Perchlorate Bioremediation: Controlling Media Loss in Ex-Situ
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Expanding the Knowledge on the Skillful Yeast Cyberlindnera Jadinii
Journal of Fungi Review Expanding the Knowledge on the Skillful Yeast Cyberlindnera jadinii Maria Sousa-Silva 1,2 , Daniel Vieira 1,2, Pedro Soares 1,2, Margarida Casal 1,2 and Isabel Soares-Silva 1,2,* 1 Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; [email protected] (M.S.-S.); [email protected] (D.V.); [email protected] (P.S.); [email protected] (M.C.) 2 Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal * Correspondence: [email protected]; Tel.: +351-253601519 Abstract: Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. -
M.Sc. Dissertation
2 ACKNOWLEDGEMENTS I wish to thank the following: God , for giving me the strength and guidance to start each day with new hope. Prof. J. L. F. Kock , for his guidance, understanding and passion for research. Prof. P. W. J. van Wyk and Miss B. Janecke for their patience and assistance with the SEM, TEM and CLSM. Dr. C. H. Pohl , for her encouragement and assistance. Mrs. A. van Wyk , for providing the yeast cultures used during this study and also for her encouragement and support. Mr. S. F. Collett , for assisting with the graphical design of this dissertation. My colleagues in Lab 28 , for always being supportive and helpful. My mother, Mrs. M. M. Swart and grandmother, Mrs. M. M. Coetzer , for their patience, love and encouragement. My family for their encouragement and for believing in me. Mr. P. S. Delport , for his love, understanding and patience. 3 CONTENTS Page Title Page 1 Acknowledgements 3 Contents 4 CHAPTER 1 Literature Review 1.1 Motivation 9 1.2 Automictic yeasts 10 1.2.1 Definition of a yeast 10 1.2.2 Automixis 11 1.3 Oxylipins 19 1.3.1 Background 19 1.3.2 3-OH oxylipins 19 1.3.2.1 Chemical structure and production 19 1.3.2.2 Distribution 20 1.3.2.3 Function 23 1.3.2.4 ASA inhibition 23 1.4 Purpose of research 24 1.5 References 26 4 CHAPTER 2 Oxylipin accumulation and acetylsalicylic acid sensitivity in fermentative and non-fermentative yeasts 2.1 Abstract 38 2.2 Introduction 40 2.3 Materials and Methods 41 2.3.1 Strains used and cultivation 41 2.3.2 Ultrastructure 42 2.3.2.1 Scanning electron microscopy (SEM) -
Some English Terms Used in Microbiology 1
Some English terms used in Microbiology 1 Shapes & Structures General terms Antibiotics and related Bacillus (pl. bacilli) Acid fast (acid fastness) ácido-alcohol resistente Acetylases Capsule Bacterial (adj.) Ampicillin Cell wall pared celular Bacterium (pl., bacteria): Beta-lactamase Coccus (cocci; and hence Staphylococcus, Bench: poyata Beta-lactamic Staphylococci) Biofilm Cephalosporin Core oligosaccharide núcleo oligosacarídico Burner (Bunsen Burner): mechero (Bunsen) Chloramphenicol Cortex Colony: colonia Colistin Fimbria (pl. fimbriae) Coverslip: (vidrio) cubreobjetos D-Cycloserine Flagellum (pl. flagella) Dye colorante DNA-gyrase Glycocalix Eukaryote or eucaryote Erythromycin Lipid A Incubator: estufa de incubación Ethambuthol Lipopolysaccharide Inoculating loop asa de siembra Fluoroquinolone Murein mureína Inoculum (inocula): Gentamicin (formerly gentamycin) Omp: outer membrane major protein proteína To flame: flamear Isoniazide de membrane externa Flask (Erlenmeyer flask): matraz Methicillin Outer membrane membrana externa Volumetric flask: matraz aforado Methylases PAMP (pathogen associated molecular pattern): Microorganism Nalidixic acid patrón molecular asociado a patógeno Motility movilidad Penicillin Peptidoglycan peptidoglucano Mycoplasm Penicillin binding protein (PBP) Periplasm periplasma Negative staining tinción negativa Phosphonomycin Periplasmic space espacio periplásmico Petri dish: placa de Petri Phosphorylases Permeability barrier barrera de permeabilidad Prokaryote or procaryote Polymyxin Pilus (pl. pili) Rack: -
The Regulation of Arsenic Metabolism in Rhizobium Sp. NT-26
The regulation of arsenic metabolism in Rhizobium sp. NT-26 Paula Corsini Madeira University College London Thesis submitted for the degree of Doctor of Philosophy 2016 I, Paula Corsini Madeira, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Date: Signed: II Abstract Arsenic (As) is a toxic metalloid and a major contaminant in terrestrial and aquatic environments. The two soluble forms, arsenite (AsIII) and arsenate (AsV) are toxic to most organisms. A range of phylogenetically distant bacteria are able to oxidize AsIII to the less toxic form, arsenate AsV using the periplasmic arsenite oxidase (AioBA). The two-component signal transduction system AioS/AioR and the AsIII-binding periplasmic protein AioX are required for AsIII oxidation and are involved in the transcriptional regulation of the aioBA operon. Most AsIII oxidisers can also reduce AsV to AsIII via the As (Ars) resistance system. The focus of this work was to understand the regulation of genes involved in AsIII oxidation and As resistance together with those involved in phosphate metabolism in the facultative chemolithoautotrophic AsIII oxidiser NT-26 grown under different conditions. Gene expression was studied by quantitative PCR in cells grown heterotrophically with and without AsIII or AsV in late-log and stationary phases. qPCR was optimised and suitable reference genes were chosen. The expression of genes involved in phosphate transport, sensing As and the genes aioX, aioS, aioR (AsIII-sensing and regulation) and aioB, aioA (AsIII oxidation) and cytC (cytochrome c) were also analysed in NT-26 grown heterotrophically in the presence or absence of AsIII or AsV at different growth stages (i.e., late-log and stationary phases). -
Oxylipin Distribution in Eremothecium
1 Oxylipin distribution in Eremothecium by Ntsoaki Joyce Leeuw Submitted in accordance with the requirements for the degree Magister Scientiae in the Department of Microbial, Biochemical and Food Biotechnology Faculty of Natural and Agricultural Sciences University of the Free State Bloemfontein South Africa Supervisor: Prof J.L.F. Kock Co- supervisors: Dr C.H. Pohl Prof P.W.J. Van Wyk November 2006 2 This dissertation is dedicated to the following people: My mother (Nkotseng Leeuw) My brother (Kabelo Leeuw) My cousins (Bafokeng, Lebohang, Mami, Thabang and Rorisang) Mr. Eugean Malebo 3 ACKNOWLEDGEMENTS I wish to thank and acknowledge the following: ) God, to You be the glory for the things You have done in my life. ) My family (especially my mom) – for always being there for me when I’m in need. ) Prof. J.L.F Kock for his patience, constructive criticisms and guidance during the course of this study. ) Dr. C.H. Pohl for her encouragement and assistance in the writing up of this dissertation. ) Mr. P.J. Botes for assistance with the GC-MS. ) Prof. P.W.J. Van Wyk and Miss B. Janecke for assistance with the CLSM and SEM. ) My fellow colleagues (especially Chantel and Desmond) for their assistance, support and encouragement. ) Mr. Eugean Malebo for always being there when I needed you. 4 CONTENTS Page Title page I Acknowledgements II Contents III CHAPTER 1 Introduction 1.1 Motivation 2 1.2 Definition and classification of yeasts 3 1.3 Classification of Eremothecium and related genera 5 1.4 Pathogenicity 12 1.5 Oxylipins 13 1.5.1 Definition -
APUNTE GEOTRICOSIS 2020.Pdf
Geotricosis GEOTRICOSIS DEFINICIÓN: es una infección oportunista causada por el hongos del género Geotrichum que produce lesiones broncopulmonares, bronquiales, bucales, vaginales, cutáneas y diseminadas. ETIOLOGÍA: actualmente se reconoce una única especie dentro del género que se asocia con infecciones en el ser humano, Geotrichum candidum. Son especies muy relacionadas: -Magnusiomyces capitatus (ex Geotrichum capitatum) y -Saprochaete clavata (ex Geotrichum clavatus) CLASIFICACIÓN TAXONÓMICA: Reino: Fungi División: Ascomycota Subdivisión: Saccharomycotina Familia: Dipodascaceae Género: Telemorfo: Galactomyces candidus Anamorfo: Geotrichum candidum ECOLOGÍA Y DISTRIBUCIÓN: Es una levadura ascosporógena (que produce ascosporos) ampliamente distribuída en la naturaleza en el suelo, agua, aire, así como en plantas, cereales, y productos lácteos. También se encuentra en la microbiota habitual en la boca , intestinos y la piel sana. CAUSAS PREDISPONENTES Y CUADROS CLÍNICOS: Dado que Geotrichum es un habitante habitual del tracto intestinal, puede causar infecciones oportunistas de origen endógeno o de origen exógeno adquiridas vía ingestión o inhalación en pacientes diabéticos, tratados con antibióticos, corticoides, citostáticos, inmunosupresores, pacientes neutropénicos, con cáncer, Sida y en general en el hospedero inmunocomprometido, produciendo infecciones bronquiales y pulmonares, bucales, vaginales y cutáneas así como fungemia e infecciones diseminadas. Geotricosis pulmonar: es una infección de evolución crónica muy similar a la tuberculosis y muchas veces secundaria a ella. Puede presentarse debilitamiento general y fiebre. El esputo es mucoide, viscoso de color gris claro y en algunos casos purulento. 1 Geotricosis Geotricosis bronquial: consiste en una infección endobronquial cuyos síntomas incluyen tos crónica intensa, esputo gelatinoso sin fiebre y estertores ligeros o roncos. En las placas de rayos X se observan engroasamientos peribronquiales difusos. -
Cell Structure and Function in the Bacteria and Archaea
4 Chapter Preview and Key Concepts 4.1 1.1 DiversityThe Beginnings among theof Microbiology Bacteria and Archaea 1.1. •The BacteriaThe are discovery classified of microorganismsinto several Cell Structure wasmajor dependent phyla. on observations made with 2. theThe microscope Archaea are currently classified into two 2. •major phyla.The emergence of experimental 4.2 Cellscience Shapes provided and Arrangements a means to test long held and Function beliefs and resolve controversies 3. Many bacterial cells have a rod, spherical, or 3. MicroInquiryspiral shape and1: Experimentation are organized into and a specific Scientificellular c arrangement. Inquiry in the Bacteria 4.31.2 AnMicroorganisms Overview to Bacterialand Disease and Transmission Archaeal 4.Cell • StructureEarly epidemiology studies suggested how diseases could be spread and 4. Bacterial and archaeal cells are organized at be controlled the cellular and molecular levels. 5. • Resistance to a disease can come and Archaea 4.4 External Cell Structures from exposure to and recovery from a mild 5.form Pili allowof (or cells a very to attach similar) to surfacesdisease or other cells. 1.3 The Classical Golden Age of Microbiology 6. Flagella provide motility. Our planet has always been in the “Age of Bacteria,” ever since the first 6. (1854-1914) 7. A glycocalyx protects against desiccation, fossils—bacteria of course—were entombed in rocks more than 3 billion 7. • The germ theory was based on the attaches cells to surfaces, and helps observations that different microorganisms years ago. On any possible, reasonable criterion, bacteria are—and always pathogens evade the immune system. have been—the dominant forms of life on Earth. -
Gram Staining Staining & Acid Fast & Acid Fast Staining
GRAM STAINING && AACCIIDD FFAASSTT SSTTAAIINNIINNGG Dr. R. Haritha Lecturer in Biotechnology Visakha Government Degree College for Women Visakhapatnam Staining Stains Principle Types Staining methods Smear Preparation Smear- Distribution of Bacterial cells on a slide Objective-To kill the microorganism & fix bacteria Method- Air Dry, Heat Fixation GRAM STAINING Gram staining is most widely Hans Christian Joachim Gram used differential staining in Microbiology. It classifies bacteria into two major groups: Gram positive Gram negative Appears violet Appears red after Gram’s stain after Gram’s stain REAGENTS 1. CRYSTAL VIOLET Primary stain Violet colored, stains all micro-organism 2. GRAM IODINE Mordant Forms Crystal violet iodine complexes 3. DECOLORIZER Acetone + Methanol Removes Crystal violet iodine complex from thin peptidoglycan layers 4. GRAM SAFRANINE Counter stain Red colored Step 1: Crystal Violet Step 2: Gram’’s Iodine Step 3: Decolorization (Aceton-Alcohol) Step 4: Safranin Red 7 PRINCIPLE : Composition of the cell wall Gram-positive bacteria Cell wall has a thick peptidoglycan layer The Crystal Violet stain gets trapped into this layer and the bacteria turned purple. Retains the color of the primary stain (crystal violet) after decolorization with alcohol. Gram-negative bacteria Cell wall has a thin peptidoglycan layer that does not retain crystal violet stain. Cell wall has a thick lipid layer which dissolves easily upon decoulorization with Aceton-Alcohol. Therefore, cells will be counterstained with safranin and turned red. Gram’s +ve Bacteria Gram’s -ve Bacteria 9 RESULT Bacteria that manage to keep the original purple are called Gram positive. Bacteria that lose the original purple dye and can therefore take up the second red dye are called Gram negative APPLICATIONS 1.Rapid preliminary diagnosis of diseases such as Bacterial meningitis. -
Metabolic Flexibility of Enigmatic SAR324 Revealed Through
bs_bs_banner Environmental Microbiology (2014) 16(1), 304–317 doi:10.1111/1462-2920.12165 Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics Cody S. Sheik,1 Sunit Jain1 and Gregory J. Dick1,2,3* deep ocean (ArÍstegui et al., 2009) is thought to constrain 1Department of Earth and Environmental Sciences and heterotrophic microbial activity. However, recent identifi- 2Center for Computational Medicine and Bioinformatics cation of carbon fixation genes in the dark ocean (> 200 m and 3Department of Ecology and Evolutionary Biology, below surface) (Swan et al., 2011) underscores auto- University of Michigan, Ann Arbor, MI 48109, USA. trophy as a metabolic strategy for many dark ocean- associated micro-organisms (Karl et al., 1984). Because autotrophy is energetically taxing (Hügler and Sievert, Summary 2011), organisms must couple carbon fixation to an Chemolithotrophy is a pervasive metabolic lifestyle electron-donating reaction such as the oxidation of for microorganisms in the dark ocean. The SAR324 ammonia, nitrite, sulfur, iron, methane, hydrogen or group of Deltaproteobacteria is ubiquitous in the formate. Yet such electron donors required to power ocean and has been implicated in sulfur oxidation and carbon fixation in the deep ocean are scarce (Reinthaler carbon fixation, but also contains genomic signatures and Van, 2010), suggesting that mixotrophy (Sorokin, of C1 utilization and heterotrophy. Here, we recon- 2003; Moran et al., 2004; Dick et al., 2008) may be nec- structed the metagenome and metatranscriptome of a essary for micro-organisms to persist until preferred population of SAR324 from a hydrothermal plume and energy sources are encountered. surrounding waters in the deep Gulf of California to Within the deep ocean, hydrothermal vents are crucial gain insight into the genetic capability and transcrip- sources of reduced compounds such as sulfur, ammonia, tional dynamics of this enigmatic group. -
Fungal and Bacterial Community Composition and Structure In
Fungal and bacterial community composition and structure in fermented `hairy' tofu (Mao tofu) Gian Maria Niccol`oBenucci1, Xinxin Wang2, Li Zhang3, Gregory Bonito2, and Fuqiang Yu3 1Michigan State university 2Michigan State University 3Kunming Institute of Botany Chinese Academy of Sciences October 22, 2020 Abstract The process of fermenting tofu extends thousands of years. Despite a resurgent interest in microbial communities and fermented foods, little knowledge exists concerning microbial diversity of communities of fermented `hairy' tofu known in China as Mao tofu. We used high-throughput metagenomic sequencing of the ITS, LSU and 16S rDNA marker genes to disentangle the Mao tofu fungal and bacterial community composition and diversity across the four most important markets in the Yunnan region of China. We show that hairy tofu in this region consists of around 170 fungal and 365 bacterial taxa. Significant differences in community structure were found between markets and niches. Machine learning random forest models were able to accurately classify both market and niche of sample origin. An over-abundance of yeast taxa were detected, and Geotrichum were the most abundant fungal taxa, followed by Torulaspora, Trichosporon, and Pichia. Mucor (Mucormycota) was also abundant in the LSU data and especially in the outside niche (rind), which consists of the visible `hairy' mycelium. The majority of the bacterial OTUs belonged to Proteobacteria, Firmicutes, and Bacteroidota, with Acinetobacter, Lactobacillus, Sphingobacterium and Flavobacterium the most abundant members. Of interest, putative fungal pathogens of plants (e.g. Cercospora, Diaporthe, Fusarium) and animal (e.g. Metarhizium, Entomomortierella, Pyxidiophora, Candida, Clavispora), as well as bacterial (e.g. Legionella) pathogens, were detected. -
Metapangenomics of the Oral Microbiome Provides Insights Into Habitat Adaptation and Cultivar Diversity Daniel R
Utter et al. Genome Biology (2020) 21:293 https://doi.org/10.1186/s13059-020-02200-2 RESEARCH Open Access Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity Daniel R. Utter1* , Gary G. Borisy2, A. Murat Eren3,4, Colleen M. Cavanaugh1* and Jessica L. Mark Welch3* * Correspondence: dutter@g. harvard.edu; [email protected]. Abstract edu; [email protected] 1Department of Organismic and Background: The increasing availability of microbial genomes and environmental Evolutionary Biology, Harvard shotgun metagenomes provides unprecedented access to the genomic differences University, Cambridge, MA 02138, within related bacteria. The human oral microbiome with its diverse habitats and USA 3The Josephine Bay Paul Center for abundant, relatively well-characterized microbial inhabitants presents an opportunity Comparative Molecular Biology and to investigate bacterial population structures at an ecosystem scale. Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, Results: Here, we employ a metapangenomic approach that combines public USA genomes with Human Microbiome Project (HMP) metagenomes to study the Full list of author information is diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, available at the end of the article and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes reveal distinct genomic groups based on shared genome content. H. parainfluenzae genomes separate into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identify an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulates species-level taxonomy and habitat preferences. However, while most R. -
Fate of Arsenate Following Arsenite Oxidation in Agrobacterium Tumefaciens GW4
bs_bs_banner Environmental Microbiology (2014) doi:10.1111/1462-2920.12465 Fate of arsenate following arsenite oxidation in Agrobacterium tumefaciens GW4 Qian Wang,1 Dong Qin,1 Shengzhe Zhang,1 Introduction Lu Wang,1 Jingxin Li,1 Christopher Rensing,2 Arsenic (As) is the most common toxic element in the Timothy R. McDermott3** and Gejiao Wang1* environment, ranking first on the U.S. Superfund List 1State Key Laboratory of Agricultural Microbiology, of Hazardous Substances and is responsible for mass College of Life Science and Technology, Huazhong poisoning throughout Asia (Chakraborti et al., 2009; Agricultural University, Wuhan 430070, China. Rodríguez-Lado et al., 2013). In the environment, trans- 2Department of Plant and Environmental Sciences, port, bioavailability and accumulation of As in biological University of Copenhagen, Frederiksberg, Denmark. endpoints is dependent on chemical speciation, with 3Department of Land Resources and Environmental arsenite (AsIII) and arsenate (AsV) being the primary Sciences, Montana State University, Bozeman, MT arsenicals found in the environment. Microbial redox 59717, USA. transformations are recognized as being important con- tributors to equilibrium levels of AsIII and AsV (Cullen and Summary Reimer, 1989; Inskeep et al., 2001; Oremland and Stolz, 2005; Stolz et al., 2006). The fate of arsenate (AsV) generated by microbial Microbial AsIII oxidation and AsV reduction both serve arsenite (AsIII) oxidation is poorly understood. as detoxification and/or energy-generating functions, Agrobacterium tumefaciens wild-type strain (GW4) depending on the organism (Stolz et al., 2006; Páez- was studied to determine how the cell copes with AsV Espino et al., 2009). Reasonable models exist for under- generated in batch culture.