Temporal Variation of Microbial Population in Acclimation and Start-Up Period of a Thermophilic Desulfurization Biofilter
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Identification of Contaminating Bacteria When Attempting to Isolate Mycobacterium Avium Subsp
Arch Med Vet 47, 97-100 (2015) COMMUNICATION Identification of contaminating bacteria when attempting to isolate Mycobacterium avium subsp. paratuberculosis (MAP) from bovine faecal and tissue samples using the BACTEC MGIT 960 system# Identificación de bacterias contaminantes al aislar Mycobacterium avium subsp. paratuberculosis (MAP) desde muestras de material fecal y tejido de bovinos, utilizando el sistema de cultivo BACTEC-MGIT 960 P Steuera, b, J de Waardc, MT Collinsd, EP Troncosoa, OA Martíneza, C Tejedaa, MA Salgadoa* aBiochemistry and Microbiology Department, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile. bGraduate School, Faculty of Veterinary Sciences, Universidad Austral de Chile, Valdivia, Chile. cLaboratorio de Tuberculosis, Instituto de Biomedicina, Caracas, Venezuela. dDeptartment of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, USA. RESUMEN El diagnóstico de la infección por Mycobacterium avium subsp. paratuberculosis (MAP) al utilizar un sistema de cultivo líquido resulta en una mayor sensibilidad, rapidez y automatización. Sin embargo, tiene como desventajas una mayor tasa de contaminación en relación con los sistemas convencionales y también es menos específico. El presente estudio identificó algunas bacterias contaminantes del sistema de cultivo BACTEC-MGIT 960 al procesar muestras clínicas de ganado bovino del sur de Chile. No se detectaron micobacterias en las muestras falsas positivas a MAP mediante la técnica Reacción en Cadena de la Polimerasa-Análisis con Enzimas de Restricción (PRA)-hsp65. Por otra parte, el Análisis de los Espaciadores Intergénicos Ribosomales (RISA) seguido de un análisis de secuenciación, reveló la presencia de Paenibacillus sp., Enterobacterias y Pseudomonas aeruginosa como contaminantes comunes. Los protocolos de eliminación de contaminantes deberían considerar esta información para mejorar los resultados diagnósticos de los sistemas de cultivo líquido. -
Product Sheet Info
Product Information Sheet for NR-2490 Paenibacillus macerans, Strain NRS 888 Citation: Acknowledgment for publications should read “The following reagent was obtained through the NIH Biodefense and Catalog No. NR-2490 Emerging Infections Research Resources Repository, NIAID, ® (Derived from ATCC 8244™) NIH: Paenibacillus macerans, Strain NRS 888, NR-2490.” For research use only. Not for human use. Biosafety Level: 2 Appropriate safety procedures should always be used with this material. Laboratory safety is discussed in the following Contributor: ® publication: U.S. Department of Health and Human Services, ATCC Public Health Service, Centers for Disease Control and Prevention, and National Institutes of Health. Biosafety in Product Description: Microbiological and Biomedical Laboratories. 5th ed. Bacteria Classification: Paenibacillaceae, Paenibacillus Washington, DC: U.S. Government Printing Office, 2007; see Species: Paenibacillus macerans (formerly Bacillus www.cdc.gov/od/ohs/biosfty/bmbl5/bmbl5toc.htm. macerans)1 Type Strain: NRS 888 (NCTC 6355; NCIB 9368) Disclaimers: Comments: Paenibacillus macerans, strain NRS 888 was ® 2 You are authorized to use this product for research use only. deposited at ATCC in 1961 by Dr. N. R. Smith. It is not intended for human use. Paenibacillus macerans are Gram-positive, dinitrogen-fixing, Use of this product is subject to the terms and conditions of spore-forming rods belonging to a class of bacilli of the the BEI Resources Material Transfer Agreement (MTA). The phylum Firmicutes. These bacteria have been isolated from MTA is available on our Web site at www.beiresources.org. a variety of sources including soil, water, plants, food, diseased insect larvae, and clinical specimens. While BEI Resources uses reasonable efforts to include accurate and up-to-date information on this product sheet, Material Provided: ® neither ATCC nor the U.S. -
Identification and Sequence Analyses of Novel Lipase Encoding Novel
Shahinyan et al. BMC Microbiology (2017) 17:103 DOI 10.1186/s12866-017-1016-4 RESEARCH ARTICLE Open Access Identification and sequence analyses of novel lipase encoding novel thermophillic bacilli isolated from Armenian geothermal springs Grigor Shahinyan1, Armine Margaryan1,2, Hovik Panosyan2 and Armen Trchounian1,2* Abstract Background: Among the huge diversity of thermophilic bacteria mainly bacilli have been reported as active thermostable lipase producers. Geothermal springs serve as the main source for isolation of thermostable lipase producing bacilli. Thermostable lipolytic enzymes, functioning in the harsh conditions, have promising applications in processing of organic chemicals, detergent formulation, synthesis of biosurfactants, pharmaceutical processing etc. Results: In order to study the distribution of lipase-producing thermophilic bacilli and their specific lipase protein primary structures, three lipase producers from different genera were isolated from mesothermal (27.5–70 °C) springs distributed on the territory of Armenia and Nagorno Karabakh. Based on phenotypic characteristics and 16S rRNA gene sequencing the isolates were identified as Geobacillus sp., Bacillus licheniformis and Anoxibacillus flavithermus strains. The lipase genes of isolates were sequenced by using initially designed primer sets. Multiple alignments generated from primary structures of the lipase proteins and annotated lipase protein sequences, conserved regions analysis and amino acid composition have illustrated the similarity (98–99%) of the lipases with true lipases (family I) and GDSL esterase family (family II). A conserved sequence block that determines the thermostability has been identified in the multiple alignments of the lipase proteins. Conclusions: The results are spreading light on the lipase producing bacilli distribution in geothermal springs in Armenia and Nagorno Karabakh. -
Biochemical Characterization and 16S Rdna Sequencing of Lipolytic Thermophiles from Selayang Hot Spring, Malaysia
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Available online at www.sciencedirect.com ScienceDirect IERI Procedia 5 ( 2013 ) 258 – 264 2013 International Conference on Agricultural and Natural Resources Engineering Biochemical Characterization and 16S rDNA Sequencing of Lipolytic Thermophiles from Selayang Hot Spring, Malaysia a a a a M.J., Norashirene , H., Umi Sarah , M.H, Siti Khairiyah and S., Nurdiana aFaculty of Applied Sciences, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia. Abstract Thermophiles are well known as organisms that can withstand extreme temperature. Thermoenzymes from thermophiles have numerous potential for biotechnological applications due to their integral stability to tolerate extreme pH and elevated temperature. Because of the industrial importance of lipases, there is ongoing interest in the isolation of new bacterial strain producing lipases. Six isolates of lipases producing thermophiles namely K7S1T53D5, K7S1T53D6, K7S1T53D11, K7S1T53D12, K7S2T51D14 and K7S2T51D19 were isolated from the Selayang Hot Spring, Malaysia. The sampling site is neutral in pH with a highest recorded temperature of 53°C. For the screening and isolation of lipolytic thermopiles, selective medium containing Tween 80 was used. Thermostability and the ability to degrade the substrate even at higher temperature was proved and determined by incubation of the positive isolates at temperature 53°C. Colonies with circular borders, convex in elevation with an entire margin and opaque were obtained. 16S rDNA gene amplification and sequence analysis were done for bacterial identification. The isolate of K7S1T53D6 was derived of genus Bacillus that is the spore forming type, rod shaped, aerobic, with the ability to degrade lipid. -
Bacterial Succession Within an Ephemeral Hypereutrophic Mojave Desert Playa Lake
Microb Ecol (2009) 57:307–320 DOI 10.1007/s00248-008-9426-3 MICROBIOLOGY OF AQUATIC SYSTEMS Bacterial Succession within an Ephemeral Hypereutrophic Mojave Desert Playa Lake Jason B. Navarro & Duane P. Moser & Andrea Flores & Christian Ross & Michael R. Rosen & Hailiang Dong & Gengxin Zhang & Brian P. Hedlund Received: 4 February 2008 /Accepted: 3 July 2008 /Published online: 30 August 2008 # Springer Science + Business Media, LLC 2008 Abstract Ephemerally wet playas are conspicuous features RNA gene sequencing of bacterial isolates and uncultivated of arid landscapes worldwide; however, they have not been clones. Isolates from the early-phase flooded playa were well studied as habitats for microorganisms. We tracked the primarily Actinobacteria, Firmicutes, and Bacteroidetes, yet geochemistry and microbial community in Silver Lake clone libraries were dominated by Betaproteobacteria and yet playa, California, over one flooding/desiccation cycle uncultivated Actinobacteria. Isolates from the late-flooded following the unusually wet winter of 2004–2005. Over phase ecosystem were predominantly Proteobacteria, partic- the course of the study, total dissolved solids increased by ularly alkalitolerant isolates of Rhodobaca, Porphyrobacter, ∽10-fold and pH increased by nearly one unit. As the lake Hydrogenophaga, Alishwenella, and relatives of Thauera; contracted and temperatures increased over the summer, a however, clone libraries were composed almost entirely of moderately dense planktonic population of ∽1×106 cells ml−1 Synechococcus (Cyanobacteria). A sample taken after the of culturable heterotrophs was replaced by a dense popula- playa surface was completely desiccated contained diverse tion of more than 1×109 cells ml−1, which appears to be the culturable Actinobacteria typically isolated from soils. -
Paenibacillaceae Cover
The Family Paenibacillaceae Strain Catalog and Reference • BGSC • Daniel R. Zeigler, Director The Family Paenibacillaceae Bacillus Genetic Stock Center Catalog of Strains Part 5 Daniel R. Zeigler, Ph.D. BGSC Director © 2013 Daniel R. Zeigler Bacillus Genetic Stock Center 484 West Twelfth Avenue Biological Sciences 556 Columbus OH 43210 USA www.bgsc.org The Bacillus Genetic Stock Center is supported in part by a grant from the National Sciences Foundation, Award Number: DBI-1349029 The author disclaims any conflict of interest. Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or by the Ohio State University. Cover: Paenibacillus dendritiformus colony pattern formation. Color added for effect. Image courtesy of Eshel Ben Jacob. TABLE OF CONTENTS Table of Contents .......................................................................................................................................................... 1 Welcome to the Bacillus Genetic Stock Center ............................................................................................................. 2 What is the Bacillus Genetic Stock Center? ............................................................................................................... 2 What kinds of cultures are available from the BGSC? ............................................................................................... 2 What you can do to help the BGSC ........................................................................................................................... -
Phylogenetic Study of Thermophilic Genera Anoxybacillus, Geobacillus
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.18.449068; this version posted June 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 bioRxiv 2 Article Type: Research article. 3 Article Title: Phylogenetic study of thermophilic genera Anoxybacillus, Geobacillus, 4 Parageobacillus, and proposal of a new classification Quasigeobacillus 5 gen. nov. 6 Authors: Talamantes-Becerra, Berenice1-2*; Carling, Jason2; Blom, Jochen3; 7 Georges, Arthur1 8 Affiliation: 1Institute for Applied Ecology, University of Canberra ACT 2601 9 Australia. 10 2Diversity Arrays Technology Pty Ltd, Bruce, Canberra ACT 2617 11 Australia. 12 3Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, 13 35392 Glessen, Hesse, Germany 14 *Correspondence: Berenice Talamantes Becerra, Institute for Applied Ecology, 15 University of Canberra ACT 2601 Australia. Email: 16 [email protected] 17 Running head: Phylogenetic study of thermophilic bacteria. 18 Word Count: Abstract: 178 Main body: 3709 References: n= 60 19 20 21 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.18.449068; this version posted June 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 22 23 Abstract 24 A phylogenetic study of Anoxybacillus, Geobacillus and Parageobacillus was performed using 25 publicly available whole genome sequences. A total of 113 genomes were selected for 26 phylogenomic metrics including calculation of Average Nucleotide Identity (ANI) and 27 Average Amino acid Identity (AAI), and a maximum likelihood tree was built from alignment 28 of a set of 662 orthologous core genes. -
Complete Genome Sequence of Cohnella Sp. HS21 Isolated from Korean Fir (Abies Koreana) Rhizospheric Soil 구상나무 근권 토
Korean Journal of Microbiology (2019) Vol. 55, No. 2, pp. 171-173 pISSN 0440-2413 DOI https://doi.org/10.7845/kjm.2019.9028 eISSN 2383-9902 Copyright ⓒ 2019, The Microbiological Society of Korea Complete genome sequence of Cohnella sp. HS21 isolated from Korean fir (Abies koreana) rhizospheric soil 1,2 1 1 1 1 2 1 Lingmin Jiang , Se Won Kang , Song-Gun Kim , Jae Cheol Jeong , Cha Young Kim , Dae-Hyuk Kim , Suk Weon Kim * , 1 and Jiyoung Lee * 1 Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Republic of Korea 2 Department of Bioactive Materials, Chonbuk National University, Jeonju 54896, Republic of Korea 구상나무 근권 토양으로부터 분리된 Cohnella sp. HS21의 전체 게놈 서열 지앙 링민1,2 ・ 강세원1 ・ 김성건1 ・ 정재철1 ・ 김차영1 ・ 김대혁2 ・ 김석원1* ・ 이지영1* 1 2 한국생명공학연구원 생물자원센터, 전북대학교 생리활성소재과학과 (Received March 19, 2019; Revised May 7, 2019; Accepted May 7, 2019) The genus Cohnella, which belongs to the family Paenibacillaceae, environmental niches, including mammals (Khianngam et al., inhabits a wide range of environmental niches. Here, we report 2012), the starch production industry (Kämpfer et al., 2006), the complete genome sequence of Cohnella sp. HS21, which fresh water (Shiratori et al., 2010), plant root nodules (Flores- was isolated from the rhizospheric soil of Korean fir (Abies Félix et al., 2014), and soils (Huang et al., 2014; Lee et al., koreana) on the top of Halla Mountain in the Republic of 2015). We have recently isolated the bacterium strain HS21 Korea. Strain HS21 features a 7,059,027 bp circular chromo- some with 44.8% GC-content. -
Genome Snapshot of Paenibacillus Polymyxa ATCC 842T
J. Microbiol. Biotechnol. (2006), 16(10), 1650–1655 Genome Snapshot of Paenibacillus polymyxa ATCC 842T JEONG, HAEYOUNG, JIHYUN F. KIM, YON-KYOUNG PARK, SEONG-BIN KIM, CHANGHOON KIM†, AND SEUNG-HWAN PARK* Laboratory of Microbial Genomics, Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), P.O. Box 115, Yuseong, Daejeon 305-600, Korea Received: May 11, 2006 Accepted: June 22, 2006 Abstract Bacteria belonging to the genus Paenibacillus are rhizosphere and soil, and their useful traits have been facultatively anaerobic endospore formers and are attracting analyzed [3, 6-8, 10, 15, 22, 26]. At present, the genus growing ecological and agricultural interest, yet their genome Paenibacillus consists of 84 species (NCBI Taxonomy information is very limited. The present study surveyed the Homepage at http://www.ncbi.nlm.nih.gov/Taxonomy/ genomic features of P. polymyxa ATCC 842 T using pulse-field taxonomyhome.html, February 2006). gel electrophoresis of restriction fragments and sample genome Nonetheless, despite the growing interest in Paenibacillus, sequencing of 1,747 reads (approximately 17.5% coverage of its genomic information is very scarce. Most of the completely the genome). Putative functions were assigned to more than sequenced organisms currently belong to the Bacillaceae 60% of the sequences. Functional classification of the sequences family, in particular to the Bacillus genus, whereas data on showed a similar pattern to that of B. subtilis. Sequence Paenibacillaceae sequences is limited even at the draft analysis suggests nitrogen fixation and antibiotic production level. P. polymyxa, the type species of the genus Paenibacillus, by P. polymyxa ATCC 842 T, which may explain its plant is also of great ecological and agricultural importance, owing growth-promoting effects. -
Complete Genome Sequence of Geobacillus Thermoglucosidasius
Brumm et al. Standards in Genomic Sciences (2015) 10:73 DOI 10.1186/s40793-015-0031-z SHORT GENOME REPORT Open Access Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park Phillip J. Brumm1,3*, Miriam L. Land2 and David A. Mead1,3 Abstract Geobacillus thermoglucosidasius C56-YS93 was one of several thermophilic organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. Comparison of 16 S rRNA sequences confirmed the classification of the strain as a G. thermoglucosidasius species. The genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute and deposited at the NCBI in December 2011 (CP002835). The genome of G. thermoglucosidasius C56-YS93 consists of one circular chromosome of 3,893,306 bp and two circular plasmids of 80,849 and 19,638 bp and an average G + C content of 43.93 %. G. thermoglucosidasius C56-YS93 possesses a xylan degradation cluster not found in the other G. thermoglucosidasius sequenced strains. This cluster appears to be related to the xylan degradation cluster found in G. stearothermophilus. G. thermoglucosidasius C56-YS93 possesses two plasmids not found in the other two strains. One plasmid contains a novel gene cluster coding for proteins involved in proline degradation and metabolism, the other contains a collection of mostly hypothetical proteins. Keywords: Geobacillus thermoglucosidasius C56-YS93, Hot springs, Biomass, Xylan, Prophage Introduction new enzyme-producing aerobic organisms from Yellow- Identification of new organisms that produce biomass- stone hot springs. degrading enzymes is of considerable interest. -
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; -
Cohnella Algarum Sp. Nov., Isolated from a Freshwater Green Alga Paulinella Chromatophora
TAXONOMIC DESCRIPTION Lee and Jeon, Int J Syst Evol Microbiol 2017;67:4767–4772 DOI 10.1099/ijsem.0.002377 Cohnella algarum sp. nov., isolated from a freshwater green alga Paulinella chromatophora Yunho Lee and Che Ok Jeon* Abstract A Gram-stain-positive, facultatively aerobic and endospore-forming bacterium, designated strain Pch-40T, was isolated from a freshwater green alga, Paulinella chromatophora. Cells were motile rods with a monotrichous polar flagellum showing catalase- and oxidase-positive reactions. Strain Pch-40T grew at 20–50 C (optimum, 37–40 C), at pH 5.0–11.0 (optimum, pH 7.0) and in the presence of 0–4.0 % (w/v) NaCl (optimum, 0 %). Menaquinone-7 was detected as the sole isoprenoid quinone. T T The genomic DNA G+C content of strain Pch-40 was 55.6 mol%. The major cellular fatty acids of strain Pch-40 were C16 : 0, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Pch-40T clearly belonged to the genus Cohnella of the family Paenibacillaceae. Strain Pch-40T was most closely related to Cohnella rhizosphaerae CSE-5610T with a 96.1 % 16S rRNA gene sequence similarity. The phenotypic and chemotaxonomic features and the phylogenetic inference clearly suggested that strain Pch-40T represents a novel species of the genus Cohnella, for which the name Cohnella algarum sp. nov. is proposed. The type strain is strain Pch-40T (=KACC 19279T=JCM 32033T). The genus Cohnella, belonging to the family Paenibacilla- useful compounds for industry [14, 15].