(12) United States Patent (10) Patent No.: US 9,157,058 B2 Dalla-Betta Et Al

Total Page:16

File Type:pdf, Size:1020Kb

(12) United States Patent (10) Patent No.: US 9,157,058 B2 Dalla-Betta Et Al US009 157058E32 (12) United States Patent (10) Patent No.: US 9,157,058 B2 Dalla-Betta et al. (45) Date of Patent: Oct. 13, 2015 (54) METHOD AND APPARATUS FOR GROWING (56) References Cited MICROBIAL CULTURES THAT REQUIRE GASEOUSELECTRON DONORS, ELECTRON U.S. PATENT DOCUMENTS ACCEPTORS, CARBON SOURCES, OR 4,279,754 A 7, 1981 Pollock OTHER NUTRENTS 4,596,778 A 6, 1986 Hitzman 4,760,027 A 7, 1988 Sublette (71) Applicant: Kiverdi, Inc., Berkeley, CA (US) 4,859,588 A 8, 1989 Sublette 5,077,208 A 12/1991 Sublette 5,173,429 A 12/1992 Gaddy et al. (72) Inventors: Peter Dalla-Betta, Hayward, CA (US); 5,593,886 A 1/1997 Gaddy John S. Reed, Berkeley, CA (US) 5,616,288 A * 4/1997 McDonald ...................... 261/76 5,645,726 A 7, 1997 Pollock (73) Assignee: Kiverdi, Inc., Berkeley, CA (US) 5,650,070 A 7, 1997 Pollock 5,807,722 A 9/1998 Gaddy (*) Notice: Subject to any disclaimer, the term of this 5,821,111 A 10/1998 Grady et al. patent is extended or adjusted under 35 5,914,441 A 6/1999 Hunter et al. U.S.C. 154(b) by 0 days. (Continued) (21) Appl. No.: 13/715,430 FOREIGN PATENT DOCUMENTS (22) Filed: Dec. 14, 2012 EP O 131220 A2 1, 1985 EP O227774 B1 9, 1990 (65) Prior Publication Data (Continued) US 2013/O189763 A1 Jul. 25, 2013 OTHER PUBLICATIONS International Search Report and Written Opinion mailed Jun. 14. Related U.S. Application Data 2013 for Application No. PCT/US2012/069830. (60) Provisional application No. 61/570,773, filed on Dec. (Continued) 14, 2011. Primary Examiner —Nathan Bowers (51) Int. C. (74) Attorney, Agent, or Firm — Jill A. Jacobson CI2M I/00 (2006.01) CI2M 3/00 (2006.01) (57) ABSTRACT CI2N L/20 (2006.01) Compositions and methods and apparatus for growth and (52) U.S. C. maintenance of microorganisms and/or bioprocesses using CPC ................. CI2N 1/20 (2013.01); CI2M 29/02 one or more gases as electron donors, electron acceptors, (2013.01); C12M 29/18 (2013.01); C12M 43/04 carbon sources, or other nutrients, and for a bioprocess that (2013.01) converts hydrogen and carbon dioxide, or syngas, or producer (58) Field of Classification Search gas into lipid products, bio-based oils, or other biochemical CPC ...... C12M 23/40; C12M 27/00; C12M 27/18: products. C12M 27/24 See application file for complete search history. 23 Claims, 12 Drawing Sheets inlet waive controited by in-line sensors Press re-relief valve gas feed marifold Gas feed port media Siface SSS 2 Cell down-tube Liquid outlet liquid circulation pump Effluent tube US 9,157,058 B2 Page 2 (56) References Cited Bergmann et al., Assimilation of carbon dioxide by hydrogen bacte ria. J Biol Chem. Jan. 1958:230(1):13-24. U.S. PATENT DOCUMENTS Bernstein et al., Climate Change 2007: Synthesis Report. IPCC Ple nary XXVII. Valencia, Spain. Nov. 12-17, 2007. 51 pages. 5,989,513 A 11, 1999 Rai 6,043,022 A 3/2000 Lueking et al. Bilal et al., Thermo-electrochemical reduction of sulfate to sulfide 6,340,581 B1 1/2002 Gaddy using a graphite cathode. Journal of Applied Electrochemistry. Oct. 6,667,171 B2 12/2003 Bayless et al. 1998:28(10): 1073-1081. 6,972,188 B2 12/2005 Maekawa et al. Bird et al., TCERs or ICERs? Choices of CDM-credits for afforsta 7,176,017 B2 2/2007 Parent et al. tion and reforestation. CDM Investment Newsletter. BEA Interna 7.285.402 B2 10/2007 Gaddy et al. tional and the Climate Business Network. 2004: 14-6. 7,332,077 B2 2, 2008 Pollock Boetius, Microfauna Macrofauna Interaction in the Seafloor: Les 2007/0275447 A1 11, 2007 Lewis et al. 2008/0302721 A1* 12/2008 Lanting et al. ................ 210,601 sons from the Tubeworm. PLoS Biol. 2005:3(3):e 102. 2009/0130704 A1* 5/2009 Gyure ............................. 435/41 Bongers, Energy generation and utilization in hydrogen bacteria. J 2010/0105116 A1 4/2010 Datta et al. Bacteriol. Oct. 1970; 104(1): 145-51. 2010, 0120104 A1 5, 2010 Reed Burton et al., Geologic carbon sequestration strategies for California: 2011/028.1314 A1 1 1/2011 Lynch The assembly bill 1925 report to the California legislature. Draft Staff 2011/0283618 A1 11/2011 Martin et al. Report. California Energy Commision. Sep. 2007. 161 pages. 2012,0003705 A1 1/2012 Jin et al. CarloZZi et al., Green energy from Rhodopseudomonas palustris 2013/0065285 A1 3/2013 Sefton ........................... 435/135 2013,0078690 A1 3/2013 Reed grown at low to high irradiance values, under fed-batch operational 2013/O149755 A1 6, 2013 Reed et al. conditions. Biotechnol Lett. Apr. 2010;32(4):477-81. Epub Dec. 16. 2014.0024.091 A1 1/2014 Reed et al. 2009. Chakraborty et al., Effect of physical irradiation and chemical FOREIGN PATENT DOCUMENTS mutagen treatment on methane production by methanogenic bacte ria. World Journal of Microbiology and Biotechnology. 2003; 19:145 EP 1099762 A1 5, 2001 50. EP 1264895 A1 12/2002 Chen et al., Coupling of Carbon Dioxide Fixation to the JP HO6-1697.83 A 6, 1994 Oxyhydrogen Reaction in the Isolated Chloroplast of WO WO 86,07604 A1 12, 1986 WO WO98,00558 A1 1, 1998 Chlamydomonas reinhardtii. Plant Physiol. Nov. 1992: 100(3): 1361 WO WOO2,08438 A2 1, 2002 5. WO WO 2008.000558 A1 1, 2008 Cheng et al., Direct biological conversion of electrical current into WO WO 2008, 128331 A1 10, 2008 methane by electromethanogenesis. Environ SciTechnol. May 15, WO WO 2011/0561.83 A1 5, 2011 2009:43(10):3953-8. WO WO 2011, 1398.04 A2 11/2011 Climate change draft scoping plan: A framework for change. Cali OTHER PUBLICATIONS fornia Air Resources Board. Technical Report. State of California. Jun. 2008. 93 pages. No Author Listed Discovery may lead to the creation of biofuel Contietal. Annual Energy Outlook 2008: With Projections to 2030. DOE Energy Information Administration. Jun. 2008. 224 pages. from CO2 in the atmosphere. SciTech Daily. Mar. 26, 2013. <http:// Cotter et al., Influence of process parameters on growth of scitechdaily.com/discovery-may-lead-to-the-creation-of-biofuel Clostridium liungaahlii and Clostridium autoethanogenium on Syn from-co2-in-the-atmospheref>. thesis gas. Enzyme and Microbial Technology. May 6, No Author Listed Evaluating the Risk of Encountering Non-hydro 2009:44(5):281-8. carbon Gas Contaminants (CO2, N2, H2S) Using Gas Geochemistry. Crueger, Biotechnology: A textbook of industrial microbiology. Weatherfold Laboratories. 2011. <http://www.gaschem.com/evalu. Sinauer Associates: Sunderland, Mass. 1990: 124-74. html>. Dushku et al., Carbon sequestration through changes in land use in No Author Listed Global Trends in Sustainable Energy Investment Oregon: Costs and opportunities. PIER Collaborative Report. Cali 2007. United Nations Environmental Programme and New Energy fornia Energy Commission. Oct. 2007. 99 pages. Finance Ltd. 2007. 54 pages. Dworkin et al., The prokaryotes: A handbook on the biology of No Author Listed U.S. DO Energy Efficiency & Renewable Energy bacteria. Third Edition. Vol. 5: Proteobacteria: Alpha and Beta Sub Biomass Program, National Algal Biofuels Technology Roadmap, classes. 2006. 964 pages. May 2010. 140 pages. Eichler et al., Oxidation of primary aliphatic alcohols by No Author Listed Vital Climate Change Graphics. United Nations Acetobacterium carbinolicum sp. Nov., a Honoacetogenic Environmetal Programme and Grid Arendal. Feb. 2005. 24 pages. anaerobe. Arch Microbiol. 1984; 140:147-52. Ackerman, Financing the Climate Mitigation and Adaptation Mea Elvert et al., Archaea mediating anaerobic methane oxidation in Sures in Developing Countries. No. 57, G-24 Discussion Papers. deep-sea sediments at cold seeps of the eastern Aleutian Subduction United Nations Conference on Trade and Development. 2009. 26 Zone. Organic Geochemistry. 2000:31:1175-87. pageS. Erbes et al., Kinetics of the Oxyhydrogen Reaction in the Presence Ahmed et al., Effects of biomass-generated producer gas constituents and Absence of Carbon Dioxide in Scenedesmus obliquus. Plant on cell growth, product distribution and hydrogenase activity of Physiol. Jan. 1981:67(1): 129-32. clostridium carboxidivorans P7T. Biomass and Bioenergy. Ercole et al., Deposition of calcium carbonate in karst caves: role of 2006:30:665-72. bacteria in Stiffe's Cave. IntJ Speleol. 2001:30:69-79. Ammann et al., Gas consumption and growth rate of Fischer et al., Selection and optimization of microbial hosts for Hydrogenomonas eutropha in continuous culture. Appl Microbiol. biofuels production. Metab Eng. Nov. 2008; 10(6):295-304. Jun. 1968; 16(6):822-6. Girguis et al., Growth and methane oxidation rates of anaerobic Atkinson et al., Biochemical engineering and biotechnology hand methanotrophic archaea in a continuous-flow bioreactor. Appl book. Second Edition. Stockton Press. New York. 1991:243-364. Environ Microbiol. Sep. 2003:69(9):5472-82. Bailey et al., Biochemical Engineering Fundamentals. 2nd Edition. Gouda et al., Bioremediation of kerosene I: A case study in liquid McGraw-Hill: New York. Feb. 1, 1986:383-384 and 620-622. media. Chemosphere. Nov. 2007:69(11): 1807-14. Epub Jul. 16, BCC Research. 2011. Carbon Capture & Storage Technologies— 2007. EGYO37B, online Available at: http://www.bccresearch.com/mar Heise et al., Sodium dependence of acetate formation by the ket-research/energy-and-resources/carbon-capture-storage-technol acetogenic bacterium Acetobacterium WOOdii. J Bacteriol. Oct. ogy-egy037b.html. 1989; 171(10):5473-8. US 9,157,058 B2 Page 3 (56) References Cited Piccolo et al., Atechno-economic comparison between two technolo gies for bioethanol production from lignocellulose. Biomass and OTHER PUBLICATIONS Bioenergy. Mar. 2009:33(3):478-91. Reducing U.S. greenhouse gas emissions: How much at what cost? Heiskanen et al., The effect of syngas composition on the growth and U.S.
Recommended publications
  • Genome-Wide Studies of Mycolic Acid Bacteria: Computational Identification And
    Genome-wide Studies of Mycolic Acid Bacteria: Computational Identification and Analysis of a Minimal Genome Dissertation by Frederick Kinyua Kamanu In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia December, 2012 2 EXAMINATION COMMITTEE APPROVALS FORM The dissertation of Frederick Kinyua Kamanu is approved by the examination committee. Committee Chairperson: Prof. Vladimir B. Bajic Committee Co-Chair: Dr. John A.C. Archer Committee Member: Prof. Pierre Magistretti Committee Member: Prof. Xin Gao Committee Member: Prof. Christoph Gehring Committee Member: Prof. Kothandaraman Narasimhan 3 COPYRIGHT © December, 2012 Frederick Kinyua Kamanu All Rights Reserved 4 ABSTRACT Genome wide studies of mycolic acid bacteria: Computational Identification and Analysis of a Minimal Genome Frederick Kinyua Kamanu The mycolic acid bacteria are a distinct suprageneric group of asporogenous Gram- positive, high GC-content bacteria, distinguished by the presence of mycolic acids in their cell envelope. They exhibit great diversity in their cell and morphology; although primarily non-pathogens, this group contains three major pathogens Mycobacterium leprae, Mycobacterium tuberculosis complex, and Corynebacterium diphtheria. Although the mycolic acid bacteria are a clearly defined group of bacteria, the taxonomic relationships between its constituent genera and species are less well defined. Two approaches were tested for their suitability in describing the taxonomy of the group. First, a Multilocus Sequence Typing (MLST) experiment was assessed and found to be superior to monophyletic (16S small ribosomal subunit) in delineating a total of 52 mycolic acid bacterial species. Phylogenetic inference was performed using the neighbor- joining method.
    [Show full text]
  • Microorganisms
    microorganisms Article Comparative Genomics of the Rhodococcus Genus Shows Wide Distribution of Biodegradation Traits Daniel Garrido-Sanz , Miguel Redondo-Nieto , Marta Martín and Rafael Rivilla * Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain; [email protected] (D.G.-S.); [email protected] (M.R.-N.); [email protected] (M.M.) * Correspondence: [email protected] Received: 15 April 2020; Accepted: 20 May 2020; Published: 21 May 2020 Abstract: The genus Rhodococcus exhibits great potential for bioremediation applications due to its huge metabolic diversity, including biotransformation of aromatic and aliphatic compounds. Comparative genomic studies of this genus are limited to a small number of genomes, while the high number of sequenced strains to date could provide more information about the Rhodococcus diversity. Phylogenomic analysis of 327 Rhodococcus genomes and clustering of intergenomic distances identified 42 phylogenomic groups and 83 species-level clusters. Rarefaction models show that these numbers are likely to increase as new Rhodococcus strains are sequenced. The Rhodococcus genus possesses a small “hard” core genome consisting of 381 orthologous groups (OGs), while a “soft” core genome of 1253 OGs is reached with 99.16% of the genomes. Models of sequentially randomly added genomes show that a small number of genomes are enough to explain most of the shared diversity of the Rhodococcus strains, while the “open” pangenome and strain-specific genome evidence that the diversity of the genus will increase, as new genomes still add more OGs to the whole genomic set. Most rhodococci possess genes involved in the degradation of aliphatic and aromatic compounds, while short-chain alkane degradation is restricted to a certain number of groups, among which a specific particulate methane monooxygenase (pMMO) is only found in Rhodococcus sp.
    [Show full text]
  • Investigation of New Actinobacteria for the Biodesulphurisation of Diesel Fuel
    Investigation of new actinobacteria for the biodesulphurisation of diesel fuel Selva Manikandan Athi Narayanan A thesis submitted in partial fulfilment of the requirements of Edinburgh Napier University, for the award of Doctor of Philosophy May 2020 Abstract Biodesulphurisation (BDS) is an emerging technology that utilises microorganisms for the removal of sulphur from fossil fuels. Commercial-scale BDS needs the development of highly active bacterial strains which allow easier downstream processing. In this research, a collection of actinobacteria that originated from oil-contaminated soils in Russia were investigated to establish their phylogenetic positions and biodesulphurisation capabilities. The eleven test strains were confirmed as members of the genus Rhodococcus based on 16S rRNA and gyrB gene sequence analysis. Two organisms namely strain F and IEGM 248, confirmed as members of the species R. qingshengii and R. opacus, respectively based on the whole- genome sequence based OrthoANIu values, exhibited robust biodesulphurisation of dibenzothiophene (DBT) and benzothiophene (BT), respectively. R. qingshengii strain F was found to convert DBT to hydroxybiphenyl (2-HBP) with DBTO and DBTO2 as intermediates. The DBT desulphurisation genes of strain F occur as a cluster and share high sequence similarity with the dsz operon of R. erythropolis IGTS8. Rhodococcus opacus IEGM 248 could convert BT into benzofuran. The BDS reaction of both strains follows the well-known 4S pathway of desulphurisation of DBT and BT. When cultured directly in a biphasic growth medium containing 10% (v/v) oil (n-hexadecane or diesel) containing 300 ppm sulphur, strain F formed a stable oil-liquid emulsion, making it unsuitable for direct industrial application despite the strong desulphurisation activity.
    [Show full text]
  • A Novel Approach to the Discovery of Natural Products from Actinobacteria Rahmy Tawfik University of South Florida, [email protected]
    University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 3-24-2017 A Novel Approach to the Discovery of Natural Products From Actinobacteria Rahmy Tawfik University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the Microbiology Commons Scholar Commons Citation Tawfik, Rahmy, "A Novel Approach to the Discovery of Natural Products From Actinobacteria" (2017). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/6766 This Thesis is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. A Novel Approach to the Discovery of Natural Products From Actinobacteria by Rahmy Tawfik A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science Department of Cell Biology, Microbiology & Molecular Biology College of Arts and Sciences University of South Florida Major Professor: Lindsey N. Shaw, Ph.D. Edward Turos, Ph.D. Bill J. Baker, Ph.D. Date of Approval: March 22, 2017 Keywords: Secondary Metabolism, Soil, HPLC, Mass Spectrometry, Antibiotic Copyright © 2017, Rahmy Tawfik Acknowledgements I would like to express my gratitude to the people who have helped and supported me throughout this degree for both scientific and personal. First, I would like to thank my mentor and advisor, Dr. Lindsey Shaw. Although my academics were lacking prior to entering graduate school, you were willing to look beyond my shortcomings and focus on my strengths.
    [Show full text]
  • Characterization of Actinobacteria Degrading and Tolerating Organic Pollutants and Tolerating Organic Pollutants
    Characterization of Actinobacteria Degrading Characterization of Actinobacteria Degrading and Tolerating Organic Pollutants and Tolerating Organic Pollutants Irina Tsitko Irina Tsitko Division of Microbiology Division of Microbiology Department of Applied Chemistry and Microbiology Department of Applied Chemistry and Microbiology Faculty of Agriculture and Forestry Faculty of Agriculture and Forestry University of Helsinki University of Helsinki Academic Dissertation in Microbiology Academic Dissertation in Microbiology To be presented, with the permission of the Faculty of Agriculture and Forestry of the To be presented, with the permission of the Faculty of Agriculture and Forestry of the University of Helsinki, for public criticism in Auditorium 1015 at Viikki Biocentre, University of Helsinki, for public criticism in Auditorium 1015 at Viikki Biocentre, Viikinkaari 5, on January 12th, 2007, at 12 o’clock noon. Viikinkaari 5, on January 12th, 2007, at 12 o’clock noon. Helsinki 2007 Helsinki 2007 Supervisor: Professor Mirja Salkinoja-Salonen Supervisor: Professor Mirja Salkinoja-Salonen Department of Applied Chemistry and Microbiology Department of Applied Chemistry and Microbiology University of Helsinki University of Helsinki Helsinki, Finland Helsinki, Finland Reviewers Doctor Anja Veijanen Reviewers Doctor Anja Veijanen Department of Biological and Environmental Science Department of Biological and Environmental Science University of Jyväskylä University of Jyväskylä Jyväskylä, Finland Jyväskylä, Finland Docent Merja Kontro Docent Merja Kontro University of Helsinki University of Helsinki Department of Ecological and Environmental Sciences Department of Ecological and Environmental Sciences Lahti, Finland Lahti, Finland Opponent: Professor Edward R.B. Moore, Opponent: Professor Edward R.B. Moore, Department of Clinical Bacteriology Department of Clinical Bacteriology Sahlgrenska University Hospital, Sahlgrenska University Hospital, Göteborg University Göteborg University Göteborg, Sweden.
    [Show full text]
  • An Innovative Approach to Resolve the Structure of Complex Prokaryotic Taxa
    www.nature.com/scientificreports OPEN Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic Received: 18 July 2016 Accepted: 08 November 2016 taxa Published: 07 December 2016 Vartul Sangal1, Michael Goodfellow2, Amanda L. Jones1, Edward C. Schwalbe1, Jochen Blom3, Paul A. Hoskisson4 & Iain C. Sutcliffe1 Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genusRhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance. It is common knowledge that prokaryotes are widely distributed in nature though the lack of understanding about their abundance and the scale of their diversity feature among the major challenges facing microbiologists1–3.
    [Show full text]
  • Lipid Accumulation by Rhodococcus Rhodochrous
    Mississippi State University Scholars Junction Theses and Dissertations Theses and Dissertations 1-1-2016 Lipid Accumulation by Rhodococcus Rhodochrous Sara Ashley Shieldsenard Follow this and additional works at: https://scholarsjunction.msstate.edu/td Recommended Citation Shieldsenard, Sara Ashley, "Lipid Accumulation by Rhodococcus Rhodochrous" (2016). Theses and Dissertations. 2958. https://scholarsjunction.msstate.edu/td/2958 This Dissertation - Open Access is brought to you for free and open access by the Theses and Dissertations at Scholars Junction. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Scholars Junction. For more information, please contact [email protected]. Template C v3.0 (beta): Created by J. Nail 06/2015 Lipid accumulation by Rhodococcus rhodochrous By TITLE PAGE Sara Ashley Shields-Menard A Dissertation Submitted to the Faculty of Mississippi State University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biological Sciences in the Department of Biological Sciences Mississippi State, Mississippi May 2016 Copyright by COPYRIGHT PAGE Sara Ashley Shields-Menard 2016 Lipid accumulation by Rhodococcus rhodochrous By APPROVAL PAGE Sara Ashley Shields-Menard Approved: ____________________________________ Janet R. Donaldson (Major Professor) ____________________________________ William Todd French (Committee Member) ____________________________________ Gary N. Ervin (Committee Member) ____________________________________
    [Show full text]
  • Diversity of Culturable Nocardioform Actinomycetes from Wastewater Treatment Plants in Spain and Their Role in the Biodegradability of Aromatic Compounds
    Document downloaded from: http://hdl.handle.net/10251/104253 This paper must be cited as: Soler Hernández, A.; García Hernández, J.; Zornoza-Zornoza, AM.; Alonso Molina, JL. (2017). Diversity of culturable nocardioform actinomycetes from wastewater treatment plants in Spain and their role in the biodegradability of aromatic compounds. Environmental Technology. 39(2):172-181. doi:10.1080/09593330.2017.1296897 The final publication is available at https://doi.org/10.1080/09593330.2017.1296897 Copyright Taylor & Francis Additional Information 1 Diversity of culturable nocardioform actinomycetes from wastewater 2 treatment plants in Spain and their role in the biodegradability of 3 aromatic compounds 4 Albert Soler1,*, Andrés Zornoza3, Jorge García-Hernández2, José Luis Alonso3 5 6 1 Departmento Microbiología III , Universidad Complutense, 28040 Madrid, Spain 7 8 2 Departamento de Biotecnología, Universitat Politècnica de València, 46022 Valencia, Spain 9 10 3 Instituto de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, 46022 11 Valencia, Spain 12 13 14 15 *Corresponding Author 16 17 Dr. Albert Soler Hernández 18 19 Phone: +34 657 74 20 21 20 21 Fax: +34 91 394 49 64 22 23 e-mail: [email protected] 24 25 26 27 28 29 30 31 32 33 Abstract 34 1 35 Currently, urban and industrial wastewater treatment plants (WWTP) are mainly 36 focused on the reduction of biological oxygen demand and sometimes on the removal of 37 nutrients such as nitrogen and phosphorus. However, there are microorganisms that 38 interfere with the process. In these environments, there is a large diversity of 39 microorganisms that have not been studied in detail and that could provide real and 40 practical solutions to the problems that could be caused by the wastewater treatment 41 process.
    [Show full text]
  • Genome-Based Taxonomic Classification of the Phylum
    ORIGINAL RESEARCH published: 22 August 2018 doi: 10.3389/fmicb.2018.02007 Genome-Based Taxonomic Classification of the Phylum Actinobacteria Imen Nouioui 1†, Lorena Carro 1†, Marina García-López 2†, Jan P. Meier-Kolthoff 2, Tanja Woyke 3, Nikos C. Kyrpides 3, Rüdiger Pukall 2, Hans-Peter Klenk 1, Michael Goodfellow 1 and Markus Göker 2* 1 School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom, 2 Department Edited by: of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Martin G. Klotz, Germany, 3 Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States Washington State University Tri-Cities, United States The application of phylogenetic taxonomic procedures led to improvements in the Reviewed by: Nicola Segata, classification of bacteria assigned to the phylum Actinobacteria but even so there remains University of Trento, Italy a need to further clarify relationships within a taxon that encompasses organisms of Antonio Ventosa, agricultural, biotechnological, clinical, and ecological importance. Classification of the Universidad de Sevilla, Spain David Moreira, morphologically diverse bacteria belonging to this large phylum based on a limited Centre National de la Recherche number of features has proved to be difficult, not least when taxonomic decisions Scientifique (CNRS), France rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft *Correspondence: Markus Göker genome sequences
    [Show full text]
  • Document Downloaded From: This Paper Must Be Cited As: the Final Publication Is Available at Copyright
    Document downloaded from: http://hdl.handle.net/10251/39737 This paper must be cited as: Cuesta Amat, G.; Soler Hernández, A.; Alonso Molina, JL.; Ruvira, M.; Lucena, T.; Arahal, D.; Goodfellow, M. (2013). Pseudonocardia hispaniensis sp. nov., a novel actinomycete isolated from industrial wastewater activated sludge. Antonie van Leeuwenhoek. 103(1):135-142. doi:10.1007/s10482-012-9792-1. The final publication is available at http://dx.doi.org/10.1007/s10482-012-9792-1 Copyright Springer Verlag (Germany) *Manuscript Click here to download Manuscript: Pseudonocardia PA3 AvL Cuesta et al revised 26-7-2012.doc Click here to view linked References 1 Pseudonocardia hispaniensis sp. nov., a novel actinomycete isolated from industrial wastewater 2 activated sludge 3 4 G. Cuesta1, A. Soler1, J.L. Alonso2, M.A. Ruvira3, T. Lucena3, D.R. Arahal3 and M. Goodfellow4 5 6 1Área de Microbiología, Departamento de Biotecnología, E.T.S.I. Agronómica y Medio Natural, 7 Universitat Politècnica de València, 46022 Valencia, Spain. 8 2Instituto Universitario de Ingeniería del Agua y Medio Ambiente, Universitat Politècnica de València, 9 46022 Valencia, Spain. 10 3Colección Española de Cultivos Tipo (CECT) and Departamento de Microbiología y Ecología, Campus 11 de Burjassot-Paterna, Universidad de Valencia, Valencia, Spain. 12 4School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK 13 14 Running title: Pseudonocardia hispaniensis sp. nov. 15 16 Key words: Pseudonocardia hispaniensis sp. nov., systematics, polyphasic taxonomy, activated sludge 17 18 19 The GenBank/EMBL/DDBJ accession number for the 16S rRNA sequence of Pseudonocardia 20 hispaniensis PA3T is FR695486 21 22 23 Corresponding author: G.
    [Show full text]
  • Provided for Non-Commercial Research and Educational Use. Not for Reproduction, Distribution Or Commercial Use
    Provided for non-commercial research and educational use. Not for reproduction, distribution or commercial use. This article was originally published in the Encyclopedia of Microbiology published by Elsevier, and the attached copy is provided by Elsevier for the author’s benefit and for the benefit of the author’s institution, for non-commercial research and educational use including without limitation use in instruction at your institution, sending it to specific colleagues who you know, and providing a copy to your institution’s administrator. All other uses, reproduction and distribution, including without limitation commercial reprints, selling or licensing copies or access, or posting on open internet sites, your personal or institution’s website or repository, are prohibited. For exceptions, permission may be sought for such use through Elsevier’s permissions site at: http://www.elsevier.com/locate/permissionusematerial E M Wellington. Actinobacteria. Encyclopedia of Microbiology. (Moselio Schaechter, Editor), pp. 26-[44] Oxford: Elsevier. Author's personal copy BACTERIA Contents Actinobacteria Bacillus Subtilis Caulobacter Chlamydia Clostridia Corynebacteria (including diphtheria) Cyanobacteria Escherichia Coli Gram-Negative Cocci, Pathogenic Gram-Negative Opportunistic Anaerobes: Friends and Foes Haemophilus Influenzae Helicobacter Pylori Legionella, Bartonella, Haemophilus Listeria Monocytogenes Lyme Disease Mycoplasma and Spiroplasma Myxococcus Pseudomonas Rhizobia Spirochetes Staphylococcus Streptococcus Pneumoniae Streptomyces
    [Show full text]
  • A Report of 12 Unrecorded Prokaryotic Species Isolated from Gastrointestinal Tracts and Feces of Various Endangered Animals in Korea
    Journal of Species Research 9(1):35-45, 2020 A report of 12 unrecorded prokaryotic species isolated from gastrointestinal tracts and feces of various endangered animals in Korea Pil Soo Kim1,§, Ki-Eun Lee2,§, Euon Jung Tak1, Myung-Suk Kang3 and Jin-Woo Bae1,* 1Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea 2Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea 3Biological Resources Utilization Department, National Institute of Biological Resources, Incheon 22689, Republic of Korea *Correspondent: [email protected] §These authors contributed equally to this work. In 2016 and 2017, as part of a comprehensive investigation to identify the prokaryotic species in Korea, a total of 12 bacterial strains were isolated from the gastrointestinal tract and/or fecal samples of four endangered species, including reptile, bird, and marine and terrestrial mammals. Phylogenetic analysis with the 16S rRNA gene sequence was used to assign these strains to the phyla, Firmicutes, Actinobacteria or Proteobacteria. Furthermore, most of the strains Firmicutes belonged to the order Lactobacillales. Interestingly, 12 of the isolated strains have not been previously reported from the Korean Peninsula. Also, based on their high 16S rRNA gene sequence similarities (>98.7%) and formation of strong monophyletic clades with the closest type species, each isolated strain of isolates was assigned to an independent, predefined bacterial species. Gram- stain reaction, colony and cell morphology, biochemical characteristics, isolation source, and NIBR IDs are described in the species description section. Keywords: ‌16S rRNA sequence, endangered animals, gut microbiota, Korean Peninsula, unrecorded species Ⓒ 2020 National Institute of Biological Resources DOI:10.12651/JSR.2020.9.1.035 INTRODUCTION al., 2009; Round and Mazmanian, 2009).
    [Show full text]