@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} }
 @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{tanwee_lipscomb_vailionis_zhang_bing_hailey c. o'quinn_poole_zhang_kelly_adams_2023, title={Metabolic engineering of <i>Caldicellulosiruptor bescii</i> for 2,3-butanediol production from unpretreated lignocellulosic biomass and metabolic strategies for improving yields and titers}, volume={12}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01951-23}, abstractNote={ABSTRACT}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Tanwee, Tania N. N. and Lipscomb, Gina L. and Vailionis, Jason L. and Zhang, Ke and Bing, Ryan G. and Hailey C. O'Quinn and Poole, Farris L. and Zhang, Ying and Kelly, Robert M. and Adams, Michael W. W.}, year={2023}, month={Dec} }
 @article{sulis_jiang_yang_marques_matthews_miller_lan_cofre-vega_liu_sun_et al._2023, title={Multiplex CRISPR editing of wood for sustainable fiber production}, volume={381}, ISSN={["1095-9203"]}, url={http://europepmc.org/abstract/med/37440632}, DOI={10.1126/science.add4514}, abstractNote={The domestication of forest trees for a more sustainable fiber bioeconomy has long been hindered by the complexity and plasticity of lignin, a biopolymer in wood that is recalcitrant to chemical and enzymatic degradation. Here, we show that multiplex CRISPR editing enables precise woody feedstock design for combinatorial improvement of lignin composition and wood properties. By assessing every possible combination of 69,123 multigenic editing strategies for 21 lignin biosynthesis genes, we deduced seven different genome editing strategies targeting the concurrent alteration of up to six genes and produced 174 edited poplar variants. CRISPR editing increased the wood carbohydrate-to-lignin ratio up to 228% that of wild type, leading to more-efficient fiber pulping. The edited wood alleviates a major fiber-production bottleneck regardless of changes in tree growth rate and could bring unprecedented operational efficiencies, bioeconomic opportunities, and environmental benefits.}, number={6654}, journal={SCIENCE}, author={Sulis, Daniel B. and Jiang, Xiao and Yang, Chenmin and Marques, Barbara M. and Matthews, Megan L. and Miller, Zachary and Lan, Kai and Cofre-Vega, Carlos and Liu, Baoguang and Sun, Runkun and et al.}, year={2023}, month={Jul}, pages={216-+} }
 @article{vailionis_zhao_zhang_rodionov_lipscomb_tanwee_hailey c. o'quinn_bing_kelly_adams_et al._2023, title={Optimizing Strategies for Bio-Based Ethanol Production Using Genome-Scale Metabolic Modeling of the Hyperthermophilic Archaeon, Pyrococcus furiosus}, volume={6}, ISSN={["1098-5336"]}, DOI={10.1128/aem.00563-23}, abstractNote={
            The bio-based production of organic chemicals provides a sustainable alternative to fossil-based production in the face of today’s climate challenges. In this work, we present a genome-scale metabolic reconstruction of
            Pyrococcus furiosus
            , a well-established platform organism that has been engineered to produce a variety of chemicals and fuels.
          }, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Vailionis, Jason L. and Zhao, Weishu and Zhang, Ke and Rodionov, Dmitry A. and Lipscomb, Gina L. and Tanwee, Tania N. N. and Hailey C. O'Quinn and Bing, Ryan G. and Kelly, Robert M. and Adams, Michael W. W. and et al.}, year={2023}, month={Jun} }
 @article{laemthong_bing_crosby_manesh_adams_kelly_2023, title={Role of cell-substrate association during plant biomass solubilization by the extreme thermophile Caldicellulosiruptor bescii}, volume={27}, ISSN={["1433-4909"]}, DOI={10.1007/s00792-023-01290-7}, abstractNote={Caldicellulosiruptor species are proficient at solubilizing carbohydrates in lignocellulosic biomass through surface (S)-layer bound and secretomic glycoside hydrolases. Tāpirins, surface-associated, non-catalytic binding proteins in Caldicellulosiruptor species, bind tightly to microcrystalline cellulose, and likely play a key role in natural environments for scavenging scarce carbohydrates in hot springs. However, the question arises: If tāpirin concentration on Caldicellulosiruptor cell walls increased above native levels, would this offer any benefit to lignocellulose carbohydrate hydrolysis and, hence, biomass solubilization? This question was addressed by engineering the genes for tight-binding, non-native tāpirins into C. bescii. The engineered C. bescii strains bound more tightly to microcrystalline cellulose (Avicel) and biomass compared to the parent. However, tāpirin overexpression did not significantly improve solubilization or conversion for wheat straw or sugarcane bagasse. When incubated with poplar, the tāpirin-engineered strains increased solubilization by 10% compared to the parent, and corresponding acetate production, a measure of carbohydrate fermentation intensity, was 28% higher for the Calkr_0826 expression strain and 18.5% higher for the Calhy_0908 expression strain. These results show that enhanced binding to the substrate, beyond the native capability, did not improve C. bescii solubilization of plant biomass, but in some cases may improve conversion of released lignocellulose carbohydrates to fermentation products.}, number={1}, journal={EXTREMOPHILES}, author={Laemthong, Tunyaboon and Bing, Ryan G. and Crosby, James R. and Manesh, Mohamad J. H. and Adams, Michael W. W. 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{bing_straub_sulis_wang_adams_kelly_2022, title={<p>Plant biomass fermentation by the extreme thermophile Caldicellulosiruptor bescii for co-production of green hydrogen and acetone: Technoeconomic analysis</p>}, volume={348}, ISSN={["1873-2976"]}, url={http://europepmc.org/abstract/med/35093526}, DOI={10.1016/j.biortech.2022.126780}, abstractNote={A variety of chemical and biological processes have been proposed for conversion of sustainable low-cost feedstocks into industrial products. Here, a biorefinery concept is formulated, modeled, and analyzed in which a naturally (hemi)cellulolytic and extremely thermophilic bacterium, Caldicellulosiruptor bescii, is metabolically engineered to convert the carbohydrate content of lignocellulosic biomasses (i.e., soybean hulls, transgenic poplar) into green hydrogen and acetone. Experimental validation of C. bescii fermentative performance demonstrated 82% carbohydrate solubilization of soybean hulls and 55% for transgenic poplar. A detailed technical design, including equipment specifications, provides the basis for an economic analysis that establishes metabolic engineering targets. This robust industrial process leveraging metabolically engineered C. bescii yields 206 kg acetone and 25 kg H2 per metric ton of soybean hull, or 174 kg acetone and 21 kg H2 per metric ton transgenic poplar. Beyond this specific case, the model demonstrates industrial feasibility and economic advantages of thermophilic fermentation.}, journal={BIORESOURCE TECHNOLOGY}, author={Bing, Ryan G. and Straub, Christopher T. and Sulis, Daniel B. and Wang, Jack P. and Adams, Michel W. W. and Kelly, Robert M.}, year={2022}, month={Mar} }
 @article{crosby_laemthong_bing_zhang_tanwee_lipscomb_rodionov_zhang_adams_kelly_2022, title={Biochemical and Regulatory Analyses of Xylanolytic Regulons in Caldicellulosiruptor bescii Reveal Genus-Wide Features of Hemicellulose Utilization}, volume={10}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01302-22}, abstractNote={
            Microbial deconstruction of lignocellulose for the production of biofuels and chemicals requires the hydrolysis of heterogeneous hemicelluloses to access the microcrystalline cellulose portion. This work extends previous
            in vivo
            and
            in vitro
            efforts to characterize hemicellulose utilization by integrating genomic reconstruction, transcriptomic data, operon structures, and biochemical characteristics of key enzymes to understand the deployment and functionality of hemicellulases by the extreme thermophile
            Caldicellulosiruptor bescii
            .
          }, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Crosby, James R. and Laemthong, Tunyaboon and Bing, Ryan G. and Zhang, Ke and Tanwee, Tania N. N. and Lipscomb, Gina L. and Rodionov, Dmitry A. and Zhang, Ying and Adams, Michael W. W. and Kelly, Robert M.}, year={2022}, month={Oct} }
 @article{laemthong_bing_crosby_adams_kelly_2022, title={Engineering Caldicellulosiruptor bescii with Surface Layer Homology Domain-Linked Glycoside Hydrolases Improves Plant Biomass Solubilization}, volume={9}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01274-22}, abstractNote={
            Caldicellulosiruptor
            species hold promise as microorganisms that can solubilize the carbohydrate portion of lignocellulose and subsequently convert fermentable sugars into bio-based chemicals and fuels. Members of the genus have surface layer (S-layer) homology domain-associated glycoside hydrolases (SLH-GHs) that mediate attachment to biomass as well as hydrolysis of carbohydrates.
            Caldicellulosiruptor bescii
            , the most studied member of the genus, has only one SLH-GH.
          }, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Laemthong, Tunyaboon and Bing, Ryan G. and Crosby, James R. and Adams, Michael W. W. and Kelly, Robert M.}, year={2022}, month={Sep} }
 @article{rodionov_rodionova_rodionov_arzamasov_zhang_rubinstein_tanwee_bing_crosby_nookaew_et al._2021, title={Genome-Scale Metabolic Model of
            Caldicellulosiruptor bescii
            Reveals Optimal Metabolic Engineering Strategies for Bio-based Chemical Production}, volume={6}, ISSN={2379-5077}, url={http://dx.doi.org/10.1128/msystems.01351-20}, DOI={10.1128/mSystems.01351-20}, abstractNote={
            The extremely thermophilic cellulolytic bacterium,
            Caldicellulosiruptor bescii
            , degrades plant biomass at high temperatures without any pretreatments and can serve as a strategic platform for industrial applications. The metabolic engineering of
            C. bescii
            , however, faces potential bottlenecks in bio-based chemical productions.
          }, number={3}, journal={mSystems}, publisher={American Society for Microbiology}, author={Rodionov, Dmitry A. and Rodionova, Irina A. and Rodionov, Vladimir A. and Arzamasov, Aleksandr A. and Zhang, Ke and Rubinstein, Gabriel M. and Tanwee, Tania N. N. and Bing, Ryan G. and Crosby, James R. and Nookaew, Intawat and et al.}, editor={Summers, Zarath M.Editor}, year={2021}, month={Jun} }
 @article{bing_sulis_wang_adams_kelly_2021, title={Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose}, volume={13}, ISSN={1758-2229 1758-2229}, url={http://dx.doi.org/10.1111/1758-2229.12943}, DOI={10.1111/1758-2229.12943}, abstractNote={Summary}, number={3}, journal={Environmental Microbiology Reports}, publisher={Wiley}, author={Bing, Ryan G. and Sulis, Daniel B. and Wang, Jack P. and Adams, Michael W. W. and Kelly, Robert M.}, year={2021}, month={Mar}, pages={272–293} }
 @article{straub_bing_otten_keller_zeldes_adams_kelly_2020, title={Metabolically engineeredCaldicellulosiruptor besciias a platform for producing acetone and hydrogen from lignocellulose}, volume={117}, ISSN={["1097-0290"]}, DOI={10.1002/bit.27529}, abstractNote={Abstract}, number={12}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Straub, Christopher T. and Bing, Ryan G. and Otten, Jonathan K. and Keller, Lisa M. and Zeldes, Benjamin M. and Adams, Michael W. W. and Kelly, Robert M.}, year={2020}, month={Dec}, pages={3799–3808} }
 @article{lee_crosby_rubinstein_laemthong_bing_straub_adams_kelly_2020, title={The biology and biotechnology of the genus Caldicellulosiruptor: recent developments in 'Caldi World'}, volume={24}, ISSN={["1433-4909"]}, url={https://doi.org/10.1007/s00792-019-01116-5}, DOI={10.1007/s00792-019-01116-5}, abstractNote={Terrestrial hot springs near neutral pH harbor extremely thermophilic bacteria from the genus Caldicellulosiruptor, which utilize the carbohydrates of lignocellulose for growth. These bacteria are technologically important because they produce novel, multi-domain glycoside hydrolases that are prolific at deconstructing microcrystalline cellulose and hemicelluloses found in plant biomass. Among other interesting features, Caldicellulosiruptor species have successfully adapted to bind specifically to lignocellulosic substrates via surface layer homology (SLH) domains associated with glycoside hydrolases and unique binding proteins (tāpirins) present only in these bacteria. They also utilize a parallel pathway for conversion of glyceraldehyde-3-phosphate into 3-phosphoglycerate via a ferredoxin-dependent oxidoreductase that is conserved across the genus. Advances in the genetic tools for Caldicellulosiruptor bescii, including the development of a high-temperature kanamycin-resistance marker and xylose-inducible promoter, have opened the door for metabolic engineering applications and some progress along these lines has been reported. While several species of Caldicellulosiruptor can readily deconstruct lignocellulose, improvements in the amount of carbohydrate released and in the production of bio-based chemicals are required to successfully realize the biotechnological potential of these organisms.}, number={1}, journal={EXTREMOPHILES}, author={Lee, Laura L. and Crosby, James R. and Rubinstein, Gabriel M. and Laemthong, Tunyaboon and Bing, Ryan G. and Straub, Christopher T. and Adams, Michael W. W. and Kelly, Robert M.}, year={2020}, month={Jan}, pages={1–15} }
 @article{straub_bing_wang_chiang_adams_kelly_2020, title={Use of the lignocellulose-degrading bacterium Caldicellulosiruptor bescii to assess recalcitrance and conversion of wild-type and transgenic poplar}, volume={13}, ISSN={["1754-6834"]}, url={http://dx.doi.org/10.1186/s13068-020-01675-2}, DOI={10.1186/s13068-020-01675-2}, abstractNote={Abstract}, number={1}, journal={BIOTECHNOLOGY FOR BIOFUELS}, author={Straub, Christopher T. and Bing, Ryan G. and Wang, Jack P. and Chiang, Vincent L. and Adams, Michael W. W. and Kelly, Robert M.}, year={2020}, month={Mar} }