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References Associated with K. Bernard's Excel File Called “Review of Clostridium April 18 2017” NOTE: Many Older Species C

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References Associated with K. Bernard’s Excel file called “Review of Clostridium April 18 2017” NOTE: Many older species cited in the Excel file are solely linked to ref 1 (Collins et al, 1994) and / or ref 2 (Bergey’s manual, 2008). Most other references cited below are linked to taxa described AFTER 1994 or 2008 and historically were NOT cited in Collins and/or the Bergey’s chapter. References are only cited once; some references describe taxa which fell into multiple clusters. Literature cited (done April 19 2017) Cluster I references 1. Collins, MD, Lawson, PA, Willems, A, Cordoba, JJ, Fernandez-Garayzabal, J, Garcia, P, Cai, J, Hippe, H, Farrow, JA. 1994. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int. J. Syst. Bacteriol. 44:812-826. 2. Rainey, FA, Hollen, BJ, Small, A. 2008. Genus I. Clostridium Prazmowski 1880, 23 AL in Bergey's Manual of Systematic Bacteriology 2nd ed., p. 738-828. In De Vos, P, Garrity, GM, Jones, D, Krieg, NR, Ludwig, W, Rainey, FA, Schleifer, K, Whitman, WB (eds.), Bergey's Manual of Systematic Bacteriology 2nd ed., 2nd ed., vol. 3 The Firmicutes. Springer, Dordrecht Heidelberg London New York. 3. Orlygsson, J, Krooneman, J, Collins, MD, Pascual, C, Gottschalk, G. 1996. Clostridum acetireducens sp. nov., a novel amino acid-oxidizing, acetate-reducing anaerobic bacterium. Int. J. Syst. Bacteriol. 46:454-459. 4. Kuhner, CH, Matthies, C, Acker, G, Schmittroth, M, Gossner, AS, Drake, HL. 2000. Clostridium akagii sp. nov. and Clostridium acidisoli sp. nov.: acid-tolerant, N2-fixing clostridia isolated from acidic forest soil and litter. Int. J. Syst. Evol. Microbiol. 50 Pt 2:873-881. 5. Lee, YJ, Romanek, CS, Wiegel, J. 2007. Clostridium aciditolerans sp. nov., an acid-tolerant spore-forming anaerobic bacterium from constructed wetland sediment. Int. J. Syst. Evol. Microbiol. 57:311-315. 6. Kim, S, Jeong, H, Chun, J. 2007. Clostridium aestuarii sp. nov., from tidal flat sediment. Int. J. Syst. Evol. Microbiol. 57:1315-1317. 7. Lawson, P, Dainty, RH, Kristiansen, N, Berg, J, Collins, MD. 1994. Characterization of a psychrotrophic Clostridium causing spoilage in vacuum-packed cooked pork: description of Clostridium algidicarnis sp. nov. Lett. Appl. Microbiol. 19:153-157. 8. Wu, YF, Zheng, H, Wu, QL, Yang, H, Liu, SJ. 2014. Clostridium algifaecis sp. nov., an anaerobic bacterial species from decomposing algal scum. Int. J. Syst. Evol. Microbiol. 64:3844-3848. 9. Shcherbakova, VA, Chuvilskaya, NA, Rivkina, EM, Pecheritsyna, SA, Laurinavichius, KS, Suzina, NE, Osipov, GA, Lysenko, AM, Gilichinsky, DA, Akimenko, VK. 2005. Novel psychrophilic anaerobic spore-forming bacterium from the overcooled water brine in permafrost: description Clostridium algoriphilum sp. nov. Extremophiles. 9:239-246. 10. O'Neal, L, Obregon-Tito, AJ, Tito, RY, Ozga, AT, Polo, SI, Lewis, CM,Jr, Lawson, PA. 2015. Clostridium amazonense sp. nov. an obliqately anaerobic bacterium isolated from a remote Amazonian community in Peru. Anaerobe. 35:33-37. 11. Jung, MY, Park, IS, Kim, W, Kim, HL, Paek, WK, Chang, YH. 2010. Clostridium arbusti sp. nov., an anaerobic bacterium isolated from pear orchard soil. Int. J. Syst. Evol. Microbiol. 60:2231-2235. 12. Hahnke, S, Striesow, J, Elvert, M, Mollar, XP, Klocke, M. 2014. Clostridium bornimense sp. nov., isolated from a mesophilic, two-phase, laboratory-scale biogas reactor. Int. J. Syst. Evol. Microbiol. 64:2792-2797. 13. Spring, S, Merkhoffer, B, Weiss, N, Kroppenstedt, RM, Hippe, H, Stackebrandt, E. 2003. Characterization of novel psychrophilic clostridia from an Antarctic microbial mat: description of Clostridium frigoris sp. nov., Clostridium lacusfryxellense sp. nov., Clostridium bowmanii sp. nov. and Clostridium psychrophilum sp. nov. and reclassification of Clostridium laramiense as Clostridium estertheticum subsp. laramiense subsp. nov. Int. J. Syst. Evol. Microbiol. 53:1019-1029. 14. Bowman, KS, Dupre, RE, Rainey, FA, Moe, WM. 2010. Clostridium hydrogeniformans sp. nov. and Clostridium cavendishii sp. nov., hydrogen-producing bacteria from chlorinated solvent-contaminated groundwater. Int. J. Syst. Evol. Microbiol. 60:358-363. 15. Kelly, WJ, Asmundson, RV, Hopcroft, DH. 1987. Isolation and characterization of a strictly anaerobic, cellulolytic spore former: Clostridium chartatabidum sp. nov. Arch. Microbiol. 147:169-173. 16. Kelly, WJ, Asmundson, RV, Hopcroft, DH. 1996. In Validation of the Publication of New Names and New Combinations previously effectively published outside the IJSB. List no. 57. Int. J. Syst. Bacteriol. 46:625-626. 17. Inglett, KS, Bae, HS, Aldrich, HC, Hatfield, K, Ogram, AV. 2011. Clostridium chromiireducens sp. nov., isolated from Cr(VI)-contaminated soil. Int. J. Syst. Evol. Microbiol. 61:2626-2631. 18. Greetham, HL, Gibson, GR, Giffard, C, Hippe, H, Merkhoffer, B, Steiner, U, Falsen, E, Collins, MD. 2003. Clostridium colicanis sp. nov., from canine faeces. Int. J. Syst. Evol. Microbiol. 53:259-262. 19. Biebl, H, Sproer, C. 2002. Taxonomy of the glycerol fermenting clostridia and description of Clostridium diolis sp. nov. Syst. Appl. Microbiol. 25:491-497. 20. Biebl, H, Sproer, C. 2003. In Validation of the Publication of New Names and New Combinations previously effectively published outside the IJSB. List no. 91. Int. J. Syst. Bacteriol. 53:627-628. 21. Liou, JS, Balkwill, DL, Drake, GR, Tanner, RS. 2005. Clostridium carboxidivorans sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov. Int. J. Syst. Evol. Microbiol. 55:2085-2091. 22. Tamburini, E, Daly, S, Steiner, U, Vandini, C, Mastromei, G. 2001. Clostridium felsineum and Clostridium acetobutylicum are two distinct species that are phylogenetically closely related. Int. J. Syst. Evol. Microbiol. 51:963-966. 23. Broda, DM, Lawson, PA, Bell, RG, Musgrave, DR. 1999. Clostridium frigidicarnis sp. nov., a psychrotolerant bacterium associated with 'blown pack' spoilage of vacuum-packed meats. Int. J. Syst. Bacteriol. 49 Pt 4:1539- 1550. 24. Kim, S, Jeong, H, Kim, S, Chun, J. 2006. Clostridium ganghwense sp. nov., isolated from tidal flat sediment. Int. J. Syst. Evol. Microbiol. 56:691-693. 25. Broda, DM, Saul, DJ, Lawson, PA, Bell, RG, Musgrave, DR. 2000. Clostridium gasigenes sp. nov., a psychrophile causing spoilage of vacuum-packed meat. Int. J. Syst. Evol. Microbiol. 50 Pt 1:107-118. 26. Mountfort, DO, Rainey, FA, Burghardt, J, Stackebrandt, E. 1994. Clostridium grantii sp. nov., a new obligately anaerobic, alginolytic bacterium isolated from mullet gut. Arch. Microbiol. 162:173-179. 27. Ruan, Z, Wang, Y, Zhang, C, Song, J, Zhai, Y, Zhuang, Y, Wang, H, Chen, X, Li, Y, Zhao, B, Zhao, B. 2014. Clostridium huakuii sp. nov., an anaerobic, acetogenic bacterium isolated from methanogenic consortia. Int. J. Syst. Evol. Microbiol. 64:4027-4032. 28. Padden, AN, Dillon, VM, Edmonds, J, Collins, MD, Alvarez, N, John, P. 1999. An indigo-reducing moderate thermophile from a woad vat, Clostridium isatidis sp. nov. Int. J. Syst. Bacteriol. 49 Pt 3:1025-1031. 29. Yin, Q, Tao, Y, Zhu, X, Zhou, Y, He, X, Cheng, L, Huang, Y, Li, D. 2015. Clostridium liquoris sp. nov., isolated from a fermentation pit used for the production of Chinese Strong-Flavored Liquor. Int. J. Syst. Evol. Microbiol. 30. Tanner, RS, Miller, LM, Yang, D. 1993. Clostridium ljungdahlii sp. nov., an acetogenic species in clostridial rRNA homology group I. Int. J. Syst. Bacteriol. 43:232-236. 31. Cirne, DG, Delgado, OD, Marichamy, S, Mattiasson, B. 2006. Clostridium lundense sp. nov., a novel anaerobic lipolytic bacterium isolated from bovine rumen. Int. J. Syst. Evol. Microbiol. 56:625-628. 32. Wang, Q, Wang, CD, Li, CH, Li, JG, Chen, Q, Li, YZ. 2015. Clostridium luticellarii sp. nov., isolated from a mud cellar used for producing strong aromatic liquors. Int. J. Syst. Evol. Microbiol. 65:4730-4733. 33. Lawson, PA, Rainey, FA. 2016. Proposal to restrict the genus Clostridium (Prazmowski) to Clostridium butyricum and related species. Int. J. Syst. Evol. Microbiol. 66:1009-1016. 34. Suresh, K, Prakash, D, Rastogi, N, Jain, RK. 2007. Clostridium nitrophenolicum sp. nov., a novel anaerobic p- nitrophenol-degrading bacterium, isolated from a subsurface soil sample. Int. J. Syst. Evol. Microbiol. 57:1886- 1890. 35. Horino, H, Ito, M, Tonouchi, A. 2015. Clostridium oryzae sp. nov., from soil of a Japanese rice field. Int. J. Syst. Evol. Microbiol. 65:943-951. 36. Wilde, E, Collins, MD, Hippe, H. 1997. Clostridium pascui sp. nov., a new glutamate-fermenting sporeformer from a pasture in Pakistan. Int. J. Syst. Bacteriol. 47:164-170. 37. Mechichi, T, Fardeau, ML, Labat, M, Garcia, JL, Verhe, F, Patel, BK. 2000. Clostridium peptidivorans sp. nov., a peptide-fermenting bacterium from an olive mill wastewater treatment digester. Int. J. Syst. Evol. Microbiol. 50 Pt 3:1259-1264. 38. Lanjekar, VB, Marathe, NP, Shouche, YS, Ranade, DR. 2015. Clostridium punense sp. nov., an obligate anaerobe isolated from healthy human faeces. Int. J. Syst. Evol. Microbiol. 65:4749-4756. 39. Keis, S, Shaheen, R, Jones, DT. 2001. Emended descriptions of Clostridium acetobutylicum and Clostridium beijerinckii, and descriptions of Clostridium saccharoperbutylacetonicum sp. nov. and Clostridium saccharobutylicum sp. nov. Int. J. Syst. Evol. Microbiol. 51:2095-2103. 40. Alam, SI, Dixit, A, Reddy, GS, Dube, S, Palit, M, Shivaji, S, Singh, L. 2006. Clostridium schirmacherense sp. nov., an obligately anaerobic, proteolytic, psychrophilic bacterium isolated from lake sediment of Schirmacher Oasis, Antarctica. Int. J. Syst. Evol. Microbiol. 56:715-720. 41. Mishra, AK, Lagier, JC, Robert, C, Raoult, D, Fournier, PE. 2012. Non-contiguous finished genome sequence and description of Clostridium senegalense sp. nov. Stand. Genomic Sci. 6:386-395. 42. Mishra, AK, Lagier, J-, Robert, C, Raoult, D, Fournier, P-. 2015. Validation List no. 165 List of New Names and New Combinations previously effectively but not validly published. Int. J. System. Evol. Microbiol. Int. J. Syst. Evol. Microbiol. 65:2777-2783. 43. Sallam, A, Steinbuchel, A. 2009. Clostridium sulfidigenes sp.
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    International Journal of Systematic and Evolutionary Microbiology (2009), 59, 981–986 DOI 10.1099/ijs.0.001719-0 Clostridium sufflavum sp. nov., isolated from a methanogenic reactor treating cattle waste Tomomi Nishiyama, Atsuko Ueki, Nobuo Kaku and Katsuji Ueki Correspondence Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Atsuko Ueki Japan [email protected] A strictly anaerobic, mesophilic, cellulolytic bacterial strain, designated CDT-1T, was isolated from rice-straw residue from a methanogenic reactor treating waste from cattle farms. The isolation was performed using enrichment culture with filter paper as a substrate. Cells stained Gram-negative, but reacted Gram-positively in the KOH test. Cells were slightly curved rods and were motile by means of peritrichous flagella. The strain produced yellow pigment when grown on filter-paper fragments. Although spore formation was not confirmed microscopically, thermotolerant cells were produced when the strain was grown on filter paper. The optimum temperature for growth was 33 6C and the optimum pH was 7.4. Oxidase, catalase and nitrate-reducing activities were absent. The strain utilized xylose, fructose, glucose, cellobiose, xylooligosaccharide, cellulose (filter-paper fragments and ball-milled filter paper) and xylan. The major fermentation products were acetate, ethanol, H2 and CO2. The major cellular fatty acids were iso-C15 : 0, iso-C14 : 0 and C16 : 0 DMA. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The genomic DNA G+C content was 40.7 mol%. On the basis of 16S rRNA gene sequence similarities, strain CDT-1T could be placed in cluster III of the genus Clostridium, being closely related to type strains of Clostridium hungatei (96.6 % sequence similarity), Clostridium termitidis (96.2 %) and Clostridium papyrosolvens (96.1 %).
  • A Report of 22 Unrecorded Bacterial Species in Korea, Isolated from Namhangang

    A Report of 22 Unrecorded Bacterial Species in Korea, Isolated from Namhangang

    Journal114 of Species Research 7(2):114-122, 2018JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2 A report of 22 unrecorded bacterial species in Korea, isolated from Namhangang Chaeyun Baek1 and Hana Yi1,2,* 1Department of Public Health Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea 2School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea *Correspondent: [email protected] As part of a larger study of indigenous prokaryotic species diversity in South Korea, various samples from Namhangang were subjected to analyses. Fresh water, underwater sediment, and moss-inhabiting aerobic and anaerobic bacteria were isolated. 22 of the isolates were identified as unrecorded bacterial species in Korea that had ≥98.7% 16S rRNA gene sequence similarity with published species. The aerobic strains isolated were Kurthia gibsonii and Massilia plicata. Also identified were four facultative anaerobic strains: Bacillus hisashii, Enterococcus rotai, Paenibacillus vini, and Pediococcus pentosaceus. 16 strictly anaerobic strains were identified as Bacteroides xylanolyticus, Carnobacterium maltaromaticum, Clostridium argentinense, Clostridium beijerinckii, Clostridium butyricum, Clostridium cavendishii, Clostridium diolis, Clostridium frigidicarnis, Clostridium perfringens, Clostridium saccharoperbutylacetonicum, Clostridium sphenoides, Clostridium subterminale, Cutibacterium acnes, Paraclostridium bifermentans, Prevotella paludivivens, and Romboutsia lituseburensis. Based on the examination of morphological, cultural, physiological, and biochemical properties of the isolates, descriptive information of these previously unrecorded species is provided here. Keywords: anaerobes, Namhangang, unrecorded species Ⓒ 2018 National Institute of Biological Resources DOI:10.12651/JSR.2018.7.2.114 INTRODUCTION and Jungnyeongcheon, are freshwater rivers with 10.19 km2, 69.11 km2, 150.5 km2, and 130.19 km2 areas, respec- While molecular methods have supplanted traditional tively.
  • Wo 2010/096550 A2

    Wo 2010/096550 A2

    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date 26 August 2010 (26.08.2010) WO 2010/096550 A2 (51) International Patent Classification: (74) Agents: SALIWANCHIK, David, R. et al; Saliwanchik, C12N 1/20 (2006.01) A61K 35/74 (2006.01) Lloyd & Saliwanchik, P.O. Box 142950, Gainesville, FL A23C 9/123 (2006.01) C12R 1/225 (2006.01) 32614-2950 (US). (21) International Application Number: (81) Designated States (unless otherwise indicated, for every PCT/US2010/024575 kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, (22) International Filing Date: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, 18 February 2010 (18.02.2010) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (25) Filing Language: English HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, (26) Publication Language: English ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, (30) Priority Data: NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, 61/153,5 16 18 February 2009 (18.02.2009) US SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, 61/297,480 22 January 2010 (22.01 .2010) US TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (71) Applicant (for all designated States except US): UNI¬ (84) Designated States (unless otherwise indicated, for every VERSITY OF FLORIDA RESEARCH FOUNDA¬ kind of regional protection available): ARIPO (BW, GH, TION, INC.
  • Membrane Fouling and Visualisation Studies

    Membrane Fouling and Visualisation Studies

    The Potential of Water Hyacinth (Eicchornia crassipes) from Hartbeespoort dam in Biogas and Soil Ameliorant production, as a Solution to Water Weed Challenges Report to the WATER RESEARCH COMMISSION by A Roopnarain, R Adeleke, R Makofane, L Obi, M Lubinga Agricultural Research Council WRC Report No. 2543/1/18 ISBN 978-0-6392-0024-8 September 2018 Obtainable from Water Research Commission Private Bag X03 GEZINA, 0031 [email protected] or download from www.wrc.org.za DISCLAIMER This report has been reviewed by the Water Research Commission (WRC) and approved for publication. Approval does not signify that the contents necessarily reflect the views and policies of the WRC nor does mention of trade names or commercial products constitute endorsement or recommendation for use. Printed in the Republic of South Africa © Water Research Commission ii iii iv EXECUTIVE SUMMARY BACKGROUND The Hartbeespoort Dam is situated in the North West province of South Africa and is one of the most significant dams in the economic hub of the province and the Crocodile (West) Marico (CWM) Water Management Area (WMA). The dam is primarily utilised for domestic, industrial, agricultural and recreational purposes. The numerous ecosystem services provided by the dam contribute to its economic significance. These services include provisioning (the availability of water for abstraction), supporting services (holiday, commercial and residential) and regulatory (waste assimilation). City dwellers are frequently attracted to the large water body that is situated within a mountainous setting. This has contributed to the increasing importance of the dam as a regional tourist and recreational centre. The socio-economic activities and facilities available at the dam include holiday resorts, conference venues, weekend cottages, golf courses, fishing, boating and water-skiing.