Rev Microbiol. 2013;67:141–60.
Hofbauer S, Howes BD, Flego N, Pirker KF, Schaffner I, Mlynek G, et al. From chlorite dismutase towards HemQ—the role of the proximal H-bonding network in haeme binding. Biosci Rep. 2016;36:e00312.
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:e00233–00215.
Coates JD, Achenbach LA. Microbial perchlorate reduction: rocket-fueled metabolism. Nat Rev Microbiol. 2004;2:569–80.
Kounaves SP, Stroble ST, Anderson RM, Moore Q, Catling DC, Douglas S, et al. Discovery of natural perchlorate in the Antarctic Dry Valleys and its global implications. Environ Sci Technol. 2010;44:2360–4.
Melnyk RA, Coates JD. The perchlorate reduction genomic island: mechanisms and pathways of evolution by horizontal gene transfer. BMC Genomics. 2015;16:862.
Coates JD, Michaelidou U, Bruce RA, O’Connor SM, Crespi JN, Achenbach LA. Ubiquity and diversity of dissimilatory (per)chlorate-reducing bacteria. Appl Environ Microbiol. 1999;65:5234–41.
Rajagopalan S, Anderson T, Cox S, Harvey G, Cheng Q, Jackson WA. Perchlorate in wet deposition across North America. Environ Sci Technol. 2009;43:616–22.
Clark IC, Youngblut M, Jacobsen G, Wetmore KM, Deutschbauer A, Lucas L, et al. Genetic dissection of chlorate respiration in Pseudomonas stutzeri PDA reveals syntrophic (per)chlorate reduction. Environ Microbiol. 2016;18:3342–54.
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.
Van de Pas-Schoonen KT, Schalk-Otte S, Haaijer S, Schmid M, Op den Camp H, Strous M, et al. Complete conversion of nitrate into dinitrogen gas in co-cultures of denitrifying bacteria. Biochem Soc Trans. 2005;33:205–9.
Daims H, Lücker S, Wagner M. A new perspective on microbes formerly known as nitrite-oxidizing bacteria. Trends Microbiol. 2016;24:699–712.
Winogradsky S. Contributions a la morphologie des organismes de la nitrification. Arch Sci Biol. 1892;1:88–137.
Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, et al. Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. ISME J. 2018;12:1715–28.
Kelly DP, Shergill JK, Lu W-P, Wood AP. Oxidative metabolism of inorganic sulfur compounds by bacteria. Antonie Van Leeuwenhoek. 1997;71:95–107.
Grostern A, Edwards EA. Growth of Dehalobacter and Dehalococcoides spp. during degradation of chlorinated ethanes. Appl Environ Microbiol. 2006;72:428–36.
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;7:13219.
Costa E, Perez J, Kreft J-U. Why is metabolic labour divided in nitrification? Trends Microbiol. 2006;14:213–9.
Dolinšek J, Goldschmidt F, Johnson DR. Synthetic microbial ecology and the dynamic interplay between microbial genotypes. FEMS Microbiol Rev. 2016;40:961–79.
Hallin S, Philippot L, Löf FE, Sanford RA, Jones CM. Genomics and ecology of novel N2O-reducing microorganisms. Trends Microbiol. 2018;26:43–55.
Lilja EE, Johnson DR. Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates. ISME J. 2016;10:1568–78.
Wolterink AFWM, Schiltz E, Hagedoorn P-l, Hagen WR. Characterization of the chlorate reductase from Pseudomonas chloritidismutans. J Bacteriol. 2003;185:3210–3.
Hofbauer S, Schaffner I, Furtmüller PG, Obinger C. Chlorite dismutases—a heme enzyme family for use in bioremediation and generation of molecular oxygen. Biotechnol J. 2014;9:461–73.
Bender KS, O’Connor SM, Chakraborty R, Coates JD, Achenbach LA. Sequencing and transcriptional analysis of the chlorite dismutase gene of Dechloromonas agitata and its use as a metabolic probe. Appl Environ Microbiol. 2002;68:4820–6.
Van Ginkel CG, Rikken GB, Kroon AGM, Kengen SWM. Purification and characterization of chlorite dismutase: A novel oxygen-generating enzyme. Arch Microbiol. 1996;166:321–6.
Clark IC, Melnyk Ra, Iavarone AT, Novichkov PS, Coates JD. Chlorate reduction in Shewanella algae ACDC is a recently acquired metabolism characterized by gene loss, suboptimal regulation, and oxidative stress. Mol Microbiol. 2014;94:107–25.
Sun Y. Physiology of microbial perchlorate reduction. PhD dissertation. Berkeley, CA, UC Berkeley 2008.
Rikken GB, Kroon AGM, Van Ginkel CG. Transformation of (per)chlorate into chloride by a newly isolated bacterium: reduction and dismutation. Appl Microbiol Biotechnol. 1996;45:420–6.
Clark IC, Melnyk Ra, Engelbrektson A, Coates JD. Structure and evolution of chlorate reduction composite transposons. mBio. 2013;4:e00379–00313.
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.
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;340:85–87.
Liebensteiner MG, MWH Pinkse, Nijsse B, PDEM Verhaert, Tsesmetzis N, AJM Stams, et al. Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes. Environ Microbiol Rep. 2015;7:936–45.
Martínez-Espinosa RM, Richardson DJ, Bonete MJ. Characterisation of chlorate reduction in the haloarchaeon Haloferax mediterranei. Biochim Biophys Acta. 2015;1850:587–94.
Malmqvist Å, Welander T, Moore E, Ternström A, Molin G, Stenström I-MJS. et al. Ideonella dechloratans gen. nov., sp. nov., a new bacterium capable of growing anaerobically with chlorate as an electron acceptor. Syst Appl Microbiol. 1994;17:58–64.
Dudley M, Nerenberg R. Microbial ecology of perchlorate-reducing bacteria that accumulate high levels of chlorate. Master’s thesis, University of Notre Dame; 2007.
Dudley M, Salamone A, Nerenberg R. Kinetics of a chlorate-accumulating, perchlorate-reducing bacterium. Water Res. 2008;42:2403–10.
Salamone AR, Nerenberg R. Kinetics of a perchlorate-reducing bacterium that accumulates high levels of chlorate. Master’s thesis, University of Notre Dame; 2006.
Nerenberg R, Kawagoshi Y, Rittmann BE. Kinetics of a hydrogen-oxidizing, perchlorate-reducing bacterium. Water Res. 2006;40:3290–6.
Cameron Thrash J, Ahmadi S, Torok T, Coates JD. Magnetospirillum bellicus sp. nov., a novel dissimilatory perchlorate-reducing alphaproteobacterium isolated from a bioelectrical reactor. Appl Environ Microbiol. 2010;76:4730–7.
Thrash JC, Pollock J, Torok T, Coates JD. Description of the novel perchlorate-reducing bacteria Dechlorobacter hydrogenophilus gen. nov., sp. nov. and Propionivibrio militaris, sp. nov. Appl Microbiol Biotechnol. 2010b;86:335–43.
Youngblut MD, Tsai CL, Clark IC, Carlson HK, Maglaqui AP, Gau-Pan PS, et al. Perchlorate reductase is distinguished by active site aromatic gate residues. J Biol Chem. 2016a;291:9190–202.
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;1–14.
Joshi N, Fass J. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software]. 2011.
Simpson JT, Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 2012;549–56.
Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:btv033.
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013. Preprint at https://arxiv.org/abs/1303.3997.
Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319.
Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 2015;31:3350–2.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;114:gr.186072.186114.
Seemann T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, et al. HMMER web server: 2015 update. Nucleic Acids Research: 2015;1–9.
Coates JD, Lonergan DJ, Philips EJP, Jenter H, Lovley DR. Desulfuromonas palmitatis sp. nov., a marine dissimilatory Fe (III) reducer that can oxidize long-chain fatty acids. Arch Microbiol. 1995;164:406–13.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST plus: architecture and applications. BMC Bioinforma. 2009;10:421.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581.
Callahan BJ, McMurdie PJ, Holmes SP. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 2017;11:2639.
Tang JY, Riley WJ. A total quasi-steady-state formulation of substrate uptake kinetics in complex networks and an example application to microbial litter decomposition. Biogeosciences. 2013;10:8329–51.
Rittmann BE, McCarty PL. Environmental biotechnology: principles and applications. McGraw-Hill Education – Europe. 2001. ISBN-13: 2001;978-0071181846.
Thrash JC, Ahmadi S, Torok T, Coates JD, Division ES, Orlando E, et al. Magnetospirillum bellicus sp. nov., a novel dissimilatory perchlorate-reducing alphaproteobacterium isolated from a bioelectrical reactor. Appl Environ Microbiol. 2010a;76:4730–7.
Dubois JL. O–O bond formation by a heme protein: the unexpected efficiency of chlorite dismutase. molecular water oxidation catalysis: a key topic for new sustainable energy conversion schemes. In: Llobet (ed.). Molecular Water Oxidation Catalysis: A Key Topic for New Sustainable Energy Conversion Schemes. John Wiley & Sons – United Kingdom. 2014.
Celis AI, Geeraerts Z, Ngmenterebo D, Machovina MM, Kurker RC, Rajakumar K, et al. A dimeric chlorite dismutase exhibits O2-generating activity and acts as a chlorite antioxidant in Klebsiella pneumoniae MGH 78578. Biochemistry. 2015;54:434–46.
Engelbrektson A, Hubbard CG, Tom LM, Boussina A, Jin YT, Wong H, et al. Inhibition of microbial sulfate reduction in a flow-through column system by (per)chlorate treatment. Front Microbiol. 2014;5:1–11.
Brundrett M, Yan W, Velazquez MC, Rao B, Jackson WA. Abiotic reduction of chlorate by Fe(II) minerals: implications for occurrence and transformation of oxy-chlorine species on earth and mars. ACS Earth Space Chem. 2019;3:700–10.
Stepanov VG, Xiao Y, Tran Q, Rojas M, Willson RC, Fofanov Y, et al. The presence of nitrate dramatically changed the predominant microbial community in perchlorate degrading cultures under saline conditions. BMC Microbiol. 2014;14:225.
Martens-Habbena W, Berube PM, Urakawa H, De La Torre JR, Stahl DA. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature. 2009;461:976–9.
Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, et al. Complete nitrification by Nitrospira bacteria. Nature. 2015;528:504–9.
Source: Ecology - nature.com
