DOCSLIB.ORG

Analysis of the Impact of Organic Pollutants on Marine Microbial Communities

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Analysis of the Impact of Organic Pollutants on Marine Microbial Communities Analysis of the impact of organic pollutants on marine microbial communities Elena Cerro Gálvez ADVERTIMENT La consulta d’aquesta tesi queda condicionada a l’acceptació de les següents condicions d'ús: La difusió d’aquesta tesi per mitjà del r e p o s i t o r i i n s t i t u c i o n a l UPCommons (http://upcommons.upc.edu/tesis) i el repositori cooperatiu TDX ( h t t p : / / w w w . t d x . c a t / ) ha estat autoritzada pels titulars dels drets de propietat intel·lectual únicament per a usos privats emmarcats en activitats d’investigació i docència. No s’autoritza la seva reproducció amb finalitats de lucre ni la seva difusió i posada a disposició des d’un lloc aliè al servei UPCommons o TDX. No s’autoritza la presentació del seu contingut en una finestra o marc aliè a UPCommons (framing). Aquesta reserva de drets afecta tant al resum de presentació de la tesi com als seus continguts. En la utilització o cita de parts de la tesi és obligat indicar el nom de la persona autora. ADVERTENCIA La consulta de esta tesis queda condicionada a la aceptación de las siguientes condiciones de uso: La difusión de esta tesis por medio del repositorio institucional UPCommons (http://upcommons.upc.edu/tesis) y el repositorio cooperativo TDR (http://www.tdx.cat/?locale- attribute=es) ha sido autorizada por los titulares de los derechos de propiedad intelectual únicamente para usos privados enmarcados en actividades de investigación y docencia. No se autoriza su reproducción con finalidades de lucro ni su difusión y puesta a disposición desde un sitio ajeno al servicio UPCommons No se autoriza la presentación de su contenido en una ventana o marco ajeno a UPCommons (framing). Esta reserva de derechos afecta tanto al resumen de presentación de la tesis como a sus contenidos. En la utilización o cita de partes de la tesis es obligado indicar el nombre de la persona autora. WARNING On having consulted this thesis you’re accepting the following use conditions: Spreading this thesis by the i n s t i t u t i o n a l r e p o s i t o r y UPCommons (http://upcommons.upc.edu/tesis) and the cooperative repository TDX (http://www.tdx.cat/?locale- attribute=en) has been authorized by the titular of the intellectual property rights only for private uses placed in investigation and teaching activities. Reproduction with lucrative aims is not authorized neither its spreading nor availability from a site foreign to the UPCommons service. Introducing its content in a window or frame foreign to the UPCommons service is not authorized (framing). These rights affect to the presentation summary of the thesis as well as to its contents. In the using or citation of parts of the thesis it’s obliged to indicate the name of the author. Analysis of the impact of organic pollutants on marine microbial communities Elena Cerro Gálvez Doctoral Thesis by compendium of publications Ph.D. Program in Marine Sciences Supervised by Dra. Maria Vila Costa and Dr. Jordi Dachs Marginet Department of Environmental Chemistry (IDAEA-CSIC) Barcelona, 2019 “Educating people to understand, to love and to protect the water systems of the planet, marine and fresh water, for the well-being of future generations.” COUSTEAU, JACQUES YVES “How inappropriate to call this planet Earth when it is quite clearly Ocean.” CLARKE, ARTHUR CHARLES TABLE OF CONTENTS List of figures List of tables List of abbreviations List of publications Abstract / Resumen PART I: GENERAL INTRODUCTION General introduction 27 Organic pollutants (OPs) 27 Description and legacy 27 OPs in the ocean 30 OPs selected in this study 33 Marine microbial communities 42 Interaction between OPs and marine microorganisms 45 Thesis aims 49 A brief overview of methodology 52 Experiments and sampling sites 52 Methodological approaches 53 References 57 PART II: MAIN CHAPTERS Chapter 1 Modulation of microbial growth and enzymatic activities 73 in the marine environment due to exposure to organic contaminants of emerging concern and hydrocarbons Chapter 2 Microbial responses to perfluoroalkyl substances and 117 perfluorooctanesulfonate (PFOS) desulfurization in the Antarctic marine environment Chapter 3 Microbial responses to anthropogenic dissolved organic 153 carbon in Arctic and Antarctic coastal seawaters Chapter 4 195 Part III: EPILOGUE General discussion 239 General conclusions 245 Recommendations for future research 247 References 250 PART IV: Annex Annex I: Supporting information of chapter 1 257 Annex II: Supporting information of chapter 2 271 Annex III: Supporting information of chapter 3 297 Annex IV: Supporting information of chapter 4 331 Acknowledgements LIST OF FIGURES PART I: GENERAL INTRODUCTION Figure 1 Bioconcentration, bioaccumulation and biomagnification concepts. 28 Figure 2 Environmental transport, cycling, and fate of organic pollutants. 31 Figure 3 Heptadecane, as an example of n-alkane with 17 carbon atoms. 33 Figure 4 List of Polycyclic aromatic hydrocarbons (PAHs). 34 Figure 5 List of Organophosphate esters (OPEs). 36 Figure 6 Perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA). 37 Figure 7 Overlaid chromatogram of a dissolved phase sample of the aromatic 39 fraction. Figure 8 Schematic illustration of the phylogeny of the major marine Archaea and 43 Bacteria clades. Figure 9 Some of the main approaches available to marine microbial ecologists. 44 Figure 10 Interaction between marine microbial communities and OPs. 48 Figure 11 Map of experiment locations. 52 Figure 12 Summary of techniques used in each chapter. 54 PART II: MAIN CHAPTERS Chapter 1 Figure 1 Location of the sampling stations. 87 Figure 2 Significant differences in cell abundances of heterotrophic bacteria and 91 picophytoplankton. Figure 3 Contribution of each bacterial phylogenetic group (% CARD-FISH). 94 Figure 4 Extracellular enzyme activities. 96 Chapter 2 Figure 1 Changes in microbial activities and community composition in dose- 130 response experiments. Figure 2 Variation of relative abundance of PFOS in the long-term experiment. 133 Figure 3 Changes in microbial community activities and composition between 135 controls and PFAA amendments in long-term experiment. Figure 4 Contribution of each taxonomical group to the total number of transcripts 136 in controls and PFAAs amendments after 24 h and 6 days. Figure 5 Total number of significantly enriched and depleted transcripts detected 139 by edgeR (FDR < 0.05). Figure 6 Relative abundance of transcripts of Sulfur metabolism. 140 Figure 7 Suggested pathways of bacterial PFOS desulfurization. 141 Chapter 3 Figure 1 Enrichment factor of growth rate of prokaryotic community microcosms 167 amended with different ADOC fractions. Figure 2 Abundance of the taxa that increased by 10-fold or were absent in 172 controls. Figure 3 Contribution of genes and transcripts differently present in ADOC 175 treatments versus controls to the total number of genes harboured or expressed by each taxa. Figure 4 Heatmap of changes in gene expression. 176 Figure 5 Schematics of the strategies to cope with hydrophobic ADOC. 181 Chapter 4 Figure 1 Location of the sampling site of the seawater used for the experiments. 208 Figure 2 Relative abundance of transposases. 213 Figure 3 Heatmap of changes between controls and ADOC amendments. 214 Figure 4 Taxonomical affiliation of metagenomes, 24 h after treatment. 218 Figure 5 Summary of up- and down-regulated transcripts detected by edgeR 221 (FDR < 0.05). Figure 6 Summary of Spearman correlations between transposases and 222 significant up- and down-regulated genes. Figure 7 Abundances in the taxa that increased by 10-fold or were absent in 223 controls after 24 h of incubation. Part III: EPILOGUE Figure 1 Interaction between OP and marine bacteria 240 PART IV: Annex Annex I: Supporting information of chapter 1 Figure S1 Concentration of alkanes, PAHs and OPEs in the initial surface waters. 264 Figure S2 Mean cell abundances of heterotrophic bacteria and picophytoplankton 265 in the controls quantified by flow cytometry. Figure S3 Bacterial community composition of initial surface waters quantified by 265 CARD-FISH. Figure S4 Cell-specific EEA in the initial time point for each sampling site. 266 Figure S5 PCA of standardized biological descriptors at the initial time. 266 Figure S6 Pearson’s correlations between microbial growth rates. 267 Annex II: Supporting information of chapter 2 Figure S1 NMDS plot showing the similarities of sample 16S rDNA composition 290 Figure S2 Relative abundance of each taxonomic affiliation by 16S rDNA. 290 Figure S3 Absolute and relative abundance of each taxonomical group in 291 metatranscriptomic profiles Figure S4 Relative abundance of general SEED categories in the 292 metatranscriptomes. Figure S5 Heatmap of changes in sulfur metabolism transcritps. 292 Annex III: Supporting information of chapter 3 Figure S1 Relative abundance of major taxonomic groups in metaG and metaT. 318 Figure S2 Comparison between relative abundance of metaG and CARD-FISH. 319 Figure S3 Taxonomical affiliation of Antarctic and Arctic metaG. 319 Figure S4 Up- and down-regulated gene expression after 0.5 and 24 h. 320 Figure S5 Heatmap of changes in gene expression. 321 Figure S6 Scheme of the main degradation routes of PAHs. 322 Figure S7 Transcript abundances of methylotrophic groups in Arctic experiment. 322 Figure S8 Taxonomical affiliation of Type I phosphodiesterase and Alk_ 323 phosphatase Pfam domains in Arctic experiment. Figure S9 Relative abundances of LPS in metaG and metaT of Arctic experiment. 323 Figure S10 Location of the sampling sites. 324 Annex IV: Supporting information of chapter 4 Figure S1 Growth rates of prokaryotic community amended with different ADOC 336 concentrations after 4, 24 and 48 h. Figure S2 Bacterial production of bacterial community. 337 Figure S3 Percentage of actively-respiring bacteria in the dose-response 338 experiment. Figure S4 Pearson’s correlations between microbial growth rates added 339 concentrations of pollutants.
Load more

Recommended publications
  • Kinetic and Functional Properties of Human Mitochondrial Phosphoenolpyruvate Carboxykinase
    Biochemistry and Biophysics Reports 7 (2016) 124–129 Contents lists available at ScienceDirect Biochemistry and Biophysics Reports journal homepage: www.elsevier.com/locate/bbrep Kinetic and functional properties of human mitochondrial phosphoenolpyruvate carboxykinase Miriam Escós b, Pedro Latorre a,b, Jorge Hidalgo a,b, Ramón Hurtado-Guerrero b,e, José Alberto Carrodeguas b,c,d,nn, Pascual López-Buesa a,b,n a Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain b Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50009 Zaragoza, Aragón, Spain c Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain d IIS Aragón, 50009 Zaragoza, Spain e Fundación ARAID, Gobierno de Aragón, Zaragoza, Spain article info abstract Article history: The cytosolic form of phosphoenolpyruvate carboxykinase (PCK1) plays a regulatory role in gluconeo- Received 21 April 2016 genesis and glyceroneogenesis. The role of the mitochondrial isoform (PCK2) remains unclear. We report Received in revised form the partial purification and kinetic and functional characterization of human PCK2. Kinetic properties of 2 June 2016 the enzyme are very similar to those of the cytosolic enzyme. PCK2 has an absolute requirement for Accepted 6 June 2016 þ þ þ Mn2 ions for activity; Mg2 ions reduce the K for Mn2 by about 60 fold. Its specificity constant is 100 Available online 8 June 2016 m fold larger for oxaloacetate than for phosphoenolpyruvate suggesting that oxaloacetate phosphorylation Keywords: À1 is the favored reaction in vivo.
    [Show full text]
  • In Situ Biodegradation, Photooxidation and Dissolution of Petroleum Compounds in Arctic Seawater and Sea Ice
    Water Research 148 (2019) 459e468 Contents lists available at ScienceDirect Water Research journal homepage: www.elsevier.com/locate/watres In situ biodegradation, photooxidation and dissolution of petroleum compounds in Arctic seawater and sea ice * Leendert Vergeynst a, b, , Jan H. Christensen c, Kasper Urup Kjeldsen b, Lorenz Meire d, e, Wieter Boone f, Linus M.V. Malmquist c, Søren Rysgaard a, f a Arctic Research Centre, Aarhus University, Aarhus, Denmark b Section for Microbiology and Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark c Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Copenhagen, Denmark d Greenland Climate Research Centre, Greenland Institute of Natural Resources, Nuuk, Greenland e Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research, Utrecht University, Yerseke, Netherlands f Centre for Earth Observation Science, University of Manitoba, Winnipeg, Canada article info abstract Article history: In pristine sea ice-covered Arctic waters the potential of natural attenuation of oil spills has yet to be Received 19 July 2018 uncovered, but increasing shipping and oil exploitation may bring along unprecedented risks of oil spills. Received in revised form We deployed adsorbents coated with thin oil films for up to 2.5 month in ice-covered seawater and sea 22 October 2018 ice in Godthaab Fjord, SW Greenland, to simulate and investigate in situ biodegradation and photooxi- Accepted 23 October 2018 dation of dispersed oil. Available online 29 October 2018 GC-MS-based chemometric methods for oil fingerprinting were used to identify characteristic signa- tures for dissolution, biodegradation and photooxidation. In sub-zero temperature seawater, fast Keywords: Oil spill degradation of n-alkanes was observed with estimated half-life times of ~7 days.
    [Show full text]
  • Simulation of Deepwater Horizon Oil Plume Reveals Substrate Specialization Within a Complex Community of Hydrocarbon Degraders
    Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders Ping Hua, Eric A. Dubinskya,b, Alexander J. Probstc, Jian Wangd, Christian M. K. Sieberc,e, Lauren M. Toma, Piero R. Gardinalid, Jillian F. Banfieldc, Ronald M. Atlasf, and Gary L. Andersena,b,1 aEcology Department, Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; bDepartment of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720; cDepartment of Earth and Planetary Science, University of California, Berkeley, CA 94720; dDepartment of Chemistry and Biochemistry, Florida International University, Miami, FL 33199; eDepartment of Energy, Joint Genome Institute, Walnut Creek, CA 94598; and fDepartment of Biology, University of Louisville, Louisville, KY 40292 Edited by Rita R. Colwell, University of Maryland, College Park, MD, and approved May 30, 2017 (received for review March 1, 2017) The Deepwater Horizon (DWH) accident released an estimated Many studies of the plume samples reported that the structure 4.1 million barrels of oil and 1010 mol of natural gas into the Gulf of the microbial communities shifted as time progressed (3–6, 11– of Mexico, forming deep-sea plumes of dispersed oil droplets and 16). Member(s) of the order Oceanospirillales dominated from dissolved gases that were largely degraded by bacteria. During the May to mid-June, after which their numbers rapidly declined and course of this 3-mo disaster a series of different bacterial taxa were species of Cycloclasticus and Colwellia dominated for the next enriched in succession within deep plumes, but the metabolic capa- several weeks (4, 5, 14).
    [Show full text]
  • Effects of Dispersants and Biosurfactants on Crude-Oil Biodegradation and Bacterial Community Succession
    microorganisms Article Effects of Dispersants and Biosurfactants on Crude-Oil Biodegradation and Bacterial Community Succession Gareth E. Thomas 1,* , Jan L. Brant 2 , Pablo Campo 3 , Dave R. Clark 1,4, Frederic Coulon 3 , Benjamin H. Gregson 1, Terry J. McGenity 1 and Boyd A. McKew 1 1 School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK; [email protected] (D.R.C.); [email protected] (B.H.G.); [email protected] (T.J.M.); [email protected] (B.A.M.) 2 Centre for Environment, Fisheries and Aquaculture Science, Pakefield Road, Lowestoft, Suffolk NR33 0HT, UK; [email protected] 3 School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK; p.campo-moreno@cranfield.ac.uk (P.C.); f.coulon@cranfield.ac.uk (F.C.) 4 Institute for Analytics and Data Science, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK * Correspondence: [email protected]; Tel.: +44-1206-873333 (ext. 2918) Abstract: This study evaluated the effects of three commercial dispersants (Finasol OSR 52, Slickgone NS, Superdispersant 25) and three biosurfactants (rhamnolipid, trehalolipid, sophorolipid) in crude- oil seawater microcosms. We analysed the crucial early bacterial response (1 and 3 days). In contrast, most analyses miss this key period and instead focus on later time points after oil and dispersant addition. By focusing on the early stage, we show that dispersants and biosurfactants, which reduce Citation: Thomas, G.E.; Brant, J.L.; the interfacial surface tension of oil and water, significantly increase the abundance of hydrocarbon- Campo, P.; Clark, D.R.; Coulon, F.; degrading bacteria, and the rate of hydrocarbon biodegradation, within 24 h.
    [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]
  • First Insights Into the Microbiology of Three Antarctic Briny Systems of the Northern Victoria Land
    diversity Review First Insights into the Microbiology of Three Antarctic Briny Systems of the Northern Victoria Land Maria Papale 1,† , Carmen Rizzo 1,2,† , Gabriella Caruso 1 , Rosabruna La Ferla 1, Giovanna Maimone 1, Angelina Lo Giudice 1,* , Maurizio Azzaro 1,‡ and Mauro Guglielmin 3,‡ 1 Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata San Raineri 86, 98122 Messina, Italy; [email protected] (M.P.); [email protected] (C.R.); [email protected] (G.C.); [email protected] (R.L.F.); [email protected] (G.M.); [email protected] (M.A.) 2 Stazione Zoologica Anton Dohrn, Department BIOTECH, National Institute of Biology, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy 3 Dipartimento di Scienze Teoriche e Applicate, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-090-6015-414 † Equal contribution as first author. ‡ Equal contribution as last author. Abstract: Different polar environments (lakes and glaciers), also in Antarctica, encapsulate brine pools characterized by a unique combination of extreme conditions, mainly in terms of high salinity and low temperature. Since 2014, we have been focusing our attention on the microbiology of brine pockets from three lakes in the Northern Victoria Land (NVL), lying in the Tarn Flat (TF) and Boulder Clay (BC) areas. The microbial communities have been analyzed for community structure by next generation sequencing, extracellular enzyme activities, metabolic potentials, and microbial abundances. In this Citation: Papale, M.; Rizzo, C.; study, we aim at reconsidering all available data to analyze the influence exerted by environmental Caruso, G.; La Ferla, R.; Maimone, G.; parameters on the community composition and activities.
    [Show full text]
  • The Long-Chain Alkane Metabolism Network of Alcanivorax Dieselolei
    ARTICLE Received 30 Jan 2014 | Accepted 5 Nov 2014 | Published 12 Dec 2014 DOI: 10.1038/ncomms6755 The long-chain alkane metabolism network of Alcanivorax dieselolei Wanpeng Wang1,2,3,4 & Zongze Shao1,2,3,4 Alkane-degrading bacteria are ubiquitous in marine environments, but little is known about how alkane degradation is regulated. Here we investigate alkane sensing, chemotaxis, signal transduction, uptake and pathway regulation in Alcanivorax dieselolei. The outer membrane protein OmpS detects the presence of alkanes and triggers the expression of an alkane chemotaxis complex. The coupling protein CheW2 of the chemotaxis complex, which is induced only by long-chain (LC) alkanes, sends signals to trigger the expression of Cyo, which participates in modulating the expression of the negative regulator protein AlmR. This change in turn leads to the expression of ompT1 and almA, which drive the selective uptake and hydroxylation of LC alkanes, respectively. AlmA is confirmed as a hydroxylase of LC alkanes. Additional factors responsible for the metabolism of medium-chain-length alkanes are also identified, including CheW1, OmpT1 and OmpT2. These results provide new insights into alkane metabolism pathways from alkane sensing to degradation. 1 State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen 361005, China. 2 Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen 361005, China. 3 Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China. 4 Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, China. Correspondence and requests for materials should be addressed to Z.S.
    [Show full text]
  • Genome Sequence and Functional Genomic Analysis of the Oil-Degrading Bacterium Oleispira Antarctica
    ARTICLE Received 30 Oct 2012 | Accepted 18 Jun 2013 | Published 23 Jul 2013 DOI: 10.1038/ncomms3156 OPEN Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica Michael Kube1,2, Tatyana N. Chernikova3,4, Yamal Al-Ramahi5, Ana Beloqui5, Nieves Lopez-Cortez5, Marı´a-Eugenia Guazzaroni5,6, Hermann J. Heipieper7, Sven Klages1, Oleg R. Kotsyurbenko3, Ines Langer1, Taras Y. Nechitaylo3, Heinrich Lu¨nsdorf3, Marisol Ferna´ndez8, Silvia Jua´rez8, Sergio Ciordia8, Alexander Singer9,10, Olga Kagan9,10, Olga Egorova10,11, Pierre Alain Petit11, Peter Stogios11, Youngchang Kim10,12, Anatoli Tchigvintsev9, Robert Flick9, Renata Denaro13, Maria Genovese13, Juan P. Albar8, Oleg N. Reva14, Montserrat Martı´nez-Gomariz15, Hai Tran4, Manuel Ferrer5, Alexei Savchenko9,10,11, Alexander F. Yakunin11, Michail M. Yakimov13, Olga V. Golyshina3,4, Richard Reinhardt1,w & Peter N. Golyshin3,4 Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis—the paradigm of mesophilic hydrocarbonoclastic bacteria—O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low tempera- tures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts.
    [Show full text]
  • Bioprospecting the Solar Panel Microbiome: High- Throughput Screening for Antioxidant Bacteria in a Caenorhabditis Elegans Model
    bioRxiv preprint doi: https://doi.org/10.1101/423731; this version posted September 23, 2018. 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. Bioprospecting the solar panel microbiome: high- throughput screening for antioxidant bacteria in a Caenorhabditis elegans model Kristie Tanner1, Patricia Martorell2, Salvador Genovés2, Daniel Ramón2, Lorenzo Zacarías3, María Jesús Rodrigo3, Juli Peretó1,4,5, Manuel Porcar*1,4 1 Darwin Bioprospecting Excellence S.L. 2 ADM Biopolis S.L. 3 Instituto de Agroquímica y Tecnología de Alimentos (IATA) 4 Institute for Integrative Systems Biology (I2SysBio, University of Valencia-CSIC) 5 Department of Biochemistry and Molecular Biology, University of Valencia *Corresponding author: [email protected] Abstract Chen et al., 2015). In humans, chronic oxidative stress has been associated on many occasions with the initiation and Microbial communities that are exposed to sunlight progression of a variety of diseases, including Alzheimer’s typically share a series of adaptations to deal with the and cardiovascular diseases (such as hypertension and radiation they are exposed to, including efficient DNA atherosclerosis) or cancer (Chen and Zhong, 2014; repair systems, pigment production and protection Milkovic et al., 2014; Dandekar et al., 2015; Siti et al., 2015). against oxidative stress, which makes these environments good candidates for the search of novel The discovery of new antioxidants from natural sources antioxidant microorganisms. In this research project, we (i.e. plants or microorganisms) is of high interest for the isolated potential antioxidant pigmented bacteria from a pharmacological and food industries (Finley et al., 2011; dry and highly-irradiated extreme environment: solar Lin et al., 2014).
    [Show full text]
  • Bacterioplankton Diversity and Distribution in Relation To
    bioRxiv preprint doi: https://doi.org/10.1101/2021.06.08.447544; this version posted June 8, 2021. 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 4.0 International license. Bacterioplankton Diversity and Distribution in Relation to Phytoplankton Community Structure in the Ross Sea surface waters Angelina Cordone1, Giuseppe D’Errico2, Maria Magliulo1,§, Francesco Bolinesi1*, Matteo Selci1, Marco Basili3, Rocco de Marco3, Maria Saggiomo4, Paola Rivaro5, Donato Giovannelli1,2,3,6,7,8* and Olga Mangoni1,9 1 Department of Biology, University of Naples Federico II, Naples, Italy 2 Department of Life Sciences, DISVA, Polytechnic University of Marche, Ancona, Italy 3 National Research Council – Institute of Marine Biological Resources and Biotechnologies CNR-IRBIM, Ancona, Italy 4 Stazione Zoologica Anton Dohrn, Naples, Italy 5 Department of Chemistry and Industrial Chemistry, University of Genoa, Genoa, Italy 6 Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, USA 7 Marine Chemistry & Geochemistry Department - Woods Hole Oceanographic Institution, MA, USA 8 Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan § now at University of Essex, Essex, UK 9 Consorzio Nazionale Interuniversitario delle Scienze del Mare (CoNISMa), Rome, Italy *corresponding author: Francesco Bolinesi [email protected] Donato Giovannelli [email protected] Keywords: bacterial diversity, bacterioplankton, phytoplankton, Ross Sea, Antarctica Abstract Primary productivity in the Ross Sea region is characterized by intense phytoplankton blooms whose temporal and spatial distribution are driven by changes in environmental conditions as well as interactions with the bacterioplankton community.
    [Show full text]
  • Amirijami Mitra Phd.Pdf
    RECOMBINANT PRODUCTION OF OMEGA-3 FATTY ACIDS IN E. COL1 USING A GENE CLUSTER ISOLATED FROM SHEWANELLA BALTICA A Thesis Presented to The Faculty of Graduate Studies of The University of Guelph By MITRA AMIRI-JAMI In partial fulfillment of requirements For the degree of Doctor of Philosophy January, 2009 © Mitra Amiri-Jami, 2009 Library and Archives Bibliotheque et 1*1 Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A 0N4 OttawaONK1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-58261 -9 Our file Notre reference ISBN: 978-0-494-58261-9 NOTICE: AVIS: The author has granted a non­ L'auteur a accorde une licence non exclusive exclusive license allowing Library and permettant a la Bibliotheque et Archives Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par I'lnternet, prefer, telecommunication or on the Internet, distribuer et vendre des theses partout dans le loan, distribute and sell theses monde, a des fins commerciales ou autres, sur worldwide, for commercial or non­ support microforme, papier, electronique et/ou commercial purposes, in microform, autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in this et des droits moraux qui protege cette these. Ni thesis. Neither the thesis nor la these ni des extraits substantiels de celle-ci substantial extracts from it may be ne doivent etre imprimes ou autrement printed or otherwise reproduced reproduits sans son autorisation.
    [Show full text]
  • Aplicación De Cepas De Microbacterium Spp. Productoras De
    Aplicación de cepas de Microbacterium spp. productoras de compuestos orgánicos volátiles (COVs) como agentes biopesticidas y fitoestimulantes en semilleros de lechuga Trabajo Fin de Grado Departamento de Biología y Geología. Área de Microbiología. Grado en Biotecnología. Facultad de Ciencias Experimentales. Universidad de Almería. Curso 2019-2020 Autora: Laura Arbeloa Gómez Director: Joaquín Moreno Casco Codirectora: Francisca Suárez Estrella Agradecimientos En primer lugar, quiero dar las gracias a todo el área de Microbiología de la Universidad de Almería por acogerme y darme la oportunidad de realizar este trabajo y permitirme aprender con ellos cómo trabajar en un laboratorio y desarrollar un proyecto como este. Ha sido una gran experiencia poder trabajar en tan buena compañía, y no habría sido posible terminar este trabajo sin todos ellos. Especial agradecimiento a mi tutor, Joaquín Moreno Casco, por enseñarme un sinfín de cosas y transmitirme su pasión por el conocimiento. Desde que comencé el grado de Biotecnología mostró gran interés e implicación en llegar a cada alumno y ayudar en lo máximo posible, la puerta de su despacho siempre estaba abierta en caso de necesitar apoyo o consejo. A mi cotutora, Paqui Suárez Estrella, por todo el esfuerzo dedicado, sacando tiempo cuando no lo tenía, siempre dispuesta a resolverme cualquier duda. Por la orientación e implicación incluso durante la pandemia, gracias por hacerme sentir acompañada telemáticamente. Por último, pero no por ello menos importante, gracias a mi familia, a mis padres y hermana, por el apoyo económico y, sobre todo, personal. Gracias por creer en mí e insistir siempre en que estudiara lo que quisiera, sin importar que hubiera tenido que irme a la otra punta del mundo o quedarme al lado de casa.
    [Show full text]