Microbial Communities and Polycyclic Aromatic Hydrocarbons
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Emendation of the Genus Sphingomonas Yabuuchi Et Al
International Journal of Systematic and Evolutionary Microbiology (2002), 52, 1485–1496 DOI: 10.1099/ijs.0.01868-0 Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola 1 Department of Eiko Yabuuchi,1 Yoshimasa Kosako,2 Nagatoshi Fujiwara,3 Microbiology, Gifu 3,4 5 5 University School of Takashi Naka, Isamu Matsunaga, Hisashi Ogura and Medicine, Tsukasa-machi Kazuo Kobayashi3 40, Gifu 500-8705, Japan 2 Japan Collection of Microorganisms, Institute Author for correspondence: Kazuo Kobayashi. Tel: j81 6 6645 3745. Fax: j81 6 6646 3662. of Physical and Chemical e-mail: kobayak!med.osaka-cu.ac.jp Research (RIKEN), Wako- shi, Saitama 351-0198, Japan The 16S rDNA sequence similarities between the type strains of Sphingomonas 3 Department of Host paucimobilis and 32 other Sphingomonas species range from 902to996%. It Defense, Osaka City might be possible to divide the genus into several new genera according to a University Graduate School dendrogram drawn from 16S rDNA sequence similarity. However, the of Medicine, 1-4-3 Asahi- machi, Abeno-ku, Osaka phenotypic and biochemical information needed to define clusters of strains 545-8585, Japan representing distinct genera within this group of organisms was not 4 Institute of Skin Sciences, previously available. Although the cellular lipids of type strains of all 28 Club Cosmetics Co. Ltd, Sphingomonas species tested contained glucuronosyl-(1 ! 1)-ceramide Ikoma-shi, Nara 630-0222, together with 2-hydroxymyristic acid, other molecular species of Japan sphingoglycolipids were distributed randomly. -
Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas Sp
microorganisms Article Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5 Karel Kopejtka 1 , Yonghui Zeng 1,2, David Kaftan 1,3 , Vadim Selyanin 1, Zdenko Gardian 3,4 , Jürgen Tomasch 5,† , Ruben Sommaruga 6 and Michal Koblížek 1,* 1 Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 81 Tˇreboˇn,Czech Republic; [email protected] (K.K.); [email protected] (Y.Z.); [email protected] (D.K.); [email protected] (V.S.) 2 Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark 3 Faculty of Science, University of South Bohemia, 370 05 Ceskˇ é Budˇejovice,Czech Republic; [email protected] 4 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 Ceskˇ é Budˇejovice,Czech Republic 5 Research Group Microbial Communication, Technical University of Braunschweig, 38106 Braunschweig, Germany; [email protected] 6 Laboratory of Aquatic Photobiology and Plankton Ecology, Department of Ecology, University of Innsbruck, 6020 Innsbruck, Austria; [email protected] * Correspondence: [email protected] † Present Address: Department of Molecular Bacteriology, Helmholtz-Centre for Infection Research, 38106 Braunschweig, Germany. Abstract: An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 Citation: Kopejtka, K.; Zeng, Y.; (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Ty- Kaftan, D.; Selyanin, V.; Gardian, Z.; rolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic Tomasch, J.; Sommaruga, R.; Koblížek, analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas M. Characterization of the Aerobic and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Anoxygenic Phototrophic Bacterium Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). -
Succession and Persistence of Microbial Communities and Antimicrobial Resistance Genes Associated with International Space Stati
Singh et al. Microbiome (2018) 6:204 https://doi.org/10.1186/s40168-018-0585-2 RESEARCH Open Access Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces Nitin Kumar Singh1, Jason M. Wood1, Fathi Karouia2,3 and Kasthuri Venkateswaran1* Abstract Background: The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms. Results: The intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii,andAspergillus lentulus.EventhoughRhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3. -
WO 2015/066625 Al 7 May 2015 (07.05.2015) P O P C T
(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 WO 2015/066625 Al 7 May 2015 (07.05.2015) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/04 (2006.01) G01N 33/15 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (21) International Application Number: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, PCT/US2014/06371 1 DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 3 November 20 14 (03 .11.20 14) KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (25) Filing Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (26) Publication Language: English SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: 61/898,938 1 November 2013 (01. 11.2013) (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (71) Applicant: WASHINGTON UNIVERSITY [US/US] GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, One Brookings Drive, St. -
Bioaugmentation: an Emerging Strategy of Industrial Wastewater Treatment for Reuse and Discharge
International Journal of Environmental Research and Public Health Review Bioaugmentation: An Emerging Strategy of Industrial Wastewater Treatment for Reuse and Discharge Alexis Nzila 1,*, Shaikh Abdur Razzak 2 and Jesse Zhu 3 1 Department of Life Sciences, King Fahd University of Petroleum and Minerals (KFUPM), P.O. Box 468, Dhahran 31261, Saudi Arabia 2 Department of Chemical Engineering, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia; [email protected] 3 Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON N6A 5B9, Canada; [email protected] * Correspondence: [email protected]; Tel.: +966-13-860-7716; Fax: +966-13-860-4277 Academic Editors: Rao Bhamidiammarri and Kiran Tota-Maharaj Received: 12 May 2016; Accepted: 9 July 2016; Published: 25 August 2016 Abstract: A promising long-term and sustainable solution to the growing scarcity of water worldwide is to recycle and reuse wastewater. In wastewater treatment plants, the biodegradation of contaminants or pollutants by harnessing microorganisms present in activated sludge is one of the most important strategies to remove organic contaminants from wastewater. However, this approach has limitations because many pollutants are not efficiently eliminated. To counterbalance the limitations, bioaugmentation has been developed and consists of adding specific and efficient pollutant-biodegrading microorganisms into a microbial community in an effort to enhance the ability of this microbial community to biodegrade contaminants. This approach has been tested for wastewater cleaning with encouraging results, but failure has also been reported, especially during scale-up. In this review, work on the bioaugmentation in the context of removal of important pollutants from industrial wastewater is summarized, with an emphasis on recalcitrant compounds, and strategies that can be used to improve the efficiency of bioaugmentation are also discussed. -
Bioaugmentation of Chlorinated Solvents
BIOAUGMENTATION FOR REMEDIATION OF CHLORINATED SOLVENTS: TECHNOLOGY DEVELOPMENT, STATUS, AND RESEARCH NEEDS October 2005 GeoSyntec Consultants TABLE OF CONTENTS LIST OF TABLES ...........................................................................................................................................III LIST OF FIGURES .........................................................................................................................................III ACRONYMNS AND ABBREVIATIONS........................................................................................................V FOREWORD...................................................................................................................................................VII EXECUTIVE SUMMARY ............................................................................................................................... IX 1. INTRODUCTION ..........................................................................................................................................1 2. EARLY DEVELOPMENT OF BIOAUGMENTATION.............................................................................5 3. RECENT PROGRESS IN CHLORINATED SOLVENT BIOREMEDIATION .....................................13 4. DEHALORESPIRATION: THE KEY PROCESS UNDERLYING CURRENT BIOAUGMENTATION PRACTICES..............................................................................................................................................................19 4.1 THE UBIQUITY CONCEPT REVISITED -
Biological Methods
Biological Methods Jerry Walsh, Jenna Bishop, Quinn Albertson, Shane Galloway, Carlos Rivera, Tom Devenney, Jeff Green Physical Mechanisms In Situ Methods Permeable Reactive Barriers Biostimulation Bioaugmentation Phytoremediation Permeable Reactive Barriers (Biobarriers) • Semi-permeable reactive media in flow path • Chemically or biologically-mediated reactions transform contaminants into non-toxic or immobile products • Hydrocarbons need to be oxidized • Chlorinated solvents and nitrate need to be reduced • Microorganisms help mediate redox reactions to gain energy and materials for synthesis Reactive Media Reactive Medium Removal Mechanism Contaminants Removed Organic Material Microbial sulfate reduction Acid mine drainage and precipitation Organic Material Microbial nitrate reduction Nitrate Oxygen/Nitrate-Releasing Microbial degradation BTEX Compounds Resting-State Microbial cometabolism Chlorinated aliphatics Microorganisms Oxidative Biodegradation • To respire electrons removed from contaminants, need electron acceptors Aerobic: • Aerobic methods Molecular Oxygen Anaerobic: • Anaerobic methods Nutrients (nitrate, sulfates, CO2, ferric iron, metal oxides, etc) • Aerobic methods are generally preferred to provide more energy to the microbes • Biochemical oxygen demands (BOD’s) often exceed available oxygen, so adding oxygen to the system can stimulate oxidative biodegradation Reductive Biodegradation • Electron donors are required, which anaerobic environments more abundantly produce • Organic matter is a well-suited electron donor for this process • This method works well for TCE, hexavalent chromium, sulfate, and nitrate contamination • Heterotrophic denitrification to remove nitrate Biostimulation • Modification of environment to stimulate existing bacteria capable of bioremediation. • Only works if correct bacteria are present. • Often done through use of phosphorous, nitrogen, carbon, and oxygen. • Chemicals usually added through injection wells. • EPA approved method. Advantages • Low Costs • Can be tailored to the specific site conditions. -
Selecting Bacteria Candidates for the Bioaugmentation of Activated Sludge to Improve the Aerobic Treatment of Landfill Leachate
water Article Selecting Bacteria Candidates for the Bioaugmentation of Activated Sludge to Improve the Aerobic Treatment of Landfill Leachate Justyna Michalska *, Artur Pi ´nski , Joanna Zur˙ and Agnieszka Mrozik Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiello´nska28, 40-032 Katowice, Poland; [email protected] (A.P.); [email protected] (J.Z.);˙ [email protected] (A.M.) * Correspondence: [email protected] Received: 6 November 2019; Accepted: 27 December 2019; Published: 1 January 2020 Abstract: In this study, a multifaceted approach for selecting the suitable candidates for bioaugmentation of activated sludge (AS) that supports leachate treatment was used. To determine the exploitation of 10 bacterial strains isolated from the various matrices for inoculating the AS contaminated with the Kalina pond leachate (KPL), their degradative potential was analyzed along with their aptitude to synthesize compounds improving remediation of pollutants in wastewater and ability to incorporate into the AS flocs. Based on their capability to degrade aromatic compounds (primarily catechol, phenol, and cresols) at a concentration of 1 mg/mL and survive in 12.5% of the KPL, Pseudomonas putida OR45a and P. putida KB3 can be considered to be the best candidates for bioaugmentation of the AS among all of the bacteria tested. Genomic analyses of these two strains revealed the presence of the genes encoding enzymes related to the metabolism of aromatic compounds. Additionally, both microorganisms exhibited a high hydrophobic propensity (above 50%) and an ability to produce biosurfactants as well as high resistance to ammonium (above 600 µg/mL) and heavy metals (especially chromium). -
Bioremediation of Groundwater: an Overview
International Journal of Applied Engineering Research ISSN 0973-4562 Volume 13, Number 24 (2018) pp. 16825-16832 © Research India Publications. http://www.ripublication.com Bioremediation of Groundwater: An Overview Shivam Mani Tripathi 1, Shri Ram2 1 ,2 Civil Engineering Department, MMMUT Gorakhpur, India Abstract can be treated on site, thus reducing exposure risks for clean- In past, we have large open area and abundant land resources up personnel, or potentially wider exposure as a result of and groundwater. But after the industrialization the use of transportation accidents. Methodology of this process is not hazardous chemicals increased due to unmanageable technically difficult, considerable experience and knowledge conditions. The chemical disposed on the ground surface & may require implementing this process, by thoroughly many other anthropogenic activities by humans like use of investigating the site and to know required condition to pesticides and oil spillage contaminated the soil and achieve. groundwater. The different type of contaminant by percolation The usual technique of remediation is to plow up through the ground reach to the aquifer and get affected which contaminated soil and take away to the site, or to cover or cap causes serious problem. We spend lot of money and use many the contaminated area. There are some drawbacks. The first technologies to extract and remediate the contamination. In method simply transport the contaminated materials which spite of different methods, bioremediation is a technology create major risks is excavation, handling, and transport of which is cost efficient and effective by using natural microbes hazardous material. It is very difficult to find the new landfill and degrades the contaminants the conditions and different sites for disposal. -
Short-Term Rhizosphere Effect on Available Carbon Sources
Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil François Thomas, Aurélie Cebron To cite this version: François Thomas, Aurélie Cebron. Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil. Fron- tiers in Microbiology, Frontiers Media, 2016, 7, pp.92. 10.3389/fmicb.2016.00092. hal-01780413 HAL Id: hal-01780413 https://hal.univ-lorraine.fr/hal-01780413 Submitted on 29 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. ORIGINAL RESEARCH published: 05 February 2016 doi: 10.3389/fmicb.2016.00092 Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil François Thomas 1, 2 † and Aurélie Cébron 1, 2* 1 CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, Vandoeuvre-lés-Nancy, France, 2 Université de Lorraine, LIEC UMR7360, Faculté des Sciences et Technologies, Vandoeuvre-lés-Nancy, France Edited by: Dimitrios Georgios Karpouzas, Over the last decades, understanding of the effects of plants on soil microbiomes has University of Thessaly, Greece greatly advanced. However, knowledge on the assembly of rhizospheric communities in Reviewed by: Antonis Chatzinotas, aged-contaminated industrial soils is still limited, especially with regard to transcriptionally Helmholtz Centre for Environmental active microbiomes and their link to the quality or quantity of carbon sources. -
Mapping the Diversity of Microbial Lignin Catabolism: Experiences from the Elignin Database
Applied Microbiology and Biotechnology (2019) 103:3979–4002 https://doi.org/10.1007/s00253-019-09692-4 MINI-REVIEW Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database Daniel P. Brink1 & Krithika Ravi2 & Gunnar Lidén2 & Marie F Gorwa-Grauslund1 Received: 22 December 2018 /Revised: 6 February 2019 /Accepted: 9 February 2019 /Published online: 8 April 2019 # The Author(s) 2019 Abstract Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database (www.elignindatabase.com), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings. Keywords Lignin . Database . Aromatic metabolism . Catabolic pathways -
ETH Zurich Research Collection
Research Collection Doctoral Thesis Identification of Indigenous Phyllosphere Isolates of the Genus Sphingomonas as Plant-Protective Bacteria Author(s): Innerebner, Gerd Publication Date: 2011 Permanent Link: https://doi.org/10.3929/ethz-a-6620246 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO. 19649 Identification of Indigenous Phyllosphere Isolates of the Genus Sphingomonas as Plant-Protective Bacteria A dissertation submitted to ETH Zurich for the degree of Doctor of Sciences Presented by Gerd Innerebner Mag. rer. nat., Leopold-Franzens-Universität Innsbruck Born on 3 January 1980 Citizen of Italy April 2011 Referees: Prof. Dr. Julia A. Vorholt Prof. Dr. Hans-Martin Fischer Prof. Dr. Leo Eberl Table of Contents Thesis Abstract ........................................................................................................................ 5 Zusammenfassung ................................................................................................................... 7 Chapter 1 General Introduction ............................................................................................................. 11 The phyllosphere as habitat for microorganisms ......................................................................... 11 Leaf-associated bacterial communities ........................................................................................