{"id":162,"date":"2024-07-15T15:13:53","date_gmt":"2024-07-15T22:13:53","guid":{"rendered":"https:\/\/dornsife.usc.edu\/lloyd\/?page_id=162"},"modified":"2024-07-15T15:13:53","modified_gmt":"2024-07-15T22:13:53","slug":"publications","status":"publish","type":"page","link":"https:\/\/dornsife.usc.edu\/lloyd\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n\n \n \n\n\n\n\n\n\n\n
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*Students and technicians of the Lloyd lab.<\/p>\n

Buongiorno*, J., K. Sipes*, K. Wasmund, A. Loy, K. G. Lloyd. Woeseiales transcriptional response to burial in Arctic fjord surface sediment, BioRxiv, https:\/\/www.biorxiv.org\/content\/10.1101\/2020.06.04.134015v1<\/a>, In press at Plos One.<\/p>\n

Lloyd, K. G., J. T. Bird*, J. Buongiorno*, E. Deas*, R. Kevorkian*, T. Noordhoek*, J. Rosalsky*, T. Roy*. Evidence for a growth zone for deep subsurface microbial clades in near-surface anoxic sediments. BioRxiv, https:\/\/www.biorxiv.org\/content\/10.1101\/2020.03.24.005512v1<\/a>, In press at Appl. Environ. Microbiol.. Volume 86, issue 19.<\/p>\n

Murray, A.E., J. Freudenstein, S. Gribaldo, R. Hatzenpichler, P. Hugenholtz, P. K\u00e4mpfer, K. Konstantinidis, C. Lane, R. Papke, D. Parks, R. Rossell\u00f3-M\u00f3ra, M. Stott, I. Sutcliffe, J. C. Thrash, S. Venter, W. Whitman, S. Acinas, R. Amann, K. Anantharaman, J. Armengaud, B. Baker, R. Barco, H. Bode, E. Boyd, C. Brady, P. Carini, P, Chain, D. Colman, K. DeAngelis, A. de los Rios, P. Estrada-de los Santos, C. Dunlap, J. Eisen, D. Emerson, T. Ettema, D. Eveillard, P. Girguis, U. Hentschel, J. Hollibaugh, L. Hug, W. Inskeep, E. Ivanova, H.-P. Klenk, W.-J. Li, K. Lloyd, F. L\u00f6ffler, T. Makhalanyane, D. Moser, T. Nunoura, M. Palmer, V. Parro, C. Pedr\u00f3s-Ali\u00f3, A. Probst, T. Smits, A. Steen, E. Steenkamp, A. Spang, F. Stewart, J. Tiedje, P. Vandamme, M. Wagner, F. Wang, B. Hedlund, A.-L. Reysenbach. A roadmap for naming uncultivated microorganisms. 2020. Nature Microbiology. 5: 987-994.<\/p>\n

Baker, B. J., V. de Anda, K. W. Seitz, N. Dombrowski, A. E. Santoro, and K. G. Lloyd. 2020. A revolution in archaeal biology. Nature Microbiology 5: 887-900.<\/p>\n

Larowe, D., S. Arndt, J. Bradley, E. Estes, A. Hoarfrost, S. Lang, K. G. Lloyd, N. Mahmoudi, W. Orsi, S. S. Walter, A. D. Steen, R. Zhao. 2020. The fate of organic carbon in marine sediments \u2013 New insights from recent data and analysis. Earth-Science Reviews. 204: 103146.<\/p>\n

Giovannelli, D., P. Barry, J. M. de Moor, K. G. Lloyd, M. Schrenk. 2020. Microbial influences on subduction zone carbon cycling. EOS. 101.<\/p>\n

Bird*, J., E. D. Tague, L. Zinke, J. M. Schmidt, A. D. Steen, B. Reese, I. P. G. Marshall, G. Webster, A. Weightman, H. F. Castro, S. R. Campagna, and K. G. Lloyd. 2019. Uncultured microbial phyla suggest mechanisms for multi-thousand-year subsistence in Baltic Sea sediments. mBio. 10(2): e02376-18.<\/p>\n

Barry, P. H., J. M. de Moor, D. Giovannelli, M. Schrenk, D. Hummer, T. Lopez, C. A. Pratt,Y. Alp\u00edzar Segura, A. Battaglia, P. Beaudry, G. Bini, M. Cascante, G. d\u2019Errico, M. di Carlo, D. Fattorini, K. Fullerton*, E. Gazel, G. Gonz\u00e1lez, S. A. Halld\u00f3rsson, K. Iacovino, J. T. Kulongoski, E. Manini, M. Mart\u00ednez, H. Miller, M. Nakagawa, S. Ono, S. Patwardhan, C. J. Ram\u00edrez, F. Regoli, F. Smedile, S. Turner, C. Vetriani, M. Y\u00fccel, C.J. Ballentine, T. P. Fischer, D. R. Hilton, and K. G. Lloyd. 2019. Forearc carbon sink reduces long-term volatile recycling into the mantle. Nature. 568: 487-492.<\/p>\n

Buongiorno*, J., L. C. Herbert, L. M. Wehrmann, A. Michaud, K. Laufer, A. Szynkiewicz, A. Faiia, H. R\u00f8y, B. B. J\u00f8rgensen, K. M. Yeager, K. Schindler, K. G. Lloyd. 2019. Complex microbial communities drive iron and sulfur cycling in Arctic fjord sediments. Applied and Environmental Microbiology. 85(14): e00949-19.<\/p>\n

Steen, A. D., A. Crits-Christoph, P. Carini, K. M. DeAngelis, N. Fierer, K. G. Lloyd, C. Thrash. 2019. High proportions of bacteria and archaea across most biomes remain uncultured. The ISME Journal. 13: 3126-3130.<\/p>\n

Barry, P. H., M. Nakagawa, D. Giovannelli, J. M. de Moor, M. Schrenk, A. M. Seltzer, E. Manini, D. Fattorini, M. di Carlo, F. Regoli, K. Fullerton*, Lloyd, K. G. 2019. Helium, inorganic and organic carbon isotopes of fluids and gases across the Costa Rica convergent margin, Scientific Data. 6: 284.<\/p>\n

Liang, R., M. Lau, T. Vishnivetskaya, K. G. Lloyd, S. Pfiffner, E. M. Rivkina, T. C. Onstott. 2019. Predominance of anaerobic, spore-forming bacteria in metabolically active microbial communities from ancient Siberian permafrost. Applied and Environmental Microbiology. 85(15): e00560-19.<\/p>\n

Lloyd, K. G., C. Sheik, B. Garcia-Moreno, and C. Royer. 2019. The genetics, biochemistry, and biophysics of carbon cycling by deep life, in Deep Carbon: Past to Present, B. Orcutt, I. Daniel, and R. Dasgupta, Eds. Cambridge University Press.<\/p>\n

Zinke, L., C. Glombitza, J. Bird*, H. R\u00f8y, B. B. J\u00f8rgensen, K. G. Lloyd, J. Amend, and B. Reese. 2019. Microbial organic matter degradation potential in Baltic Sea sediments is influenced by depositional conditions and in situgeochemistry. Applied and Environmental Microbiology. 85:e02164-18.<\/p>\n

Zhou, Z, Liu, Y., K. G. Lloyd, J. Pan, Y. Yang, J-D Gu, M. Li. 2019. Genomic and transcriptomic insights into the ecology and metabolism of global benthic archaealcosmopolitan, Thermoprofundales (MBG-D archaea). The ISME Journal. 13: 885-901.<\/p>\n

Lloyd, K. G., A. D. Steen, J. Ladau, J. Yin, L. Crosby. 2018. Phylogenetically novel uncultured microbial cells dominate Earth microbiomes. mSystems. 3(5): e00055-18.<\/p>\n

Kevorkian*, R. T., J. T. Bird*, A. Shumaker*, K. G. Lloyd. 2018. Estimating population turnover rates by relative quantification methods reveals microbial dynamics in marine sediment. Applied and Environmental Microbiology.84(1): e01443-17.<\/p>\n

Vishnivetskaya, T. A., J. Buongiorno*, K. Krivushin, E. Spirina, V. Oshurkova, G. Wilson, K. G. Lloyd, E. M. Rivkina. 2018. Methanogens in the Antarctic Dry Valley permafrost. FEMS Microbiology Ecology 94(8): fiy109.<\/p>\n

Buongiorno*, J., S. Turner, G. Webster, M. Asai, A. Shumaker*, T. Roy*, A. Weightman, A. Schippers, K. G. Lloyd. 2017. Interlaboratory quantification of Bacteria and Archaea in deeply buried sediments of the Baltic Sea (IODP Expedition 347). FEMS Microbiology Ecology 93 (3): fix007.<\/p>\n

Zinke, L. A., M. M. Mullis, J. T. Bird*, I. P. G. Marshall, B. B. J\u00f8rgensen, K. G. Lloyd, J. P. Amend, B. K. Reese. 2017. Thriving or Surviving? Evaluating active microbial guilds in Baltic Sea sediment. Environmental Microbiology Reports. 9(5): 528-536.<\/p>\n

Lloyd, K. G. 2016. (Biogeochemical) cycling in \u201cThe Microbe Olympics\u201d. Nature Microbiology. 1(8): 16122.<\/p>\n

Bird*, J. T., B. J. Baker, A. Probst, M. Podar, K. G. Lloyd. 2016. Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales. Frontiers in Microbiology. 7: 1221.<\/p>\n

Underwood, S., L. Lapham, A. Teske. K. G. Lloyd. 2016. Microbial community structure and methane-cycling activity of subsurface sediments at Mississippi Canyon 118 before the Deepwater Horizon disaster. Deep-Sea Research II. 129: 148-156.<\/p>\n

Solden, L, K. G. Lloyd, K. Wrighton. 2016. The bright side of microbial dark matter: Lessons learned from the uncultivated majority. Current Opinion in Microbiology. 31:217-226.<\/p>\n

Buongiorno*, J., J. T. Bird*, K. G. Lloyd, T. Vishnivetskaya. 2016. Draft Genome Sequence of Antarctic Methanogen enriched from Dry Valley Permafrost. Genome Announcements. 4(6): e01362-16.<\/p>\n

Wasmund, K. C., M. Cooper, L. Schreiber, K. G. Lloyd, B. J. Baker, D. G. Petersen, B. B. J\u00f8rgensen, R. Stepanauskas, R. Reinhardt, A. Schramm, A. Loy, L. Adrian. 2016. Single-cell genome and group-specific dsrABsequencing implicate marine members of the class Dehalococcoidia (Phylum Chloroflexi) in sulfur cycling. mBio. 7:e00266-16.<\/p>\n

Teske, A., D. de Beer, L. McKay, J. Biddle, M. Tivey, D. Hoer, K. G. Lloyd, M. A. Lever, H. R\u00f8y, D. B. Albert, H. Mendlovitz, B. MacGregor. 2016. The Guaymas Basin hiking guide to hydrothermal mounds, chimneys and microbial mats: complex seafloor expressions of subsurface hydrothermal circulation. Frontiers in Microbiology. 7: 75.<\/p>\n

Dowell, F., Z. Cardman, L. J. McKay, B. MacGregor, S. E. Ruff, J. F. Biddle, S. Dasarathy, K. G. Lloyd, H. Mendlovitz, D. Albert, A. Teske. 2016. Methane-processing microbial communities in hot sediments at the base of a hydrothermal mount (Mat Mound) in Guaymas Basin. Frontiers in Microbiology. 7: 17.<\/p>\n

Lloyd, K. G. 2015. Beyond known methanogens. Science. 350: 384.<\/p>\n

Michalska, K., A. Steen, G. Chhor, M. Endres, J. Bird*, K. G. Lloyd, A. Joachimiak. 2015. Discovery of novel aminopeptidase from \u201cMicrobial Dark Matter\u201d, The FASEB Journal. 29:1-9.<\/p>\n

Lever, M. A., K. Rogers, K. G. Lloyd, J. Overmann, B. Schink, R. K. Thauer, T. M. Hoehler, B. B. J\u00f8rgensen. 2015. Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations. FEMS Microbiology Reviews. 39(5):688-728.<\/p>\n

Wasmund, K., C. Algora, J. Muller, M. Kr\u00fcger, K. G. Lloyd, R. Reinhardt, L. Adrian. 2015. Development and application of primers for the class Dehalococcoidetes (phylum Chloroflexi) enables deep insights into diversity and stratification of sub-groups in the marine subsurface. Environmental Microbiology. 17: 3540-56.<\/p>\n

Lloyd, K. G.2014 . Importance of microbial quantification in the marine subseafloor. In Microbial Life of the Deep Biosphere, Jens Kallmeyer, Ed. (DeGruyter GmbH). 1 citation.<\/p>\n

Lloyd, K. G. 2014. Quantitative methods applied to methane-cycling archaea in the marine sediments of the White Oak River estuary. In Skovhus, T.L., Caffrey, S., and Hubert, C. Molecular Methods and Applications in Microbiology (Norfolk, UK: Caister Academic Press).<\/p>\n

Orcutt, B. N., D. LaRowe, K. G. Lloyd, H. Mills, W. Orsi, B. Kiel-Reese, J. Sauvage. 2014. IODP Deep Biosphere Research workshop report \u2013 A synthesis of recent investigations, and discussion of new research questions and drilling targets. Scientific Drilling. 17: 61-66.<\/p>\n

Wasmund, K., L. Schreiber, K. G. Lloyd, D. G. Petersen, A. Schramm, R. Reinhardt, B. B. J\u00f8rgensen, L. Adrian. 2014. Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidetes, phylum Chloroflexi. The ISME Journal. 8: 383-397.<\/p>\n

Lloyd, K. G., L. Schreiber, D. G. Petersen, K. Kjeldsen, M. A. Lever, A. D. Steen, R. Stepanauskas, M. Richter, S. Kleindienst, S. Lenk, A. Schramm, B. B. J\u00f8rgensen. 2013. Predominant archaea in marine sediments degrade detrital proteins. Nature. 496: 215-219.<\/p>\n

Lloyd, K. G., M. May*, R. Kevorkian*, A. D. Steen. 2013. A meta-analysis shows that archaea and bacteria have similar abundances in the subseafloor. Applied and Environmental Microbiology. 79:7790-7799.<\/p>\n

Meyer, S., G. Wegener, K. G. Lloyd, A. Teske, A. Boetius, A. Ramette. 2013. Microbial community connectivity across spatial scales and hydrothermal temperature gradients at Guaymas Basin. Frontiers in Marine Microbiology. 4:207.<\/p>\n

Kubo, K., Lloyd, K. G., Biddle, J., Teske, A., Amann, R. Knittel, K. 2012. Archaea of the Miscellaneous Crenarchaeotal Group (MCG) are abundant, diverse, and widespread in marine sediments, The ISME Journal. 6, 1949-1965.<\/p>\n

Biddle, J. F., Z. Cardman, H. Mendlovitz, D. B. Albert, K. G. Lloyd, A. Boetius, A. Teske. 2012. Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments. The ISME Journal 6: 1018-1031.<\/p>\n

McKay, L. J., B. J. MacGregor, J. F. Biddle, D. B. Albert, H. P.Mendlovitz, D. R. Hoer, J. S. Lipp, K. G. Lloyd, A. P. Teske. 2012. Spatial heterogeneity and underlying geochemistry of phylogenetically diverse orange and white Beggiatoa mats in Guaymas Basin hydrothermal sediments. Deep-Sea Research Part I. 67:21-31.<\/p>\n

Lloyd, K. G., M. J. Alperin, A. Teske. 2011. Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea. Environmental Microbiology 13(9): 2548-2564.<\/p>\n

Lloyd, K. G., D. Albert, J. F. Biddle, J. Chanton, O. Pizarro, and A. Teske. 2010. Spatial structure and activity of sedimentary microbial communities underlying a Beggiatoa spp. mat in a Gulf of Mexico hydrocarbon seep. PLoS One, 5(1): e8738.<\/p>\n

Lloyd, K. G., B. J. MacGregor, and A. Teske. 2010. Quantitative PCR methods for RNA and DNA in marine sediments: Maximizing yield while overcoming inhibition. FEMS Microbiology Ecology. 72: 143-151.<\/p>\n

Joye, S. B., V. A. Samarkin, B. N. Orcutt, I. R. MacDonald, K. U. Hinrichs, M. Elvert, A. P. Teske, K. G. Lloyd, C. D. Meile, J. P. Montoya. 2009. Metabolic variability in seafloor brines revealed by carbon and sulphur dynamics. Nature Geoscience. 2(5): 349-354.<\/p>\n

Edgcomb, V. P., S. J. Molyneaux, S. B\u00f6er, C. O. Wirsen, M. Saito, M. S. Atkins, K. G. Lloyd, A. Teske. 2007. Survival and growth of two heterotrophic hydrothermal vent archaea, Pyrococcus strain GB-D and Thermococcus fumicolans, under low pH and high sulfide concentrations in combination with high temperature and pressure regimes. Extremophiles. 11(2): 329-342.<\/p>\n

Lloyd, K.G., L. Lapham, A. Teske. 2006. An anaerobic methane oxidizing community of ANME-1b archaea in hypersaline Gulf of Mexico sediments. Applied and Environmental Microbiology. 72: 7218-7230.<\/p>\n

Biddle, J. F., J. S. Lipp, M. Lever, K. G. Lloyd, K. B. S\u00f8rensen, R. Anderson, H. F. Fredricks, M. Elvert, T. Kelly, D. P. Schrag, M. L. Sogin, J. Brenchley, A. Teske, C. H. House, K. U. Hinrichs. 2006. Heterotrophic archaea dominate sedimentary subsurface ecosystems off Peru. Proceedings of the National Academy of Sciences USA. 103(10): 3846-3851.<\/p>\n

Lloyd, K.G., V.P. Edgcomb, S. M. Molyneaux, S. B\u00f6er, C.O. Wirsen, M. Atkins, A. Teske. 2005. Effect of dissolved sulfide, pH, and temperature on the growth and survival of marine hyperthermophilic archaea. Applied and Environmental Microbiology 71: 6383-6387.<\/p>\n

Dhillon, A., M. Lever, K. Lloyd, D. Albert, M. L. Sogin, A. Teske. 2005 .Methanogen diversity based on molecular characterization of Methyl Coenzyme M Reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin. Applied and Environmental Microbiology. 71 (8): 4592-4601.<\/p>\n

Edgcomb, V., S.J. Molyneaux, M.A. Saito, K. Lloyd, S. B\u00f6er, C.O. Wirsen, M.S. Atkins, and A. Teske. 2004. Sulfide ameliorates metal toxicity for deep-sea hydrothermal vent archaea. 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