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[72] Kashyap S, Sklute EC, Wang P, Tague Jr TJ, Dyar MD, Holden JF (2023) Spectral detection of nanophase iron minerals produced by Fe(III)-reducing hyperthermophilic crenarchaea. Astrobiology 23:43-56.
[71] Jung JH, Hong S, Jeon EJ, Kim MK, Seo DH, Woo EJ, Holden JF, Park CS (2022) Acceptor dependent catalytic properties of GH57 4-α-glucanotransferase from Pyrococcus sp. ST04. Front Microbiol. 13:1016675.
[70] Kashyap S, Musa M, Neat KA, Leopo DA, Holden JF (2022) Desulfovulcanus ferrireducens gen. nov., sp. nov., a thermophilic autotrophic iron and sulfur reducing bacterium from subseafloor basalt that grows on nanophase akaganéite and lepidocrocite minerals. Extremophiles 26:13.
[69] Fortunato CS, Butterfield DA, Larson B, Lawrence-Slavas N, Algar CK, Zeigler Allen L, Holden JF, Proskurowski G, Reddington E, Stewart LC, Topcuoglu BD, Vallino JJ, Huber JA (2021) Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressure and lag time on autotrophic microbial communities. Appl Environ Microbiol 87:e00078-21.
[68] Kashyap S, Holden JF (2021) Microbe-mineral interaction and novel proteins for iron oxide reduction in the hyperthermophilic crenarchaeon Pyrodictium delaneyi. Appl Environ Microbiol 87:e02330-20.
[67] Clague DA, Martin JF, Paduan JB, Butterfield DA, Jamieson JW, Le Saout M, Caress DW, Thomas H, Holden JF, Kelley DS (2020) Hydrothermal chimney distribution on the Endeavour Segment, Juan de Fuca Ridge. Geochem Geophys Geosyst 21:e2020GC008917.
[66] Holden JF, Bardwell CP, Kashyap K (2020) Draft genome sequence of Desulfurobacterium thermolithotrophum strain HR11, a novel thermophilic autotrophic subspecies from a deep-sea hydrothermal vent. Microbiol Resour Announc 9:e00167-20.
[65] Nguyen TB, Topcuoglu BD, Holden JF, LaRowe DE, Lang SQ (2020) Low hydrogen flux leads to larger carbon isotopic fractionation of methane and biomarkers during hydrogenotrophic methanogenesis. Geochim Cosmochim Acta 271:212-226.
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[63] Stewart LC, Algar CK, Fortunato CS, Larson BI, Vallino JJ, Huber JA, Butterfield DA, Holden JF (2019) Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents. ISME J 13:1711-1721.
[62] Topcuoglu BD, Meydan C, Nguyen TB, Lang SQ, Holden JF (2019) Growth kinetics, carbon isotope fractionation, and gene expression in the hyperthermophile Methanocaldococcus jannaschii during hydrogen-limited growth and interspecies hydrogen transfer. Appl Environ Microbiol 85:e00180-19.
[61] Gruen DS, Wang DT, Könneke M, Topcuoglu BD, Stewart LC, Goldhammer T, Holden JF, Hinrichs KU, Ono S (2018) Experimental investigation on the controls of clumped isotopologue and hydrogen isotope ratios in microbial methane. Geochim Cosmochim Acta 237:339-356.
[60] Kashyap S, Sklute EC, Dyar MD, Holden JF (2018) Reduction and morphological transformation of synthetic nanophase iron oxide minerals by hyperthermophilic archaea. Front Microbiol 9:1550.
[59] Topcuoglu BD, Meydan C, Orellana R, Holden JF (2018) Formate hydrogenlyase and formate secretion ameliorate H2 inhibition in the hyperthermophilic archaeon Thermococcus paralvinellae. Environ Microbiol 20:949-957.
[58] Sklute EC, Kashyap S, Dyar MD, Holden JF, Tague T, Wang P, Jaret SJ (2018) Spectral and morphological characteristics of synthetic nanophase iron (oxyhydr)oxides. Phys Chem Miner 45:1-26.
[57] Vaccaro BJ, Clarkson SM, Holden JF, Lee DW, Wu CH, Poole FL, Cotelesage JJH, Hackett MJ, Mohebbi S, Sun J, Li H, Johnson MK, George GN, Adams MWW (2017) Biological iron-sulfur storage in a thioferrate-protein nanoparticle. Nat Commun 8:16110.
[56] Jung JH, Seo DH, Holden JF, Kim HS, Baik MY, Park CS (2016) Broad substrate specificity of a hyperthermophilic α-glucosidase from Pyrobaculum arsenaticum. Food Sci Biotechnol 25:1665-1669.
[55] Topcuoglu BD, Stewart LC, Morrison HG, Butterfield DA, Huber JA, Holden JF (2016) Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents. Front Microbiol 7:1240.
[54] Lin TJ, El Sebae G, Jung JH, Jung DH, Park CS, Holden JF (2016) Pyrodictium delaneyi sp. nov., a hyperthermophilic autotrophic archaeon that reduces Fe(III) oxide and nitrate. Int J Syst Evol Microbiol 66:3372-3376.
[53] Jangi S, Gandhi R, Cox LM, Li N, Von Glehn F, Yan R, Patel B, Antonietta Mazzola M, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topcuoglu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L, Weiner HL (2016) Alterations of the human gut microbiome in multiple sclerosis. Nat Commun 7:12015.
[52] Hensley SA, Moreira E, Holden JF (2016) Hydrogen production and enzyme activities in the hyperthermophile Thermococcus paralvinellae grown on maltose, tryptone and agricultural waste. Front Microbiol. 7:167.
[51] Lin TJ, Ver Eecke HC, Breves EA, Dyar MD, Jamieson JW, Hannington MD, Dahle H, Bishop JL, Lane MD, Butterfield DA, Kelley DS, Lilley MD, Baross JA, Holden JF (2016) Linkages between mineralogy, fluid chemistry and microbial communities within hydrothermal chimneys from the Endeavour Segment, Juan de Fuca Ridge. Geochem Geophys Geosyst 17:300-323.
[50] Stewart LC, Llewellyn JG, Butterfield DA, Lilley MD, Holden JF (2016) Hydrogen and thiosulfate limits for growth of a thermophilic, autotrophic Desulfurobacterium species from a deep-sea hydrothermal vent. Environ Microbiol Rep 8:196-200.
[49] Kim YT, Jung JH, Stewart LC, Kwon SW, Holden JF, Park CS (2015) Complete genome sequence of the hyperthermophilic methanogen Methanocaldococcus bathoardescens JH146T isolated from the basalt subseafloor. Mar Genomics 24:229-230.
[48] Wang DT, Gruen DS, Sherwood Lollar B, Hinrichs KU, Stewart LC, Holden JF, Hristov AN, Pohlman JW, Morrill PL, Könneke M, Delwiche KB, Reeves EP, Sutcliffe CN, Ritter DJ, Seewald JS, McIntosh JC, Hemond HF, Kubo MD, Cardace D, Hoehler TM, Ono S (2015) Unique non-equilibrium clumped isotope signals in microbial methane. Science 348:428-431.
[47] Stewart LC, Jung JH, Kim YT, Kwon SW, Park CS, Holden JF (2015) Methanocaldococcus bathoardescens sp. nov., a hyperthermophilic methanogen isolated from a volcanically active deep-sea hydrothermal vent. Int J Syst Evol Microbiol 65:1280-1283.
[46] Hensley SA, Jung JH, Park CS, Holden JF (2014) Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents. Int J Syst Evol Microbiol. 64:3655-3659.
[45] Lin TJ, Breves EA, Dyar MD, Ver Eecke HC, Jamieson JW, Holden JF (2014) Magnetite formation from ferrihydrite by hyperthermophilic archaea from Endeavour Segment, Juan de Fuca Ridge hydrothermal vent chimneys. Geobiology 12:200-211.
[44] Park KH, Jung JH, Park SG, Lee ME, Holden JF, Park CS, Woo EJ (2014) Structural features underlying the selective cleavage of a novel exo-type maltose-forming amylase from Pyrococcus sp. ST04. Acta Cryst D70:1659-1668.
[43] Jeon EJ, Jung JH, Seo DH, Jung DH, Holden JF, Park CS (2014) Bioinformatic and biochemical analysis of a novel maltose-forming α-amylase of the GH57 family in the hyperthermophilic archaeon Thermococcus sp. CL1. Enzyme Microb Tech 60:9-15.
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[1] Holden JF, Baross JA (1993) Enhanced thermotolerance and temperature induced changes in protein composition in the hyperthermophilic archaeon ES4. J Bacteriol 175:2839-2843.
[72] Kashyap S, Sklute EC, Wang P, Tague Jr TJ, Dyar MD, Holden JF (2023) Spectral detection of nanophase iron minerals produced by Fe(III)-reducing hyperthermophilic crenarchaea. Astrobiology 23:43-56.
[71] Jung JH, Hong S, Jeon EJ, Kim MK, Seo DH, Woo EJ, Holden JF, Park CS (2022) Acceptor dependent catalytic properties of GH57 4-α-glucanotransferase from Pyrococcus sp. ST04. Front Microbiol. 13:1016675.
[70] Kashyap S, Musa M, Neat KA, Leopo DA, Holden JF (2022) Desulfovulcanus ferrireducens gen. nov., sp. nov., a thermophilic autotrophic iron and sulfur reducing bacterium from subseafloor basalt that grows on nanophase akaganéite and lepidocrocite minerals. Extremophiles 26:13.
[69] Fortunato CS, Butterfield DA, Larson B, Lawrence-Slavas N, Algar CK, Zeigler Allen L, Holden JF, Proskurowski G, Reddington E, Stewart LC, Topcuoglu BD, Vallino JJ, Huber JA (2021) Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressure and lag time on autotrophic microbial communities. Appl Environ Microbiol 87:e00078-21.
[68] Kashyap S, Holden JF (2021) Microbe-mineral interaction and novel proteins for iron oxide reduction in the hyperthermophilic crenarchaeon Pyrodictium delaneyi. Appl Environ Microbiol 87:e02330-20.
[67] Clague DA, Martin JF, Paduan JB, Butterfield DA, Jamieson JW, Le Saout M, Caress DW, Thomas H, Holden JF, Kelley DS (2020) Hydrothermal chimney distribution on the Endeavour Segment, Juan de Fuca Ridge. Geochem Geophys Geosyst 21:e2020GC008917.
[66] Holden JF, Bardwell CP, Kashyap K (2020) Draft genome sequence of Desulfurobacterium thermolithotrophum strain HR11, a novel thermophilic autotrophic subspecies from a deep-sea hydrothermal vent. Microbiol Resour Announc 9:e00167-20.
[65] Nguyen TB, Topcuoglu BD, Holden JF, LaRowe DE, Lang SQ (2020) Low hydrogen flux leads to larger carbon isotopic fractionation of methane and biomarkers during hydrogenotrophic methanogenesis. Geochim Cosmochim Acta 271:212-226.
[64] Topcuoglu BD, Holden JF (2019) Extremophiles: hot environments, pp. 263-269. In Schmidt TM (ed.), Encyclopedia of Microbiology, 4th Edition, Elsevier Publishing, Oxford, UK.
[63] Stewart LC, Algar CK, Fortunato CS, Larson BI, Vallino JJ, Huber JA, Butterfield DA, Holden JF (2019) Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents. ISME J 13:1711-1721.
[62] Topcuoglu BD, Meydan C, Nguyen TB, Lang SQ, Holden JF (2019) Growth kinetics, carbon isotope fractionation, and gene expression in the hyperthermophile Methanocaldococcus jannaschii during hydrogen-limited growth and interspecies hydrogen transfer. Appl Environ Microbiol 85:e00180-19.
[61] Gruen DS, Wang DT, Könneke M, Topcuoglu BD, Stewart LC, Goldhammer T, Holden JF, Hinrichs KU, Ono S (2018) Experimental investigation on the controls of clumped isotopologue and hydrogen isotope ratios in microbial methane. Geochim Cosmochim Acta 237:339-356.
[60] Kashyap S, Sklute EC, Dyar MD, Holden JF (2018) Reduction and morphological transformation of synthetic nanophase iron oxide minerals by hyperthermophilic archaea. Front Microbiol 9:1550.
[59] Topcuoglu BD, Meydan C, Orellana R, Holden JF (2018) Formate hydrogenlyase and formate secretion ameliorate H2 inhibition in the hyperthermophilic archaeon Thermococcus paralvinellae. Environ Microbiol 20:949-957.
[58] Sklute EC, Kashyap S, Dyar MD, Holden JF, Tague T, Wang P, Jaret SJ (2018) Spectral and morphological characteristics of synthetic nanophase iron (oxyhydr)oxides. Phys Chem Miner 45:1-26.
[57] Vaccaro BJ, Clarkson SM, Holden JF, Lee DW, Wu CH, Poole FL, Cotelesage JJH, Hackett MJ, Mohebbi S, Sun J, Li H, Johnson MK, George GN, Adams MWW (2017) Biological iron-sulfur storage in a thioferrate-protein nanoparticle. Nat Commun 8:16110.
[56] Jung JH, Seo DH, Holden JF, Kim HS, Baik MY, Park CS (2016) Broad substrate specificity of a hyperthermophilic α-glucosidase from Pyrobaculum arsenaticum. Food Sci Biotechnol 25:1665-1669.
[55] Topcuoglu BD, Stewart LC, Morrison HG, Butterfield DA, Huber JA, Holden JF (2016) Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents. Front Microbiol 7:1240.
[54] Lin TJ, El Sebae G, Jung JH, Jung DH, Park CS, Holden JF (2016) Pyrodictium delaneyi sp. nov., a hyperthermophilic autotrophic archaeon that reduces Fe(III) oxide and nitrate. Int J Syst Evol Microbiol 66:3372-3376.
[53] Jangi S, Gandhi R, Cox LM, Li N, Von Glehn F, Yan R, Patel B, Antonietta Mazzola M, Liu S, Glanz BL, Cook S, Tankou S, Stuart F, Melo K, Nejad P, Smith K, Topcuoglu BD, Holden J, Kivisäkk P, Chitnis T, De Jager PL, Quintana FJ, Gerber GK, Bry L, Weiner HL (2016) Alterations of the human gut microbiome in multiple sclerosis. Nat Commun 7:12015.
[52] Hensley SA, Moreira E, Holden JF (2016) Hydrogen production and enzyme activities in the hyperthermophile Thermococcus paralvinellae grown on maltose, tryptone and agricultural waste. Front Microbiol. 7:167.
[51] Lin TJ, Ver Eecke HC, Breves EA, Dyar MD, Jamieson JW, Hannington MD, Dahle H, Bishop JL, Lane MD, Butterfield DA, Kelley DS, Lilley MD, Baross JA, Holden JF (2016) Linkages between mineralogy, fluid chemistry and microbial communities within hydrothermal chimneys from the Endeavour Segment, Juan de Fuca Ridge. Geochem Geophys Geosyst 17:300-323.
[50] Stewart LC, Llewellyn JG, Butterfield DA, Lilley MD, Holden JF (2016) Hydrogen and thiosulfate limits for growth of a thermophilic, autotrophic Desulfurobacterium species from a deep-sea hydrothermal vent. Environ Microbiol Rep 8:196-200.
[49] Kim YT, Jung JH, Stewart LC, Kwon SW, Holden JF, Park CS (2015) Complete genome sequence of the hyperthermophilic methanogen Methanocaldococcus bathoardescens JH146T isolated from the basalt subseafloor. Mar Genomics 24:229-230.
[48] Wang DT, Gruen DS, Sherwood Lollar B, Hinrichs KU, Stewart LC, Holden JF, Hristov AN, Pohlman JW, Morrill PL, Könneke M, Delwiche KB, Reeves EP, Sutcliffe CN, Ritter DJ, Seewald JS, McIntosh JC, Hemond HF, Kubo MD, Cardace D, Hoehler TM, Ono S (2015) Unique non-equilibrium clumped isotope signals in microbial methane. Science 348:428-431.
[47] Stewart LC, Jung JH, Kim YT, Kwon SW, Park CS, Holden JF (2015) Methanocaldococcus bathoardescens sp. nov., a hyperthermophilic methanogen isolated from a volcanically active deep-sea hydrothermal vent. Int J Syst Evol Microbiol 65:1280-1283.
[46] Hensley SA, Jung JH, Park CS, Holden JF (2014) Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents. Int J Syst Evol Microbiol. 64:3655-3659.
[45] Lin TJ, Breves EA, Dyar MD, Ver Eecke HC, Jamieson JW, Holden JF (2014) Magnetite formation from ferrihydrite by hyperthermophilic archaea from Endeavour Segment, Juan de Fuca Ridge hydrothermal vent chimneys. Geobiology 12:200-211.
[44] Park KH, Jung JH, Park SG, Lee ME, Holden JF, Park CS, Woo EJ (2014) Structural features underlying the selective cleavage of a novel exo-type maltose-forming amylase from Pyrococcus sp. ST04. Acta Cryst D70:1659-1668.
[43] Jeon EJ, Jung JH, Seo DH, Jung DH, Holden JF, Park CS (2014) Bioinformatic and biochemical analysis of a novel maltose-forming α-amylase of the GH57 family in the hyperthermophilic archaeon Thermococcus sp. CL1. Enzyme Microb Tech 60:9-15.
[42] Jung JH, Kim YT, Eun-Jung J, Seo DH, Hensley SA, Holden JF, Park CS (2014) Complete genome sequence of hyperthermophilic archaeon Thermococcus sp. ES1. J Biotechnol 174:14-15.
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[1] Holden JF, Baross JA (1993) Enhanced thermotolerance and temperature induced changes in protein composition in the hyperthermophilic archaeon ES4. J Bacteriol 175:2839-2843.