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Arxiv:2105.11503V2 [Physics.Bio-Ph] 26 May 2021 3.1 Geometry and Swimming Speeds of the Cells
The Bank Of Swimming Organisms at the Micron Scale (BOSO-Micro) Marcos F. Velho Rodrigues1, Maciej Lisicki2, Eric Lauga1,* 1 Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, United Kingdom. 2 Faculty of Physics, University of Warsaw, Warsaw, Poland. *Email: [email protected] Abstract Unicellular microscopic organisms living in aqueous environments outnumber all other creatures on Earth. A large proportion of them are able to self-propel in fluids with a vast diversity of swimming gaits and motility patterns. In this paper we present a biophysical survey of the available experimental data produced to date on the characteristics of motile behaviour in unicellular microswimmers. We assemble from the available literature empirical data on the motility of four broad categories of organisms: bacteria (and archaea), flagellated eukaryotes, spermatozoa and ciliates. Whenever possible, we gather the following biological, morphological, kinematic and dynamical parameters: species, geometry and size of the organisms, swimming speeds, actuation frequencies, actuation amplitudes, number of flagella and properties of the surrounding fluid. We then organise the data using the established fluid mechanics principles for propulsion at low Reynolds number. Specifically, we use theoretical biophysical models for the locomotion of cells within the same taxonomic groups of organisms as a means of rationalising the raw material we have assembled, while demonstrating the variability for organisms of different species within the same group. The material gathered in our work is an attempt to summarise the available experimental data in the field, providing a convenient and practical reference point for future studies. Contents 1 Introduction 2 2 Methods 4 2.1 Propulsion at low Reynolds number . -
Bakterielle Diversität in Einer Wasserbehandlungsanlage Zur Reini- Gung Saurer Grubenwässer
Bakterielle Diversität in einer Wasserbehandlungsanlage zur Reini- gung saurer Grubenwässer E. Heinzel1, S. Hedrich1, G. Rätzel2, M. Wolf2, E. Janneck2, J. Seifert1, F. Glombitza2, M. Schlömann1 1AG Umweltmikrobiologie, IÖZ, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, [email protected], 2Fa. G.E.O.S. Ingenieurgesellschaft mbH, Gewerbepark „Schwarze Kiefern“, 09633 Halsbrücke In einer Versuchsanlage zur Gewinnung von Eisenhydroxysulfaten durch biologische Oxidation von zweiwertigem Eisen wurde die Zusammensetzung der bakteriellen Lebensgemeinschaft mit moleku- largenetischen Methoden analysiert. Die 16S rDNA-Klonbank wurde von zwei Sequenztypen, denen 68 % der Klone zugeordnet werden konnten, dominiert. Ein Sequenztyp kann phylogenetisch in die Ordnung der Nitrosomonadales eingeordnet werden, zu deren Vertretern sowohl chemo-heterotrophe Bakterien als auch autotrophe Eisen und Ammonium oxidierende Bakterien gehören. Der zweite Se- quenztyp ist ähnlich zu „Ferrimicrobium acidiphilum“, einem heterotrophen Eisenoxidierer. The microbial community of a pilot plant for the production of iron hydroxysulfates by biological oxidation of ferrous iron was studied using molecular techniques. The 16S rDNA clone library was dominated by two sequence types, to which 68 % of all clones could be assigned. One sequence type is phylogenetically classified to the order of Nitrosomonadales. Both chemoheterotrophic bacteria and autotrophic iron or ammonium oxidizing bacteria belong to this order. The second sequence type is related to “Ferrimicrobium acidiphilum”, a heterotrophic iron oxidizing bacteria. 1 Einleitung und Projektziel die biologische Oxidationskapazität zu optimie- ren. Zur Gewährleistung einer konstanten Pro- Stark eisenhaltige und saure Bergbauwässer aus duktqualität muss die Oxidation sicher be- Tagebaufolgelandschaften bedingen einen erheb- herrscht und gesteuert werden können. Dies er- lichen Sanierungsaufwand. Die konventionelle fordert die Analyse der mikrobiellen Lebens- Reinigung dieser Wässer findet durch pH- gemeinschaft. -
Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju. -
Contents Topic 1. Introduction to Microbiology. the Subject and Tasks
Contents Topic 1. Introduction to microbiology. The subject and tasks of microbiology. A short historical essay………………………………………………………………5 Topic 2. Systematics and nomenclature of microorganisms……………………. 10 Topic 3. General characteristics of prokaryotic cells. Gram’s method ………...45 Topic 4. Principles of health protection and safety rules in the microbiological laboratory. Design, equipment, and working regimen of a microbiological laboratory………………………………………………………………………….162 Topic 5. Physiology of bacteria, fungi, viruses, mycoplasmas, rickettsia……...185 TOPIC 1. INTRODUCTION TO MICROBIOLOGY. THE SUBJECT AND TASKS OF MICROBIOLOGY. A SHORT HISTORICAL ESSAY. Contents 1. Subject, tasks and achievements of modern microbiology. 2. The role of microorganisms in human life. 3. Differentiation of microbiology in the industry. 4. Communication of microbiology with other sciences. 5. Periods in the development of microbiology. 6. The contribution of domestic scientists in the development of microbiology. 7. The value of microbiology in the system of training veterinarians. 8. Methods of studying microorganisms. Microbiology is a science, which study most shallow living creatures - microorganisms. Before inventing of microscope humanity was in dark about their existence. But during the centuries people could make use of processes vital activity of microbes for its needs. They could prepare a koumiss, alcohol, wine, vinegar, bread, and other products. During many centuries the nature of fermentations remained incomprehensible. Microbiology learns morphology, physiology, genetics and microorganisms systematization, their ecology and the other life forms. Specific Classes of Microorganisms Algae Protozoa Fungi (yeasts and molds) Bacteria Rickettsiae Viruses Prions The Microorganisms are extraordinarily widely spread in nature. They literally ubiquitous forward us from birth to our death. Daily, hourly we eat up thousands and thousands of microbes together with air, water, food. -
International Journal of Systematic and Evolutionary Microbiology
University of Plymouth PEARL https://pearl.plymouth.ac.uk 01 University of Plymouth Research Outputs University of Plymouth Research Outputs 2017-05-01 Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the 'Proteobacteria', and four new families within the orders Nitrosomonadales and Rhodocyclales Boden, R http://hdl.handle.net/10026.1/8740 10.1099/ijsem.0.001927 International Journal of Systematic and Evolutionary Microbiology All content in PEARL is protected by copyright law. Author manuscripts are made available in accordance with publisher policies. Please cite only the published version using the details provided on the item record or document. In the absence of an open licence (e.g. Creative Commons), permissions for further reuse of content should be sought from the publisher or author. International Journal of Systematic and Evolutionary Microbiology Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov. Transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the 'Proteobacteria', and 4 new families within the orders Nitrosomonadales and Rhodocyclales. --Manuscript Draft-- Manuscript Number: IJSEM-D-16-00980R2 Full Title: Reclassification of Thiobacillus aquaesulis (Wood & Kelly, -
Biology 2 Lab Packet for Practical 1
Biology 2: LAB PRACTICUM 1 1 Biology 2 Lab Packet For Practical 1 Biology 2: LAB PRACTICUM 1 2 CLASSIFICATION: Domain: Bacteria Domain: Archaea Group: Proteobacteria Group: Methanogens Group: Chlamydias Group: Halophiles Group: Spirochetes Group: Thermophiles Group: Cyanobacteria Group: Gram-Positive Bacteria Viruses Station 1 – Prokaryotic Cells 1. What general characteristics and structures are found in the clade Prokaryotes? 2. When did the first prokaryote appear in the fossil record? 3. What form did the fossil Prokaryote take? 4. How long were prokaryotes on earth by themselves? 5. Where are prokaryotes found? 6. Be able to label the diagram below. Biology 2: LAB PRACTICUM 1 3 Station 2 – Bacterial Shapes Be able to identify the following shapes: Coccus, Bacillus, Helical and Filamentous Use the slide of Streptococcus lactis (in a chain) to become familiar with this shape. Streptococcus lactis Clostridium tetani Spirillum volutans Oscillatoria sp. Station 3 – Gram Stain (Gram Positive and Gram Negative) Be able to recognize the difference between a slide that is gram-positive and one that is gram-negative. 1. What do cell walls of prokaryotes contain? 2. What is the structure of the cell wall in gram-positive bacteria? What color does it Gram Stain? 3. What is the structure of the cell wall in gram-negative bacteria? What color does it Gram Stain? Biology 2: LAB PRACTICUM 1 4 Station 4 – Bacterial Colonies When growing on a nutrient medium which has been hardened with agar (a derivative of red algae), each species of bacteria will form a characteristic colony that can be identified. A colony is a cluster of millions of bacteria. -
Tikrit University Microbiology Science Collage Forth Class Biology
Tikrit University Microbiology Science Collage Forth class Biology Department Bacterial Taxonomy Lecture 6 ●The Betaproteobacteria: There is considerable overlap between the betaproteobacteria and the alphaproteobacteria, for example, among the nitrifying bacteria discussed earlier. The betaproteobacteria often use nutrient substances that diffuse away from areas of anaerobic decomposition of organic matter, such as hydrogen gas, ammonia, and methane. Several important pathogenic bacteria are found in this group. ●Thiobacillus: Thiobacillus (thī-ō-ba-silʹ lus) species and other sulfur-oxidizing bacteria are important in the sulfur cycle. These chemoautotrophic bacteria are capable of obtaining energy by oxidizing the reduced forms of sulfur, such as hydrogen sulfide (H2S), or elemental sulfur (S0), into sulfates (SO42−). ●Spirillum: The habitat of the genus Spirillum (spī-rilʹ lum) is mainly fresh water. An important morphological difference from the helical spirochetes is that Spirillum bacteria are motile by conventional polar flagella, rather than axial filaments. The spirilla are relatively large, gram-negative, aerobic bacteria. Spirillum volutans (vō-lū-tans) is often used as a demonstration slide when microbiology students are first introduced to the operation of the microscope. ●Sphaerotilus: Sheathed bacteria, which include Sphaerotilus natans (sfe-raʹ ti-lus naʹ tans), are found in freshwater and in sewage. These gram-negative bacteria with polar flagella form a hollow, filamentous sheath in which to live. Sheaths are protective and also aid in nutrient accumulation. Sphaerotilus probably contributes to bulking, an important problem in sewage treatment. ●Burkholderia: The genus Burkholderia was formerly grouped with the genus Pseudomonas, which is now classified under the gammaproteobacteria. Like the pseudomonads, almost all Burkholderia species are motile by a single polar flagellum or tuft of flagella. -
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VOL. 7 NO.2 September 201 8 - ISSN 2233 – 1859 : DOI: 10.21533/scjournal.v7i2.14 4 Southeast Europe Journal of Soft Computing Available online: http://scjournal.ius.edu.ba Longest Common Subsequences in Bacteria Taxonomic Classification M. Can O. Gürsoy Faculty of Engineering and Natural Sciences, International University of Sarajevo International University of Sarajevo, Hrasnicka Cesta 15, Ilidža 71210 Sarajevo, Bosnia and Herzegovina [email protected] [email protected] Article Info ABSTRACT: In 1980s, Carl Woese made a ground breaking contribution to Article history: Article received on 10 June 2018 microbiology using rRNA-genes for phylogenetic classifications . He used it not Received in revised form 1 August 2018 only to explore microbial diversity but also as a method for bacterial annotation. Today, rRNA-based analysis remains a central method in microbiology . Many researchers followed this track, using several new generations of Artificial Keywords: Neural Networks obtained high accuracies using available datasets of their time. 16S ribosomal RNA; gene segments; diagnosis; bacteria annotation By the time, the number of bacteria increased enormously. I n this article we used Longest Common Subsequence similarity measure to classify bacterial 16S rRNA gene sequences of 1.820.414 bacteria in SILVA, 3.196.038 bacteria in RDP, and 198.509 bacteria in Greengenes . The last two taxonomy have six taxonomical lev els, phylum, class, order, family, genus, and species , while SILVA has two more levels subclass and suborder, but lacks species level . The majority of classifications (98%) were of high accuracy (98%). 1. INTRODUCTION Bacteria are often identifi ed as the causes of human and laboratory conditions (Ash et. -
1 Bridging 200 Years of Bacterial Classification
1 Bridging 200 Years of Bacterial Classification Ramon Rosselló-Móra1 and Erko Stackebrandt2,* 1Grup de Microbiologia Marina, Department Animal and Microbial Diversity, IMEDEA (CSIC-UIB), Esporles, Spain; 2Kneitlingen, OT Ampleben, Germany Introduction bacterial names and classification systems. The first was the establishment of the Approved List The history of bacterial systematics reflects of Bacterial Names (Skerman et al., 1980) that scientific progress in which approaches (often brought order into the huge number of syn- developed in non-biological disciplines) were onyms based on obscure species descriptions; adopted to improve the accuracy of bacterial the second was the perception that proper classi- taxonomy and to develop comprehensible rela- fication needed to be based upon phylogenetic tionships. What started two centuries ago with a relationships. Within a short period of 20 blurred vision of the simplest properties of the years the tree of life began to unfold, and what bacterial cell became more focused once pure originally was founded on a single evolutionary cultures were achievable. At an amazing speed, conservative gene has now been extended to their existence as both harmful pathogens for genome sequences. Moreover, the era in which humans, plants and animals and as beneficial pure cultures were needed to assess phylogenetic partners in agriculture, food and industrial ap- novelty has been extended to the direct applica- plications was disclosed. Microbiology as a scien- tion of metagenome and microbiome studies to tific discipline in its own right was established, environmental samples. As a result, the ‘trad- although the historical connection to botany was itional’ bacteriologists are confronted with the still recognizable until recently. -
Report of 21 Unrecorded Bacterial Species in Korea Belonging to Betaproteobacteria and Epsilonproteobacteria
Journal of Species Research 6(1):1524, 2017 Report of 21 unrecorded bacterial species in Korea belonging to Betaproteobacteria and Epsilonproteobacteria MinKyeong Kim1, ChiNam Seong2, Kwangyeop Jahng3, ChangJun Cha4, Kiseong Joh5, JinWoo Bae6, JangCheon Cho7, WanTaek Im8 and SeungBum Kim1,* 1Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Republic of Korea 2Department of Biology, Sunchon National University, Suncheon 57922, Republic of Korea 3Department of Biological Sciences, Chonbuk National Universty, Jeonju 54896, Republic of Korea 4Department of Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea 5Department of Biotechnology, Hankuk University of Foreign Studies, Yongin 17035, Republic of Korea 6Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea 7Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea 8Department of Biotechnology, Hankyoung National University, Anseong 17579, Republic of Korea *Correspondent: [email protected] During the extensive survey of the prokaryotic species diversity in Korea, bacterial strains belonging to Betaproteobacteria and Epsilonproteobacteria were isolated from various sources including freshwater, sediment, soil and fish. A total of 23 isolates were obtained, among which 22 strains were assigned to the class Betaproteobacteria and one strain to the class Epsilonproteobacteria. The 22 betaproteobacterial strains were further assigned to Comamonadaceae (11 strains), Burkholderiaceae -
Archaeal and Bacterial Community Composition of a Pristine Coastal Aquifer in Doñana National Park, Spain
AQUATIC MICROBIAL ECOLOGY Vol. 47: 123–139, 2007 Published May 16 Aquat Microb Ecol Archaeal and bacterial community composition of a pristine coastal aquifer in Doñana National Park, Spain Ana Isabel López-Archilla1,*, David Moreira2, Sergio Velasco1, Purificación López-García2 1Departamento de Ecología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain 2Unité d’Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, bâtiment 360, 91405 Orsay Cedex, France ABSTRACT: We studied the biological activity and prokaryotic diversity associated with 2 samples of different physico-chemical characteristics in a pristine coastal aquifer at Doñana National Park, south-western Spain. Sulphate reduction, denitrification and iron-metabolising activities were detected in the aquifer, as well as different enzymatic activities related to the degradation of labile and complex pools of organic matter. Prokaryotic diversity was assessed by environmental 16S rRNA gene amplification, cloning and sequencing. Bacterial diversity was greater in the shallower aquifer sample (49S1, 15 m depth), including members of the Proteobacteria, Acidobacteria, Planctomycetes, Nitrospirae, some divergent lineages and the candidate divisions SPAM, OP3, OP11, ‘Endomicrobia’ or Termite Group 1 and a novel division-level group including denitrifying bacteria associated to anaerobic methane-oxidising archaea, whereas only Proteobacteria and Firmicutes were detected in the deeper sample (56S, 80 m depth). By contrast, archaea seemed much more diverse in the deeper aquifer sample, with members of the Methanomicrobiales, ANME2-related Methanosarcinales and other divergent lineages, whereas only Group I Crenarchaeota were detected in the shallower sam- ple. Betaproteobacteria were the most abundant and diverse group in both sample libraries, together with the Gammaproteobacteria in the deeper and more saline 56S sample. -
The Gammaproteobacteria
Chapter 11 The Prokaryotes: Domains of Bacteria and Archaea © 2013 Pearson Education, Inc. Lectures prepared by Christine L. Case Lectures prepared by Christine L. Case Copyright © 2013 Pearson Education, Inc. © 2013 Pearson Education, Inc. The Prokaryotes © 2013 Pearson Education, Inc. Domain Bacteria . Proteobacteria . From the mythical Greek god Proteus, who could assume many shapes . Gram-negative . Chemoheterotrophic © 2013 Pearson Education, Inc. The Alphaproteobacteria Learning Objective 11-1 Differentiate the alphaproteobacteria described in this chapter by drawing a dichotomous key. © 2013 Pearson Education, Inc. The Alphaproteobacteria . Pelagibacter ubique . Discovered by FISH technique . 20% of prokaryotes in oceans . 0.5% of all prokaryotes . 1354 genes © 2013 Pearson Education, Inc. The Alphaproteobacteria . Human pathogens . Bartonella − B. henselae: cat-scratch disease . Brucella: brucellosis . Ehrlichia: tickborne © 2013 Pearson Education, Inc. The Alphaproteobacteria . Obligate intracellular parasites . Ehrlichia: tickborne, ehrlichiosis . Rickettsia: arthropod-borne, spotted fevers − R. prowazekii: epidemic typhus − R. typhi: endemic murine typhus − R. rickettsii: Rocky Mountain spotted fever © 2013 Pearson Education, Inc. Figure 11.1 Rickettsias. Slime layer Chicken Scattered embryo cell rickettsias Nucleus Masses of rickettsias in nucleus A rickettsial cell that has Rickettsias grow only within a host cell, just been released from a such as the chicken embryo cell shown host cell here. Note the scattered rickettsias within the cell and the compact masses of rickettsias in the cell nucleus. © 2013 Pearson Education, Inc. The Alphaproteobacteria . Wolbachia: live in insects and other animals © 2013 Pearson Education, Inc. Applications of Microbiology 11.1a Wolbachia are red inside the cells of this fruit fly embryo. © 2013 Pearson Education, Inc. Applications of Microbiology 11.1b In an infected pair, only female hosts can reproduce.