@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 The complete genome sequence of the thermoacidophilic archaeon Metallosphaera sedula (DSM 5348) is reported here. M. sedula, originally isolated from a volcanic field in Italy, is a prolific iron-oxidizing archaeon with applications in bioleaching of sulfide minerals.}, 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{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. ABSTRACT 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. ABSTRACT 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 Reported here is the complete genome sequence (2,191,724 bp) for the thermoacidophilic archaeon Sulfuracidifex (f. Sulfolobus) metallicus DSM 6482 (Topt 65°C, pHopt 2.0). This obligately chemolithoautotrophic microorganism is a prolific metal and sulfur oxidizer and has application in metal bioleaching operations. A multi-assembly reconciliation approach enabled closure of the genome.}, 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={Thermoacidophilic archaea lack sigma factors and the large inventory of heat shock proteins (HSP) widespread in bacterial genomes, suggesting other strategies for handling thermal stress are involved. Heat shock transcriptomes for the thermoacidophilic archaeon Saccharolobus (f. Sulfolobus) solfataricus 98/2 revealed genes that were highly responsive to thermal stress, including transcriptional regulators YtrASs (Ssol_2420) and FadRSs (Ssol_0314), as well as Type II Toxin-Antitoxin (TA) loci VapBC6 (Ssol_2337, Ssol_2338) and VapBC22 (Ssol_0819, Ssol_0818). The role, if any, of Type II TA loci during stress response in microorganisms, such as Escherichia coli, is controversial. But, when genes encoding YtrASs , FadRSs , VapC22, VapB6, and VapC6 were systematically mutated in Sa. solfataricus 98/2, significant up-regulation of the other genes within this set was observed, implicating an interconnected regulatory network during thermal stress response. VapBC6 and VapBC22 have close homologs in other Sulfolobales, as well as in other archaea (e.g., Pyrococcus furiosus and Archaeoglobus fulgidus), and their corresponding genes were also heat shock responsive. The interplay between VapBC TA loci and heat shock regulators in Sa. solfataricus 98/2 not only indicates a cellular mechanism for heat shock response that differs from bacteria but one that could have common features within the thermophilic archaea. This article is protected by copyright. All rights reserved.}, 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. ABSTRACT A type II VapB14 antitoxin regulates biofilm dispersal in the archaeal thermoacidophile Sulfolobus acidocaldarius through traditional toxin neutralization but also through noncanonical transcriptional regulation. Type II VapC toxins are ribonucleases that are neutralized by their proteinaceous cognate type II VapB antitoxin. VapB antitoxins have a flexible tail at their C terminus that covers the toxin’s active site, neutralizing its activity. VapB antitoxins also have a DNA-binding domain at their N terminus that allows them to autorepress not only their own promoters but also distal targets. VapB14 antitoxin gene deletion in S. acidocaldarius stunted biofilm and planktonic growth and increased motility structures (archaella). Conversely, planktonic cells were devoid of archaella in the ΔvapC14 cognate toxin mutant. VapB14 is highly conserved at both the nucleotide and amino acid levels across the Sulfolobales, extremely unusual for type II antitoxins, which are typically acquired through horizontal gene transfer. Furthermore, homologs of VapB14 are found across the Crenarchaeota, in some Euryarchaeota, and even bacteria. S. acidocaldarius vapB14 and its homolog in the thermoacidophile Metallosphaera sedula (Msed_0871) were both upregulated in biofilm cells, supporting the role of the antitoxin in biofilm regulation. In several Sulfolobales species, including M. sedula, homologs of vapB14 and vapC14 are not colocalized. Strikingly, Sulfuracidifex tepidarius has an unpaired VapB14 homolog and lacks a cognate VapC14, illustrating the toxin-independent conservation of the VapB14 antitoxin. The findings here suggest that a stand-alone VapB-type antitoxin was the product of selective evolutionary pressure to influence biofilm formation in these archaea, a vital microbial community behavior. IMPORTANCE 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. Here, a VapBC type II toxin-antitoxin system in the thermoacidophilic archaeon Sulfolobus acidocaldarius was shown to control biofilm dispersal through a multifaceted regulation of the archaeal motility structure, the archaellum. The VapC14 toxin degrades an RNA that causes an increase in archaella and swimming. The VapB14 antitoxin decreases archaella and biofilm dispersal by binding the VapC14 toxin and neutralizing its activity, while also repressing the archaellum genes. VapB14-like antitoxins are highly conserved across the Sulfolobales and respond similarly to biofilm growth. In fact, VapB14-like antitoxins are also found in other archaea, and even in bacteria, indicating an evolutionary pressure to maintain this protein and its role in biofilm formation.}, 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={Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered more than 50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further the probe novel features of these microbes, but have also paved the way for potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes, and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.}, 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} }