DOCSLIB.ORG

Novel Method of Probe Design for Characterising Unclassified Microbial Taxa in Wastewater

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Novel Method of Probe Design for Characterising Unclassified Microbial Taxa in Wastewater Novel method of probe design for characterising unclassified microbial taxa in wastewater TAN SHI MING Interdisciplinary Graduate School The Singapore Centre for Environmental Life Sciences Engineering (SCELSE) 2017 Novel method of probe design for characterising unclassified microbial taxa in wastewater TAN SHI MING Interdisciplinary Graduate School The Singapore Centre for Environmental Life Sciences Engineering (SCELSE) A thesis submitted to the Nanyang Technological University in partial fulfilment of the requirement for the degree of Doctor of Philosophy 2017 Acknowledgements First and foremost, I will like to express my gratitude towards my supervisor, Professor Yehuda Cohen for providing me with the academic freedom to pursue my PhD candidature in SCELSE. I thank him for the countless opportunities he has provided, the financial stability for the projects that I have pursued and his strong resolve in moulding me into an independent researcher. Secondly, I will like to express my thanks to Dr Paul William, Mr Teo Guo Hui and Mr Ryan Lim for their tremendous help with the flow cytometry work. The flow cytometry work would not have gone smoothly without their invaluable expertise and advice. Prof Federico Lauro had proposed the use of FISH-FACS tool for the enrichment of the unclassified bacteria and I appreciate his input. The sequencing team in SCELSE has helped with the sequencing aspect of my thesis. Special thanks go to Dr Daniela Moses whom I have consulted on the type of sequencing platform to use and Mr Alexander Putra who has efficiently handled my samples for sequencing. Mr Larry Liew was instrumental in obtaining sludge samples from Ulu Pandan Water Reclamation Plant, and I will like to thank him for his time and effort. Dr Xie Chao was the author of the RiboTagger software and he suggested the design of FISH probes from RiboTags. Mr Wesley Goi rendered advice in the updating of the SILVA database in the RiboTagger software. Dr Xiang Hui Liu was instrumental in attempting genomic binning using other software that was not covered in this thesis. Recovery of draft genomes from enriched samples was influenced through discussions with Dr Rohan Williams. My sincerest appreciation goes towards Dr Muhammud Hafiz, Dr Martin Tay, Dr Rasmus Kirkegaard and Miss Krithika Arumugam for their kind patience in imparting basic bioinformatics knowledge to me. The thesis would not have been a success without the acquisition of these essential skills. i I will like to show my appreciation to Dr Nguyen Quoc Mai Phuong, Mr Muhamma d Jasrie, Dr Maria Yung, Dr Lim Chun Ping and Prof Cao Bin for their invaluable advice and feedback on my thesis. Heartfelt thanks to my friends in SCELSE: Syed Munir, Chan Siew Herng, Rosalie Chai, Choo Pei Yi, Adelicia Li, Wong Jun Jie, Kelvin Chong and many more for creating a fun-filled environment to do my PhD in. The wonderful friendships forged have helped me through the tough times. I am extremely grateful to the Environmental and Water Industry (EWI) and SCELSE for their generous scholarship and financial support during my PhD journey. Finally, I will like to extend my utmost gratitude towards my family members: Dad, Mum and sister for their emotional support and pampering. Thank you for putting me through the wonder education system in Singapore. Last but not least, a big thank you to my wonderful girlfriend, Julianna Ng for her unwavering faith in my abilities. Your constant encouragements have spurred me in every little way possible. ii Publications 1.) Shi Ming Tan, Maria Yung, Chao Xie, Paul Hutchinson, Guo Hui Teo, Muhammad Hafiz Ismail, Martin Tay Qi Xiang, Rohan Williams, Yehuda Cohen. Design of next generation FISH probes from omics dataset for targeted visualisation and enrichment of environmental samples. Manuscript in preparation. 2.) Shi Ming Tan, Maria Yung, Chao Xie, Paul Hutchinson, Guo Hui Teo, Rohan Williams, Yehuda Cohen. Genome analysis of an unclassified and rare bacterial taxon in activated sludge recovered with next generation FISH probes. Manuscript in preparation. 3.) Shi Ming Tan, Chao Xie, Paul Hutchinson, Guo Hui Teo, Yehuda Cohen. Deciphering different spatial structures of Haliangium species in activated sludge with FISH and cell sorting. Manuscript in preparation. iii Table of Contents Acknowledgements ............................................................................................................................ i Publications ...................................................................................................................................... iii Table of Contents ............................................................................................................................. iv List of Figures .................................................................................................................................... x List of Tables................................................................................................................................... xvi List of Abbreviations .................................................................................................................... xviii Abstract ........................................................................................................................................... xx Chapter 1 Introduction ................................................................................................................. 1 1.1 Background ...................................................................................................................... 1 1.2 Research gap .................................................................................................................... 2 1.3 Aims and scopes ............................................................................................................... 4 Chapter 2 Introduction ................................................................................................................. 7 2.1 Activated sludge process for biological wastewater treatment ...................................... 7 2.2 Unclassified microbial taxa present in floccular sludge community drives biological wastewater treatment under tropical conditions ..................................................................... 10 2.3 Approaches to identification and classification of prokaryotes .................................... 15 2.3.1 Culture-dependent approach................................................................................. 15 2.3.2 Culture-independent approach.............................................................................. 16 2.3.3 Methods of FISH probe design ............................................................................... 24 2.3.4 Methods for enrichment of target bacterial taxa .................................................. 29 Chapter 3 Novel method of probe design driven by next generation sequencing reads ........... 35 3.1 Introduction ................................................................................................................... 35 iv 3.2 Materials and methods .................................................................................................. 37 3.2.1 Sample preparation ................................................................................................ 38 3.2.2 Sample fixation ....................................................................................................... 39 3.2.3 Fluorescence in situ hybridisation (FISH) ............................................................... 39 3.2.3.1 Evaluation of the in silico specificity and coverage of probes ........................... 42 3.2.4 Probe dissociation curve ........................................................................................ 43 3.2.5 Sequencing of the 16S rRNA gene ......................................................................... 44 3.2.6 Visualisation of probe accessibility site of the16S rRNA gene ............................... 45 3.2.7 Co-localisation analyses ......................................................................................... 45 3.3 Results ............................................................................................................................ 46 3.3.1 Evaluation of the in silico specificity and coverage of FISH probes ....................... 46 3.3.2 In silico accessibility of 16S rRNA to RiboProbe ..................................................... 48 In situ validation of RiboProbe ............................................................................................... 49 3.3.3 Determining probe stringency of RiboProbe ......................................................... 51 3.3.4 Hybridisation of RiboProbe with activated sludge ................................................. 52 3.3.5 Co-localisation assays ............................................................................................. 54 3.3.6 Applications of RiboProbe ...................................................................................... 57 3.4 Discussion ....................................................................................................................... 61 3.4.1 Design of RiboProbe ............................................................................................... 61 3.4.2 Validation of RiboProbe ......................................................................................... 62 3.4.3 Evaluation of RiboProbe ........................................................................................
Load more

Recommended publications
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • Downloads/Bin/Fastq Quality Filter -Q20 -P90 -Q33
    Biological Reduction of Selenium Oxyanions in the Presence of Nitrate anions using Anaerobic Microbes by Gaurav Subedi B.Sc., Jacobs University Bremen, 2010 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Chemical and Biological Engineering) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) July 2016 © Gaurav Subedi, 2016 Abstract Biological selenium reduction has emerged as a viable solution for the removal of toxic selenium from the environment. However, the presence of nitrate hinders selenium reduction by acting as a competitive electron acceptor. The present thesis investigated the use of local mine-impacted sediment as an inoculum for selenium reduction and studied the affect of nitrate on the removal of selenium. Sediment samples, impacted by mining activities, were collected from two vastly different sites of the Elk River Valley. These sediments namely; Goddard Marsh and Mature Tailing Coal, were enriched for selenium reducing bacterial consortium under high selenium and varying nitrate concentrations to put additional selection pressure. Ultimately, two cultures from Goddard Marsh enriched under low and high nitrate condition as well as one culture from Mature Tailing Coal enriched under moderate nitrate condition were used to access the affect of nitrate on selenium reduction using central composite design matrix. The extent of Se reduction was highest in the Goddard Marsh enrichment with no nitrate while enrichment with moderate and high nitrate reduced selenium poorly. ANOVA results from the CCD experiment in Goddard Marsh enrichment with no nitrate indicated no affect of nitrate in Se reduction. Two primer sets targeting the selenate redutase (serA) from Thauera selenatis and nitrite reductase (nirK) from denitrifying population were used to quantify the population of selenium reducing and denitrifying population in the CCD experiment.
    [Show full text]
  • Taxonomy JN869023
    Species that differentiate periods of high vs. low species richness in unattached communities Species Taxonomy JN869023 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 JN674641 Bacteria; Bacteroidetes; [Saprospirae]; [Saprospirales]; Chitinophagaceae; Sediminibacterium JN869030 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 U51104 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae; Limnohabitans JN868812 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae JN391888 Bacteria; Planctomycetes; Planctomycetia; Planctomycetales; Planctomycetaceae; Planctomyces HM856408 Bacteria; Planctomycetes; Phycisphaerae; Phycisphaerales GQ347385 Bacteria; Verrucomicrobia; [Methylacidiphilae]; Methylacidiphilales; LD19 GU305856 Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Pelagibacteraceae GQ340302 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales JN869125 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae New.ReferenceOTU470 Bacteria; Cyanobacteria; ML635J-21 JN679119 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae HM141858 Bacteria; Acidobacteria; Holophagae; Holophagales; Holophagaceae; Geothrix FQ659340 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; auto67_4W AY133074 Bacteria; Elusimicrobia; Elusimicrobia; Elusimicrobiales FJ800541 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; R4-41B JQ346769 Bacteria; Acidobacteria; [Chloracidobacteria]; RB41; Ellin6075
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Metabarcoding for Bacterial Diversity Assessment: Looking Inside Didymosphenia Geminata Mats in Patagonian Aquatic Ecosystems
    Aquatic Invasions (2021) Volume 16, Issue 1: 43–61 Special Issue: Proceedings of the 21st International Conference on Aquatic Invasive Species Guest editors: Sarah Bailey, Bonnie Holmes and Oscar Casas-Monroy CORRECTED PROOF Research Article Metabarcoding for bacterial diversity assessment: looking inside Didymosphenia geminata mats in Patagonian aquatic ecosystems Ana Victoria Suescún1,*, Karla Martinez-Cruz2, Maialen Barret3 and Leyla Cárdenas1,4 1Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile 2Environmental Biogeochemistry in Extreme Ecosystems Laboratory, Universidad de Magallanes, Punta Arenas, Chile 3Laboratory of Functional Ecology and Environment, Université de Toulouse, CNRS, Toulouse, France 4Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Chile Author e-mails: [email protected] (AVS), [email protected] (KM), [email protected] (MB), [email protected] (LC) *Corresponding author Co-Editors’ Note: This study was contributed in relation to the 21st International Conference Abstract on Aquatic Invasive Species held in Montreal, Canada, October 27–31, 2019 (http://www.icais. The number of organisms that spread and invade new habitats has increased in recent org/html/previous21.html). This conference has decades as a result of drastic environmental changes such as climate change and provided a venue for the exchange of anthropogenic activities. Microbial species invasions occur worldwide in terrestrial information on various aspects of aquatic and aquatic systems and represent an emerging challenge to our understanding of invasive species since its inception in 1990. The conference continues to provide an the interplay between biodiversity and ecosystem functioning. Due to the difficulty opportunity for dialog between academia, of detecting and evaluating non-indigenous microorganisms, little is known about industry and environmental regulators.
    [Show full text]
  • Aerosol Microbiome Over the Mediterranean Sea Diversity and Abundance
    atmosphere Article Aerosol Microbiome over the Mediterranean Sea Diversity and Abundance Esra Mescioglu 1,* , Eyal Rahav 2, Natalia Belkin 2, Peng Xian 3, Jordan M. Eigenza 4 , Ania Vichik 2, Barak Herut 2 and Adina Paytan 5 1 Earth and Planetary Science, University of California, Santa Cruz, CA 95060, USA 2 Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa 3108000, Israel 3 Marine Meteorology Division, Naval Research Laboratory, 7 Grace Hopper Avenue, Monterey, CA 93940, USA 4 Biomolecular Engineering, University of California, Santa Cruz, CA 95060, USA 5 Institute of Marine Science, University of California, Santa Cruz, CA 95060, USA * Correspondence: [email protected] Received: 18 June 2019; Accepted: 24 July 2019; Published: 1 August 2019 Abstract: Prokaryotic microbes can become aerosolized and deposited into new environments located thousands of kilometers away from their place of origin. The Mediterranean Sea is an oligotrophic to ultra-oligotrophic marginal sea, which neighbors northern Africa (a major source of natural aerosols) and Europe (a source of mostly anthropogenic aerosols). Previous studies demonstrated that airborne bacteria deposited during dust events over the Mediterranean Sea may significantly alter the ecology and function of the surface seawater layer, yet little is known about their abundance and diversity during ‘background’ non-storm conditions. Here, we describe the abundance and genetic diversity of airborne bacteria in 16 air samples collected over an East-West transect of the entire Mediterranean Sea during non-storm conditions in April 2011. The results show that airborne bacteria represent diverse groups with the most abundant bacteria from the Firmicutes (Bacilli and Clostridia) and Proteobacteria (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) phyla.
    [Show full text]
  • Download/Splitstree5)
    bioRxiv preprint doi: https://doi.org/10.1101/2021.05.31.446453; this version posted June 1, 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. Phylogenetic context using phylogenetic outlines Caner Bagcı1, David Bryant2, Banu Cetinkaya3, and Daniel H. Huson1;4;∗ 1 Algorithms in Bioinformatics, University of T¨ubingen,72076 T¨ubingen,Germany 2 Department of Mathematics, University of Otago, Dunedin, New Zealand 3 Computer Science program, Sabancı University, 34956 Tuzla/Istanbul,_ Turkey 4 Cluster of Excellence: Controlling Microbes to Fight Infection, T¨ubingen,Germany *[email protected] Abstract 1 Microbial studies typically involve the sequencing and assembly of draft genomes for 2 individual microbes or whole microbiomes. Given a draft genome, one first task is to 3 determine its phylogenetic context, that is, to place it relative to the set of related reference 4 genomes. We provide a new interactive graphical tool that addresses this task using Mash 5 sketches to compare against all bacterial and archaeal representative genomes in the 6 GTDB taxonomy, all within the framework of SplitsTree5. The phylogenetic context of the 7 query sequences is then displayed as a phylogenetic outline, a new type of phylogenetic 8 network that is more general that a phylogenetic tree, but significantly less complex than 9 other types of phylogenetic networks. We propose to use such networks, rather than trees, 10 to represent phylogenetic context, because they can express uncertainty in the placement 11 of taxa, whereas a tree must always commit to a specific branching pattern.
    [Show full text]
  • Marine Cyanolichens from Different Littoral Zones Are
    bioRxiv preprint doi: https://doi.org/10.1101/209320; this version posted February 6, 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. 1 Marine cyanolichens from different littoral 2 zones are associated with distinct bacterial 3 communities 4 Nyree J. West*1, Delphine Parrot2†, Claire Fayet1, Martin Grube3, Sophie Tomasi2 5 and Marcelino T. Suzuki4 6 1 Sorbonne Universités, UPMC Univ Paris 06, CNRS, Observatoire Océanologique de Banyuls (OOB), 7 F-66650, Banyuls sur mer, France 8 2 UMR CNRS 6226, Institut des Sciences chimiques de Rennes, Equipe CORINT « Chimie Organique 9 et Interfaces », UFR Sciences Pharmaceutiques et Biologiques, Univ. Rennes 1, Université Bretagne 10 Loire, F-35043, Rennes, France 11 3 Institute of Plant Sciences, University of Graz, A-8010 Graz, Austria 12 4 Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies 13 Microbiennes (LBBM), Observatoire Océanologique, F-66650, Banyuls sur mer, France 14 †Current address: GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Marine 15 Natural Products Chemistry, GEOMAR Centre for Marine Biotechnology, 24106 Kiel, Germany 16 *Corresponding author: 17 Observatoire Océanologique de Banyuls sur mer, F-66650 Banyuls sur mer, France 18 19 Tel: +33 (0)4 30 19 24 29, Fax: +33 (0)4 68 88 73 98 20 Email: [email protected] 21 1 bioRxiv preprint doi: https://doi.org/10.1101/209320; this version posted February 6, 2018.
    [Show full text]
  • Dynamics of Naphthenic Acids and Microbial Community Structures in A
    Electronic Supplementary Material (ESI) for RSC Advances. This journal is © The Royal Society of Chemistry 2017 Supporting Information: Dynamics of naphthenic acids and microbial community structures in a membrane bioreactor treating oil sands process- affected water: impacts of supplemented inorganic nitrogen and hydraulic retention time 1, 2 1, 3 1 1 Jinkai Xue , Yanyan Zhang , Yang Liu , Mohamed Gamal El-Din 1 Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada; 2 Department of Civil, Environmental, and Geo- Engineering, University of Minnesota, Minneapolis, Minnesota 55404, United States; 3 Department of Civil Engineering, New Mexico State University, Las Cruces, New Mexico, United States Supporting information includes 7 tables, 5 figures, and 17 pages in total. 1 Water chemistry analyses Samples were collected weekly from the feed by using a disposable syringe, and from the permeate by leaving the effluent tubing in a clean glass bottle untill a volume of 100 mL was achieved. Right after sample collection, Thermo Scientific™ Target2™ Nylon Syringe Filters (0.22 μm) were used to filter water samples prior to analyses. Conventional water chemistry parameters including pH, COD, nitrate nitrogen (NO3-N), ammonium nitrogen (NH4-N), and nitrite nitrogen (NO2-N) were measured for the feed and permeate samples in duplicates according to the standard methods (Federation and Association, 2005). To measure the mixed liquor suspended solids (MLSS) and mixed liquor volatile suspended solids (MLVSS) concentration (an indicator of microbial growth), a 30 mL sludge sample was collected weekly from the middle depth of the anoxic and aerobic tanks by using a disposable syringe.
    [Show full text]
  • Halophilic Bacteroidetes As an Example on How Their Genomes Interact with the Environment
    DOCTORAL THESIS 2020 PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez DOCTORAL THESIS 2020 Doctoral Programme of Environmental and Biomedical Microbiology PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez Thesis Supervisor: Ramon Rosselló Móra Thesis Supervisor: Rudolf Amann Thesis tutor: Elena I. García-Valdés Pukkits Doctor by the Universitat de les Illes Balears Publications resulted from this thesis Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Systematic and Applied Microbiology, 39(5), 281–296 Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Corrigendum to “Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov.” [Syst. Appl. Microbiol. 39 (5) (2016) 281–296]. Systematic and Applied Microbiology, 39, 491–492. Munoz, R., Amann, R., & Rosselló-Móra, R. (2019). Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics. Systematic and Applied Microbiology, 43(2), 126065. Dr. Ramon Rosselló Móra, of the Institut Mediterrani d’Estudis Avançats, Esporles and Dr. Rudolf Amann, of the Max-Planck-Institute für Marine Mikrobiologie, Bremen WE DECLARE: That the thesis titled Phylogenomics of Bacteroidetes; halophilic Bacteroidetes as an example on how their genomes interact with the environment, presented by Raúl Muñoz Jiménez to obtain a doctoral degree, has been completed under our supervision and meets the requirements to opt for an International Doctorate. For all intents and purposes, we hereby sign this document.
    [Show full text]
  • Dynamics of Bacterial Assemblages and Removal of Polycyclic Aromatic
    Dynamics of bacterial assemblages and removal of polycyclic aromatic hydrocarbons in oil-contaminated coastal marine sediments subjected to contrasted oxygen regimes Cécile Militon, Ronan Jezequel, Franck Gilbert, Yannick Corsellis, Léa Sylvi, Cristiana Cravo-Laureau, Robert Duran, Philippe Cuny To cite this version: Cécile Militon, Ronan Jezequel, Franck Gilbert, Yannick Corsellis, Léa Sylvi, et al.. Dynamics of bac- terial assemblages and removal of polycyclic aromatic hydrocarbons in oil-contaminated coastal marine sediments subjected to contrasted oxygen regimes. Environmental Science and Pollution Research, Springer Verlag, 2015, 22 (20), pp.15260-15272. 10.1007/s11356-015-4510-y. hal-01233392 HAL Id: hal-01233392 https://hal.archives-ouvertes.fr/hal-01233392 Submitted on 25 Nov 2015 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. Open Archive TOULOUSE Archive Ouverte ( OATAO ) OATAO is an open access repository that collects the work of Toulouse researchers and makes it freely available over the web where possible. This is an author-deposited version published in : http://oatao.univ-toulouse.fr/ Eprints ID : 14472 To link to this article : doi: 10.1007/s11356-015-4510-y URL : http://dx.doi.org/10.1007/s11356-015-4510-y To cite this version : Militon, Cécile and Jezequel, Ronan and Gilbert, Franck and Corsellis, Yannick and Sylvi, Léa and Cravo-Laureau, Cristiana and Duran, Robert and Cuny, Philippe Dynamics of bacterial assemblages and removal of polycyclic aromatic hydrocarbons in oil- contaminated coastal marine sediments subjected to contrasted oxygen regimes.
    [Show full text]
  • Dinghuibacter Silviterrae Gen. Nov., Sp. Nov., Isolated from Forest Soil Ying-Ying Lv, Jia Wang, Mei-Hong Chen, Jia You and Li-Hong Qiu
    International Journal of Systematic and Evolutionary Microbiology (2016), 66, 1785–1791 DOI 10.1099/ijsem.0.000940 Dinghuibacter silviterrae gen. nov., sp. nov., isolated from forest soil Ying-Ying Lv, Jia Wang, Mei-Hong Chen, Jia You and Li-Hong Qiu Correspondence State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Li-Hong Qiu Guangzhou, 510275, PR China [email protected] A novel Gram-stain negative, non-motile, rod-shaped, aerobic bacterial strain, designated DHOA34T, was isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, China. Comparative 16S rRNA gene sequence analysis showed that it exhibited highest similarity with Flavisolibacter ginsengiterrae Gsoil 492T and Flavitalea populi HY-50RT, at 90.89 and 90.83 %, respectively. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, DHOA34T formed an independent lineage within the family Chitinophagaceae but was distinct from all recognized species and genera of the family. T The major cellular fatty acids of DHOA34 included iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1v6c and/or C16 : 1v7c). The DNA G+C content was 51.6 mol% and the predominant quinone was menaquinone 7 (MK-7). Flexirubin pigments were produced. The phenotypic, chemotaxonomic and phylogenetic data demonstrate consistently that strain DHOA34T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Dinghuibacter silviterrae gen. nov., sp. nov. is proposed. The type strain of Dinghuibacter silviterrae is DHOA34T (5CGMCC 1.15023T5KCTC 42632T). The family Chitinophagaceae, belonging to the class Sphingo- For isolation of DHOA34T, the soil sample was thoroughly bacteriia of the phylum Bacteroidetes, was proposed by suspended with 100 mM PBS (pH 7.0) and the suspension Ka¨mpfer et al.
    [Show full text]