@article{manesh_bing_willard_adams_kelly_2024, title={Complete genome sequence for the extremely thermophilic bacterium Anaerocellum danielii (DSM:8977)}, volume={1}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/mra.01229-23}, DOI={10.1128/mra.01229-23}, abstractNote={ABSTRACT The complete genome sequence of the extremely thermophilic bacterium Anaerocellum (f. Caldicellulosiruptor) danielii (DSM:8977) is reported here. A. danielii is a fermentative anaerobe and capable of lignocellulose degradation with potential applications in biomass degradation and production of chemicals and fuels from renewable feedstocks.}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Manesh, Mohamad J. H. and Bing, Ryan G. and Willard, Daniel J. and Adams, Michael W. W. and Kelly, Robert M.}, editor={Stedman, Kenneth M.Editor}, year={2024}, month={Jan} }
 @article{manesh_bing_willard_kelly_2024, title={Complete genome sequence for the thermoacidophilic archaeon <i>Metallosphaera sedula</i> (DSM:5348)}, volume={2}, ISSN={["2576-098X"]}, DOI={10.1128/mra.01228-23}, abstractNote={ABSTRACT}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Manesh, Mohamad J. H. and Bing, Ryan G. and Willard, Daniel J. and Kelly, Robert M.}, year={2024}, month={Feb} }
 @misc{manesh_willard_lewis_kelly_2024, title={Extremely thermoacidophilic archaea for metal bioleaching:<i> What</i><i> do</i><i> their</i> genomes tell Us?}, volume={391}, ISSN={["1873-2976"]}, DOI={10.1016/j.biortech.2023.129988}, abstractNote={Elevated temperatures favor bioleaching processes through faster kinetics, more favorable mineral chemistry, lower cooling requirements, and less surface passivation. Extremely thermoacidophilic archaea from the order Sulfolobales exhibit novel mechanisms for bioleaching metals from ores and have great potential. Genome sequences of many extreme thermoacidophiles are now available and provide new insights into their biochemistry, metabolism, physiology and ecology as these relate to metal mobilization from ores. Although there are some molecular genetic tools available for extreme thermoacidophiles, further development of these is sorely needed to advance the study and application of these archaea for bioleaching applications. The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. The need for critical metals and the diminishing primary deposits for copper should provide incentives for high temperature bioleaching.}, journal={BIORESOURCE TECHNOLOGY}, author={Manesh, Mohamad J. H. and Willard, Daniel J. and Lewis, April M. and Kelly, Robert M.}, year={2024}, month={Jan} }
 @article{willard_manesh_bing_alexander_kelly_2024, title={Phenotype-driven assessment of the ancestral trajectory of sulfur biooxidation in the thermoacidophilic archaea Sulfolobaceae}, volume={7}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.01033-24}, journal={MBIO}, author={Willard, Daniel J. and Manesh, Mohamad J. H. and Bing, Ryan G. and Alexander, Benjamin H. and Kelly, Robert M.}, year={2024}, month={Jul} }
 @article{bing_willard_manesh_laemthong_crosby_adams_kelly_2023, title={Complete Genome Sequences of Caldicellulosiruptor acetigenus DSM 7040, Caldicellulosiruptor morganii DSM 8990 (RT8.B8), and Caldicellulosiruptor naganoensis DSM 8991 (NA10)}, volume={2}, ISSN={["2576-098X"]}, DOI={10.1128/mra.01292-22}, abstractNote={
            The genome sequences of three extremely thermophilic, lignocellulolytic
            Caldicellulosiruptor
            species were closed, improving previously reported multiple-contig assemblies. All 14 classified
            Caldicellulosiruptor
            spp. now have closed genomes. Genome closure will enhance bioinformatic analysis of the species, including identification of carbohydrate-active enzymes (CAZymes) and comparison against other
            Caldicellulosiruptor
            species and lignocellulolytic microorganisms.
          }, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Bing, Ryan G. G. and Willard, Daniel J. J. and Manesh, Mohamad J. H. and Laemthong, Tunyaboon and Crosby, James R. R. and Adams, Michael W. W. and Kelly, Robert M. M.}, year={2023}, month={Feb} }
 @article{bing_willard_manesh_laemthong_crosby_adams_kelly_2023, title={Complete Genome Sequences of Two Thermophilic Indigenous Bacteria Isolated from Wheat Straw, Thermoclostridium stercorarium subsp. Strain RKWS1 and Thermoanaerobacter sp. Strain RKWS2}, volume={12}, ISSN={["2576-098X"]}, DOI={10.1128/mra.01193-22}, abstractNote={
            Reported here are complete genome sequences for two anaerobic, thermophilic bacteria isolated from wheat straw, i.e., the (hemi)cellulolytic
            Thermoclostridium stercorarium
            subspecies strain RKWS1 (3,029,933 bp) and the hemicellulolytic
            Thermoanaerobacter
            species strain RKWS2 (2,827,640 bp). Discovery of indigenous thermophiles in plant biomass suggests that high-temperature microorganisms are more ubiquitous than previously thought.
          }, number={3}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Bing, Ryan G. and Willard, Daniel J. and Manesh, Mohamad J. H. and Laemthong, Tunyaboon and Crosby, James R. and Adams, Michael W. W. and Kelly, Robert M.}, year={2023}, month={Mar} }
 @article{willard_manesh_bing_kelly_2023, title={Complete genome sequence for the thermoacidophilic archaeon <i>Sulfuracidifex</i> (f<i>. Sulfolobus</i>) <i>metallicus</i> DSM 6482}, volume={12}, ISSN={["2576-098X"]}, DOI={10.1128/mra.00981-23}, abstractNote={ABSTRACT}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Willard, Daniel J. and Manesh, Mohamad J. H. and Bing, Ryan G. and Kelly, Robert M.}, year={2023}, month={Dec} }
 @article{bing_carey_laemthong_willard_crosby_sulis_wang_adams_kelly_2023, title={Fermentative conversion of unpretreated plant biomass: A thermophilic threshold for indigenous microbial growth}, volume={367}, ISSN={["1873-2976"]}, url={http://europepmc.org/abstract/med/36347479}, DOI={10.1016/j.biortech.2022.128275}, abstractNote={Naturally occurring, microbial contaminants were found in plant biomasses from common bioenergy crops and agricultural wastes. Unexpectedly, indigenous thermophilic microbes were abundant, raising the question of whether they impact thermophilic consolidated bioprocessing fermentations that convert biomass directly into useful bioproducts. Candidate microbial platforms for biomass conversion, Acetivibrio thermocellus (basionym Clostridium thermocellum; Topt 60 °C) and Caldicellulosiruptor bescii (Topt 78 °C), each degraded a wide variety of plant biomasses, but only A. thermocellus was significantly affected by the presence of indigenous microbial populations harbored by the biomass. Indigenous microbial growth was eliminated at ≥75 °C, conditions where C. bescii thrives, but where A. thermocellus cannot survive. Therefore, 75 °C is the thermophilic threshold to avoid sterilizing pre-treatments on the biomass that prevents native microbes from competing with engineered microbes and forming undesirable by-products. Thermophiles that naturally grow at and above 75 °C offer specific advantages as platform microorganisms for biomass conversion into fuels and chemicals.}, journal={BIORESOURCE TECHNOLOGY}, author={Bing, Ryan G. and Carey, Morgan J. and Laemthong, Tunyaboon and Willard, Daniel J. and Crosby, James R. and Sulis, Daniel B. and Wang, Jack P. and Adams, Michael W. W. and Kelly, Robert M.}, year={2023}, month={Jan} }
 @article{cooper_lewis_notey_mukherjee_willard_blum_kelly_2023, title={Interplay between transcriptional regulators and VapBC toxin-antitoxin loci during thermal stress response in extremely thermoacidophilic archaea}, volume={2}, ISSN={["1462-2920"]}, DOI={10.1111/1462-2920.16350}, abstractNote={Abstract}, journal={ENVIRONMENTAL MICROBIOLOGY}, author={Cooper, Charlotte R. and Lewis, April M. and Notey, Jaspreet S. and Mukherjee, Arpan and Willard, Daniel J. and Blum, Paul H. and Kelly, Robert M.}, year={2023}, month={Feb} }
 @article{lewis_willard_manesh_sivabalasarma_albers_kelly_2023, title={Stay or Go: Sulfolobales Biofilm Dispersal Is Dependent on a Bifunctional VapB Antitoxin}, volume={4}, ISSN={["2150-7511"]}, DOI={10.1128/mbio.00053-23}, abstractNote={Biofilms allow microbes to resist a multitude of stresses and stay proximate to vital nutrients. The mechanisms of entering and leaving a biofilm are highly regulated to ensure microbial survival, but are not yet well described in archaea.}, journal={MBIO}, author={Lewis, April M. and Willard, Daniel J. and Manesh, Mohamad J. H. J. and Sivabalasarma, Shamphavi and Albers, Sonja-Verena and Kelly, Robert M.}, year={2023}, month={Apr} }
 @article{bing_willard_crosby_adams_kelly_2023, title={Whither the genus Caldicellulosiruptor and the order Thermoanaerobacterales: phylogeny, taxonomy, ecology, and phenotype}, volume={14}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2023.1212538}, abstractNote={The order Thermoanaerobacterales currently consists of fermentative anaerobic bacteria, including the genus Caldicellulosiruptor. Caldicellulosiruptor are represented by thirteen species; all, but one, have closed genome sequences. Interest in these extreme thermophiles has been motivated not only by their high optimal growth temperatures (≥70°C), but also by their ability to hydrolyze polysaccharides including, for some species, both xylan and microcrystalline cellulose. Caldicellulosiruptor species have been isolated from geographically diverse thermal terrestrial environments located in New Zealand, China, Russia, Iceland and North America. Evidence of their presence in other terrestrial locations is apparent from metagenomic signatures, including volcanic ash in permafrost. Here, phylogeny and taxonomy of the genus Caldicellulosiruptor was re-examined in light of new genome sequences. Based on genome analysis of 15 strains, a new order, Caldicellulosiruptorales, is proposed containing the family Caldicellulosiruptoraceae, consisting of two genera, Caldicellulosiruptor and Anaerocellum. Furthermore, the order Thermoanaerobacterales also was re-assessed, using 91 genome-sequenced strains, and should now include the family Thermoanaerobacteraceae containing the genera Thermoanaerobacter, Thermoanaerobacterium, Caldanaerobacter, the family Caldanaerobiaceae containing the genus Caldanaerobius, and the family Calorimonaceae containing the genus Calorimonas. A main outcome of ANI/AAI analysis indicates the need to reclassify several previously designated species in the Thermoanaerobacterales and Caldicellulosiruptorales by condensing them into strains of single species. Comparative genomics of carbohydrate-active enzyme inventories suggested differentiating phenotypic features, even among strains of the same species, reflecting available nutrients and ecological roles in their native biotopes.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Bing, Ryan G. G. and Willard, Daniel J. J. and Crosby, James R. R. and Adams, Michael W. W. and Kelly, Robert M. M.}, year={2023}, month={Aug} }
 @article{willard_kelly_2021, title={Intersection of Biotic and Abiotic Sulfur Chemistry Supporting Extreme Microbial Life in Hot Acid}, volume={125}, ISSN={["1520-5207"]}, DOI={10.1021/acs.jpcb.1c02102}, abstractNote={Microbial life on Earth exists within wide ranges of temperature, pressure, pH, salinity, radiation, and water activity. Extreme thermoacidophiles, in particular, are microbes found in hot, acidic biotopes laden with heavy metals and reduced inorganic sulfur species. As chemolithoautotrophs, they thrive in the absence of organic carbon, instead using sulfur and metal oxidation to fuel their bioenergetic needs, while incorporating CO2 as a carbon source. Metal oxidation by these microbes takes place extracellularly, mediated by membrane-associated oxidase complexes. In contrast, sulfur oxidation involves extracellular, membrane-associated, and cytoplasmic biotransformations, which intersect with abiotic sulfur chemistry. This novel lifestyle has been examined in the context of early aerobic life on this planet, but it is also interesting when considering the prospects of life, now or previously, on other solar bodies. Here, extreme thermoacidophily (growth at pH below 4.0, temperature above 55 °C), a characteristic of species in the archaeal order Sulfolobales, is considered from the perspective of sulfur chemistry, both biotic and abiotic, as it relates to microbial bioenergetics. Current understanding of the mechanisms involved are reviewed which are further expanded through recent experimental results focused on imparting sulfur oxidation capacity on a natively nonsulfur oxidizing extremely thermoacidophilic archaeon, Sulfolobus acidocaldarius, through metabolic engineering.}, number={20}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Willard, Daniel J. and Kelly, Robert M.}, year={2021}, month={May}, pages={5243–5257} }
 @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} }