DOCSLIB.ORG

PAH Biodegradation by Sphingomonas and Mycobacterium Spp in Two Different Set Ups

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
PAH Biodegradation by Sphingomonas and Mycobacterium Spp in Two Different Set Ups FACULTEIT LANDBOUWKUNDIGE EN TOEGEPASTE BIOLOGISCHE WETENSCHAPPEN Academiejaar 2003 - 2004 PAH-BIODEGRADATION BY SPHINGOMONAS AND MYCOBACTERIUM : STUDY OF THEIR NATURAL ABUNDANCE, DIVERSITY AND NUTRIENT DEMANDS IN PAH-CONTAMINATED SOILS. PAK-BIODEGRADATIE DOOR SPHINGOMONAS EN MYCOBACTERIUM : STUDIE VAN HUN NATUURLIJKE VERSPREIDING, DIVERSITEIT EN NUTRIËNT EISEN IN PAK-GECONTAMINEERDE BODEMS. door ir. Natalie Leys Thesis submitted in fulfillment of the requirements for the degree of Doctor (Ph.D.) in Applied Biological Sciences Proefschrift voorgedragen tot het bekomen van de graad van Doctor in de Toegepaste Biologische Wetenschappen op gezag van Rector: prof. dr. apr. A. DE LEENHEER Decaan: Promotoren: prof. dr. ir. H. VAN LANGENHOVE prof. dr. ir. W. VERSTRAETE prof. dr. ir. E. TOP dr. ir. D. SPRINGAEL dr. ir. L. BASTIAENS ISBN 90-5989-016-7 Auteur en promotoren geven de toelating dit doctoraatswerk voor consultatie beschikbaar te stellen en delen ervan te kopiëren voor persoonlijk gebruik. Elk ander gebruik valt onder de beperkingen van het auteursrecht, in het bijzonder met betrekking tot de verplichting uitdrukkelijk de bron te vermelden bij het aanhalen van de resultaten van dit werk. The author and the promoters give the authorization to consult and to copy parts of this work for personal use only. Every other use is subjected to the copyright laws. Permission to reproduce any material contained in this work should be obtained from the author. Gent, 28 maart 2004 De auteur: ir. Natalie Leys De promotoren: Prof. dr. ir. Willy Verstraete, Dr. ir. Eva Top, Dr. ir. Dirk Springael, Dr. ir. Leen Bastiaens " Research is what I'm doing when I don't know what I'm doing." - Wernher von Braun – Dankwoord ~ THE END ~ Cast The Doctor…................................................................... Natalie Leys Partners in crime…………..……………………….….........Karolien & Zita Co-stars…....................................Cindy, Barbara, David, Jan & Joke Colleagues.....................................Annemie Ryngaert & the Vito crew Assistants................................................Students Els, Tine & Carlos Supporters...................................................................All my friends! Boyfriend.….............................................................Joachim De Baer Anti-stress ball……........................................................Yazoo the cat Mom & Dad.…........................................Erna Van Hool & Louis Leys Sister & her family.…..................Isabella Leys & Ivan Eulaers & Cato The in-laws..........................................Hilda Ringoot & Hugo De Baer Catherine De Baer & Jeroen Stuur Dankwoord Review comity…..............Prof. H. Van Langenhove, Prof. P. Sorgeloos, Prof. E. Vandamme, Dr. K. Smalla, Prof. M. Höfte, Prof. P. De Vos Producer.............................................................Prof. Willy Verstaete Assistant Producer.........................................................Prof. Eva Top Director..................................................................Dr. Dirk Springael Assistant Director.................................................Dr. Leen Bastiaens Logistics supervisor......................................................Dr. Ludo Diels Production support.……….……………………………………The SCK crew ~ Thank you all very much !!! ~ That's all folks! Summary SUMMARY Polycyclic aromatic hydrocarbons (PAHs) are major soil pollutants in many industrialized countries. Microbial degradation is considered to be the major route through which PAHs are removed from contaminated environments and therefore bioremediation is considered as a feasible remediation technology for cleaning PAH- contaminated soil. Mycobacterium and Sphingomonas strains using polycyclic aromatic hydrocarbons (PAHs) as sole source of carbon and energy could be essential members of such PAH-degrading bacterial communities, as they are often isolated during enrichments of PAH-degrading bacteria from such soil. Therefore, for future optimization of bioremediation process, it is of interest to study more in detail the distribution and diversity and specific nutrient requirements of Mycobacterium and Sphingomonas in PAH-polluted soil. Four new culture-independent PCR-based detection methods targeting the 16S rRNA genes were developed to analyze PAH-degrading Mycobacterium and Sphingomonas communities in PAH-contaminated soils. Genus-specific primers were developed for PCR detection of either Sphingomonas species (Sphingo108f and Sphingo420r), or ‘fast-growing’ Mycobacterium species (Myco66f and Myco600r). The resulting amplicons were separated by Denaturing Gradient Gel Electrophoresis (DGGE) for generating Mycobacterium and Sphingomonas community fingerprints. Both Mycobacterium and Sphingomonas specific primer sets proved to be highly selective for the target group and single-band DGGE profiles were obtained for most strains tested. Strains belonging to the same species had identical DGGE fingerprints, and in most cases but not all, these fingerprints were typical for one species, allowing partial differentiation between species in a Mycobacterium or Sphingomonas population. Inoculated Sphingomonas and Mycobacterium strains could be detected at a cell concentration of 104 respectively 106 cells per gram of soil using the new primer set alone or 102 cells per gram of soil in a nested PCR approach in combination with eubacterial primers. In addition, 2 species specific primer sets were designed to detect bacteria related to Sphingomonas sp. EPA505 (EPAf and EPAr) and M. frederiksbergense (MYCOFf and MYCOFr). Using DNA extracts of a variety of inoculated PAH-contaminated soils, the EPA505 specific primer pair was able to Summary detect EPA505 in concentrations as low as 102 cells per gram of soil. The MYCOF primer set could detect M. frederiksbergense in soil at a cell concentration of 104 cells per g soil via direct PCR and subsequent DNA-DNA hybridization of the PCR products or at a cell concentration of 102 cells per g soil via a nested PCR approach. The new detection methods were used to rapidly asses the Mycobacterium and Sphingomonas population structure of several PAH-contaminated soils of diverse origin and different overall contamination profiles, pollution concentrations and chemical-physical soil characteristics. Using the Mycobacterium genus-specific detection method, fast-growing Mycobacterium species were detected in most uncontaminated soils and PAH-contaminated soils tested. By sequencing of cloned PCR products amplified from DNA from PAH-contaminated soil, well-known PAH- degrading species like M. frederiksbergense and M. austroafricanum were detected. However, in all PAH-contaminated soils bacteria were detected with 16S rRNA gene sequences related to the 16S rRNA gene of M. tusciae, a Mycobacterium species so far not reported in relation to biodegradation of PAHs. Using the species-specific detection method, M. frederiksbergense strains were detected in most PAH- contaminated soils, including soils in which no M. frederiksbergense strains were detected using the Mycobacterium genus-specific detection method. The new Sphingomonas specific PCR-DGGE method revealed the presence of Sphingomonas communities in all tested PAH-contaminated soils, with less diversity in soils containing highest phenanthrene concentrations. Sequence analysis of cloned PCR products revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates. Sequences from environmental clones grouped phylogenetically with other environmental clone sequences available in data bases and possibly originated from several potential new species, not previously detected with culture-dependent detection techniques. In most of the tested PAH-contaminated soils, we detected also 16S rRNA gene fragments from Sphingomonas sp. EPA505 related strains. By adding different inorganic supplements of nitrogen (N) and phosphorus (P) affecting the overall Carbon/Nitrogen/Phosphorus-ratio of soil, we investigated the impact of soil inorganic N and P nutrient conditions on PAH degradation by PAH- degrading Sphingomonas and Mycobacterium strains by means of soil slurry Summary degradation tests. The general theoretical calculated C/N/P-ratio of 120/14/3 [expressed in mg] allowed rapid PAH metabolisation by Sphingomonas and Mycobacterium strains without limitation. In addition, PAH-degradation activity was not affected when circa 10 times lower concentrations of nitrogen and phosphorus were available, indicating that Sphingomonas and Mycobacterium strains are capable of metabolizing PAHs under low nutrient conditions. In addition, PAH-degradation was not affected by an excess of nitrogen and/or phosphorus unbalancing the C/N/P ratio in the soil. Supplements of nitrogen and phosphorus salts increased however the salinity of the soil slurry solutions and seriously limited or even completely blocked biodegradation. The results presented in this thesis suggest an important role for Mycobacterium and Sphingomonas species in the PAH-degrading bacterial communities naturally colonizing PAH-contaminated soils with very different contamination profiles and different origin. Sphingomonas populations seem to dominate in soils contaminated with high concentrations of more bioavailable and more easily degradable PAHs such as phenanthrene, while Mycobacterium populations may be better adapted to flourish in soils enriched in less bioavailable higher molecular weight PAHs. In addition, the results and
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • Natural Gas and Temperature Structured a Microbial Community Response to the Deepwater Horizon Oil Spill
    Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill Molly C. Redmond and David L. Valentine1 Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106 Edited by Paul G. Falkowski, Rutgers, The State University of New Jersey, New Brunswick, Brunswick, NJ, and approved September 7, 2011 (received for review June 1, 2011) Microbial communities present in the Gulf of Mexico rapidly Although the ability to degrade hydrocarbons is found in many responded to the Deepwater Horizon oil spill. In deep water types of bacteria, the most abundant oil-degraders in marine plumes, these communities were initially dominated by members environments are typically Gammaproteobacteria, particularly of Oceanospirillales, Colwellia, and Cycloclasticus. None of these organisms such as Alcanivorax, which primarily degrades alkanes, groups were abundant in surface oil slick samples, and Colwellia or Cycloclasticus, which specializes in the degradation of aro- was much more abundant in oil-degrading enrichment cultures in- matic compounds (16). However, most studies of microbial cubated at 4 °C than at room temperature, suggesting that the community response to hydrocarbons have been conducted in colder temperatures at plume depth favored the development of oil-amended mesocosm experiments with sediment, beach sand, these communities. These groups decreased in abundance after the or surface water (16), and little is known about the response to well was capped in July, but the addition of hydrocarbons in labo- oil inputs in the deep ocean or the impact of natural gas on these ratory incubations of deep waters from the Gulf of Mexico stimu- communities.
    [Show full text]
  • Cycloclasticus Pugetii Gen. Nov., Sp. Nov., an Aromatic Hydrocarbon-Degrading Bacterium from Marine Sediments SHERYL E
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1995, p. 116-123 Vol. 45, No. 1 0020-7713/95/$04.00+0 Copyright 0 1995, International Union of Microbiological Societies Cycloclasticus pugetii gen. nov., sp. nov., an Aromatic Hydrocarbon-Degrading Bacterium from Marine Sediments SHERYL E. DYKSTERHOUSE,? JAMES P. GRAY, RUSSELL P. HERWIG," J. CAN0 LARA, AND JAMES T. STALEY Department of Microbiology, SC-42) University of Washington, Seattle, Washington 981 95 Three heterotrophic bacterial strains were isolated from different locations in Puget Sound, Washington, by using biphenyl as the principal carbon source. These strains grow by using a limited number of organic compounds, including the aromatic hydrocarbons naphthalene, phenanthrene, anthracene, and toluene, as sole carbon sources. These aerobic, gram-negative rods are motile by means of single polar flagella. Their 16s rRNA sequences indicate that they are all members of the y subdivision of the Proteobacteriu. Their closest known relatives are the genera Methylobacter and Methylomonas (genera of methane-oxidizing bacteria), uncultured sulfur-oxidizing symbionts found in marine invertebrates, and clone FL5 containing 16s ribosomal DNA amplified from an environmental source. However, the Puget Sound bacteria do not use methane or methanol as a carbon source and do not oxidize reduced sulfur compounds. Furthermore, a 16s rRNA base similarity comparison revealed that these bacteria are sufficiently different from other bacteria to justify establishment of a new genus. On the basis of the information summarized above, we describe a new genus and species, Cycloclasticuspugetii, for these bacteria; strain PS-1 is the type strain of C. pugetii. Nearshore marine environments receive a wide variety of as their sole sources of organic carbon.
    [Show full text]
  • Metabolic and Spatio-Taxonomic Response of Uncultivated Seafloor Bacteria Following the Deepwater Horizon Oil Spill
    The ISME Journal (2017) 11, 2569–2583 © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej ORIGINAL ARTICLE Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill KM Handley1,2,3, YM Piceno4,PHu4, LM Tom4, OU Mason5, GL Andersen4, JK Jansson6 and JA Gilbert2,3,7 1School of Biological Sciences, University of Auckland, Auckland, New Zealand; 2Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA; 3Institute for Genomic and Systems Biology, Argonne National Laboratory, Lemont, IL, USA; 4Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; 5Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA; 6Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA and 7The Microbiome Center, Department of Surgery, The University of Chicago, Chicago, IL, USA The release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecology of the water and sediment. Here, we reconstructed the genomes of 57 widespread uncultivated bacteria from post-spill deep-sea sediments, and recovered their gene expression pattern across the seafloor. These genomes comprised a common collection of bacteria that were enriched in heavily affected sediments around the wellhead. Although rare in distal sediments, some members were still detectable at sites up to 60 km away. Many of these genomes exhibited phylogenetic clustering indicative of common trait selection by the environment, and within half we identified 264 genes associated with hydrocarbon degradation.
    [Show full text]
  • Metabolic and Spatio-Taxonomic Response of Uncultivated Seafloor Bacteria Following the Deepwater Horizon Oil Spill
    bioRxiv preprint doi: https://doi.org/10.1101/084707; this version posted October 31, 2016. 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-NC-ND 4.0 International license. Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill Authors Handley KMa,b,c, $, Piceno YMd, Hu Pd, Tom LMd, Mason OUe, Andersen GLd, Jansson JKf, Gilbert JAa,b,g,1 Author Affiliation aSchool of Biological Sciences, University of Auckland, Auckland 1010, New Zealand bDepartment of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA cInstitute for Genomic and Systems Biology, Argonne National Laboratory, IL 60439, USA dEarth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA eEarth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32304, USA fEarth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA gThe Microbiome Center, Department of Surgery, The University of Chicago, Chicago, IL 60637, USA 1Correspondence should be addressed to Jack A. Gilbert, Ph.D. Department of Surgery, University of Chicago, 5842 South Maryland Avenue, Chicago, IL, 60637, USA; email: [email protected]; and Kim M. Handley, School of Biological Sciences, University of Auckland, Auckland, New Zealand, email: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/084707; this version posted October 31, 2016. 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.
    [Show full text]
  • Chapter 4 Results
    University of Pretoria etd – Surridge, A K J (2007) Chapter 4 Results 85 University of Pretoria etd – Surridge, A K J (2007) Results 4.1 Phylogeny of microbial communities from crude oil-polluted soil according to DGGE profiles DGGE with the 16S rDNA PCR product from soil samples 1-8 (Table 1) resulted in a gel displaying a denser (closer spaced and higher number) banded fingerprint pattern with a higher colour intensity in unpolluted soil (lanes 5-7) than in the diesel-polluted soils (lanes1-4 and 8) (Fig. 6). Each band on the gel is assumed to be representative of only one distinct species, which was proved upon sequencing of the band. The gel also revealed a decrease in microbial diversity, i.e. number of bands, in subsoil layers (lanes 2 and 8) in comparison with topsoil. This was to be expected since these two samples should have very low species diversity as few organisms are present 1m and 1.5m deep in soil (Zhou et al. 2002). Of the polluted topsoil samples (lanes 1, 3 and 4), lane 3 DNA, extracted from the rhizosphere of plants growing in the soil, showed the greatest array of bands. This could have been due to plant root exudates enriching the soil around the roots, thus providing a nutrient boost within the polluted soil for microbes growing in the immediate vicinity of the roots. However, lane 4, which was from barren soil, displayed only slightly fewer bands than lane 3. 86 University of Pretoria etd – Surridge, A K J (2007) S 12 3456 78S 16 17 18 2019 21 11 22 12 23 1 24 6 25 7 26 13 2 28 27 14 8 4 29 15 30 3 5 9 10 Figure 6: Denaturing gradient gel fingerprints resulting from assessing bacterial diversity between communities isolated from site 1 in Table 1, using a gradient of 15-55%.
    [Show full text]
  • Sphingomonas Alaskensis Sp. Nov., a Dominant Bacterium from a Marine Oligotrophic Environment
    International Journal of Systematic and Evolutionary Microbiology (2001), 51, 73–79 Printed in Great Britain Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment M. Vancanneyt,1 F. Schut,2 C. Snauwaert,1 J. Goris,3 J. Swings1,3 and J. C. Gottschal2 Author for correspondence: M. Vancanneyt. Tel: j32 9 2645115. Fax: j32 9 2645092. e-mail: marc.vancanneyt!rug.ac.be 1,3 BCCM/LMG Bacteria Seven Gram-negative strains, isolated in 1990 from a 106-fold dilution series of Collection, K. L. seawater from Resurrection Bay, a deep fjord of the Gulf of Alaska, were Ledeganckstraat 351 and Laboratorium voor identified in a polyphasic taxonomic study. Analysis of 16S rDNA sequences Microbiology3 , University and DNA-homology studies confirmed the phylogenetic position of all strains of Gent, B-9000 Gent, in the genus Sphingomonas and further indicated that all of the strains Belgium constitute a single homogeneous genomic species, distinct from all validly 2 Department of described Sphingomonas species. The ability to differentiate the species, both Microbiology, University of Groningen, N-9750 AA phenotypically and chemotaxonomically, from its nearest neighbours justifies Haren, The Netherlands the proposal of a new species name, Sphingomonas alaskensis sp. nov., for this taxon. Strain LMG 18877T (l RB2256T l DSM 13593T) was selected as the type strain. Keywords: Sphingomonas alaskensis sp. nov., identification, polyphasic taxonomy, marine ultramicrobacterium INTRODUCTION readily obtained in culture but which mostly belong to a minority of the total community. Microbiologists have been intrigued by the phenom- Culture-independent molecular techniques are now enon of ‘unculturability’ for over half a century, widely used to obtain a thorough understanding of the especially with respect to bacteria in the open ocean identity and nature of the bacteria comprising marine (MacLeod, 1985).
    [Show full text]
  • Microbial Communities and Polycyclic Aromatic Hydrocarbons
    Microbial Communities and Polycyclic Aromatic Hydrocarbons: Exposure Related Adaptations in Environmental Microbiomes and Their Potential for Bioremediation by Lauren Kathleen Redfern Department of Civil and Environmental Engineering Duke University Date:_______________________ Approved: ___________________________ Claudia K. Gunsch, Supervisor ___________________________ Patrick L. Ferguson ___________________________ Scott H. Harrison ___________________________ Richard T. Di Giulio Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Civil and Environmental Engineering in the Graduate School of Duke University 2017 ABSTRACT Microbial Communities and Chemical Pollutants: Exposure Related Adaptations in Prokaryotic Microbiomes and Their Influence on Environmental and Ecological Health by Lauren Kathleen Redfern Department of Civil and Environmental Engineering Duke University Date:_______________________ Approved: ___________________________ Claudia K. Gunsch, Supervisor ___________________________ Patrick L. Ferguson ___________________________ Scott H. Harrison ___________________________ Richard T. Di Giulio An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Civil and Environmental Engineering in the Graduate School of Duke University 2017 Copyright by Lauren Kathleen Redfern 2017 Abstract Bioremediation is a treatment strategy that involves the removal of chemical pollutants
    [Show full text]
  • Bacterial-Invertebrate Symbioses: from an Asphalt Cold Seep to Shallow Waters
    Bacterial-invertebrate symbioses: from an asphalt cold seep to shallow waters Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften - Dr. rer. nat. - dem Fachbereich Biologie/Chemie der Universit¨at Bremen vorgelegt von Luciana Raggi Hoyos Bremen September 2010 Die vorliegende Arbeit wurde in der Zeit von April 2007 bis August 2010 in der Symbiose Gruppe am Max-Planck Institut f¨ur marine Mikrobiologie in Bremen angefertigt. 1. Gutachterin: Dr. Nicole Dubilier 2. Gutachter: Prof. Dr. Ulrich Fischer Tag des Promotionskolloquiums: 18. Oktober 2010 To Pablo to my family ‘La simbiosis, la uni´on de distintos organismos para formar nuevos colectivos, ha resultado ser la m´as importante fuerza de cambio sobre la Tierra’ L. Margulis & D. Sagan, 1995 ‘La uni´on hace la fuerza’ - Frase popular Abstract Symbiotic associations are complex partnerships that can lead to new metabolic capabilities and the establishment of novel organisms. The diversity of these as- sociations is very broad and there are still many mysteries about the origin and the exact relationship between the organisms that are involved in a symbiosis (host and symbiont). Some of these associations are essential to the hosts, such as the chemosynthetic symbioses occurring in invertebrates of the deep-sea. In others the host probably would rather not be the host, as in the case of parasitic microbes. My PhD research focuses on symbiotic and parasitic associations in chemosynthetic and non-chemosynthetic invertebrates. This thesis describes and discusses three different aspects of associations between bacteria and marine in- vertebrates. The first aspect focuses on chemosynthetic associations from a unique asphalt seep called Chapopote in the Gulf of Mexico (GoM).
    [Show full text]
  • Enhanced Crude Oil Biodegradative Potential of Natural Phytoplankton- Associated Hydrocarbonoclastic Bacteria
    Thompson H, Angelova A, Bowler B, Jones M, Gutierrez T. Enhanced crude oil biodegradative potential of natural phytoplankton- associated hydrocarbonoclastic bacteria. Environmental Microbiology 2017, 19(7), 2843-2861. Copyright: This is the peer reviewed version of the following article: Thompson H, Angelova A, Bowler B, Jones M, Gutierrez T. Enhanced crude oil biodegradative potential of natural phytoplankton-associated hydrocarbonoclastic bacteria. Environmental Microbiology 2017, 19(7), 2843-2861, which has been published in final form at https://doi.org/10.1111/1462-2920.13811. This article may be used for non- commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving. DOI link to article: https://doi.org/10.1111/1462-2920.13811 Date deposited: 25/08/2017 Embargo release date: 05 June 2018 Newcastle University ePrints - eprint.ncl.ac.uk 1 Enhanced crude oil biodegradative potential of natural phytoplankton-associated 2 hydrocarbonoclastic bacteria 3 4 Haydn Thompson1, Angelina Angelova1, Bernard Bowler2, Martin Jones2, Tony Gutierrez1* 5 6 1 School of Life Sciences, Heriot Watt University, Edinburgh, UK 7 2 School of Civil Engineering and Geosciences, University of Newcastle, Newcastle Upon Tyne, UK 8 9 10 *Correspondence to: 11 Dr. Tony Gutierrez 12 School of Life Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K. 13 [email protected] 14 15 Running title: Phytoplankton-bacterial biodegradation of crude oil PAHs 16 17 Keywords: eukaryotic phytoplankton; hydrocarbon-degrading bacteria (HCB); crude oil; micro- 18 algae; biodegradation; marine environment 19 20 21 The authors declare no conflict of interest. 22 23 24 25 1 26 Summary 27 Phytoplankton have been shown to harbour a diversity of hydrocarbonoclastic bacteria (HCB), yet it 28 is not understood how these phytoplankton-associated HCB would respond in the event of an oil spill 29 at sea.
    [Show full text]