@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{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{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{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{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{crosby_laemthong_lewis_straub_adams_kelly_2019, title={Extreme thermophiles as emerging metabolic engineering platforms}, volume={59}, ISSN={0958-1669}, url={http://dx.doi.org/10.1016/j.copbio.2019.02.006}, DOI={10.1016/j.copbio.2019.02.006}, abstractNote={Going forward, industrial biotechnology must consider non-model metabolic engineering platforms if it is to have maximal impact. This will include microorganisms that natively possess strategic physiological and metabolic features but lack either molecular genetic tools or such tools are rudimentary, requiring further development. If non-model platforms are successfully deployed, new avenues for production of fuels and chemicals from renewable feedstocks or waste materials will emerge. Here, the challenges and opportunities for extreme thermophiles as metabolic engineering platforms are discussed.}, journal={Current Opinion in Biotechnology}, publisher={Elsevier BV}, author={Crosby, James R and Laemthong, Tunyaboon and Lewis, April M and Straub, Christopher T and Adams, Michael WW and Kelly, Robert M}, year={2019}, month={Oct}, pages={55–64} }
 @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{conway_crosby_hren_southerland_lee_lunin_alahuhta_himmel_bomble_adams_et al._2018, title={Novel multidomain, multifunctional glycoside hydrolases from highly lignocellulolytic Caldicellulosiruptor species}, volume={64}, ISSN={["1547-5905"]}, DOI={10.1002/aic.16354}, abstractNote={Biological hydrolysis of microcrystalline cellulose is an uncommon feature in the microbial world, especially among bacteria and archaea growing optimally above 70°C (the so‐called extreme thermophiles). In fact, among this group only certain species in the genus Caldicellulosiruptor are capable of rapid and extensive cellulose degradation. Four novel multidomain glycoside hydrolases (GHs) from Caldicellulosiruptor morganii and Caldicellulosiruptor danielii were produced recombinantly in Caldicellulosiruptor bescii and characterized. These GHs are structurally organized with two or three catalytic domains flanking carbohydrate binding modules from Family 3. Collectively, these enzymes represent GH families 5, 9, 10, 12, 44, 48, and 74, and hydrolyze crystalline cellulose, glucan, xylan, and mannan, the primary carbohydrates in plant biomass. Degradation of microcrystalline cellulose by cocktails of GHs from three Caldicellulosiruptor species demonstrated that synergistic interactions enable mixtures of multiple enzymes to outperform single enzymes, suggesting a community mode of action for lignocellulose utilization in thermal environments. © 2018 American Institute of Chemical Engineers AIChE J, 64: 4218–4228, 2018}, number={12}, journal={AICHE JOURNAL}, author={Conway, Jonathan M. and Crosby, James R. and Hren, Andrew P. and Southerland, Robert T. and Lee, Laura L. and Lunin, Vladimir V. and Alahuhta, Petri and Himmel, Michael E. and Bomble, Yannick J. and Adams, Michael W. W. and et al.}, year={2018}, month={Dec}, pages={4218–4228} }
 @article{conway_crosby_mckinley_seals_adams_kelly_2018, title={Parsing in vivo and in vitro contributions to microcrystalline cellulose hydrolysis by multidomain glycoside hydrolases in the Caldicellulosiruptor bescii secretome}, volume={115}, ISSN={["1097-0290"]}, DOI={10.1002/bit.26773}, abstractNote={Abstract}, number={10}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Conway, Jonathan M. and Crosby, James R. and McKinley, Bennett S. and Seals, Nathaniel L. and Adams, Michael W. W. and Kelly, Robert M.}, year={2018}, month={Oct}, pages={2426–2440} }