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1. Fe(III) (oxyhydr)oxide reduction by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens

Author

Elizabeth C. Sklute, Deborah A. Leopo, Kaylee A. Neat, Kenneth J. T. Livi, M. Darby Dyar, and James F. Holden

Subjects
thermophile, iron reduction, ferrihydrite, akaganeite, lepidocrocite, magnetite, Microbiology, QR1-502
Abstract

Some thermophilic bacteria from deep-sea hydrothermal vents grow by dissimilatory iron reduction, but our understanding of their biogenic mineral transformations is nascent. Mineral transformations catalyzed by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens during growth at 55°C were examined using synthetic nanophase ferrihydrite, akaganeite, and lepidocrocite separately as terminal electron acceptors. Spectral analyses using visible-near infrared (VNIR), Fourier-transform infrared attenuated total reflectance (FTIR-ATR), and Mössbauer spectroscopies were complemented with x-ray diffraction (XRD) and transmission electron microscopy (TEM) using selected area electron diffraction (SAED) and energy dispersive X-ray (EDX) analyses. The most extensive biogenic mineral transformation occurred with ferrihydrite, which produced a magnetic, visibly dark mineral with spectral features matching cation-deficient magnetite. Desulfovulcanus ferrireducens also grew on akaganeite and lepidocrocite and produced non-magnetic, visibly dark minerals that were poorly soluble in the oxalate solution. Bioreduced mineral products from akaganeite and lepidocrocite reduction were almost entirely absorbed in the VNIR spectroscopy in contrast to both parent minerals and the abiotic controls. However, FTIR-ATR and Mössbauer spectra and XRD analyses of both biogenic minerals were almost identical to the parent and control minerals. The TEM of these biogenic minerals showed the presence of poorly crystalline iron nanospheres (50–200 nm in diameter) of unknown mineralogy that were likely coating the larger parent minerals and were absent from the controls. The study demonstrated that thermophilic bacteria transform different types of Fe(III) (oxyhydr)oxide minerals for growth with varying mineral products. These mineral products are likely formed through dissolution-reprecipitation reactions but are not easily predictable through chemical equilibrium reactions alone.

Published
2023
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2. Formate and hydrogen in hydrothermal vents and their use by extremely thermophilic methanogens and heterotrophs

Author

James F. Holden and Harita Sistu

Subjects
formate, hydrogen, hydrothermal vent, hyperthermophiles, formate dehydrogenase, hydrogenase, Microbiology, QR1-502
Abstract

Extremely thermophilic methanogens in the Methanococci and heterotrophs in the Thermococci are common in deep-sea hydrothermal vents. All Methanococci use H2 as an electron donor, and a few species can also use formate. Most Methanococci have a coenzyme F420-reducing formate dehydrogenase. All Thermococci reduce S0 but have hydrogenases and produce H2 in the absence of S0. Some Thermococci have formate hydrogenlyase (Fhl) that reversibly converts H2 and CO2 to formate or an NAD(P)+-reducing formate dehydrogenase (Nfd). Questions remain if Methanococci or Thermococci use or produce formate in nature, why only certain species can grow on or produce formate, and what the physiological role of formate is? Formate forms abiotically in hydrothermal fluids through chemical equilibrium with primarily H2, CO2, and CO and is strongly dependent upon H2 concentration, pH, and temperature. Formate concentrations are highest in hydrothermal fluids where H2 concentrations are also high, such as in ultramafic systems where serpentinization reactions occur. In nature, Methanococci are likely to use formate as an electron donor when H2 is limiting. Thermococci with Fhl likely convert H2 and CO2 to formate when H2 concentrations become inhibitory for growth. They are unlikely to grow on formate in nature unless formate is more abundant than H2 in the environment. Nearly all Methanococci and Thermococci have a gene for at least one formate dehydrogenase catalytic subunit, which may be used to provide free formate for de novo purine biosynthesis. However, only species with a membrane-bound formate transporter can grow on or secrete formate. Interspecies H2 transfer occurs between Thermococci and Methanococci. This and putative interspecies formate transfer may support Methanococci in low H2 environments, which in turn may prevent growth inhibition of Thermococci by its own H2. Future research directions include understanding when, where, and how formate is used and produced by these organisms in nature, and how transcription of Thermococci genes encoding formate-related enzymes are regulated.

Published
2023
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3. Acceptor dependent catalytic properties of GH57 4-α-glucanotransferase from Pyrococcus sp. ST04

Author

Jong-Hyun Jung, Seungpyo Hong, Eun Jung Jeon, Min-Kyu Kim, Dong-Ho Seo, Eui-Jeon Woo, James F. Holden, and Cheon-Seok Park

Subjects
acceptor binding site, disproportionation, 4-α-glucanotransferase, hyperthermophilic archaea, glycoside hydrolase family 57, Pyrococcus, Microbiology, QR1-502
Abstract

The 4-α-glucanotransferase (4-α-GTase or amylomaltase) is an essential enzyme in maltodextrin metabolism. Generally, most bacterial 4-α-GTase is classified into glycoside hydrolase (GH) family 77. However, hyperthermophiles have unique 4-α-GTases belonging to GH family 57. These enzymes are the main amylolytic protein in hyperthermophiles, but their mode of action in maltooligosaccharide utilization is poorly understood. In the present study, we investigated the catalytic properties of 4-α-GTase from the hyperthermophile Pyrococcus sp. ST04 (PSGT) in the presence of maltooligosaccharides of various lengths. Unlike 4-α-GTases in GH family 77, GH family 57 PSGT produced maltotriose in the early stage of reaction and preferred maltose and maltotriose over glucose as the acceptor. The kinetic analysis showed that maltotriose had the lowest KM value, which increased amylose degradation activity by 18.3-fold. Structural models of PSGT based on molecular dynamic simulation revealed two aromatic amino acids interacting with the substrate at the +2 and +3 binding sites, and the mutational study demonstrated they play a critical role in maltotriose binding. These results clarify the mode of action in carbohydrate utilization and explain acceptor binding mechanism of GH57 family 4-α-GTases in hyperthermophilic archaea.

Published
2022
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4. Hydrothermal Chimney Distribution on the Endeavour Segment, Juan de Fuca Ridge

Author

David A. Clague, Julie F. Martin, Jennifer B. Paduan, David A. Butterfield, John W. Jamieson, Morgane Le Saout, David W. Caress, Hans Thomas, James F. Holden, and Deborah S. Kelley

Subjects
hydrothermal chimneys, Endeavour Ridge, AUV mapping, Geophysics. Cosmic physics, QC801-809, Geology, QE1-996.5
Abstract

Abstract The Endeavour Segment of the Juan de Fuca Ridge is well known for its abundance of hydrothermal vents and chimneys. One‐meter scale multibeam mapping data collected by an autonomous undersea vehicle revealed 572 chimneys along the central 14 km of the segment, although only 47 are named and known to be active. Hydrothermal deposits are restricted to the axial graben and the near‐rims of the graben above a seismically mapped axial magma lens. The sparse eruptive activity on the segment during the last 4,300 years has not buried inactive chimneys, as occurs at more magmatically robust mid‐ocean ridges.

Published
2020
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5. Biological iron-sulfur storage in a thioferrate-protein nanoparticle

Author

Brian J. Vaccaro, Sonya M. Clarkson, James F. Holden, Dong-Woo Lee, Chang-Hao Wu, Farris L. Poole II, Julien J. H. Cotelesage, Mark J. Hackett, Sahel Mohebbi, Jingchuan Sun, Huilin Li, Michael K. Johnson, Graham N. George, and Michael W. W. Adams

Subjects
Science
Abstract

The biosynthesis of iron-sulfur clusters in anaerobic organisms has not been extensively investigated. Here, the authors identify and characterize a multi-subunit protein that stores iron and sulfur in thioferrate for the assembly of the clusters inPyrococcus furiosus.

Published
2017
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6. Reduction and Morphological Transformation of Synthetic Nanophase Iron Oxide Minerals by Hyperthermophilic Archaea

Author

Srishti Kashyap, Elizabeth C. Sklute, M. Darby Dyar, and James F. Holden

Subjects
hyperthermophile, archaea, iron oxide, magnetite, nanophase, Microbiology, QR1-502
Abstract

Fe(III) (oxyhydr)oxides are electron acceptors for some hyperthermophilic archaea in mildly reducing geothermal environments. However, the kinds of iron oxides that can be used, growth rates, extent of iron reduction, and the morphological changes that occur to minerals are poorly understood. The hyperthermophilic iron-reducing crenarchaea Pyrodictium delaneyi and Pyrobaculum islandicum were grown separately on six different synthetic nanophase Fe(III) (oxyhydr)oxides. For both organisms, growth on ferrihydrite produced the highest growth rates and the largest amounts of Fe(II), although P. delaneyi produced four times more Fe(II) (25 mM) than P. islandicum (6 mM). Both organisms grew on lepidocrocite and akaganéite and produced 2 and 3 mM Fe(II). Modest growth occurred for both organisms on goethite, hematite, and maghemite where ≤1 mM Fe(II) was produced. The diameters of the spherical mineral end-products following P. delaneyi growth increased by 30 nm for ferrihydrite and 50–150 nm for lepidocrocite relative to heated abiotic controls. For akaganéite, spherical particle sizes were the same for P. delaneyi-reacted samples and heated abiotic controls, but the spherical particles were more numerous in the P. delaneyi samples. For P. islandicum, there was no increase in grain size for the mineral end-products following growth on ferrihydrite, lepidocrocite, or akaganéite relative to the heated abiotic controls. High-resolution transmission electron microscopy of lattice fringes and selected-area electron diffraction of the minerals produced by both organisms when grown on ferrihydrite showed that magnetite and/or possibly maghemite were the end-products while the heated abiotic controls only contained ferrihydrite. These results expand the current view of bioavailable Fe(III) (oxyhydr)oxides for reduction by hyperthermophilic archaea when presented as synthetic nanophase minerals. They show that growth and reduction rates are inversely correlated with the iron (oxyhydr)oxide crystallinity and that iron (oxyhydr)oxide mineral transformation takes different forms for these two organisms.

Published
2018
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7. FCC Physics Opportunities

Author

A. Abada, M. Abbrescia, S. S. AbdusSalam, I. Abdyukhanov, J. Abelleira Fernandez, A. Abramov, M. Aburaia, A. O. Acar, P. R. Adzic, P. Agrawal, J. A. Aguilar-Saavedra, J. J. Aguilera-Verdugo, M. Aiba, I. Aichinger, G. Aielli, A. Akay, A. Akhundov, H. Aksakal, J. L. Albacete, S. Albergo, A. Alekou, M. Aleksa, R. Aleksan, R. M. Alemany Fernandez, Y. Alexahin, R. G. Alía, S. Alioli, N. Alipour Tehrani, B. C. Allanach, P. P. Allport, M. Altınlı, W. Altmannshofer, G. Ambrosio, D. Amorim, O. Amstutz, L. Anderlini, A. Andreazza, M. Andreini, A. Andriatis, C. Andris, A. Andronic, M. Angelucci, F. Antinori, S. A. Antipov, M. Antonelli, M. Antonello, P. Antonioli, S. Antusch, F. Anulli, L. Apolinário, G. Apollinari, A. Apollonio, D. Appelö, R. B. Appleby, Ara. Apyan, Arm. Apyan, A. Arbey, A. Arbuzov, G. Arduini, V. Arı, S. Arias, N. Armesto, R. Arnaldi, S. A. Arsenyev, M. Arzeo, S. Asai, E. Aslanides, R. W. Aßmann, D. Astapovych, M. Atanasov, S. Atieh, D. Attié, B. Auchmann, A. Audurier, S. Aull, S. Aumon, S. Aune, F. Avino, G. Avrillaud, G. Aydın, A. Azatov, G. Azuelos, P. Azzi, O. Azzolini, P. Azzurri, N. Bacchetta, E. Bacchiocchi, H. Bachacou, Y. W. Baek, V. Baglin, Y. Bai, S. Baird, M. J. Baker, M. J. Baldwin, A. H. Ball, A. Ballarino, S. Banerjee, D. P. Barber, D. Barducci, P. Barjhoux, D. Barna, G. G. Barnaföldi, M. J. Barnes, A. Barr, J. Barranco García, J. Barreiro Guimarães da Costa, W. Bartmann, V. Baryshevsky, E. Barzi, S. A. Bass, A. Bastianin, B. Baudouy, F. Bauer, M. Bauer, T. Baumgartner, I. Bautista-Guzmán, C. Bayındır, F. Beaudette, F. Bedeschi, M. Béguin, I. Bellafont, L. Bellagamba, N. Bellegarde, E. Belli, E. Bellingeri, F. Bellini, G. Bellomo, S. Belomestnykh, G. Bencivenni, M. Benedikt, G. Bernardi, J. Bernardi, C. Bernet, J. M. Bernhardt, C. Bernini, C. Berriaud, A. Bertarelli, S. Bertolucci, M. I. Besana, M. Besançon, O. Beznosov, P. Bhat, C. Bhat, M. E. Biagini, J.-L. Biarrotte, A. Bibet Chevalier, E. R. Bielert, M. Biglietti, G. M. Bilei, B. Bilki, C. Biscari, F. Bishara, O. R. Blanco-García, F. R. Blánquez, F. Blekman, A. Blondel, J. Blümlein, T. Boccali, R. Boels, S. A. Bogacz, A. Bogomyagkov, O. Boine-Frankenheim, M. J. Boland, S. Bologna, O. Bolukbasi, M. Bomben, S. Bondarenko, M. Bonvini, E. Boos, B. Bordini, F. Bordry, G. Borghello, L. Borgonovi, S. Borowka, D. Bortoletto, D. Boscherini, M. Boscolo, S. Boselli, R. R. Bosley, F. Bossu, C. Botta, L. Bottura, R. Boughezal, D. Boutin, G. Bovone, I. Božović Jelisavc̆ić, A. Bozbey, C. Bozzi, D. Bozzini, V. Braccini, S. Braibant-Giacomelli, J. Bramante, P. Braun-Munzinger, J. A. Briffa, D. Britzger, S. J. Brodsky, J. J. Brooke, R. Bruce, P. Brückman De Renstrom, E. Bruna, O. Brüning, O. Brunner, K. Brunner, P. Bruzzone, X. Buffat, E. Bulyak, F. Burkart, H. Burkhardt, J.-P. Burnet, F. Butin, D. Buttazzo, A. Butterworth, M. Caccia, Y. Cai, B. Caiffi, V. Cairo, O. Cakir, R. Calaga, S. Calatroni, G. Calderini, G. Calderola, A. Caliskan, D. Calvet, M. Calviani, J. M. Camalich, P. Camarri, M. Campanelli, T. Camporesi, A. C. Canbay, A. Canepa, E. Cantergiani, D. Cantore-Cavalli, M. Capeans, R. Cardarelli, U. Cardella, A. Cardini, C. M. Carloni Calame, F. Carra, S. Carra, A. Carvalho, S. Casalbuoni, J. Casas, M. Cascella, P. Castelnovo, G. Castorina, G. Catalano, V. Cavasinni, E. Cazzato, E. Cennini, A. Cerri, F. Cerutti, J. Cervantes, I. Chaikovska, J. Chakrabortty, M. Chala, M. Chamizo-Llatas, H. Chanal, D. Chanal, S. Chance, A. Chancé, P. Charitos, J. Charles, T. K. Charles, S. Chattopadhyay, R. Chehab, S. V. Chekanov, N. Chen, A. Chernoded, V. Chetvertkova, L. Chevalier, G. Chiarelli, G. Chiarello, M. Chiesa, P. Chiggiato, J. T. Childers, A. Chmielińska, A. Cholakian, P. Chomaz, M. Chorowski, W. Chou, M. Chrzaszcz, E. Chyhyrynets, G. Cibinetto, A. K. Ciftci, R. Ciftci, R. Cimino, M. Ciuchini, P. J. Clark, Y. Coadou, M. Cobal, A. Coccaro, J. Cogan, E. Cogneras, F. Collamati, C. Colldelram, P. Collier, J. Collot, R. Contino, F. Conventi, C. T. A. Cook, L. Cooley, G. Corcella, A. S. Cornell, G. H. Corral, H. Correia-Rodrigues, F. Costanza, P. Costa Pinto, F. Couderc, J. Coupard, N. Craig, I. Crespo Garrido, A. Crivellin, J. F. Croteau, M. Crouch, E. Cruz Alaniz, B. Curé, J. Curti, D. Curtin, M. Czech, C. Dachauer, R. T. D’Agnolo, M. Daibo, A. Dainese, B. Dalena, A. Daljevec, W. Dallapiazza, L. D’Aloia Schwartzentruber, M. Dam, G. D’Ambrosio, S. P. Das, S. DasBakshi, W. da Silva, G. G. da Silveira, V. D’Auria, S. D’Auria, A. David, T. Davidek, A. Deandrea, J. de Blas, C. J. Debono, S. De Curtis, N. De Filippis, D. de Florian, S. Deghaye, S. J. de Jong, C. Del Bo, V. Del Duca, D. Delikaris, F. Deliot, A. Dell’Acqua, L. Delle Rose, M. Delmastro, E. De Lucia, M. Demarteau, D. Denegri, L. Deniau, D. Denisov, H. Denizli, A. Denner, D. d’Enterria, G. de Rijk, A. De Roeck, F. Derue, O. Deschamps, S. Descotes-Genon, P. S. B. Dev, J. B. de Vivie de Régie, R. K. Dewanjee, A. Di Ciaccio, A. Di Cicco, B. M. Dillon, B. Di Micco, P. Di Nezza, S. Di Vita, A. Doblhammer, A. Dominjon, M. D’Onofrio, F. Dordei, A. Drago, P. Draper, Z. Drasal, M. Drewes, L. Duarte, I. Dubovyk, P. Duda, A. Dudarev, L. Dudko, D. Duellmann, M. Dünser, T. du Pree, M. Durante, H. Duran Yildiz, S. Dutta, F. Duval, J. M. Duval, Ya. Dydyshka, B. Dziewit, S. Eisenhardt, M. Eisterer, T. Ekelof, D. El Khechen, S. A. Ellis, J. Ellis, J. A. Ellison, K. Elsener, M. Elsing, Y. Enari, C. Englert, H. Eriksson, K. J. Eskola, L. S. Esposito, O. Etisken, E. Etzion, P. Fabbricatore, A. Falkowski, A. Falou, J. Faltova, J. Fan, L. Fanò, A. Farilla, R. Farinelli, S. Farinon, D. A. Faroughy, S. D. Fartoukh, A. Faus-Golfe, W. J. Fawcett, G. Felici, L. Felsberger, C. Ferdeghini, A. M. Fernandez Navarro, A. Fernández-Téllez, J. Ferradas Troitino, G. Ferrara, R. Ferrari, L. Ferreira, P. Ferreira da Silva, G. Ferrera, F. Ferro, M. Fiascaris, S. Fiorendi, C. Fiorio, O. Fischer, E. Fischer, W. Flieger, M. Florio, D. Fonnesu, E. Fontanesi, N. Foppiani, K. Foraz, D. Forkel-Wirth, S. Forte, M. Fouaidy, D. Fournier, T. Fowler, J. Fox, P. Francavilla, R. Franceschini, S. Franchino, E. Franco, A. Freitas, B. Fuks, K. Furukawa, S. V. Furuseth, E. Gabrielli, A. Gaddi, M. Galanti, E. Gallo, S. Ganjour, Jia. Gao, Jie. Gao, V. Garcia Diaz, M. García Pérez, L. García Tabarés, C. Garion, M. V. Garzelli, I. Garzia, S. M. Gascon-Shotkin, G. Gaudio, P. Gay, S.-F. Ge, T. Gehrmann, M. H. Genest, R. Gerard, F. Gerigk, H. Gerwig, P. Giacomelli, S. Giagu, E. Gianfelice-Wendt, F. Gianotti, F. Giffoni, S. S. Gilardoni, M. Gil Costa, M. Giovannetti, M. Giovannozzi, P. Giubellino, G. F. Giudice, A. Giunta, L. K. Gladilin, S. Glukhov, J. Gluza, G. Gobbi, B. Goddard, F. Goertz, T. Golling, D. Gonçalves, V. P. Goncalves, R. Gonçalo, L. A. Gonzalez Gomez, S. Gorgi Zadeh, G. Gorine, E. Gorini, S. A. Gourlay, L. Gouskos, F. Grancagnolo, A. Grassellino, A. Grau, E. Graverini, H. M. Gray, Ma. Greco, Mi. Greco, J.-L. Grenard, O. Grimm, C. Grojean, V. A. Gromov, J. F. Grosse-Oetringhaus, A. Grudiev, K. Grzanka, J. Gu, D. Guadagnoli, V. Guidi, S. Guiducci, G. Guillermo Canton, Y. O. Günaydin, R. Gupta, R. S. Gupta, J. Gutierrez, J. Gutleber, C. Guyot, V. Guzey, C. Gwenlan, Ch. Haberstroh, B. Hacışahinoğlu, B. Haerer, K. Hahn, T. Hahn, A. Hammad, C. Han, M. Hance, A. Hannah, P. C. Harris, C. Hati, S. Haug, J. Hauptman, V. Haurylavets, H-J. He, A. Hegglin, B. Hegner, K. Heinemann, S. Heinemeyer, C. Helsens, Ana. Henriques, And. Henriques, P. Hernandez, R. J. Hernández-Pinto, J. Hernandez-Sanchez, T. Herzig, I. Hiekkanen, W. Hillert, T. Hoehn, M. Hofer, W. Höfle, F. Holdener, S. Holleis, B. Holzer, D. K. Hong, C. G. Honorato, S. C. Hopkins, J. Hrdinka, F. Hug, B. Humann, H. Humer, T. Hurth, A. Hutton, G. Iacobucci, N. Ibarrola, L. Iconomidou-Fayard, K. Ilyina-Brunner, J. Incandela, A. Infantino, V. Ippolito, M. Ishino, R. Islam, H. Ita, A. Ivanovs, S. Iwamoto, A. Iyer, S. Izquierdo Bermudez, S. Jadach, D. O. Jamin, P. Janot, P. Jarry, A. Jeff, P. Jenny, E. Jensen, M. Jensen, X. Jiang, J. M. Jiménez, M. A. Jones, O. R. Jones, J. M. Jowett, S. Jung, W. Kaabi, M. Kado, K. Kahle, L. Kalinovskaya, J. Kalinowski, J. F. Kamenik, K. Kannike, S. O. Kara, H. Karadeniz, V. Karaventzas, I. Karpov, S. Kartal, A. Karyukhin, V. Kashikhin, J. Katharina Behr, U. Kaya, J. Keintzel, P. A. Keinz, K. Keppel, R. Kersevan, K. Kershaw, H. Khanpour, S. Khatibi, M. Khatiri Yanehsari, V. V. Khoze, J. Kieseler, A. Kilic, A. Kilpinen, Y.-K. Kim, D. W. Kim, U. Klein, M. Klein, F. Kling, N. Klinkenberg, S. Klöppel, M. Klute, V. I. Klyukhin, M. Knecht, B. Kniehl, F. Kocak, C. Koeberl, A. M. Kolano, A. Kollegger, K. Kołodziej, A. A. Kolomiets, J. Komppula, I. Koop, P. Koppenburg, M. Koratzinos, M. Kordiaczyńska, M. Korjik, O. Kortner, P. Kostka, W. Kotlarski, C. Kotnig, T. Köttig, A. V. Kotwal, A. D. Kovalenko, S. Kowalski, J. Kozaczuk, G. A. Kozlov, S. S. Kozub, A. M. Krainer, T. Kramer, M. Krämer, M. Krammer, A. A. Krasnov, F. Krauss, K. Kravalis, L. Kretzschmar, R. M. Kriske, H. Kritscher, P. Krkotic, H. Kroha, M. Kucharczyk, S. Kuday, A. Kuendig, G. Kuhlmann, A. Kulesza, Mi. Kumar, Mu. Kumar, A. Kusina, S. Kuttimalai, M. Kuze, T. Kwon, F. Lackner, M. Lackner, E. La Francesca, M. Laine, G. Lamanna, S. La Mendola, E. Lançon, G. Landsberg, P. Langacker, C. Lange, A. Langner, A. J. Lankford, J. P. Lansberg, T. Lari, P. J. Laycock, P. Lebrun, A. Lechner, K. Lee, S. Lee, R. Lee, T. Lefevre, P. Le Guen, T. Lehtinen, S. B. Leith, P. Lenzi, E. Leogrande, C. Leonidopoulos, I. Leon-Monzon, G. Lerner, O. Leroy, T. Lesiak, P. Lévai, A. Leveratto, E. Levichev, G. Li, S. Li, R. Li, D. Liberati, M. Liepe, D. A. Lissauer, Z. Liu, A. Lobko, E. Locci, E. Logothetis Agaliotis, M. P. Lombardo, A. J. Long, C. Lorin, R. Losito, A. Louzguiti, I. Low, D. Lucchesi, M. T. Lucchini, A. Luciani, M. Lueckhof, A. J. G. Lunt, M. Luzum, D. A. Lyubimtsev, M. Maggiora, N. Magnin, M. A. Mahmoud, F. Mahmoudi, J. Maitre, V. Makarenko, A. Malagoli, J. Malclés, L. Malgeri, P. J. Mallon, F. Maltoni, S. Malvezzi, O. B. Malyshev, G. Mancinelli, P. Mandrik, P. Manfrinetti, M. Mangano, P. Manil, M. Mannelli, G. Marchiori, F. Marhauser, V. Mariani, V. Marinozzi, S. Mariotto, P. Marquard, C. Marquet, T. Marriott-Dodington, R. Martin, O. Martin, J. Martin Camalich, T. Martinez, H. Martinez Bruzual, M. I. Martínez-Hernández, D. E. Martins, S. Marzani, D. Marzocca, L. Marzola, S. Masciocchi, I. Masina, A. Massimiliano, A. Massironi, T. Masubuchi, V. A. Matveev, M. A. Mazzoni, M. McCullough, P. A. McIntosh, P. Meade, L. Medina, A. Meier, J. Meignan, B. Mele, J. G. Mendes Saraiva, F. Menez, M. Mentink, E. Meoni, P. Meridiani, M. Merk, P. Mermod, V. Mertens, L. Mether, E. Métral, M. Migliorati, A. Milanese, C. Milardi, G. Milhano, B. L. Militsyn, F. Millet, I. Minashvili, J. V. Minervini, L. S. Miralles, D. Mirarchi, S. Mishima, D. P. Missiaen, G. Mitselmakher, T. Mitsuhashi, J. Mnich, M. Mohammadi Najafabadi, R. N. Mohapatra, N. Mokhov, J. G. Molson, R. Monge, C. Montag, G. Montagna, S. Monteil, G. Montenero, E. Montesinos, F. Moortgat, N. Morange, G. Morello, M. Moreno Llácer, M. Moretti, S. Moretti, A. K. Morley, A. Moros, I. Morozov, V. Morretta, M. Morrone, A. Mostacci, S. Muanza, N. Muchnoi, M. Mühlegger, M. Mulder, M. Mulders, B. Müller, F. Müller, A.-S. Müller, J. Munilla, M. J. Murray, Y. Muttoni, S. Myers, M. Mylona, J. Nachtman, T. Nakamoto, M. Nardecchia, G. Nardini, P. Nason, Z. Nergiz, A. V. Nesterenko, A. Nettsträter, C. Neubüser, J. Neundorf, F. Niccoli, O. Nicrosini, Y. Nie, U. Niedermayer, J. Niedziela, A. Niemi, S. A. Nikitin, A. Nisati, J. M. No, M. Nonis, Y. Nosochkov, M. Novák, A. Novokhatski, J. M. O’Callaghan, C. Ochando, S. Ogur, K. Ohmi, K. Oide, V. A. Okorokov, Y. Okumura, C. Oleari, F. I. Olness, Y. Onel, M. Ortino, J. Osborne, P. Osland, T. Otto, K. Y. Oyulmaz, A. Ozansoy, V. Özcan, K. Özdemir, C. E. Pagliarone, H. F. Pais da Silva, E. Palmieri, L. Palumbo, A. Pampaloni, R.-Q. Pan, M. Panareo, O. Panella, G. Panico, G. Panizzo, A. A. Pankov, V. Pantsyrny, C. G. Papadopoulos, A. Papaefstathiou, Y. Papaphilippou, M. A. Parker, V. Parma, M. Pasquali, S. K. Patra, R. Patterson, H. Paukkunen, F. Pauss, S. Peggs, J.-P. Penttinen, G. Peón, E. E. Perepelkin, E. Perez, J. C. Perez, G. Perez, F. Pérez, E. Perez Codina, J. Perez Morales, M. Perfilov, H. Pernegger, M. Peruzzi, C. Pes, K. Peters, S. Petracca, F. Petriello, L. Pezzotti, S. Pfeiffer, F. Piccinini, T. Pieloni, M. Pierini, H. Pikhartova, G. Pikurs, E. Pilicer, P. Piminov, C. Pira, R. Pittau, W. Płaczek, M. Plagge, T. Plehn, M.-A. Pleier, M. Płoskoń, M. Podeur, H. Podlech, T. Podzorny, L. Poggioli, A. Poiron, G. Polesello, M. Poli Lener, A. Polini, J. Polinski, S. M. Polozov, L. Ponce, M. Pont, L. Pontecorvo, T. Portaluri, K. Potamianos, C. Prasse, M. Prausa, A. Preinerstorfer, E. Premat, T. Price, M. Primavera, F. Prino, M. Prioli, J. Proudfoot, A. Provino, T. Pugnat, N. Pukhaeva, S. Puławski, D. Pulikowski, G. Punzi, M. Putti, A. Pyarelal, H. Quack, M. Quispe, A. Racioppi, H. Rafique, V. Raginel, M. Raidal, N. S. Ramírez-Uribe, M. J. Ramsey-Musolf, R. Rata, P. Ratoff, F. Ravotti, P. Rebello Teles, M. Reboud, S. Redaelli, E. Renner, A. E. Rentería-Olivo, M. Rescigno, J. Reuter, A. Ribon, A. M. Ricci, W. Riegler, S. Riemann, B. Riemann, T. Riemann, J. M. Rifflet, R. A. Rimmer, R. Rinaldesi, L. Rinolfi, O. Rios Rubiras, T. Risselada, A. Rivetti, L. Rivkin, T. Rizzo, T. Robens, F. Robert, A. J. Robson, E. Rochepault, C. Roda, G. Rodrigo, M. Rodríguez-Cahuantzi, C. Rogan, M. Roig, S. Rojas-Torres, J. Rojo, G. Rolandi, G. Rolando, P. Roloff, A. Romanenko, A. Romanov, F. Roncarolo, A. Rosado Sanchez, G. Rosaz, L. Rossi, A. Rossi, R. Rossmanith, B. Rousset, C. Royon, X. Ruan, I. Ruehl, V. Ruhlmann-Kleider, R. Ruiz, L. Rumyantsev, R. Ruprecht, A. I. Ryazanov, A. Saba, R. Sadykov, D. Saez de Jauregui, M. Sahin, B. Sailer, M. Saito, F. Sala, G. P. Salam, J. Salfeld-Nebgen, C. A. Salgado, S. Salini, J. M. Sallese, T. Salmi, A. Salzburger, O. A. Sampayo, S. Sanfilippo, J. Santiago, E. Santopinto, R. Santoro, A. Sanz Ull, X. Sarasola, I. H. Sarpün, M. Sauvain, S. Savelyeva, R. Sawada, G. F. R. Sborlini, A. Schaffer, M. Schaumann, M. Schenk, C. Scheuerlein, I. Schienbein, K. Schlenga, H. Schmickler, R. Schmidt, D. Schoerling, A. Schoning, T. Schörner-Sadenius, M. Schott, D. Schulte, P. Schwaller, C. Schwanenberger, P. Schwemling, N. Schwerg, L. Scibile, A. Sciuto, E. Scomparin, C. Sebastiani, B. Seeber, M. Segreti, P. Selva, M. Selvaggi, C. Senatore, A. Senol, L. Serin, M. Serluca, N. Serra, A. Seryi, L. Sestini, A. Sfyrla, M. Shaposhnikov, E. Shaposhnikova, B. Yu. Sharkov, D. Shatilov, J. Shelton, V. Shiltsev, I. P. Shipsey, G. D. Shirkov, A. Shivaji, D. Shwartz, T. Sian, S. Sidorov, A. Siemko, L. Silvestrini, N. Simand, F. Simon, B. K. Singh, A. Siódmok, Y. Sirois, E. Sirtori, R. Sirvinskaite, B. Sitar, T. Sjöstrand, P. Skands, E. Skordis, K. Skovpen, M. Skrzypek, E. Slade, P. Slavich, R. Slovak, V. Smaluk, V. Smirnov, W. Snoeys, L. Soffi, P. Sollander, O. Solovyanov, H. K. Soltveit, H. Song, P. Sopicki, M. Sorbi, L. Spallino, M. Spannowsky, B. Spataro, P. Sphicas, H. Spiesberger, P. Spiller, M. Spira, T. Srivastava, J. Stachel, A. Stakia, J. L. Stanyard, E. Starchenko, A. Yu. Starikov, A. M. Staśto, M. Statera, R. Steerenberg, J. Steggemann, A. Stenvall, F. Stivanello, D. Stöckinger, L. S. Stoel, M. Stöger-Pollach, B. Strauss, M. Stuart, G. Stupakov, S. Su, A. Sublet, K. Sugita, L. Sulak, M. K. Sullivan, S. Sultansoy, T. Sumida, K. Suzuki, G. Sylva, M. J. Syphers, A. Sznajder, M. Taborelli, N. A. Tahir, E. Tal Hod, M. Takeuchi, C. Tambasco, J. Tanaka, K. Tang, I. Tapan, S. Taroni, G. F. Tartarelli, G. Tassielli, L. Tavian, T. M. Taylor, G. N. Taylor, A. M. Teixeira, G. Tejeda-Muñoz, V. I. Telnov, R. Tenchini, H. H. J. ten Kate, K. Terashi, A. Tesi, M. Testa, C. Tetrel, D. Teytelman, J. Thaler, A. Thamm, S. Thomas, M. T. Tiirakari, V. Tikhomirov, D. Tikhonov, H. Timko, V. Tisserand, L. M. Tkachenko, J. Tkaczuk, J. Ph. Tock, B. Todd, E. Todesco, R. Tomás Garcia, D. Tommasini, G. Tonelli, F. Toral, T. Torims, R. Torre, Z. Townsend, R. Trant, D. Treille, L. Trentadue, A. Tricoli, A. Tricomi, W. Trischuk, I. S. Tropin, B. Tuchming, A. A. Tudora, B. Turbiarz, I. Turk Cakir, M. Turri, T. Tydecks, J. Usovitsch, J. Uythoven, R. Vaglio, A. Valassi, F. Valchkova, M. A. Valdivia Garcia, P. Valente, R. U. Valente, A.-M. Valente-Feliciano, G. Valentino, L. Vale Silva, J. M. Valet, R. Valizadeh, J. W. F. Valle, S. Vallecorsa, G. Vallone, M. van Leeuwen, U. H. van Rienen, L. van Riesen-Haupt, M. Varasteh, L. Vecchi, P. Vedrine, G. Velev, R. Veness, A. Ventura, W. Venturini Delsolaro, M. Verducci, C. B. Verhaaren, C. Vernieri, A. P. Verweij, O. Verwilligen, O. Viazlo, A. Vicini, G. Viehhauser, N. Vignaroli, M. Vignolo, A. Vitrano, I. Vivarelli, S. Vlachos, M. Vogel, D. M. Vogt, V. Völkl, P. Volkov, G. Volpini, J. von Ahnen, G. Vorotnikov, G. G. Voutsinas, V. Vysotsky, U. Wagner, R. Wallny, L.-T. Wang, R. Wang, K. Wang, B. F. L. Ward, T. P. Watson, N. K. Watson, Z. Wa̧s, C. Weiland, S. Weinzierl, C. P. Welsch, J. Wenninger, M. Widorski, U. A. Wiedemann, H.-U. Wienands, G. Wilkinson, P. H. Williams, A. Winter, A. Wohlfahrt, T. Wojtoń, D. Wollmann, J. Womersley, D. Woog, X. Wu, A. Wulzer, M. K. Yanehsari, G. Yang, H. J. Yang, W.-M. Yao, E. Yazgan, V. Yermolchik, Ay. Yilmaz, Al. Yilmaz, H.-D. Yoo, S. A. Yost, T. You, C. Young, T.-T. Yu, F. Yu, A. Zaborowska, S. G. Zadeh, M. Zahnd, M. Zanetti, L. Zanotto, L. Zawiejski, P. Zeiler, M. Zerlauth, S. M. Zernov, G. Zevi Dell Porta, Z. Zhang, Y. Zhang, C. Zhang, H. Zhang, Z. Zhao, Y.-M. Zhong, J. Zhou, D. Zhou, P. Zhuang, G. Zick, F. Zimmermann, J. Zinn-Justin, L. Zivkovic, A. V. Zlobin, M. Zobov, J. Zupan, J. Zurita, and The FCC Collaboration

Subjects
Astrophysics, QB460-466, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798
Abstract

Abstract We review the physics opportunities of the Future Circular Collider, covering its e+e-, pp, ep and heavy ion programmes. We describe the measurement capabilities of each FCC component, addressing the study of electroweak, Higgs and strong interactions, the top quark and flavour, as well as phenomena beyond the Standard Model. We highlight the synergy and complementarity of the different colliders, which will contribute to a uniquely coherent and ambitious research programme, providing an unmatchable combination of precision and sensitivity to new physics.

Published
2019
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8. Complete Genome Sequence of the Hyperthermophilic Archaeon Thermococcus sp. Strain CL1, Isolated from a Paralvinella sp. Polychaete Worm Collected from a Hydrothermal Vent.

Author

Jong-Hyun Jung, James F. Holden, Dong-Ho Seo, Kwan-Hwa Park, Hakdong Shin, Sangryeol Ryu, Ju-Hoon Lee, and Cheon-Seok Park

Subjects
*POLYCHAETA, *GENOMES, *AMINO acids, *BIOSYNTHESIS, *HABITATS
Abstract

Thermococcus sp. strain CL1 is a hyperthermophilic, anaerobic, and heterotrophic archaeon isolated from a Paralvinella sp. polychaete worm living on an active deep-sea hydrothermal sulfide chimney on the Cleft Segment of the Juan de Fuca Ridge. To further understand the distinct characteristics of this archaeon at the genome level, its genome was completely sequenced and analyzed. Here, we announce the complete genome sequence (1,950,313 bp) of Thermococcus sp. strain CL1, with a focus on H2- and energy-producing capabilities and its amino acid biosynthesis and acquisition in an extreme habitat. [ABSTRACT FROM AUTHOR]

Published
2012
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9. Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents

Author

Begüm D. Topçuoğlu, Lucy C. Stewart, Hilary G Morrison, David A. Butterfield, Julie A Huber, and James F. Holden

Subjects
Hydrogen, Hydrothermal Vents, Methanococcales, Thermococcales, methanogenesis, syntrophy, Microbiology, QR1-502
Abstract

Thermophilic methanogens are common autotrophs at hydrothermal vents, but their growth constraints and dependence on H2 syntrophy in situ are poorly understood. Between 2012 and 2015, methanogens and H2-producing heterotrophs were detected by growth at 80°C and 55°C at most diffuse (7-40°C) hydrothermal vent sites at Axial Seamount. Microcosm incubations of diffuse hydrothermal fluids at 80°C and 55°C demonstrated that growth of thermophilic and hyperthermophilic methanogens is primarily limited by H2 availability. Amendment of microcosms with NH4+ generally had no effect on CH4 production. However, annual variations in abundance and CH4 production were observed in relation to the eruption cycle of the seamount. Microcosm incubations of hydrothermal fluids at 80°C and 55°C supplemented with tryptone and no added H2 showed CH4 production indicating the capacity in situ for methanogenic H2 syntrophy. 16S rRNA genes were found in 80°C microcosms from H2-producing archaea and H2-consuming methanogens, but not for any bacteria. In 55°C microcosms, sequences were found from the H2-producing bacteria and H2-consuming methanogens and sulfate-reducing bacteria. A co-culture of representative organisms showed that Thermococcus paralvinellae supported the syntrophic growth of Methanocaldococcus bathoardescens at 82°C and Methanothermococcus sp. strain BW11 at 60°C. The results demonstrate that modeling of subseafloor methanogenesis should focus primarily on H2 availability and temperature, and that thermophilic H2 syntrophy can support methanogenesis within natural microbial assemblages and may be an important energy source for thermophilic autotrophs in marine geothermal environments.

Published
2016
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10. Hydrogen production and enzyme activities in the hyperthermophile Thermococcus paralvinellae grown on maltose, tryptone and agricultural waste

Author

Sarah A. Hensley, Emily eMoreira, and James F. Holden

Subjects
Archaea, Hydrogenase, Hydrothermal Vents, Physiology, Thermococcus, bioenergy, Microbiology, QR1-502
Abstract

Thermococcus may be an important alternative source of H2 in the hot subseafloor in otherwise low H2 environments such as some hydrothermal vents and oil reservoirs. It may also be useful in industry for rapid agricultural waste treatment and concomitant H2 production. Thermococcus paralvinellae grown at 82°C without sulfur produced up to 5 mmol of H2 L-1 at rates of 5-36 fmol H2 cell-1 h-1 on 0.5% (wt vol-1) maltose, 0.5% (wt vol-1) tryptone, and 0.5% maltose + 0.05% tryptone media. Two potentially inhibiting conditions, the presence of 10 mM acetate and low pH (pH 5) in maltose-only medium, did not significantly affect growth or H2 production. Growth rates, H2 production rates, and cell yields based on H2 production were the same as those for Pyrococcus furiosus grown at 95°C on the same media for comparison. Acetate, butyrate, succinate, isovalerate and formate were also detected as end products. After 100 h, T. paralvinellae produced up to 5 mmol of H2 L-1 of medium when grown on up to 70% (vol vol-1) waste milk from cows undergoing treatment for mastitis with the bacterial antibiotic Ceftiofur and from untreated cows. The amount of H2 produced by T. paralvinellae increased with increasing waste concentrations, but decreased in P. furiosus cultures supplemented with waste milk above 1% concentration. All mesophilic bacteria from the waste milk that grew on Luria Bertani, Sheep’s Blood (selective for Staphylococcus, the typical cause of mastitis), and MacConkey (selective for Gram-negative enteric bacteria) agar plates were killed by heat during incubation at 82°C. Ceftiofur, which is heat labile, was below the detection limit following incubation at 82°C. T. paralvinellae also produced up to 6 mmol of H2 L-1 of medium when grown on 0.1-10% (wt vol-1) spent brewery grain while P. furiosus produced < 1 mmol of H2 L-1. Twelve of 13 enzyme activities in T. paralvinellae showed significant (p

Published
2016
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11. Introduction to the Special Issue: From RIDGE to Ridge 2000

Author

Daniel J. Fornari, Stace E. Beaulieu, James F. Holden, Lauren S. Mullineaux, and Maya Tolstoy

Subjects
Ridge 2000, mid-ocean ridges, spreading centers, Integrated Study Sites, Oceanography, GC1-1581
Abstract

Articles in this special issue of Oceanography represent a compendium of research that spans the disciplinary and thematic breadth of the National Science Foundation's Ridge 2000 Program, as well as its geographic focal points. The mid-ocean ridge (MOR) crest is where much of Earth's volcanism is focused and where most submarine volcanic activity occurs. If we could look down from space at our planet with the ocean drained, the MOR's topography and shape, along with its intervening fracture zones, would resemble the seams on a baseball, with the ocean basins dominating our planetary panorama. The volcanic seafloor is hidden beneath the green-blue waters of the world's ocean, yet therein lie fundamental clues to how our planet works and has evolved over billions of years, something that was not clearly understood 65 years ago—witness the following quote from H.H. Hess (1962) in his essay on "geopoetry" and commentary on J.H.F. Umbgrove's (1947) comprehensive summary of Earth and ocean history: The birth of the oceans is a matter of conjecture, the subsequent history is obscure, and the present structure is just beginning to be understood. Fascinating speculation on these subjects has been plentiful, but not much of it predating the last decade [the 1950s] holds water.

Published
2012

12. Biogeochemical Processes at Hydrothermal Vents: Microbes and Minerals, Bioenergetics, and Carbon Fluxes

Author

James F. Holden, John A. Breier, Karyn L. Rogers, Mitchell D. Schulte, and Brandy M. Toner

Subjects
Ridge 2000, mid-ocean ridges, spreading centers, hydrothermal vents, extreme environment, global geochemical cycles, Oceanography, GC1-1581
Abstract

Hydrothermal vents are among the most biologically active regions of the deep ocean. However, our understanding of the limits of life in this extreme environment, the extent of biogeochemical transformation that occurs in the crust and overlying ocean, and the impact of vent life on regional and global ocean chemistry is in its infancy. Recently, scientific studies have expanded our view of how vent microbes gain metabolic energy at vents through their use of dissolved chemicals and minerals contained in ocean basalts, seafloor sulfide deposits, and hydrothermal plumes and, in turn, how they catalyze chemical and mineral transformations. The scale of vent environments and the difficulties inherent in the study of life above, on, and below the deep seafloor have led to the development of geochemical and bioenergetic models. These models predict habitability and biological activity based on the chemical composition of hydrothermal fluids, seawater, and the surrounding rock, balanced by the physiological energy demand of cells. This modeling, coupled with field sampling for ground truth and discovery, has led to a better understanding of how hydrothermal vents affect the ocean and global geochemical cycles, and how they influence our views of life on the early Earth and the search for life beyond our own planet.

Published
2012

13. On the Potential for Bioenergy and Biofuels from Hydrothermal Vent Microbes

Author

Peter R. Girguis and James F. Holden

Subjects
Ridge 2000, mid-ocean ridges, spreading centers, biofuels, Oceanography, GC1-1581
Abstract

The discovery of deep-sea hydrothermal vents caused scientists to reconsider their notions about life in the deep sea. In these seemingly inhospitable environments, free-living microbes, as well as microbial-animal symbioses, thrive in the warm waters around vents. The biomass per unit area in this environment is comparable to that of rainforests. Uniquely, these highly productive ecosystems are based on microbial chemoautotrophic metabolism, wherein microbes generate metabolic energy by drawing oxygen or nitrate from surrounding seawater to oxidize reduced chemicals (e.g., sulfide) found in the vent fluids (Sievert and Vetriani, 2012, in this issue). The rapid and voluminous fluid flux through hydrothermal vents replenishes these substrates at a rate sufficient to support this substantial community. The tremendous microbial productivity observed at vents raises the question as to whether these microorganisms are also well suited for bioenergy and biofuel production. Here, we discuss the utility and issues associated with two example approaches: in situ bioelectricity generation and microbially mediated large-scale biofuel production.

Published
2012

14. Endeavour Segment of the Juan de Fuca Ridge: One of the Most Remarkable Places on Earth

Author

Deborah S. Kelley, Suzanne M. Carbotte, David W. Caress, David A. Clague, John R. Delaney, James B. Gill, Hunter Hadaway, James F. Holden, Emilie E.E. Hooft, Jonathan P. Kellogg, Marvin D. Lilley, Mark Stoermer, Doug Toomey, Robert Weekly, and William S.D. Wilcock

Subjects
Ridge 2000, mid-ocean ridges, spreading centers, Integrated Study Sites, Endeavour Segment, Juan de Fuca Ridge, hydrothermal vents, Oceanography, GC1-1581
Abstract

Endeavour Segment of the Juan de Fuca Ridge is one of three Integrated Study Sites for the Ridge 2000 Program. It is a remarkable, dynamic environment hosting five major hydrothermal fields, numerous smaller fields, and myriad diffuse-flow sites; magma chambers underlie all fields. Over 800 individual extinct and active chimneys have been documented within the central ~ 15 km portion of the ridge, with some edifices reaching 50 m across and up to 45 m tall. Fluid flow is focused along faults within the rift zone, and seismically active faults along the western axial valley wall have been used by both magmas and upwelling hydrothermal fluids. There is significant chemical heterogeneity in basalt compositions within the axial rift valley, with the greatest diversity occurring near the base of the western axial valley wall where normal, transitional, and enriched type mid-ocean ridge basalts occur within tens of meters of each other. Endeavour is the only site where seismic intensity has been linked directly to heat flux at the individual vent field scale. Installation of the world's first high-power and high-bandwidth cabled observatory at Endeavour via NEPTUNE Canada ensures that new discoveries along the Juan de Fuca Ridge will continue into the future.

Published
2012

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