@article{counts_vitko_kelly_2021, title={Fox Cluster determinants for iron biooxidation in the extremely thermoacidophilic Sulfolobaceae}, volume={8}, ISSN={["1462-2920"]}, DOI={10.1111/1462-2920.15727}, abstractNote={Summary}, journal={ENVIRONMENTAL MICROBIOLOGY}, author={Counts, James A. and Vitko, Nicholas P. and Kelly, Robert M.}, year={2021}, month={Aug} }
 @article{lewis_recalde_bräsen_counts_nussbaum_bost_schocke_shen_willard_quax_et al._2021, title={The biology of thermoacidophilic archaea from the order Sulfolobales}, volume={45}, ISSN={1574-6976}, url={http://dx.doi.org/10.1093/femsre/fuaa063}, DOI={10.1093/femsre/fuaa063}, abstractNote={ABSTRACT}, number={4}, journal={FEMS Microbiology Reviews}, publisher={Oxford University Press (OUP)}, author={Lewis, April M and Recalde, Alejandra and Bräsen, Christopher and Counts, James A and Nussbaum, Phillip and Bost, Jan and Schocke, Larissa and Shen, Lu and Willard, Daniel J and Quax, Tessa E F and et al.}, year={2021}, month={Jan} }
 @article{counts_vitko_kelly_2020, title={Genome Sequences of Five Type Strain Members of the Archaeal Family Sulfolobaceae, Acidianus ambivalens, Acidianus infernus, Stygiolobus azoricus, Sulfuracidifex metallicus, and Sulfurisphaera ohwakuensis}, volume={9}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.01490-19}, abstractNote={
            Presented are five genomes from the polyextremophilic (optimal temperature of >65°C and optimal pH of <3.5) archaeal family
            Sulfolobaceae
            , greatly expanding order-wide genomic diversity. Included are the only obligate anaerobic species, several facultative sulfur utilizers, two metal mobilizers, one facultative chemolithoautotroph with robust metabolic versatility, and some of the most thermophilic thermoacidophiles reported to date.
          }, number={11}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Counts, James A. and Vitko, Nicholas P. and Kelly, Robert M.}, year={2020}, month={Mar} }
 @article{counts_willard_kelly_2020, title={Life in hot acid: a genome‐based reassessment of the archaeal order
            Sulfolobales}, volume={23}, ISSN={1462-2912 1462-2920}, url={http://dx.doi.org/10.1111/1462-2920.15189}, DOI={10.1111/1462-2920.15189}, abstractNote={Summary}, number={7}, journal={Environmental Microbiology}, publisher={Wiley}, author={Counts, James A. and Willard, Daniel J. and Kelly, Robert M.}, year={2020}, month={Sep}, pages={3568–3584} }
 @article{zeldes_loder_counts_haque_widney_keller_albers_kelly_2019, title={Determinants of sulphur chemolithoautotrophy in the extremely thermoacidophilic Sulfolobales}, volume={21}, ISSN={["1462-2920"]}, DOI={10.1111/1462-2920.14712}, abstractNote={Summary}, number={10}, journal={ENVIRONMENTAL MICROBIOLOGY}, author={Zeldes, Benjamin M. and Loder, Andrew J. and Counts, James A. and Haque, Mashkurul and Widney, Karl A. and Keller, Lisa M. and Albers, Sonja-Verena and Kelly, Robert M.}, year={2019}, month={Oct}, pages={3696–3710} }
 @article{wheaton_vitko_counts_dulkis_podolsky_mukherjee_kelly_2019, title={Extremely Thermoacidophilic Metallosphaera Species Mediate Mobilization and Oxidation of Vanadium and Molybdenum Oxides}, volume={85}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.02805-18}, abstractNote={
            In order to effectively leverage extremely thermoacidophilic archaea for the microbially based solubilization of solid-phase metal substrates (e.g., sulfides and oxides), understanding the mechanisms by which these archaea solubilize metals is important. Physiological analysis of
            Metallosphaera
            species growth in the presence of molybdenum and vanadium oxides revealed an indirect mode of metal mobilization, catalyzed by iron cycling. However, since the mobilized metals exist in more than one oxidation state, they could potentially serve directly as energetic substrates. Transcriptomic response to molybdenum and vanadium oxides provided evidence for new biomolecules participating in direct metal biooxidation. The findings expand the knowledge on the physiological versatility of these extremely thermoacidophilic archaea.
          }, number={5}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Wheaton, Garrett H. and Vitko, Nicholas P. and Counts, James A. and Dulkis, Jessica A. and Podolsky, Igor and Mukherjee, Arpan and Kelly, Robert M.}, year={2019}, month={Mar} }
 @misc{straub_counts_nguyen_wu_zeldes_crosby_conway_otten_lipscomb_schut_et al._2018, title={Biotechnology of extremely thermophilic archaea}, volume={42}, ISSN={["1574-6976"]}, DOI={10.1093/femsre/fuy012}, abstractNote={Although the extremely thermophilic archaea (Topt ≥ 70°C) may be the most primitive extant forms of life, they have been studied to a limited extent relative to mesophilic microorganisms. Many of these organisms have unique biochemical and physiological characteristics with important biotechnological implications. These include methanogens that generate methane, fermentative anaerobes that produce hydrogen gas with high efficiency, and acidophiles that can mobilize base, precious and strategic metals from mineral ores. Extremely thermophilic archaea have also been a valuable source of thermoactive, thermostable biocatalysts, but their use as cellular systems has been limited because of the general lack of facile genetics tools. This situation has changed recently, however, thereby providing an important avenue for understanding their metabolic and physiological details and also opening up opportunities for metabolic engineering efforts. Along these lines, extremely thermophilic archaea have recently been engineered to produce a variety of alcohols and industrial chemicals, in some cases incorporating CO2 into the final product. There are barriers and challenges to these organisms reaching their full potential as industrial microorganisms but, if these can be overcome, a new dimension for biotechnology will be forthcoming that strategically exploits biology at high temperatures.}, number={5}, journal={FEMS MICROBIOLOGY REVIEWS}, author={Straub, Christopher T. and Counts, James A. and Nguyen, Diep M. N. and Wu, Chang-Hao and Zeldes, Benjamin M. and Crosby, James R. and Conway, Jonathan M. and Otten, Jonathan K. and Lipscomb, Gina L. and Schut, Gerrit J. and et al.}, year={2018}, month={Sep}, pages={543–578} }
 @article{counts_vitko_kelly_2018, title={Complete Genome Sequences of Extremely Thermoacidophilic Metal-Mobilizing Type Strain Members of the Archaeal Family Sulfolobaceae, Acidianus brierleyi DSM-1651, Acidianus sulfidivorans DSM-18786, and Metallosphaera hakonensis DSM-7519}, volume={7}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.00831-18}, abstractNote={
            The family
            Sulfolobaceae
            contains extremely thermoacidophilic archaea that are found in terrestrial environments. Here, we report three closed genomes from two currently defined genera within the family, namely,
            Acidianus brierleyi
            DSM-1651
            T
            ,
            Acidianus sulfidivorans
            DSM-18786
            T
            , and
            Metallosphaera hakonensis
            DSM-7519
            T
            .
          }, number={2}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Counts, James A. and Vitko, Nicholas P. and Kelly, Robert M.}, year={2018}, month={Jul} }
 @misc{counts_zeldes_lee_straub_adams_kelly_2017, title={Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms}, volume={9}, ISSN={["1939-005X"]}, DOI={10.1002/wsbm.1377}, abstractNote={The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as ‘extreme thermophiles’ and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs—basically, anywhere there is hot water. Initial efforts to study extreme thermophiles faced challenges with their isolation from difficult to access locales, problems with their cultivation in laboratories, and lack of molecular tools. Fortunately, because of their relatively small genomes, many extreme thermophiles were among the first organisms to be sequenced, thereby opening up the application of systems biology‐based methods to probe their unique physiological, metabolic and biotechnological features. The bacterial genera Caldicellulosiruptor, Thermotoga and Thermus, and the archaea belonging to the orders Thermococcales and Sulfolobales, are among the most studied extreme thermophiles to date. The recent emergence of genetic tools for many of these organisms provides the opportunity to move beyond basic discovery and manipulation to biotechnologically relevant applications of metabolic engineering. WIREs Syst Biol Med 2017, 9:e1377. doi: 10.1002/wsbm.1377}, number={3}, journal={WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE}, author={Counts, James A. and Zeldes, Benjamin M. and Lee, Laura L. and Straub, Christopher T. and Adams, Michael W. W. and Kelly, Robert M.}, year={2017}, month={May} }
 @article{mukherjee_wheaton_counts_ijeomah_desai_kelly_2017, title={VapC toxins drive cellular dormancy under uranium stress for the extreme thermoacidophile Metallosphaera prunae}, volume={19}, ISSN={["1462-2920"]}, DOI={10.1111/1462-2920.13808}, abstractNote={Summary}, number={7}, journal={ENVIRONMENTAL MICROBIOLOGY}, author={Mukherjee, Arpan and Wheaton, Garrett H. and Counts, James A. and Ijeomah, Brenda and Desai, Jigar and Kelly, Robert M.}, year={2017}, month={Jul}, pages={2831–2842} }
 @misc{wheaton_counts_mukherjee_kruh_kelly_2015, title={The Confluence of Heavy Metal Biooxidation and Heavy Metal Resistance: Implications for Bioleaching by Extreme Thermoacidophiles}, volume={5}, ISSN={["2075-163X"]}, DOI={10.3390/min5030397}, abstractNote={Abstract: Extreme thermoacidophiles ( T opt > 65 °C, pH opt < 3.5) inhabit unique environments fraught with challenges, including extremely high temperatures, low pH, as well as high levels of soluble metal species. In fact, certain members of this group thrive by metabolizing heavy metals, creating a dynamic equilibrium between biooxidation to meet bioenergetic needs and mechanisms for tolerating and resisting the toxic effects of solubilized metals. Extremely thermoacidophilic archaea dominate bioleaching operations at elevated temperatures and have been considered for processing certain mineral types (e.g., chalcopyrite), some of which are recalcitrant to their mesophilic counterparts. A key issue to consider, in addition to temperature and pH, is the extent to which solid phase heavy metals are solubilized and the concomitant impact of these mobilized metals on the microorganism’s growth physiology. Here, extreme thermoacidophiles are examined from the perspectives of biodiversity, heavy metal biooxidation, metal resistance mechanisms, microbe-solid interactions, and application of these archaea in biomining operations.}, number={3}, journal={MINERALS}, author={Wheaton, Garrett and Counts, James and Mukherjee, Arpan and Kruh, Jessica and Kelly, Robert}, year={2015}, month={Sep}, pages={397–451} }