Microbial Diversity in Aged Bentonites
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Kaistella Soli Sp. Nov., Isolated from Oil-Contaminated Soil
A001 Kaistella soli sp. nov., Isolated from Oil-contaminated Soil Dhiraj Kumar Chaudhary1, Ram Hari Dahal2, Dong-Uk Kim3, and Yongseok Hong1* 1Department of Environmental Engineering, Korea University Sejong Campus, 2Department of Microbiology, School of Medicine, Kyungpook National University, 3Department of Biological Science, College of Science and Engineering, Sangji University A light yellow-colored, rod-shaped bacterial strain DKR-2T was isolated from oil-contaminated experimental soil. The strain was Gram-stain-negative, catalase and oxidase positive, and grew at temperature 10–35°C, at pH 6.0– 9.0, and at 0–1.5% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence analysis suggested that the strain DKR-2T was affiliated to the genus Kaistella, with the closest species being Kaistella haifensis H38T (97.6% sequence similarity). The chemotaxonomic profiles revealed the presence of phosphatidylethanolamine as the principal polar lipids;iso-C15:0, antiso-C15:0, and summed feature 9 (iso-C17:1 9c and/or C16:0 10-methyl) as the main fatty acids; and menaquinone-6 as a major menaquinone. The DNA G + C content was 39.5%. In addition, the average nucleotide identity (ANIu) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain DKR-2T and phylogenically closest members were below the threshold values for species delineation. The polyphasic taxonomic features illustrated in this study clearly implied that strain DKR-2T represents a novel species in the genus Kaistella, for which the name Kaistella soli sp. nov. is proposed with the type strain DKR-2T (= KACC 22070T = NBRC 114725T). [This study was supported by Creative Challenge Research Foundation Support Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF- 2020R1I1A1A01071920).] A002 Chitinibacter bivalviorum sp. -
Pentachlorophenol Degradation by Janibacter Sp., a New Actinobacterium Isolated from Saline Sediment of Arid Land
Hindawi Publishing Corporation BioMed Research International Volume 2014, Article ID 296472, 9 pages http://dx.doi.org/10.1155/2014/296472 Research Article Pentachlorophenol Degradation by Janibacter sp., a New Actinobacterium Isolated from Saline Sediment of Arid Land Amel Khessairi,1,2 Imene Fhoula,1 Atef Jaouani,1 Yousra Turki,2 Ameur Cherif,3 Abdellatif Boudabous,1 Abdennaceur Hassen,2 and Hadda Ouzari1 1 UniversiteTunisElManar,Facult´ e´ des Sciences de Tunis (FST), LR03ES03 Laboratoire de Microorganisme et Biomolecules´ Actives, Campus Universitaire, 2092 Tunis, Tunisia 2 Laboratoire de Traitement et Recyclage des Eaux, Centre des Recherches et Technologie des Eaux (CERTE), Technopoleˆ Borj-Cedria,´ B.P. 273, 8020 Soliman, Tunisia 3 Universite´ de Manouba, Institut Superieur´ de Biotechnologie de Sidi Thabet, LR11ES31 Laboratoire de Biotechnologie et Valorization des Bio-Geo Resources, Biotechpole de Sidi Thabet, 2020 Ariana, Tunisia Correspondence should be addressed to Hadda Ouzari; [email protected] Received 1 May 2014; Accepted 17 August 2014; Published 17 September 2014 Academic Editor: George Tsiamis Copyright © 2014 Amel Khessairi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Many pentachlorophenol- (PCP-) contaminated environments are characterized by low or elevated temperatures, acidic or alkaline pH, and high salt concentrations. PCP-degrading microorganisms, adapted to grow and prosper in these environments, play an important role in the biological treatment of polluted extreme habitats. A PCP-degrading bacterium was isolated and characterized from arid and saline soil in southern Tunisia and was enriched in mineral salts medium supplemented with PCP as source of carbon and energy. -
A Numerical Taxonomy of 604 Strains of the Genera Arthrobacter, Aureo
J. Gen. Appl. Microbiol., 39, 135-214 (1993) NUMERICAL CLASSIFICATION OF CORYNEFORM BACTERIA AND RELATED TAXA PETER KAMPFER,* HERI3ERT SEILER,' AND WOLFGANG DOTT Fachgebiet Hygiene, Technische Universitat Berlin, Amrumerstr. 32, D-13353 Berlin, Federal Republic of Germany 'Suddeutsche Versuchs - and Forschungsanstalt fur Milchwirtschaft, Vottingerstr. 45, D-85354 Freising, Federal Republic of Germany (Received August 14, 1992) A numerical taxonomy of 604 strains of the genera Arthrobacter, Aureo- bacterium, Brevibacterium, Cellulomonas, Clavibacter, Corynebacterium, Curtobacterium, Microbacterium, Nocardia, Nocardioides, Rhodococcus, Terrabacter and Tsukamurella was undertaken based on 280 physiological characters with the aid of miniaturized tests. Clustering was by the unweighted pair group method (UPGMA) with 12 different measures of similarity. Test error, overlap between the phena and cophenetic correla- tion coefficients for the classifications obtained with the Jaccard coefficient (SJ), the Pearson coefficient (SP), the simple-matching coefficient (SsM), and the Dice coefficient (SE,) as measures of similarity were within acceptable limits. Clusters were defined at the 55.0 to 70.5% levels (SJ). The compositions of clusters corresponded largely the delineations of 81.1 to 93.5% (SSM),29.1 to 55.0% (Se), and 55.3 to 81.1% (SD). A total of 31 major clusters (containing five or more strains), 41 minor clusters and subclusters (containing less than five strains), and 54 single-member clusters were obtained in the UPGMA/SJ study. The following conclu- sions were reached: (i) A high degree of similarity between the genera Aureobacterium, Cellulomonas, Clavibacter, Curtobacterium and Microbac- terium found in phylogenetic-based studies could be shown also pheneti- cally. Strains belonging to these genera were found in SJ clusters 1 to 45, often representing closely related, or single species. -
Nocardioides Zeicaulis Sp. Nov., an Endophyte Actinobacterium of Maize Peter Ka¨Mpfer,1 Stefanie P
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 1869–1874 DOI 10.1099/ijsem.0.000959 Nocardioides zeicaulis sp. nov., an endophyte actinobacterium of maize Peter Ka¨mpfer,1 Stefanie P. Glaeser,1 John A. McInroy2 and Hans-Ju¨rgen Busse3 Correspondence 1Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t Giessen, D-35392 Giessen, Peter Ka¨mpfer Germany peter.kaempfer@ 2Entomology and Plant Pathology Dept., Auburn University, Alabama, AL 36849, USA umwelt.uni-giessen.de 3Abteilung fu¨r Klinische Mikrobiologie und Infektionsbiologie, Institut fu¨r Mikrobiologie, Veterina¨rmedizinische Universita¨t Wien, A-1210 Wien, Austria A Gram-stain-positive, aerobic organism was isolated as an endophyte from the stem tissue of healthy maize (Zea mays) and investigated in detail for its taxonomic position. On the basis of the 16S rRNA gene sequence analysis, strain JM-601T was shown to be most closely related to Nocardioides alpinus (98.3 %), and Nocardioides ganghwensis (98.0 %). The 16S rRNA gene sequence similarity to all other species of the genus Nocardioides was j98.0 %. The diagnostic diamino acid of the peptidoglycan was LL-diaminopimelic acid. The major T quinone of strain JM-601 was menaquinone MK-8(H4). The polar lipid profile revealed the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylcholine and an unidentified phospholipid. The polyamine pattern contained predominantly spermine and moderate amounts of spermidine. In the fatty acid profile, iso-C16 : 0,C17 : 1v8c and 10-methyl C17 : 0 were present in major amounts. All these data support the allocation of the strain to the genus Nocardioides. The results of physiological and biochemical characterization allow in addition a phenotypic differentiation of strain JM-601T from N. -
Complete Genome of Isoprene Degrading Nocardioides Sp. WS12
microorganisms Brief Report Complete Genome of Isoprene Degrading Nocardioides sp. WS12 Lisa Gibson, Nasmille L. Larke-Mejía and J. Colin Murrell * School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK; [email protected] (L.G.); [email protected] (N.L.L.-M.) * Correspondence: [email protected] Received: 5 May 2020; Accepted: 5 June 2020; Published: 12 June 2020 Abstract: Isoprene is a climate-active gas whose wide-spread global production stems mostly from terrestrial plant emissions. The biodegradation of isoprene is carried out by a number of different bacteria from a wide range of environments. This study investigates the genome of a novel isoprene degrading bacterium Nocardioides sp. WS12, isolated from soil associated with Salix alba (Willow), a tree known to produce high amounts of isoprene. The Nocardioides sp. WS12 genome was fully sequenced, revealing the presence of a complete isoprene monooxygenase gene cluster, along with associated isoprene degradation pathway genes. Genes associated with rubber degradation were also present, suggesting that Nocardioides sp. WS12 may also have the capacity to degrade poly-cis-1,4-isoprene. Keywords: isoprene; isolate; genome; degradation; Nocardioides; rubber 1. Introduction Isoprene (2-methyl-1,3-butadiene) is a major biogenic volatile compound (BVOC) with atmospheric 1 emissions of 400–600 Tg y− , making it similar in scale to methane [1,2]. As a climate-active gas, it plays a wide and varied role in the Earth’s atmospheric chemistry. With an atmospheric lifetime ranging from 0.8 h to 1.3 days, it is highly reactive and susceptible to attack by hydroxyl, nitrate and ozone radicals [3]. -
Transfer of Pimelobacter Tumescens to Terrabacter Gen. Nov. As Terrabacter Tumescens Comb. Nov. and of Pimelobacter Jensenii To
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1989, p. 1-6 Vol. 39, No. 1 0020-7713/89/010001-06$02.OO/O Copyright 0 1989, International Union of Microbiological Societies Transfer of Pimelobacter tumescens to Terrabacter gen. nov. as Terrabacter tumescens comb. nov. and of Pimelobacter jensenii to Nocardioides as Nocardioides jensenii comb. nov. M. D. COLLINS,l M. DORSCH,’ AND E. STACKEBRANDT’” Department of Microbiology, Agricultural Food Research Council, Institute of Food Research, Reading Laboratory, Shinjield, Reading RG2 9AT, United Kingdom,’ and Institut fur Allgemeine Mikrobiologie, Christian-Albrechts- Universitat, 2300 Kiel, Federal Republic of Germany’ The phylogenetic interrelationship of members of the genera Nocardioides and Pimelobacter were examined by using reverse transcriptase sequencing of 16s ribosomal ribonucleic acid. The sequence studies demon- strated that Nocardioides albus, Nocardioides luteus, Pimelobacter jensenii, and Pimelobacter simplex represent a coherent phylogenetic group at the genus level, whereas Pimelobacter tumescens occupies a separate line of descent. On the basis of sequence data and the chemotaxonomic distinctiveness of the latter organism, we propose that Pimelobacter tumescens be reclassified in a new genus, Terrabacter, as Terrabacter tumescens comb. nov. Arthrobacter simplex and Arthrobacter tumescens are mycelium), and its placement within the genus Nocardioides among the few named species of coryneform bacteria which has been questioned (14). contain cell wall peptidoglycans based on ~~-2,6-diaminopi- 16s ribosomal ribonucleic acid (rRNA) cataloging shows melic acid (5, 16). The two species thus differ in peptidogly- that P. simplex is well removed from the arthrobacters sensu can composition from Arthrobacter globiformis, the type strict0 and indicates that this species occupies a line of species of the genus, which contains lysine as the dibasic descent the branching point of which is as low as that of amino acid (16). -
(ΐ2) United States Patent (ΐο) Patent No.: US 10,596,255 Β2 Clube (45) Date of Patent: *Mar
US010596255B2 US010596255B2 (ΐ2) United States Patent (ΐο) Patent No.: US 10,596,255 Β2 Clube (45) Date of Patent: *Mar. 24, 2020 (54) SELECTIVELY ALTERING MICROBIOTA 39/0258; C07K 14/315; C07K 14/245; FOR IMMUNE MODULATION C07K 14/285; C07K 14/295; C12N 2310/20; C12N 2320/30 (71) Applicant: SNIPR Technologies Limited, London See application file for complete search history. (GB) (72) Inventor: Jasper Clube, London (GB) (56) References Cited (73) Assignee: SNIPR Technologies Limited, London U.S. PATENT DOCUMENTS (GB) 4,626,504 A 12/1986 Puhler et al. 5,633,154 A 5/1997 Schaefer et al. (*) Notice: Subject to any disclaimer, the term of this 8,241,498 Β2 8/2012 Summer et al. patent is extended or adjusted under 35 8,252,576 Β2 8/2012 Campbell et al. U.S.C. 154(b) by 0 days. 8,906,682 Β2 12/2014 June et al. 8,911,993 Β2 12/2014 June et al. This patent is subject to a terminal dis 8,916,381 Β1 12/2014 June et al. 8,975,071 Β1 3/2015 June et al. claimer. 9,101,584 Β2 8/2015 June et al. 9,102,760 Β2 8/2015 June et al. (21) Appl. No.: 16/389,376 9,102,761 Β2 8/2015 June et al. 9,113,616 Β2 8/2015 MacDonald et al. (22) Filed: Apr. 19, 2019 9,328,156 Β2 5/2016 June et al. 9,464,140 Β2 10/2016 June et al. (65) Prior Publication Data 9,481,728 Β2 11/2016 June et al. -
Nocardioides Daeguensis Sp. Nov., a Nitrate- Reducing Bacterium Isolated from Activated Sludge of an Industrial Wastewater Treatment Plant
International Journal of Systematic and Evolutionary Microbiology (2013), 63, 3727–3732 DOI 10.1099/ijs.0.047043-0 Nocardioides daeguensis sp. nov., a nitrate- reducing bacterium isolated from activated sludge of an industrial wastewater treatment plant Yingshun Cui,13 Sung-Geun Woo,2,33 Jangho Lee,2 Sahastranshu Sinha,3,4 Myung-Suk Kang,5 Long Jin,6 Kwang Kyu Kim,7 Joonhong Park,2 Myungjin Lee8 and Sung-Taik Lee1 Correspondence 1Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Sung-Taik Lee 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea [email protected] 2School of Civil and Environmental Engineering, Yonsei University, Seoul 120-749, Myungjin Lee Republic of Korea [email protected] 3Research and Development Division, H-Plus Eco Ltd, BVC #301, KRIBB, Eoeun-dong, Yuseong-gu, Daejeon 305-333, Republic of Korea 4Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India 5National Institute of Biological Resources, Environmental Research Complex, Gyeongseo-dong, Seo-gu, Incheon 404-708, Republic of Korea 6Environmental Biotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology, 52 Eoeun-dong, Yuseong-gu, Daejeon 305-806, Republic of Korea 7Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, 52 Eoeun-dong, Yuseong-gu, Daejeon 305-806, Republic of Korea 8WIZCHEM Co., Ltd. Inno-Biz Park No. 403 HNU, 461-6 Jeonmin-dong, Yuseong-gu, Daejeon, 305- 811, Republic of Korea A Gram-reaction-positive, rod-shaped, non-spore-forming bacterium (strain 2C1-5T) was isolated from activated sludge of an industrial wastewater treatment plant in Daegu, South Korea. -
Diversity and Distribution of Actinobacteria Associated with Reef Coral Porites Lutea
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 21 October 2015 doi: 10.3389/fmicb.2015.01094 Diversity and distribution of Actinobacteria associated with reef coral Porites lutea Weiqi Kuang 1, 2 †, Jie Li 1 †, Si Zhang 1 and Lijuan Long 1* 1 CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China, 2 College of Earth Science, University of Chinese Academy of Sciences, Beijing, China Actinobacteria is a ubiquitous major group in coral holobiont. The diversity and spatial Edited by: and temporal distribution of actinobacteria have been rarely documented. In this Sheng Qin, study, diversity of actinobacteria associated with mucus, tissue and skeleton of Porites Jiangsu Normal University, China lutea and in the surrounding seawater were examined every 3 months for 1 year on Reviewed by: Syed Gulam Dastager, Luhuitou fringing reef. The population structures of the P.lutea-associated actinobacteria National Collection of Industrial were analyzed using phylogenetic analysis of 16S rRNA gene clone libraries, which Microorganisms Resource Center, demonstrated highly diverse actinobacteria profiles in P. lutea. A total of 25 described India Wei Sun, families and 10 unnamed families were determined in the populations, and 12 genera Shanghai Jiao Tong University, China were firstly detected in corals. The Actinobacteria diversity was significantly different P. Nithyanand, SASTRA University, India between the P. lutea and the surrounding seawater. Only 10 OTUs were shared by *Correspondence: the seawater and coral samples. -
Polycyclic Aromatic Hydrocarbon Degrading Bacteria from the Indonesian Marine Environment
BIODIVERSITAS ISSN: 1412-033X Volume 17, Number 2, October 2016 E-ISSN: 2085-4722 Pages: 857-864 DOI: 10.13057/biodiv/d170263 Polycyclic aromatic hydrocarbon degrading bacteria from the Indonesian Marine Environment ELVI YETTI♥, AHMAD THONTOWI, YOPI Laboratory of Biocatalyst and Fermentation, Research Centre for Biotechnology, Indonesian Institute of Sciences. Cibinong Science Center, Jl. Raya Bogor Km 46 Cibinong-Bogor 16911, West Java, Indonesia. Tel. +62-21-8754587, Fax. +62-21-8754588, ♥email: [email protected] Manuscript received: 20 April 2016. Revision accepted: 20 October 2016. Abstract. Yetti E, Thontowi A, Yopi. 2016. Polyaromatic hydrocarbon degrading bacteria from the Indonesian Marine Environment. Biodiversitas 17: 857-864. Oil spills are one of the main causes of pollution in marine environments. Oil degrading bacteria play an important role for bioremediation of oil spill in environment. We collected 132 isolates of marine bacteria isolated from several Indonesia marine areas, i.e. Pari Island, Jakarta, Kamal Port, East Java and Cilacap Bay, Central Java. These isolates were screened for capability to degrade polyaromatic hydrocarbons (PAHs). Selection test were carried out qualitatively using sublimation method and growth assay of the isolates on several PAHs i.e. phenanthrene, dibenzothiophene, fluorene, naphtalene, phenotiazine, and pyrene. The fifty-eight isolates indicated in having capability to degrade PAHs, consisted of 25 isolates were positive on naphthalene (nap) and 20 isolates showed ability to grow in phenanthrene (phen) containing media. Further, 38 isolates were selected for dibenzothiophene (dbt) degradation and 25 isolates were positive on fluorene (flr). On the other hand, 23 isolates presented capability to degrade in phenothiazine (ptz) and 15 isolates could grow in media with pyrene (pyr). -
Compile.Xlsx
Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge; -
Nocardioides Deserti Sp. Nov., an Actinobacterium Isolated from Desert Soil
International Journal of Systematic and Evolutionary Microbiology (2015), 65, 1604–1610 DOI 10.1099/ijs.0.000147 Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil Li Tuo,1 Yan-Ping Dong,1,2 Xugela Habden,3 Jia-Meng Liu,1 Lin Guo,1 Xian-Fu Liu,4 Li Chen,4 Zhong-Ke Jiang,1 Shao-Wei Liu,1 Yu-Bin Zhang,2 Yu-Qin Zhang1 and Cheng-Hang Sun1 Correspondence 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Yu-Qin Zhang Medical College, Beijing 100050, PR China [email protected] 2College of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, Cheng-Hang Sun PR China [email protected] 3College of Life Science and Chemistry, Xinjiang Normal University, Urumchi 830054, PR China 4Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China A rod- or coccus-shaped, non-spore-forming actinobacterium, designated strain SC8A-24T, was isolated from a soil sample collected from the rhizosphere of Alhagi sparsifolia on the southern edge of the Taklimakan desert, Xinjiang, China, and examined by a polyphasic approach to clarify its taxonomic position. This actinobacterium was Gram-staining-positive and aerobic. Substrate and aerial mycelia were not observed, and no diffusible pigments were observed on the media tested. Strain SC8A-24T grew optimally without NaCl at 28–30 6C and pH 7.0–8.0. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain SC8A-24T belonged to the genus Nocardioides and shared the highest 16S rRNA gene sequence similarity with Nocardioides salarius CL-Z59T (96.51 %), N.