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<I>Thauera Aminoaromatica</I> Strain MZ1T

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University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln US Department of Energy Publications U.S. Department of Energy 2012 Complete genome sequence of Thauera aminoaromatica strain MZ1T Ke Jiang The University of Tennessee John Sanseverino The University of Tennessee Archana Chauhan The University of Tennessee Susan Lucas DOE Joint Genome Institute Alex Copeland DOE Joint Genome Institute See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/usdoepub Part of the Bioresource and Agricultural Engineering Commons Jiang, Ke; Sanseverino, John; Chauhan, Archana; Lucas, Susan; Copeland, Alex; Lapidus, Alla; Glavina Del Rio, Tijana; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Sims, David; Brettin, Thomas; Detter, John C.; Han, Cliff; Chang, Y.J.; Larimer, Frank; Land, Miriam; Hauser, Loren; Kyrpides, Nikos C.; Mikhailova, Natalia; Moser, Scott; Jegier, Patricia; Close, Dan; DeBruyn, Jennifer M.; Wang, Ying; Layton, Alice C.; Allen, Michael S.; and Sayler, Gary S., "Complete genome sequence of Thauera aminoaromatica strain MZ1T" (2012). US Department of Energy Publications. 292. https://digitalcommons.unl.edu/usdoepub/292 This Article is brought to you for free and open access by the U.S. Department of Energy at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in US Department of Energy Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Ke Jiang, John Sanseverino, Archana Chauhan, Susan Lucas, Alex Copeland, Alla Lapidus, Tijana Glavina Del Rio, Eileen Dalin, Hope Tice, David Bruce, Lynne Goodwin, Sam Pitluck, David Sims, Thomas Brettin, John C. Detter, Cliff Han, Y.J. Chang, Frank Larimer, Miriam Land, Loren Hauser, Nikos C. Kyrpides, Natalia Mikhailova, Scott Moser, Patricia Jegier, Dan Close, Jennifer M. DeBruyn, Ying Wang, Alice C. Layton, Michael S. Allen, and Gary S. Sayler This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ usdoepub/292 Standards in Genomic Sciences (2012) 6:325-335 DOI:10.4056/sigs.2696029 Complete genome sequence of Thauera aminoaromatica strain MZ1T Ke Jiang1, John Sanseverino1, Archana Chauhan1, Susan Lucas2, Alex Copeland2, Alla Lapidus2, Tijana Glavina Del Rio2, Eileen Dalin2, Hope Tice2, David Bruce2, Lynne Goodwin2, Sam Pitluck2, David Sims3, Thomas Brettin2, John C. Detter 2, Cliff Han3, Y.J. Chang4, Frank Larimer4, Miriam Land4, Loren Hauser4, Nikos C. Kyrpides2, Natalia Mikhailova2, Scott Moser1, Patricia Jegier1, Dan Close1, Jennifer M. DeBruyn5, Ying Wang1, Alice C. Layton1, Michael S. Allen6 and Gary S. Sayler1* 1Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Tennessee, USA 2DOE Joint Genome Institute, Walnut Creek, California, USA 3Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Tennessee, USA 6Department of Biological Sciences, University of North Texas, Denton, Texas, USA *Corresponding Author: Gary S. Sayler ([email protected]) Keywords: Thauera aminoaromatica, MZ1T, genome. Thauera aminoaromatica strain MZ1T, an isolate belonging to genus Thauera, of the family Rhodocyclaceae and the class the Betaproteobacteria, has been characterized for its ability to produce abundant exopolysaccharide and degrade various aromatic compounds with nitrate as an electron acceptor. These properties, if fully understood at the genome-sequence level, can aid in environmental processing of organic matter in anaerobic cycles by short-circuiting a central anaerobic metabolite, acetate, from microbiological conversion to methane, a criti- cal greenhouse gas. Strain MZ1T is the first strain from the genus Thauera with a completely sequenced genome. The 4,496,212 bp chromosome and 78,374 bp plasmid contain 4,071 protein-coding and 71 RNA genes, and were sequenced as part of the DOE Community Se- quencing Program CSP_776774. Introduction Strain MZ1T (=DSM 25461 =MTCC 11151=LMG German microbiologist Rudolf Thauer and was 26735), a Gram-negative bacterium, was isolated described by Macy et al. [3]. Currently, this genus from activated sludge samples from the industrial consists of nine species with validly published wastewater treatment facility of Eastman Chemi- names. These species have been isolated from a cal Company, Kingsport, Tennessee [1]. It is relat- wide range of environments including wastewater ed to the genera Azoarcus and another prominent activated sludge, water and soil, and typically de- community member of activated sludge, Zoogloea. grade aromatic compounds such as benzoic acid Strain MZ1T was identified as a significant com- or toluene under anaerobic conditions [3-8]. Here ponent of microbial clusters formed during vis- we present a summary classification and a set of cous bulking that resulted in poor sludge features for T. aminoaromatica MZ1T, along with dewaterability and increased costs for dewatering, the description of the complete genomic sequenc- incineration and disposal [2]. Subsequently, MZ1T ing and annotation. was found to produce a novel exopolysaccharide which contributed to the viscous bulking phe- nomenon. The genus Thauera is named after the The Genomic Standards Consortium Thauera aminoaromatica strain MZ1T Classification and features 59.6% to T. selenatis ATCC 55363, respectively. Strain MZ1T originally was identified as belonging When the recommended threshold value of 70% to Thauera genus based on the 16S rRNA phyloge- DNA-DNA similarity is used for the definition of netic analysis [1].The sequences of the four 16S bacterial species [4], MZ1T does not belong to the rRNA gene copies in the genome do not differ from same species as T. selenatis ATCC 55363 but does each other. However, they differ from the previous- belong to the same species as strain S2. Based on ly published 16S rRNA sequence (AF110005), these results we recommend MZ1T be classified as which contains one gap and eleven ambiguous base Thauera aminoaromatica strain MZ1T. calls. Figure 1 shows the phylogenetic relationship Morphologically, cells of strain MZ1T are Gram of T. aminoaromatica MZ1T in a 16S rRNA based negative, short rods (0.5 x 1.1-1.8 µm) and motile tree to other Thauera species. Based on this tree, due to the presence of a polar flagellum (Figure 2). strain MZ1T is closely grouped with T. Colonies are slimy, creamy white in color at the op- aminoaromatica S2, T. phenylacetica B4P and T. timal growth temperature of 30 ºC and pH 7.2, re- selenatis and the cluster of these four strains is spectively. Strain MZ1T grows aerobically in well-separated from strains of T. aromatica, T. Stoke’s medium at 30 ºC shaking at 150 rpm and chlorobenzoica, T. mechernichensis, T. terpenica, T. produces copious quantities of extracellular poly- butanivorans and T. linaloolentis. saccharide from relatively simple short chain fatty DNA-DNA hybridization was performed between acids at early stationery stage [2]. However, when strain MZ1T and T. selenatis ATCC 55363, T. grown on agar plates, no obvious phenylacetica B4P DSM 14743 and T. exopolysaccharide is observed. Under aerobic con- aminoaromatica S2 DSM 14742 by Deutsche ditions, benzoate, succinate, aspartate, glutamate, Sammlung von Mikroorganismen und Zellkulturen proline, leucine, serine and alanine are utilized. Un- GmbH (DSMZ) (Braunschweig, Germany). DNA- der anaerobic conditions MZ1T is capable of DNA hybridization studies showed that MZ1T was growth on benzoate with nitrate as the terminal 100% similar to strain S2, 78.9% to strain B4P and electron acceptor. The characteristic features of the organism are listed in Table 1. Figure 1. 16S rDNA based phylogenetic tree depicting the relationship between Thauera aminoaromatica MZ1T and other members of the genus Thauera. The tree was constructed by using the Neighbor-Joining method and Jukes & Cantor evolutionary distance matrix from aligned 16S rDNA gene sequences and rooted using Azoarcus indigens as the outgroup. Bootstrap values (expressed as percentage of 500 replications) greater than 50 % are shown at the branch points. The branches are scaled as the number of base substitutions per site. 326 Standards in Genomic Sciences Jiang et al. Table 1. Classification and general features of T. aminoaromatica MZ1T according to the MIGS recommendations [5]. MIGS ID Property Term Evidence code Domain Bacteria TAS [6] Phylum ‘Proteobacteria’ TAS [7]] Class Betaproteobacteria TAS [8,9] Order Rhodocyclales TAS [8,10] Current classification Family Rhodocyclaceae TAS [8,11] Genus Thauera TAS [3,12] Species Thauera aminoaromatica IDA [3,13,14] Strain MZ1T TAS [1] Gram stain negative TAS [1] Cell shape rod TAS [1] Motility motile TAS [1] Sporulation not reported Temperature range 28-37 oC TAS [1] Optimum temperature 30 oC TAS [1] Salinity not reported MIGS-22 Oxygen requirement aerobic, facultative TAS [1] Carbon source numerous 1- and multi-C compounds TAS [1] Energy metabolism chemolithoautotroph TAS [1] MIGS-6 Habitat fresh water, waste water TAS [1] MIGS-15 Biotic relationship free living NAS MIGS-14 Pathogenicity none NAS Biosafety level 1 TAS [1] Isolation wastewater treatment plant TAS [1] MIGS-4 Geographic location Kingsport, Tennessee, USA TAS [1] MIGS-5 Sample collection time 1997 TAS [1] MIGS-4.1 Latitude 36.548 NAS MIGS-4.2 Longitude -82.561 NAS
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    G C A T T A C G G C A T genes Article Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera Roberto Tadeu Raittz 1,*,† , Camilla Reginatto De Pierri 2,† , Marta Maluk 3 , Marcelo Bueno Batista 4, Manuel Carmona 5 , Madan Junghare 6, Helisson Faoro 7, Leonardo M. Cruz 2 , Federico Battistoni 8, Emanuel de Souza 2,Fábio de Oliveira Pedrosa 2, Wen-Ming Chen 9, Philip S. Poole 10, Ray A. Dixon 4,* and Euan K. James 3,* 1 Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technical Education Sector—SEPT, UFPR, Curitiba, PR 81520-260, Brazil 2 Department of Biochemistry and Molecular Biology, UFPR, Curitiba, PR 81531-980, Brazil; [email protected] (C.R.D.P.); [email protected] (L.M.C.); [email protected] (E.d.S.); [email protected] (F.d.O.P.) 3 The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; [email protected] 4 John Innes Centre, Department of Molecular Microbiology, Norwich NR4 7UH, UK; [email protected] 5 Centro de Investigaciones Biológicas Margarita Salas-CSIC, Department of Biotechnology of Microbes and Plants, Ramiro de Maeztu 9, 28040 Madrid, Spain; [email protected] 6 Faculty of Chemistry, Biotechnology and Food Science, NMBU—Norwegian University of Life Sciences, 1430 Ås, Norway; [email protected] 7 Laboratory for Science and Technology Applied in Health, Carlos Chagas Institute, Fiocruz, Curitiba, PR 81310-020, Brazil; helisson.faoro@fiocruz.br 8 Department of Microbial Biochemistry and Genomics, IIBCE, Montevideo 11600, Uruguay; [email protected] Citation: Raittz, R.T.; Reginatto De 9 Laboratory of Microbiology, Department of Seafood Science, NKMU, Kaohsiung City 811, Taiwan; Pierri, C.; Maluk, M.; Bueno Batista, [email protected] M.; Carmona, M.; Junghare, M.; Faoro, 10 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; H.; Cruz, L.M.; Battistoni, F.; Souza, [email protected] E.d.; et al.
  • Cross-Feeding Between Thauera Aminoaromatica and Rhodococcus

    Cross-Feeding Between Thauera Aminoaromatica and Rhodococcus

    bioRxiv preprint doi: https://doi.org/10.1101/2020.01.31.929745; this version posted February 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 Cross-feeding between Thauera aminoaromatica and Rhodococcus 2 pyridinivorans drove quinoline biodegradation in a denitrifying 3 bioreactor 4 5 Xinxin Wu, Xiaogang Wu, Ji Li, Qiaoyu Wu, Yiming Ma, Weikang Sui, Liping Zhao, 6 Xiaojun Zhang* 7 8 State Key Laboratory of Microbial Metabolism, Joint International Research 9 Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & 10 Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China 11 12 Running title: Syntrophic denitrifying degradation of quinoline 13 14 * Corresponding author: Dr. Xiaojun Zhang, 15 Tel: +86 21 34204878, E-mail: [email protected] 16 800 Dongchuan Road, Minhang District, Shanghai, 200240, China 17 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.31.929745; this version posted February 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 18 Abstract 19 The complex bacterial community is predominated by several taxa, such as 20 Thauera and Rhodococcus, in a quinoline-degrading denitrifying bioreactor. Yet it 21 remains unclear about how the interactions between the different bacteria mediate the 22 quinoline metabolism in denitrifying condition.