UPI000BB50957 Cytochrome P450 [N993]
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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 -
Urban Forestry & Urban Greening
Urban Forestry & Urban Greening 60 (2021) 127065 Contents lists available at ScienceDirect Urban Forestry & Urban Greening journal homepage: www.elsevier.com/locate/ufug Long-term storage affects resource availability and occurrence of bacterial taxa linked to pollutant degradation and human health in landscaping materials Laura Soininen a, Mira Gronroos¨ a, Marja I. Roslund a, Aki Sinkkonen b,* a Ecosystems and Environment Research Programme, Department of Biological and Environmental Sciences, University of Helsinki, Niemenkatu 73, FI-15140 Lahti, Finland b Natural Resources Institute Finland, Horticulture Technologies, Itainen¨ Pitkakatu¨ 4, Turku, Finland ARTICLE INFO ABSTRACT Handling Editor: Wendy Chen Man-made landscaping materials form uppermost soil layers in urban green parks and lawns. To optimize effects of landscaping materials on biodiversity, plant growth and human health, it is necessary to understand microbial Keywords: community dynamics and physicochemical characteristics of the landscaping materials during storage. In the Community shifts current three-year study, the consequences of long-term storage on biotic and abiotic characteristics of eight Degradation potential commercial landscaping materials were evaluated. We hypothesized that long-term storage results in changes in Diversity microbial utilization of various energy sources and the diversity and relative abundance of bacteria with path Health-associated bacteria Nutrient availability ogenic or immunomodulatory characteristics. Three-year storage led to remarkable changes in bacterial com Resource utilization munity composition. Diversity and richness of taxa associated with immune modulation, particularly phylum Proteobacteria and class Gammaproteobacteria, decreased over time. Bacteroidetes decreased while Actino bacteria increased in relative abundance. Functional orthologs associated with biosynthesis of antibiotics and degradation of complex carbon sources increased during storage. -
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Proposal of Henriciella barbarensis sp. nov. and Henriciella algicola sp. nov., stalked species of the genus and emendation of the genus Henriciella. Item Type Article Authors Abraham, Wolf-Rainer; de Carvalho, Maira Peres; da Costa Neves, Thais Souto Paula; Memoria, Marina Torquato; Tartuci, Iago Toledo; Vancanneyt, Marc; Smit, John; Rohde, M Citation Proposal of Henriciella barbarensis sp. nov. and Henriciella algicola sp. nov., stalked species of the genus and emendation of the genus Henriciella. 2017, 67 (8):2804-2810 Int. J. Syst. Evol. Microbiol. DOI 10.1099/ijsem.0.002024 Journal International journal of systematic and evolutionary microbiology Download date 06/10/2021 03:29:09 Item License http://creativecommons.org/licenses/by-nc-sa/4.0/ Link to Item http://hdl.handle.net/10033/621103 1Proposal of Henriciella barbarensis sp. nov. and Henriciella algicola sp. nov., stalked 2species of the genus and emendation of the genus Henriciella 3 4Wolf-Rainer Abraham*1, Maira Peres de Carvalho1, Thaís Souto Paula da Costa Neves1, 5Marina Torquato Memória1, Iago Toledo Tartuci1, Marc Vancanneyt2, John Smit3, and 6Manfred Rohde4 7 81Helmholtz Centre for Infection Research, Chemical Microbiology, Inhoffenstrasse 7, 38124 9Braunschweig, Germany; 2BCCM/LMG Bacteria Collection, Universiteit Gent, K.L. 10Ledeganckstraat 35, Gent; Belgium; 3Dept. of Microbiology and Immunology, University of 11British Columbia, Vancouver, British Columbia, Canada; 4Central Facility for Microscopy, 12Helmholtz Centre for Infection Research 13 14 15Running title: Henricella barbarensis and H. algicola sp. nov. 16 17Subject category: New taxa; Subsection: Alphaproteobacteria 18 19Keywords: Henriciella, Hyphomonadaceae, lipids, marine bacteria 20 21 22*Corresponding author: 23Dr. Wolf-Rainer Abraham 24Helmholtz Centre for Infection Research, Chemical Microbiology 25Inhoffenstrasse 7, 38124 Braunschweig, Germany 26Tel. -
Bacteria Associated with Vascular Wilt of Poplar
Bacteria associated with vascular wilt of poplar Hanna Kwasna ( [email protected] ) Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu https://orcid.org/0000-0001- 6135-4126 Wojciech Szewczyk Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu Marlena Baranowska Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu Jolanta Behnke-Borowczyk Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu Research Article Keywords: Bacteria, Pathogens, Plantation, Poplar hybrids, Vascular wilt Posted Date: May 27th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-250846/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/30 Abstract In 2017, the 560-ha area of hybrid poplar plantation in northern Poland showed symptoms of tree decline. Leaves appeared smaller, turned yellow-brown, and were shed prematurely. Twigs and smaller branches died. Bark was sunken and discolored, often loosened and split. Trunks decayed from the base. Phloem and xylem showed brown necrosis. Ten per cent of trees died in 1–2 months. None of these symptoms was typical for known poplar diseases. Bacteria in soil and the necrotic base of poplar trunk were analysed with Illumina sequencing. Soil and wood were colonized by at least 615 and 249 taxa. The majority of bacteria were common to soil and wood. The most common taxa in soil were: Acidobacteria (14.757%), Actinobacteria (14.583%), Proteobacteria (36.872) with Betaproteobacteria (6.516%), Burkholderiales (6.102%), Comamonadaceae (2.786%), and Verrucomicrobia (5.307%).The most common taxa in wood were: Bacteroidetes (22.722%) including Chryseobacterium (5.074%), Flavobacteriales (10.873%), Sphingobacteriales (9.396%) with Pedobacter cryoconitis (7.306%), Proteobacteria (73.785%) with Enterobacteriales (33.247%) including Serratia (15.303%) and Sodalis (6.524%), Pseudomonadales (9.829%) including Pseudomonas (9.017%), Rhizobiales (6.826%), Sphingomonadales (5.646%), and Xanthomonadales (11.194%). -
Microbial Communities Associated with Farmed Genypterus Chilensis: Detection in Water Prior to Bacterial Outbreaks Using Culturing and High-Throughput Sequencing
animals Article Microbial Communities Associated with Farmed Genypterus chilensis: Detection in Water Prior to Bacterial Outbreaks Using Culturing and High-Throughput Sequencing Arturo Levican 1,* , Jenny C. Fisher 2, Sandra L. McLellan 3 and Ruben Avendaño-Herrera 4,5,6,* 1 Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Valparaíso 2373223, Chile 2 Biology Department, Indiana University Northwest, Gary, IN 46408, USA; fi[email protected] 3 School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53204, USA; [email protected] 4 Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar 2571015, Chile 5 Interdisciplinary Center for Aquaculture Research (INCAR), Concepción 4030000, Chile 6 Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Casablanca 2480000, Chile * Correspondence: [email protected] or [email protected] (A.L.); [email protected] or [email protected] (R.A.-H.) Received: 5 May 2020; Accepted: 15 June 2020; Published: 18 June 2020 Simple Summary: Aquaculture can supplement traditional fisheries to meet the demands of growing populations and may help reduce the overfishing of natural resources. The Chilean Aquaculture Diversification Program has encouraged technological developments for rearing native species such as the red conger eel (Genypterus chilensis), but intensive aquaculture practices have led to bacterial outbreaks of Vibrio spp. and Tenacibaculum spp. in farmed fish. This retrospective study analyzed the natural bacterial community associated with the recirculating seawater used in an experimental G. chilensis aquaculture facility to determine if outbreak strains could be identified through regular monitoring. -
A Taxonomic Framework for Emerging Groups of Ecologically
Spring S, Scheuner C, Göker M, Klenk H-P. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Frontiers in Microbiology 2015, 6, 281. Copyright: Copyright © 2015 Spring, Scheuner, Göker and Klenk. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. DOI link to article: http://dx.doi.org/10.3389/fmicb.2015.00281 Date deposited: 07/03/2016 This work is licensed under a Creative Commons Attribution 4.0 International License Newcastle University ePrints - eprint.ncl.ac.uk ORIGINAL RESEARCH published: 09 April 2015 doi: 10.3389/fmicb.2015.00281 A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data Stefan Spring 1*, Carmen Scheuner 1, Markus Göker 1 and Hans-Peter Klenk 1, 2 1 Department Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 School of Biology, Newcastle University, Newcastle upon Tyne, UK Edited by: Marcelino T. Suzuki, Sorbonne Universities (UPMC) and In recent years a large number of isolates were obtained from saline environments that are Centre National de la Recherche phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, Scientifique, France which were originally identified in seawater samples using cultivation independent Reviewed by: Fabiano Thompson, methods and are characterized by high seasonal abundances in coastal environments. -
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. -
Abstract Tracing Hydrocarbon
ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants. -
Characterization of Culturable Bacterial Flora in Yolk-Sac Larvae of Atlantic Halibut (Hippoglossus Hippoglossus L.) with “Gaping Jaws” Syndrome
Lat. Am. J. Aquat. Res., 42(1): 97-110, 2014 Bacterial flora and immune response in Atlantic halibut 97 DOI: 103856/vol42-issue1-fulltext-7 Research Article Characterization of culturable bacterial flora in yolk-sac larvae of Atlantic halibut (Hippoglossus hippoglossus L.) with “gaping jaws” syndrome Rocío Urtubia1, Pablo Gallardo2, Paris Lavin1, Nick Brown3 & Marcelo González1 1Laboratorio de Biorrecursos Antárticos, Departamento Científico, Instituto Antártico Chileno Plaza Muñoz Gamero 1055, Punta Arenas, Chile 2Centro de Cultivos Marinos Bahía Laredo, Facultad de Ciencias, Universidad de Magallanes Avda. Bulnes 01855, Punta Arenas, Chile 3Center for Cooperative Aquaculture Research, School of Marine Sciences, University of Maine 33 Salmon Farm Road Franklin, ME 05634-3144, USA ABSTRACT. One of the main problems facing Atlantic halibut hatcheries is the high mortality in the early stages of larval development. Several factors could be involved, for example: water quality, diseases or abnormalities, such as deformities occurring in the yolk sac larvae prior to exogenous feeding. The aim of this study was to identify differences in bacterial flora associated with yolk sac larvae with oral deformity. We also aimed to establish whether there is any relationship between bacterial strains and the “gaping jaws” syndrome. During our study, 74 bacterial isolates were obtained using three different nutrient media: Marine Agar, R2A and TCBS. Some of these bacteria were characterized using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and 16S rRNA sequencing. The immune response in larvae exhibiting the “gaping jaws” condition was measured by real time PCR. Our results showed significant differences in bacterial flora between normal and gaping larvae. -
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. -
Effects of Oenanthe Javanica on Nitrogen Removal in Free-Water
Article Effects of Oenanthe javanica on Nitrogen Removal in Free‐Water Surface Constructed Wetlands under Low‐Temperature Conditions Siyuan Song 1,2,†, Penghe Wang 1,3,†, Yongxia Liu 1, Dehua Zhao 1,2,*,∙Xin Leng 1,2 and Shuqing An 1,2 1 Institute of Wetland Ecology, School of Life Science, Nanjing University, Nanjing 210046, China; [email protected] (S.S.); [email protected] (P.W.); [email protected] (Y.L.); [email protected] (X.L.); [email protected] (S.A.) 2 Nanjing University Ecology Research Institute of Changshu (NJUecoRICH), Changshu 215500, China 3 Shanghai Investigation, Design & Research Institute Co., Ltd. (SIDRI), Shanghai 200434, China * Correspondence: [email protected] (D.Z.); [email protected] (X.L.); Tel.: +86‐25‐89681309 † Siyuan Song and Penghe Wang are co‐first authors. Received: 5 March 2019; Accepted: 8 April 2019; Published: 19 April 2019 Abstract: To investigate the role and microorganism‐related mechanisms of macrophytes and assess the feasibility of Oenanthe javanica (Blume) DC. in promoting nitrogen removal in free‐water surface constructed wetlands (FWS‐CWS) under low temperatures (<10 °C), pilot‐scale FWS‐CWS, planted with O. javanica, were set up and run for batch wastewater treatment in eastern China during winter. The presence of macrophytes observably improved the removal rates of ammonia nitrogen (65%– 71%) and total nitrogen (41%–48%) (p < 0.05), with a sharp increase in chemical oxygen demand concentrations (about 3–4 times). Compared to the unplanted systems, the planted systems not only exhibited higher richness and diversity of microorganisms, but also significantly higher abundances of bacteria, ammonia monooxygenase gene (amoA), nitrous oxide reductase gene (nosZ), dissimilatory cd1‐containing nitrite reductase gene (nirS), and dissimilatory copper‐containing nitrite reductase gene (nirK) in the substrate. -
Articles (Mansour Et Al., and Particularly on Aquatic Environments (Konrad and Booth, 2018)
Hydrol. Earth Syst. Sci., 24, 4257–4273, 2020 https://doi.org/10.5194/hess-24-4257-2020 © Author(s) 2020. This work is distributed under the Creative Commons Attribution 4.0 License. Coalescence of bacterial groups originating from urban runoffs and artificial infiltration systems among aquifer microbiomes Yannick Colin1,a, Rayan Bouchali1, Laurence Marjolet1, Romain Marti1, Florian Vautrin1,2, Jérémy Voisin1,2, Emilie Bourgeois1, Veronica Rodriguez-Nava1, Didier Blaha1, Thierry Winiarski2, Florian Mermillod-Blondin2, and Benoit Cournoyer1 1Research Team “Bacterial Opportunistic Pathogens and Environment”, UMR Ecologie Microbienne Lyon (LEM), Université Claude Bernard Lyon 1, VetAgro Sup, INRA 1418, CNRS 5557, University of Lyon, 69680 Marcy-l’Étoile, France 2UMR Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), CNRS 5023, ENTPE, Université Claude Bernard Lyon 1, University of Lyon, 69622 Villeurbanne, France apresent address: UMR Morphodynamique Continentale et Côtière, CNRS 6143, Normandie University, UNIROUEN, UNICAEN, 76000 Rouen, France Correspondence: Yannick Colin ([email protected]) and Benoit Cournoyer ([email protected]) Received: 26 January 2020 – Discussion started: 17 February 2020 Revised: 28 May 2020 – Accepted: 20 July 2020 – Published: 31 August 2020 Abstract. The invasion of aquifer microbial communities by enabled the tracking of bacterial species from 24 genera in- aboveground microorganisms, a phenomenon known as com- cluding Pseudomonas, Aeromonas and Xanthomonas, among munity coalescence, is likely to be exacerbated in groundwa- these communities. Several tpm sequence types were found ters fed by stormwater infiltration systems (SISs). Here, the to be shared between the aboveground and aquifer samples. incidence of this increased connectivity with upslope soils Reads related to Pseudomonas were allocated to 50 species, and impermeabilized surfaces was assessed through a meta- of which 16 were found in the aquifer samples.