{Replace with the Title of Your Dissertation}
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
A Polysaccharide-Degrading Marine Bacterium Flammeovirga Sp. MY04 and Its Extracellular Agarase System
中国科技论文在线 http://www.paper.edu.cn J. Ocean Univ. China (Oceanic and Coastal Sea Research) DOI 10.1007/s11802-012-1929-3 ISSN 1672-5182, 2012 11 (3): 375-382 http://www.ouc.edu.cn/xbywb/ E-mail:[email protected] A Polysaccharide-Degrading Marine Bacterium Flammeovirga sp. MY04 and Its Extracellular Agarase System HAN Wenjun1), 2), 3), GU Jingyan1), 3), YAN Qiujie2), LI Jungang2), WU Zhihong3), *, GU Qianqun1), *, and LI Yuezhong3) 1) Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, P. R . C hi n a 2) School of Life Science and Biotechnology, Mianyang Normal University, Mianyang 621000, P. R. China 3) State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, P. R. China (Received February 2, 2012; revised April 8, 2012; accepted May 29, 2012) © Ocean University of China, Science Press and Springer-Verlag Berlin Heidelberg 2012 Abstract Bacteria of the genus Flammeovirga can digest complex polysaccharides (CPs), but no details have been reported re- garding the CP depolymerases of these bacteria. MY04, an agarolytic marine bacterium isolated from coastal sediments, has been identified as a new member of the genus Flammeovirga. The MY04 strain is able to utilize multiple CPs as a sole carbon source and -1 -1 grows well on agarose, mannan, or xylan. This strain produces high concentrations of extracellular proteins (490 mg L ± 18.2 mg L liquid culture) that exhibit efficient and extensive degradation activities on various polysaccharides, especially agarose. These pro- -1 -1 teins have an activity of 310 U mg ± 9.6 U mg proteins. -
The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. -
Imperialibacter Roseus Gen. Nov., Sp. Nov., a Novel Bacterium of the Family Flammeovirgaceae Isolated from Permian Groundwater
International Journal of Systematic and Evolutionary Microbiology (2013), 63, 4136–4140 DOI 10.1099/ijs.0.052662-0 Imperialibacter roseus gen. nov., sp. nov., a novel bacterium of the family Flammeovirgaceae isolated from Permian groundwater Hui Wang,1,2,3 Junde Li,1 Tianling Zheng,2 Russell T. Hill3 and Xiaoke Hu1 Correspondence 1Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China Xiaoke Hu 2Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, [email protected] Xiamen University, Xiamen 361005, China 3Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA A novel bacterial strain, designated P4T, was isolated from Permian groundwater and identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics. Cells were aerobic, Gram-stain-negative rods. 16S rRNA gene sequence-based phylogenetic analysis revealed that P4T is affiliated with the family Flammeovirgaceae in the phylum Bacteroidetes, but forms a distinct cluster within this family. The DNA G+C content of strain P4T was 45.2 mol%. The predominant cellular fatty acids were C16 : 1v6c/C16 : 1v7c and iso-C15 : 0. MK-7 was the main respiratory quinone. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid, unidentified glycoli- pids and unidentified polar lipids. Based on our extensive polyphasic analysis, a novel species in a new genus, Imperialibacter roseus gen. nov., sp. nov., is proposed. The type strain of Imperialibacter roseus is P4T (5CICC 10659T5KCTC 32399T). Bacteria affiliated with the family Flammeovirgaceae of the staining was performed according to the method described phylum Bacteroidetes are widely distributed in various by Gerhardt et al. -
Raineya Orbicola Gen. Nov., Sp. Nov. a Slightly Thermophilic Bacterium of the Phylum Bacteroidetes and the Description of Raineyaceae Fam
TAXONOMIC DESCRIPTION Albuquerque et al., Int J Syst Evol Microbiol 2018;68:982–989 DOI 10.1099/ijsem.0.002556 Raineya orbicola gen. nov., sp. nov. a slightly thermophilic bacterium of the phylum Bacteroidetes and the description of Raineyaceae fam. nov. Luciana Albuquerque,1 Ana Rita M. Polónia,1 Cristina Barroso,1,2 Hugo J. C. Froufe,2 Olga Lage,3,4 Alexandre Lobo-da-Cunha,4,5 Conceiçao~ Egas1,2 and Milton S. da Costa1,* Abstract An isolate, designated SPSPC-11T, with an optimum growth temperature of about 50 C and an optimum pH for growth between 7.5 and 8.0, was recovered from a hot spring in central Portugal. Based on phylogenetic analysis of its 16S rRNA sequence, the new organism is most closely related to the species of the genus Thermonema but with a pairwise sequence similarity of <85 %. The isolate was orange-pigmented, formed non-motile long filaments and rod-shaped cells that stain Gram-negative. The organism was strictly aerobic, oxidase-positive and catalase-positive. The major fatty acids were iso- C15:0, iso-C15 : 0 2-OH and iso-C17 : 0 3-OH. The major polar lipids were one aminophospholipid, two aminolipids and three unidentified lipids. Menaquinone 7 was the major respiratory quinone. The DNA G+C content of strain SPSPC-11T was 37.6 mol% (draft genome sequence). The high quality draft genome sequence corroborated many of the phenotypic characteristics of strain SPSPC-11T. Based on genotypic, phylogenetic, physiological and biochemical characterization we describe a new species of a novel genus represented by strain SPSPC-11T (=CECT 9012T=LMG 29233T) for which we propose the name Raineya orbicola gen. -
Depthwise Microbiome and Isotopic Profiling of a Moderately Saline
www.nature.com/scientificreports OPEN Depthwise microbiome and isotopic profling of a moderately saline microbial mat in a solar saltern Varun Paul1*, Yogaraj Banerjee2, Prosenjit Ghosh2,3 & Susheel Bhanu Busi4 The solar salterns in Tuticorin, India, are man-made, saline to hypersaline systems hosting some uniquely adapted populations of microorganisms and eukaryotic algae that have not been fully characterized. Two visually diferent microbial mats (termed ‘white’ and ‘green’) developing on the reservoir ponds (53 PSU) were isolated from the salterns. Firstly, archaeal and bacterial diversity in diferent vertical layers of the mats were analyzed. Culture-independent 16S rRNA gene analysis revealed that both bacteria and archaea were rich in their diversity. The top layers had a higher representation of halophilic archaea Halobacteriaceae, phylum Chlorofexi, and classes Anaerolineae, Delta- and Gamma- Proteobacteria than the deeper sections, indicating that a salinity gradient exists within the mats. Limited presence of Cyanobacteria and detection of algae-associated bacteria, such as Phycisphaerae, Phaeodactylibacter and Oceanicaulis likely implied that eukaryotic algae and other phototrophs could be the primary producers within the mat ecosystem. Secondly, predictive metabolic pathway analysis using the 16S rRNA gene data revealed that in addition to the regulatory microbial functions, methane and nitrogen metabolisms were prevalent. Finally, stable carbon 13 and nitrogen isotopic compositions determined from both mat samples showed that the δ Corg 15 and δ Norg values increased slightly with depth, ranging from − 16.42 to − 14.73‰, and 11.17 to 13.55‰, respectively. The isotopic signature along the microbial mat profle followed a pattern that is distinctive to the community composition and net metabolic activities, and comparable to saline mats in other salterns. -
A Robust Metaproteomics Pipeline for a Holistic Taxonomic and Functional
bioRxiv preprint doi: https://doi.org/10.1101/667428; this version posted June 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 Title: A robust metaproteomics pipeline for a holistic taxonomic and functional 3 characterization of microbial communities from marine particles 4 Authors: Doreen Schultz,1 Daniela Zühlke,1 Jörg Bernhardt,1 Thomas Ben Francis,2 Dirk 5 Albrecht,1 Claudia Hirschfeld,1 Stephanie Markert,3 and Katharina Riedel 1* 6 7 Addresses: 1 Institute of Microbiology, University of Greifswald, Greifswald, Germany. 8 2 Max-Planck Institute for Marine Microbiology, Bremen, Germany. 9 3 Institute of Pharmacy, University of Greifswald, Greifswald, Germany. 10 11 *Corresponding author mailing address: Institute of Microbiology, Center for Functional 12 Genomics of Microbes (C_FunGene), University of Greifswald, Felix-Hausdorff-Straße 8, DE- 13 17487 Greifswald, Germany. E-mail [email protected]; Tel (+49) 3834 420 5900 14 15 Running title: Metaproteomic pipeline to analyse marine particles 1 bioRxiv preprint doi: https://doi.org/10.1101/667428; this version posted June 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 16 Originality-Significance Statement 17 Marine particles consist of organic particulate matter (e.g. phyto- or zooplankton) and 18 particle-associated (PA) microbial communities, which are often embedded in a sugary 19 matrix. A significant fraction of the decaying algal biomass in marine ecosystems is expected 20 to be mineralized by PA heterotrophic communities, which are thus greatly contributing to 21 large-scale carbon fluxes. -
University of Florida Thesis Or Dissertation Formatting
CHARACTERIZING THE MOLECULAR MECHANISMS CONTRIBUTING TO BIOLOGICALLY INDUCED CARBONATE MINERALIZATION AND THROMBOLITE FORMATION By ARTEMIS S. LOUYAKIS A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2017 © 2017 Artemis S. Louyakis To my mother, for supporting every single goal I’ve ever had, the memory of my father, for keeping me focused, and my partner, for all he’s done ACKNOWLEDGMENTS I would like to begin by acknowledging and thanking my mentor, Dr. Jamie Foster, for all her guidance throughout this Ph.D. I thank my committee members for all of their advice and support - Drs. Eric Triplett, Julie Maupin, Nian Wang, and Eric McLamore. I’d like to thank the rest of the Department of Microbiology and Cell Science, staff for always keeping my academic life in order, faculty for never turning me away when I came to use equipment or ask for help, especially Drs. K.T. Shanmugan and Wayne Nicholson, as well as Dr. Andy Schuerger from the Dept. of Plant Pathology for his advice over the years. I’d also like to acknowledge those lab members and extended lab members who made themselves readily available to talk through any problems I came up against and celebrate when all went well, including Drs. Rafael Oliveira, Jennifer Mobberley, and Giorgio Casaburi, and Lexi Duscher, Rachelle Banjawo, Maddie Vroom, Hadrien Gourlé, and so many more. I’d also like to profusely thank my family and friends who have never been anything less than completely supportive of me, specifically my partner Nathan Prince, my mother and siblings Denise Louyakis, Bobbi Louyakis, Nick Newman, Cori Sergi, extended parents and siblings Carol Prince, Barry Prince, Aaron Prince, my nieces and nephew Bailey O’Regan, Bella O’Regan, Layla Newman, Colton Prince, and Summer Prince, and my dearest friends Tina Pontbriand, Tom Pontbriand, Karen Chan, Dalal Haouchar, Alexi Casaburi, and Eloise Stikeman. -
The Influence of Bacteria on the Adaptation to Changing Environments in Ectocarpus : a Systems Biology Approach Hetty Kleinjan
The influence of bacteria on the adaptation to changing environments in Ectocarpus : a systems biology approach Hetty Kleinjan To cite this version: Hetty Kleinjan. The influence of bacteria on the adaptation to changing environments in Ectocar- pus : a systems biology approach. Molecular biology. Sorbonne Université, 2018. English. NNT : 2018SORUS267. tel-02868508 HAL Id: tel-02868508 https://tel.archives-ouvertes.fr/tel-02868508 Submitted on 15 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Sorbonne Université ED 227 - Sciences de la Nature et de l'Homme : écologie & évolution Laboratoire de Biologie Intégrative des Modèles Marins Equipe Biologie des algues et interactions avec l'environnement The influence of bacteria on the adaptation to changing environments in Ectocarpus: a systems biology approach Par Hetty KleinJan Thèse de doctorat en Biologie Marine Dirigée par Simon Dittami et Catherine Boyen Présentée et soutenue publiquement le 24 septembre 2018 Devant un jury composé de : Pr. Ute Hentschel Humeida, Rapportrice GEOMAR, Kiel, Germany Dr. Suhelen Egan, Rapportrice UNSW Sydney, Australia Dr. Fabrice Not, Examinateur Sorbonne Université – CNRS Dr. David Green, Examinateur SAMS, Oban, UK Dr. Aschwin Engelen, Examinateur CCMAR, Faro, Portugal Dr. -
Genome-Based Taxonomic Classification Of
ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G. Klotz, Queens College, City University of trees inferred from genome-scale data. No significant conflict between 16S rRNA gene New York, USA and whole-genome phylogenetic analysis is found, whereas many but not all of the Reviewed by: involved taxa are supported as monophyletic groups, particularly in the genome-scale Eddie Cytryn, trees. Phenotypic and phylogenomic features support the separation of Balneolaceae Agricultural Research Organization, Israel as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new John Phillip Bowman, class Saprospiria from Chitinophagia. -
The Influence of Invasive Jellyfish Blooms on The
Biol Invasions DOI 10.1007/s10530-014-0810-2 MOLECULAR TOOLS The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy Caterina Manzari • Bruno Fosso • Marinella Marzano • Anita Annese • Rosa Caprioli • Anna Maria D’Erchia • Carmela Gissi • Marianna Intranuovo • Ernesto Picardi • Monica Santamaria • Simonetta Scorrano • Giuseppe Sgaramella • Loredana Stabili • Stefano Piraino • Graziano Pesole Received: 14 November 2013 / Accepted: 31 October 2014 Ó The Author(s) 2014. This article is published with open access at Springerlink.com Abstract The rapid expansion of multicellular microbial taxonomic and functional diversity. Here native and alien species outbreaks in aquatic and we used an effective and highly sensitive experimental terrestrial ecosystems (bioinvasions) may produce strategy, bypassing the efficiency bottleneck of the significant impacts on bacterial community dynamics traditional bacterial isolation and culturing method, to and nutrient pathways with major ecological implica- identify changes of the planktonic microbial commu- tions. In aquatic ecosystems, bioinvasions may cause nity inhabiting a marine coastal lagoon (Varano, adverse effects on the water quality resulting from Adriatic Sea) under the influence of an outbreak- changes in biological, chemical and physical proper- forming alien jellyfish species. Water samples were ties linked to significant transformations of the collected from two areas that differed in their level of confinement inside in the lagoon and jellyfish densities (W, up to 12.4 medusae m-3; E, up to 0.03 medusae Caterina Manzari, Bruno Fosso and Marinella Marzano have -3 contributed equally to this work. m ) to conduct a snapshot microbiome analysis by a metagenomic approach. -
Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga Pacifica WPAGA1
ORIGINAL RESEARCH published: 10 April 2017 doi: 10.3389/fmicb.2017.00600 Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1 Boliang Gao 1, Min Jin 2, Li Li 2, Wu Qu 1 and Runying Zeng 2, 3, 4* 1 School of Life Sciences, Xiamen University, Xiamen, China, 2 State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, SOA, Xiamen, China, 3 Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China, 4 South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, China Flammeovirga pacifica strain WPAGA1 is a Gram-negative, polysaccharide-degrading bacterium isolated from the marine sediment of the West Pacific Ocean. This strain is a cosmopolitan marine bacterium that uses complex polysaccharides as exclusive source of carbon and energy and plays a key role in the marine carbon cycle. Genome sequence Edited by: analysis of strain WPAGA1 revealed that the assembled fine genome contains 6,610,326 Télesphore Sime-Ngando, Centre National de la Recherche bp with 32.89% G+C content, 5036 open reading frames (ORFs) and abundant genomic Scientifique (CNRS), France elements. Amongst these ORFs, 1022 genes encoding carbohydrate enzymes were Reviewed by: found in the F. pacifica WPAGA1 genome. In addition, abundant putative enzymes Claire Geslin, involved in degrading polysaccharide were found. These enzymes include amylase, University of Western Brittany, France Sébastien Monchy, xylosidase, cellulase, alginate lyase, pectate lyase, rhamnogalacturonan lyase, chitinase, Université du Littoral Côte d’Opale, carrageenase, heparinase and fucosidase. To further investigate the use of these France polysaccharides in strain WPAGA1, a schematic of various polysaccharide-degrading *Correspondence: Runying Zeng metabolic pathways were deduced from the genome sequence. -
Microbial Diversity of the Namib Desert Salt Pans
Microbial Diversity of the Namib Desert Salt Pans By Melissa Cloete Submitted in partial fulfilment of the requirements for the degree of Magistrate Scientiae (M.Sc.) in the Department of Biotechnology, University of the Western Cape Supervisor: Prof. I. M Trindade Co-Supervisor: Dr. B.M. Kirby December 2015 Declaration I declare that ‘The Microbial Diversity of the Namib Desert Salt Pans’ is my own work, that is has not been submitted for any degree or examination in any other university, and that all the resources I have used or quoted have been indicated and acknowledged by complete references. --------------------------------------------- Melissa (Du Plessis) Cloete ii Abstract Salt pans are a characteristic feature of many dry deserts. The microbial communities inhabiting salt pans are thought to be particularly complex and are generally dominated by halophilic microorganisms. Although saline pools are frequently found within the hyper-arid Namib Desert, the microbial communities of these saline sites have been scarcely investigated. The aim of the present study was to characterise the archaeal, bacterial and cyanobacterial diversity inhabiting these extreme saline pools using three culture independent molecular techniques (DGGE, T-RFLP and 16S rRNA clone libraries). The physiochemical results, mainly the conductivity readings recorded from the sampling sites, indicated that the Gobabeb (103.0mS/cm) region was less saline than the two Swakopmund [(Sps01) (150.0mS/cm) and Sps02 (180.0mS/cm)] sites. Results obtained from DGGE and T-RFLP data were in agreement for both bacterial and cyanobacterial analysis indicating that the Gobabeb site was more diverse than the two Swakopmund sites (Sps01 and Sps02).