DOCSLIB.ORG

Aix Marseille Université Ecole Doctorale Des Sciences De La Vie Et De La Santé

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Aix Marseille Université Ecole Doctorale Des Sciences De La Vie Et De La Santé Aix Marseille Université Ecole Doctorale des Sciences de la Vie et de la Santé THESE Pour l’obtention du grade de Docteur d’Aix Marseille Université en Microbiologie Thèse présentée et soutenue par Nicolas CHABERT Le 21 décembre 2017 Sous la direction de Dr. ACHOUAK Wafa (Directrice de recherche, UMR 7265 CNRS-CEA-AMU) Conception de biocathode et implication du fer dans de nouveaux modes de transfert d’électrons Rapporteurs Dr. BERGEL Alain (Directeur de recherche, CNRS) Dr. BOUSSERRHINE Noureddine (Maitre de conférence, UPEC) Examinateurs Dr. LOJOU Elisabeth (Directeur de recherche, CNRS) Dr. HAICHAR Feteh-El-Zahar (Maitre de conférence, Université de Lyon 1) Pr. CUNY Philippe (Professeur, Aix Marseille Université) Invités Dr. BONNEFOY Violaine (Directeur de recherche, CNRS) Dr. ROSE Jérôme (Directeur de recherche, CNRS) Résumé : Les piles à combustible microbiennes (PCMs) sont une technologie convertissant l’énergie chimique stockée dans la matière organique en énergie électrique à l’anode à l’aide de bactéries dites électroactives. Actuellement, les performances sont limitées par l’utilisation de cathodes abiotiques. L’intérêt porté aux cathodes biologiques est récent et ces dernières sont encore peu étudiées. Les objectifs de ces recherches ont donc été d’identifier et de décrire des bactéries ainsi que les mécanismes permettant de catalyser une réduction cathodique notamment celle de l’oxygène. La première partie des travaux portant sur la réalisation d’un criblage pour la formation de biocathodes a révélé l’inefficacité du métabolisme hétérotrophe pour la conception de biocathodes performantes. De ce fait, la suite des travaux a porté sur la bactérie chimiolithoautotrophe acidophile Acidithiobacillus ferrooxidans. Deux mécanismes de transfert d’électrons dépendant du fer ont été mis en évidence générant un courant maximal de -3,8 A.m-2. Nous avons également abordé les mécanismes de transfert d’électrons en milieu neutre chez une bactérie hétérotrophe, Pseudomonas brassicacearum NFM421 bien que peu performante en terme de production de courant. Cette dernière permet une catalyse indirecte de la réduction de l’oxygène à la cathode à pH neutre via un métabolite secondaire le 2,4-diacéthylphloroglucinol associé au fer, mettant encore une fois en lumière l’importance du fer dans le transfert d’électrons. Ce travail a également porté sur la potentielle application des biopiles dans des environnements anthropisés en vue de l’extraction de métaux et plus particulièrement de terre rares qui s’avèrent être une voie de recherche prometteuse. Mots-clés : Biocathode ; Fer ; Acidithiobacillus ferrooxidans ; Pseudomonas brassicacearum ; DAPG ; extraction de métaux Abstract : Microbial fuel cells (MFCs) are devices that convert chemical energy contained in organic matter into electrical energy using electroactive bacteria that act at the anode. Currently, MFCs performances are limited by the use of abiotic cathode. The interest in biological cathode has recently started and less is known about bacterial diversity and mechanism that catalyze cathodic reduction. The aims of the research work are therefor to identify and describe potential bacteria and mechanism involved in such catalysis. The first part of the work is the realization of a screening that did not show conclusive results and might indicate that heterotrophic metabolism was not an efficient choice. Next, Acidithiobacillus ferrooxidans had been used and shown two extracellular electron transfer mechanism depending on iron. A maximum current intensity of -3,8 A.m-2 had been reached. To be close to operational condition of MFC, Pseudomonas brassicacearum NFM 421 has also be use and shown capacity to indirectly catalyze the oxygen reduction at a neutral pH using the 2,4-diacethylphloroglucinol, a secondary metabolite, associated to iron. However, current reach remained weak. Considering difficulty to build efficiant biocathode at a neutral pH, the end of this work had been focused on a new application of the MFC: metal and rare earth extraction from soil and contaminated site that appeared to be a great research opportunity to follow. Key-words : Biocathode; Iron; Acidithiobacillus ferrooxidans; Pseudomonas brassicacearum; DAPG, metals extraction 3 4 Remerciements C’est en écrivant ces quelques lignes que je me rends compte que l’aventure touche à sa fin… Mais ce fût une belle aventure ! Tout d’abord, j’aimerais remercier Wafa Achouak. Un grand merci pour m’avoir accueilli dans le laboratoire, m’avoir permis de réaliser cette thèse et pour la confiance que tu as eue en moi dans la réalisation de ce projet. Merci aussi pour ces petits voyages qui ont ponctué ces trois années. Merci également d’avoir rendu cette thèse aussi agréable et désolé d’avoir été aussi stressant ces derniers mois… bref merci pour tout ! J’en profite également pour remercier tout le personnel du LEMiRE. Un grand Merci à Sylvain Fochesato et Marie Bertrand pour votre soutien et votre aide. Philippe Ortet et Mohamed Barakat, merci beaucoup pour votre travail, que je n’ai pas toujours complètement compris mais qui m’a toujours beaucoup servi. Catherine Santaella, merci pour ton aide en chimie. Merci aussi d’avoir bien voulu partager ton café avec moi quand c’était la crise locale du café. Merci aussi à Gilles pour les (très) longues discussions du café matinal. Thierry Heulin, merci de m’avoir accueilli dans ton institut avant que celui- ci ne passe dans d’autres mains… Et merci de croire en moi pour le futur. Je souhaiterais aussi remercier toutes les Post-doctorantes pour l’ensemble de leurs œuvres, pour les fous rires et les moments de pause scientifique ! Blanche Collin, merci de m’avoir initié au bio, je ne suis toujours pas convaincu et surtout, merci de ne pas m’avoir rendu intolérant au gluten car tu en as fait des victimes ! Wei Liu, la fin fut intense mais je te promets, on découvrira les secrets de la pyramide. Merci de t’être investie dans les travaux avec moi à la fin, ce n’était pas la meilleure période mais on aura réussi à faire quelque chose de bien sur une petite période ! Merci Agnès Roux et Oulfat Amin Ali. Merci d’avoir vécu cette thèse de l’intérieur et de vous être autant impliquées pour moi. Vous avez grandement contribué à la réussite de celle-ci et vraiment, je ne pourrais jamais assez vous remercier pour ça. Je remercie également Catherine Berthomieu du LIPM pour s’être grandement investie dans une partie de ce travail et aussi Didier Marcelin à qui j’ai pris un temps fou… Merci également à Bernard Angeletti du CEREGE pour le temps passé à doser le presque ensemble du tableau périodique des éléments sur mes échantillons. Je tiens à remercier aussi Andréa Campos du CP2M pour la microscopie, ta grande pédagogie et de 5 t’intéresser de près à notre travail. Je souhaiterais également à remercier Violaine Bonnefoy du LCB. Tout d’abord merci d’avoir répondu présente à chaque fois que nous t’avons sollicitée, merci de nous avoir fait bénéficier de ton expertise sur « Acidithio » et enfin, merci vraiment pour ta gentillesse. Mes remerciements les plus sincères vont également à l’ensemble du consortium BioElec. Merci pour les partages, vos accueils respectifs lors des différentes réunions et pour votre sympathie. Ce fût un plaisir de travailler avec vous ! Je tiens aussi à adresser mes plus sincères remerciements à Noureddine Bousserrhine et à Alain Bergel d’avoir accepté d’être rapporteurs pour cette thèse. Mes remerciements vont également à Elisabeth Lojou, Zahar Haichar et Philippe Cuny pour avoir accepter d’évaluer cette thèse lors de la soutenance. Merci également à Jérôme Rose et, encore une fois, Violaine Bonnefoy d’avoir accepté l’invitation pour assister à la soutenance. Enfin, merci à tous mes proches pour m’avoir soutenu et d’avoir supporté mon humeur massacrante ces derniers mois… C’était pour la bonne cause ! Sincèrement, merci à vous tous d’avoir participé de près ou de loin à cette thèse. Je n’en serai pas là sans vous ! 6 Sommaire LISTE DES ABBREVIATIONS 11 CONTEXTE GENERAL 13 CHAPITRE I INTRODUCTION BIBLIOGRAPHIQUE 19 1. LES PILES A COMBUSTIBLES MICROBIENNES 21 1.1. PRINCIPE GENERAL DE LA PILE A COMBUSTIBLE MICROBIENNE 21 1.1.1. Historique 21 1.1.2. Fonctionnement d’une pile à combustible microbienne 21 1.2. BIOFILMS BACTERIENS 22 1.2.1. Notions de biofilm 22 1.2.2. Formation d’un biofilm 23 1.2.3. Quorum-sensing 25 1.3. BIOFILMS ELECTROACTIFS ET TRANSFERT D’ELECTRONS 27 1.4. CARACTERISATION D’UN BIOFILM ELECTROACTIF 28 2. LES BIOANODES 31 2.1. TRANSFERT EXTRACELLULAIRE D’ELECTRONS A L’ANODE 31 2.1.1. Transfert indirect d’électrons 31 2.1.2. Transfert direct d’électrons 34 2.1.3. Composition des biofilms électroactifs anodiques 36 3. LES BIOCATHODES 36 3.1. PRINCIPE GENERAL 37 3.2. DIVERSITE BACTERIENNE CATALYSANT LA REACTION DE REDUCTION A LA BIOCATHODE 38 3.3. LES TRANSFERTS EXTRACELLULAIRES D’ELECTRONS A LA CATHODE 39 4. INTERACTION BACTERIES-METAUX 44 4.1. GENERALITE 44 4.2. CYCLE BIOGEOCHIMIqUE DU FER 46 4.3. ACQUISITION DU FER 47 4.4. METABOLISME ENERGETIqUE DU FER 48 4.4.1. La réduction du fer ferrique 49 4.4.2. L’oxydation du fer ferreux 50 4.4.2.1. Les bactéries ferro-oxydantes neutrophiles 50 4.4.2.2. Les bactéries ferro-oxydantes acidophiles 53 4.5. CAPACITE ELECTROACTIVE DES BACTERIES FERRO-OXYDANTES 54 5. LES APPLICATIONS POTENTIELLES DES PCMS 55 7 5.1. ALIMENTATION ELECTRIqUE EN ZONE DEPOURVUE DE RESEAU ELECTRIqUE 55 5.2. BIOREMEDIATION 57 5.3. ELECTROSYNTHESE DE MOLECULES A HAUTE VALEUR AJOUTEE 58 5.4. BIOSENSEURS 59 5.5. DESALINISATION 60 5.6. ELECTROSYNTHESE DE NANOPARTICULES 61 6. CONCLUSION 62 7. OBJECTIFS DE TRAVAIL 62 8. REVUE BILIOGRAPHIQUE 63 REVUE BIBLIOGRAPHIQUE: ALL ECOSYSTEMS POTENTIALLY HOST ELECTROGENIC BACTERIA 65 CHAPITRE II: RESULTATS PRELIMINAIRES : CRIBLAGE DE SOUCHES ET CONSORTIA HETEROTROPHES.
Load more

Recommended publications
  • Arthrobacter Paludis Sp. Nov., Isolated from a Marsh
    TAXONOMIC DESCRIPTION Zhang et al., Int J Syst Evol Microbiol 2018;68:47–51 DOI 10.1099/ijsem.0.002426 Arthrobacter paludis sp. nov., isolated from a marsh Qi Zhang,1 Mihee Oh,1 Jong-Hwa Kim,1 Rungravee Kanjanasuntree,1 Maytiya Konkit,1 Ampaitip Sukhoom,2 Duangporn Kantachote2 and Wonyong Kim1,* Abstract A novel Gram-stain-positive, strictly aerobic, non-endospore-forming bacterium, designated CAU 9143T, was isolated from a hydric soil sample collected from Seogmo Island in the Republic of Korea. Strain CAU 9143T grew optimally at 30 C, at pH 7.0 and in the presence of 1 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain CAU 9143T belonged to the genus Arthrobacter and was closely related to Arthrobacter ginkgonis SYP-A7299T (97.1 % T similarity). Strain CAU 9143 contained menaquinone MK-9 (H2) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two glycolipids and two unidentified phospholipids as the major polar lipids. The whole-cell sugars were glucose and galactose. The peptidoglycan type was A4a (L-Lys–D-Glu2) and the major cellular fatty T acid was anteiso-C15 : 0. The DNA G+C content was 64.4 mol% and the level of DNA–DNA relatedness between CAU 9143 and the most closely related strain, A. ginkgonis SYP-A7299T, was 22.3 %. Based on phenotypic, chemotaxonomic and genetic data, strain CAU 9143T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter paludis sp. nov. is proposed. The type strain is CAU 9143T (=KCTC 13958T,=CECT 8917T).
    [Show full text]
  • Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample
    geosciences Article Stress-Tolerance and Taxonomy of Culturable Bacterial Communities Isolated from a Central Mojave Desert Soil Sample Andrey A. Belov 1,*, Vladimir S. Cheptsov 1,2 , Elena A. Vorobyova 1,2, Natalia A. Manucharova 1 and Zakhar S. Ezhelev 1 1 Soil Science Faculty, Lomonosov Moscow State University, Moscow 119991, Russia; [email protected] (V.S.C.); [email protected] (E.A.V.); [email protected] (N.A.M.); [email protected] (Z.S.E.) 2 Space Research Institute, Russian Academy of Sciences, Moscow 119991, Russia * Correspondence: [email protected]; Tel.: +7-917-584-44-07 Received: 28 February 2019; Accepted: 8 April 2019; Published: 10 April 2019 Abstract: The arid Mojave Desert is one of the most significant terrestrial analogue objects for astrobiological research due to its genesis, mineralogy, and climate. However, the knowledge of culturable bacterial communities found in this extreme ecotope’s soil is yet insufficient. Therefore, our research has been aimed to fulfil this lack of knowledge and improve the understanding of functioning of edaphic bacterial communities of the Central Mojave Desert soil. We characterized aerobic heterotrophic soil bacterial communities of the central region of the Mojave Desert. A high total number of prokaryotic cells and a high proportion of culturable forms in the soil studied were observed. Prevalence of Actinobacteria, Proteobacteria, and Firmicutes was discovered. The dominance of pigmented strains in culturable communities and high proportion of thermotolerant and pH-tolerant bacteria were detected. Resistance to a number of salts, including the ones found in Martian regolith, as well as antibiotic resistance, were also estimated.
    [Show full text]
  • Isolation of Arthrobacter Species from the Phyllosphere and Demonstration of Their Epiphytic fitness Tanja R
    ORIGINAL RESEARCH Isolation of Arthrobacter species from the phyllosphere and demonstration of their epiphytic fitness Tanja R. Scheublin1 & Johan H. J. Leveau1,2 1Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands 2Department of Plant Pathology, University of California, One Shields Avenue, Davis, California 95616 Keywords Abstract Arthrobacter, biodegradation, phylloplane, phylloremediation, soil, triadimenol Bacteria of the genus Arthrobacter are common inhabitants of the soil environ- ment, but can also be recovered from leaf surfaces (the phyllosphere). Using Correspondence enrichment cultures on 4-chlorophenol, we succeeded in specifically isolating Johan Leveau, University of California, Arthrobacter bacteria from ground cover vegetation in an apple orchard. Based Department of Plant Pathology, One Shields on 16S rRNA gene sequencing, the isolates were found to belong to at least Avenue, Davis, CA 95616. three different species of Arthrobacter. Compared to the model bacterial epi- Tel: +1 (530) 752 5046; Fax: +1 (530) 752 5674; E-mail: [email protected] phyte Pantoea agglomerans, the Arthrobacter isolates performed as well or even better in a standardized laboratory test of phyllosphere fitness. A similar perfor- Funding Information mance was observed with the well-characterized soil isolate Arthrobacter chloro- This work was supported as part of the phenolicus A6. These findings suggest that the frequently reported presence of BACSIN project within
    [Show full text]
  • Arthrobacter Pokkalii Sp Nov, a Novel Plant Associated Actinobacterium with Plant Beneficial Properties, Isolated from Saline Tolerant Pokkali Rice, Kerala, India
    RESEARCH ARTICLE Arthrobacter pokkalii sp nov, a Novel Plant Associated Actinobacterium with Plant Beneficial Properties, Isolated from Saline Tolerant Pokkali Rice, Kerala, India Ramya Krishnan1¤, Rahul Ravikumar Menon1, Naoto Tanaka2, Hans-Jürgen Busse3, Srinivasan Krishnamurthi4, Natarajan Rameshkumar1¤* 1 Biotechnology Department, National Institute for Interdisciplinary Science and Technology (CSIR), Thiruvananthapuram, 695 019, Kerala, India, 2 NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156–8502, Japan, 3 Institute of Microbiology, Veterinary University Vienna, A-1210, Vienna, Austria, 4 Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh, 160036, India ¤ Current address: Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110 001, India * [email protected] OPEN ACCESS Citation: Krishnan R, Menon RR, Tanaka N, Busse Abstract H-J, Krishnamurthi S, Rameshkumar N (2016) Arthrobacter pokkalii sp nov, a Novel Plant A novel yellow colony-forming bacterium, strain P3B162T was isolated from the pokkali rice Associated Actinobacterium with Plant Beneficial rhizosphere from Kerala, India, as part of a project study aimed at isolating plant growth Properties, Isolated from Saline Tolerant Pokkali Rice, Kerala, India. PLoS ONE 11(3): e0150322. beneficial rhizobacteria from saline tolerant pokkali rice and functionally evaluate their abili- doi:10.1371/journal.pone.0150322 ties to promote plant growth
    [Show full text]
  • Diversity of Thermophilic Bacteria in Hot Springs and Desert Soil of Pakistan and Identification of Some Novel Species of Bacteria
    Diversity of Thermophilic Bacteria in Hot Springs and Desert Soil of Pakistan and Identification of Some Novel Species of Bacteria By By ARSHIA AMIN BUTT Department of Microbiology Quaid-i-Azam University Islamabad, Pakistan 2017 Diversity of Thermophilic Bacteria in Hot Springs and Desert Soil of Pakistan and Identification of Some Novel Species of Bacteria By ARSHIA AMIN BUTT Thesis Submitted to Department of Microbiology Quaid-i-Azam University, Islamabad In the partial fulfillment of the requirements for the degree of Doctor of Philosophy In Microbiology Department of Microbiology Quaid-i-Azam University Islamabad, Pakistan 2017 ii IN THE NAME OF ALLAH, THE MOST COMPASSIONATE, THE MOST MERCIFUL, “And in the earth are tracts and (Diverse though) neighboring, gardens of vines and fields sown with corn and palm trees growing out of single roots or otherwise: Watered with the same water. Yet some of them We make more excellent than others to eat. No doubt, in that are signs for wise people.” (Sura Al Ra’d, Ayat 4) iii Author’s Declaration I Arshia Amin Butt hereby state that my PhD thesis titled A “Diversity of Thermophilic Bacteria in Hot Springs and Deserts Soil of Pakistan and Identification of Some Novel Species of Bacteria” is my own work and has not been submitted previously by me for taking any degree from this University (Name of University) Quaid-e-Azam University Islamabad. Or anywhere else in the country/world. At any time if my statement is found to be incorrect even after my Graduate the university has the right to withdraw my PhD degree.
    [Show full text]
  • [N1596] Paraburkholderia Mimosarum A
    A0A1M3AD22 Metal-dependent hydrolase [N1592] Alphaproteobacteria UPI0004A75132 cyclase family protein [N1592] Polycyclovorans algicola A0A2D4SCK2 Metal-dependent hydrolase [N1592] Salinisphaeraceae bacterium UPI000F5B58FD cyclase family protein [N1592] Burkholderia contaminans A0A1D7ZKG3 Metal-dependent hydrolase [N1592] Burkholderia stabilis UPI0007563C6D cyclase family protein [N1592] Burkholderia cepacia A0A2X1H2X8 Cyclase family protein [N1592] Burkholderia cepacia A0A072TDP7 Secreted metal-dependent cyclase [N1592] cellular organisms UPI00075CC8DF cyclase family protein [N1592] Burkholderia cepacia UPI00075798BB cyclase family protein [N1592] Burkholderia cepacia UPI000755DBD3 cyclase family protein [N1592] Burkholderia cepacia A0A3P0WXC1 Cyclase family protein [N1592] Burkholderia cepacia A0A3P0NGC3 Cyclase family protein [N1592] Burkholderia sp. Bp9031 J7J3Q6 Uncharacterized protein [N1592] Burkholderia cepacia GG4 A0A0C4YJR9 Uncharacterized protein [N1592] Cupriavidus basilensis A0A0F0FIF4 Metal-dependent hydrolase [N1592] Burkholderiaceae bacterium 16 A0A069II47 Metal-dependent hydrolase [N1592] Cupriavidus sp. SK-3 A0A1A5X974 Metal-dependent hydrolase [N1592] Paraburkholderia tropica A0A1H6WKL3 Cyclase family protein [N1592] Paraburkholderia tropica UPI0004828DE5 cyclase family protein [N1592] Paraburkholderia bannensis A0A2S4LVJ1 Putative cyclase [N1592] Paraburkholderia eburnea A0A1D9H8T7 Metal-dependent hydrolase [N1592] Cupriavidus sp. USMAA2-4 A0A2L0X359 Cyclase family protein [N1592] Cupriavidus Q1LEV6 Uncharacterized
    [Show full text]
  • Description of Unrecorded Bacterial Species Belonging to the Phylum Actinobacteria in Korea
    Journal of Species Research 10(1):23­45, 2021 Description of unrecorded bacterial species belonging to the phylum Actinobacteria in Korea Mi­Sun Kim1, Seung­Bum Kim2, Chang­Jun Cha3, Wan­Taek Im4, Won­Yong Kim5, Myung­Kyum Kim6, Che­Ok Jeon7, Hana Yi8, Jung­Hoon Yoon9, Hyung­Rak Kim10 and Chi­Nam Seong1,* 1Department of Biology, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology, Chungnam National University, Daejeon 34134, Republic of Korea 3Department of Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea 4Department of Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea 5Department of Microbiology, College of Medicine, Chung-Ang University, Seoul 06974, Republic of Korea 6Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, Seoul 01797, Republic of Korea 7Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea 8School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea 9Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea 10Department of Laboratory Medicine, Saint Garlo Medical Center, Suncheon 57931, Republic of Korea *Correspondent: [email protected] For the collection of indigenous prokaryotic species in Korea, 77 strains within the phylum Actinobacteria were isolated from various environmental samples, fermented foods, animals and clinical specimens in 2019. Each strain showed high 16S rRNA gene sequence similarity (>98.8%) and formed a robust phylogenetic clade with actinobacterial species that were already defined and validated with nomenclature. There is no official description of these 77 bacterial species in Korea.
    [Show full text]
  • First High Quality Draft Genome Sequence of a Plant Growth Promoting and Cold Active Enzyme Producing Psychrotrophic Arthrobacter Agilis Strain L77 Ram N
    Singh et al. Standards in Genomic Sciences (2016) 11:54 DOI 10.1186/s40793-016-0176-4 EXTENDED GENOME REPORT Open Access First high quality draft genome sequence of a plant growth promoting and cold active enzyme producing psychrotrophic Arthrobacter agilis strain L77 Ram N. Singh1, Sonam Gaba1, Ajar N. Yadav1, Prakhar Gaur1, Sneha Gulati1, Rajeev Kaushik1 and Anil K. Saxena1,2* Abstract Arthrobacter agilis strain L77, is a plant growth promoting and cold active hydrolytic enzymes producing psychrotrophic bacterium, isolated from Pangong Lake, a subglacial lake in north western Himalayas, India. Genome analysis revealed metabolic versatility with genes involved in metabolism and cold shock adaptation, utilization and biosynthesis of diverse structural and storage polysaccharides such as plant based carbon polymers. The genome of Arthrobacter agilis strain L77 consists of 3,608,439 bp (3.60 Mb) of a circular chromosome. The genome comprises of 3316 protein coding genes and 74 RNA genes, 725 hypothetical proteins, 25 pseudo-genes and 1404 unique genes. Keywords: Arthrobacter, Psychrotrophic, PGPB, Cold-active enzymes, Pangong Lake, Himalayas Abbreviations: AFCs, Anti-freeze compounds; EPS, Exopolysaccharides Introduction industry, agriculture and biotechnology. Arthrobacter The microorganisms from extreme environments are of agilis [9] strain L77 was isolated from Pangong Lake, a particular importance in global ecology since the major- subglacial lake in north western Himalayas, India and ity of terrestrial and aquatic ecosystems of our planet are exhibit plant growth promoting attributes as well as pro- permanently or seasonally submitted to cold tempera- duction of hydrolytic enzymes. The culture was further tures. Microorganisms capable of coping with low tem- characterized for production of EPS and anti-freeze peratures are widespread in these natural environments compounds (AFCs).
    [Show full text]
  • UNIVERSITY of NEVADA, RENO Dimensions of Antarctic Microbial
    UNIVERSITY OF NEVADA, RENO Dimensions of Antarctic microbial life revealed through microscopic, cultivation-based, molecular phylogenetic and environmental genomic characterization A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry by Emanuele Kuhn Dr. Alison E. Murray/Dissertation Advisor May, 2014 Copyright by Emanuele Kuhn 2014 All Rights Reserved P age | i Abstract Extreme cold temperatures have shaped Antarctic environments and the life that lives within them. Microorganisms affiliated with the three domains of life - Bacteria, Archaea, and Eukaryote - can be found in Antarctic environments from deep subglacial lakes to dry deserts and from deep oceans to cold and dark winter surface seawaters. This dissertation focused on the investigation of the microbial assemblage in two Antarctic environments: Lake Vida, located in the McMurdo Dry Valleys, and the surface seawater from the Antarctic Peninsula. Lake Vida has a thick (27+ m) ice cover which seals a cryogenic brine reservoir within the lake ice below 16 m. This brine’s environment challenges the conditions for the existence of life. Despite the perceived challenges of aphotic, anoxic and freezing conditions, the brine contained an abundant assemblage (6.13 ± 1.65 × 10 7 cells mL -1) of ultra-small cells 0.192 ± 0.065 μm in diameter and a less abundant assemblage (1.47 ± 0.25 × 10 5 cells mL -1) of microbial cells ranging from > 0.2 to 1.5 μm in length. Scanning electron microscopy provided supporting evidence for cell membranes associated with the ~ 0.2 μm cells and helped discern a second smaller size class of particles (0.084 ± 0.063 μm).
    [Show full text]
  • Universidade Federal Do Rio Grande Do Sul
    UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL CENTRO DE BIOTECNOLOGIA DA UFRGS PROGRAMA DE PÓS-GRADUAÇÃO EM BIOLOGIA CELULAR E MOLECULAR DIVERSIDADE MICROBIANA NA ILHA REI GEORGE (PENÍNSULA ANTÁRTICA) E PROSPECÇÃO DE ENZIMAS QUERATINOLÍTICAS Igor Stelmach Pessi Dissertação submetida ao Programa de Pós- Graduação em Biologia Celular e Molecular da UFRGS como requisito parcial para a obtenção do grau de Mestre em Ciências. Orientador: Alexandre José Macedo Porto Alegre Fevereiro de 2012. Data de aprovação: 29/02/2012 Banca examinadora: ______________________________ ______________________________ Fátima Menezes Bento Luciane Maria Pereira Passaglia Depto. de Microbiologia/UFRGS Depto. de Genética/UFRGS ______________________________ Siu Mui Tsai CENA/USP Este trabalho foi desenvolvido nas seguintes instituições: Laboratório de Biofilmes & Diversidade Microbiana Centro de Biotecnologia Universidade Federal do Rio Grande do Sul Laboratório de Tecnologia Bioquímica Departamento de Produção de Matéria-Prima Faculdade de Farmácia Universidade Federal do Rio Grande do Sul Agências de fomento: CAPES, CNPq, FAPERGS "O homem se torna civilizado, não proporcionalmente à sua vontade de acreditar, mas proporcionalmente à sua capacidade de duvidar." Henry Louis Mencken AGRADECIMENTOS Primeiramente agradeço ao meu orientador, Prof. Alexandre Macedo, por ter me recebido e aceitado ser meu orientador em um projeto que durante muito tempo havia permanecido como um sonho distante de ser realizado. Graças ao seu esforço, pude me dedicar a estudar a microbiologia do continente Antártico, tema que sempre me causou muito encantamento. Não menos importante, gostaria de agradecer ao Prof. Jefferson Simões (CPC/UFRGS) e Felipe Lorenz Simões, pela enorme ajuda durante a realização deste trabalho, fornecendo tanto as amostras utilizadas quanto sugestões; Agradeço à minha família, por motivos óbvios que não precisam ser descritos, dentre eles a ajuda e compreensão em todos os aspectos dessa nova fase da minha vida.
    [Show full text]
  • Hans-Jurgen Busse
    International Journal of Systematic and Evolutionary Microbiology (2016), 66, 9–37 DOI 10.1099/ijsem.0.000702 Review Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus Hans-Ju¨rgen Busse Correspondence Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Hans-Ju¨rgen Busse Veterina¨rplatz, 1A-1210 Vienna, Austria hans-juergen.busse@ vetmeduni.ac.at In this paper, the taxonomy of the genus Arthrobacter is discussed, from its first description in 1947 to the present state. Emphasis is given to intrageneric phylogeny and chemotaxonomic characteristics, concentrating on quinone systems, peptidoglycan compositions and polar lipid profiles. Internal groups within the genus Arthrobacter indicated from homogeneous chemotaxonomic traits and corresponding to phylogenetic grouping and/or high 16S rRNA gene sequence similarities are highlighted. Furthermore, polar lipid profiles and quinone systems of selected species are shown, filling some gaps concerning these chemotaxonomic traits. Based on phylogenetic groupings, 16S rRNA gene sequence similarities and homogeneity in peptidoglycan types, quinone systems and polar lipid profiles, a description of the genus Arthrobacter sensu lato and an emended description of Arthrobacter roseus are provided. Furthermore, reclassifications of selected species of the genus Arthrobacter into novel genera are proposed, namely Glutamicibacter gen. nov. (nine species), Paeniglutamicibacter gen. nov. (six species), Pseudoglutamicibacter gen. nov. (two species), Paenarthrobacter gen. nov. (six species) and Pseudarthrobacter gen.
    [Show full text]
  • Biodegradation of Poly(Ethylene Terephthalate) by Marine Bacteria, and Strategies for Its Enhancement
    Biodegradation of poly(ethylene terephthalate) by marine bacteria, and strategies for its enhancement Submitted in total fulfillment of the requirements for the degree of Doctor of Philosophy by Hayden Webb Environmental and Biotechnology Centre Faculty of Life and Social Sciences Swinburne University of Technology May 2012 ___________________________________________________________________ Abstract Plastic accumulation, particularly in the world’s oceans is of increasing environmental concern. One of the major components of plastic waste is poly(ethylene terephthalate) (PET), a polymer frequently used in many applications, including textiles and food packaging. The current methods of disposal of PET waste, landfill, incineration and recycling, each have inherent drawbacks and limitations, and as such there is a need for efficient and cost-effective alternative. Biodegradation is an attractive option for environmentally friendly and efficient disposal of plastic waste. To date, no protocol has yet been developed to feasibly dispose of PET by biodegradation con a commercial scale. The current works aims to investigate the potential of PET biodegradation as a plastic disposal procedure by providing fundamental knowledge of biodegradation processes, and to develop strategies for improving biodegradation efficiency. PET samples were incubated in marine bacterial community enrichment cultures, and the dynamics of the polymer – bacterial interactions traced. Modifications to polymer surfaces were monitored using a variety of surface characterisation techniques, including atomic force microscopy (AFM), x-ray photoelectron spectroscopy (XPS) and infrared microspectroscopy using Synchrotron radiation. Taxonomic members of the bacterial enrichment cultures that developed in the presence of PET were recovered and identified via 16S rRNA gene sequencing. Marine bacteria were shown to possess the ability to degrade PET surfaces.
    [Show full text]