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Granulicella Tundricola Type Strain MP5ACTX9T, an Acidobacteria from Tundra Soil
Standards in Genomic Sciences (2014) 9:449-461 DOI:10.4056/sig s.4648353 Complete genome sequence of Granulicella tundricola type strain MP5ACTX9T, an Acidobacteria from tundra soil Suman R. Rawat1, Minna K. Männistö 2, Valentin Starovoytov3, Lynne Goodwin4, Matt Nolan5 Loren Hauser6, Miriam Land 6, Karen Walston Davenport4, Tanja Woyke5 and Max M. Häggblom1* 1 Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey USA 2 Finnish Forest Research Institute, Rovaniemi, Finland 3 Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA. 4 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 5 DOE Joint Genome Institute, Walnut Creek, California, USA 6 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA *Correspondence: Max M Häggblom ([email protected]) Keywords: cold adapted, acidophile, tundra soil, Acidobacteria Granulicella tundricola strain MP5ACTX9T is a novel species of the genus Granulicella in subdivision 1 Acidobacteria. G. tundricola is a predominant member of soil bacterial communities, active at low temperatures and nutrient limiting conditions in Arctic alpine tundra. The organism is a cold-adapted acidophile and a versatile heterotroph that hydro- lyzes a suite of sugars and complex polysaccharides. Genome analysis revealed metabolic versatility with genes involved in metabolism and transport of carbohydrates, including g ene modules encoding for the carbohydrate-active enzyme (CAZy) families for the break- down, utilization and biosy nthesis of diverse structural and storag e polysaccharides suc h as plant based carbon polymers. The g enome of G. tundricola strain MP5ACTX9T consists of 4,309,151 bp of a circular chromosome and five meg a plasmids with a total genome con- tent of 5,503,984 bp. -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
Halanaerobaculum Jean Luc Cayol
Halanaerobaculum Jean Luc Cayol To cite this version: Jean Luc Cayol. Halanaerobaculum. Bergey’s Manual of Systematics of Archaea and Bacteria (BMSAB), Hoboken, New Jersey : Wiley, [2015]-, 2019, 10.1002/9781118960608.gbm01725. hal- 02883868 HAL Id: hal-02883868 https://hal.archives-ouvertes.fr/hal-02883868 Submitted on 29 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. 1 gbm01725 2 3 Halanaerobaculum 4 5 Hedi, Fardeau, Sadfi, Boudabous, Ollivier and Cayol 2009, 317 VP 6 7 Jean-Luc Cayol 8 9 Aix Marseille Université, IRD, Université de Toulon, CNRS, Mediterranean Institute of 10 Oceanography (MIO), UM 110, 13288 Marseille cedex 9, France 11 12 Hal.an.ae.ro.ba’cu.lum. Gr. masc. n. hals, salt; Gr. pref. an, not; Gr. masc. or fem. n. aer, air; 13 L. neut. n. baculum, stick; N.L. neut. n. Halanaerobaculum, salt stick not living in air. 14 15 Abstract 16 The genus Halanaerobaculum comprises one species with validly published name, 17 Halanaerobaculum tunisiense, which was isolated from hypersaline surface sediments of El- 18 Djerid Chott, Tunisia. The genus is halophilic, strict anaerobic and chemoorganotrophic. The 19 genus Halanaerobaculum belongs to the family Halobacteroidaceae; order Halanaerobiales; 20 class Clostridia. -
The Round Goby (Neogobius Melanostomus):A Review of European and North American Literature
ILLINOI S UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN PRODUCTION NOTE University of Illinois at Urbana-Champaign Library Large-scale Digitization Project, 2007. CI u/l Natural History Survey cF Library (/4(I) ILLINOIS NATURAL HISTORY OT TSrX O IJX6V E• The Round Goby (Neogobius melanostomus):A Review of European and North American Literature with notes from the Round Goby Conference, Chicago, 1996 Center for Aquatic Ecology J. Ei!en Marsden, Patrice Charlebois', Kirby Wolfe Illinois Natural History Survey and 'Illinois-Indiana Sea Grant Lake Michigan Biological Station 400 17th St., Zion IL 60099 David Jude University of Michigan, Great Lakes Research Division 3107 Institute of Science & Technology Ann Arbor MI 48109 and Svetlana Rudnicka Institute of Fisheries Varna, Bulgaria Illinois Natural History Survey Lake Michigan Biological Station 400 17th Sti Zion, Illinois 6 Aquatic Ecology Technical Report 96/10 The Round Goby (Neogobius melanostomus): A Review of European and North American Literature with Notes from the Round Goby Conference, Chicago, 1996 J. Ellen Marsden, Patrice Charlebois1, Kirby Wolfe Illinois Natural History Survey and 'Illinois-Indiana Sea Grant Lake Michigan Biological Station 400 17th St., Zion IL 60099 David Jude University of Michigan, Great Lakes Research Division 3107 Institute of Science & Technology Ann Arbor MI 48109 and Svetlana Rudnicka Institute of Fisheries Varna, Bulgaria The Round Goby Conference, held on Feb. 21-22, 1996, was sponsored by the Illinois-Indiana Sea Grant Program, and organized by the -
Using Stable Isotopes to Investigate Movement of Fish in Rice Paddy Fields
Int Aquat Res DOI 10.1007/s40071-015-0105-y ORIGINAL RESEARCH Using stable isotopes to investigate movement of fish in rice paddy fields Jaeyong Lee . Jae-Ok Kim . Jeffrey S. Owen . Bomchul Kim Received: 7 January 2015 / Accepted: 17 April 2015 Ó The Author(s) 2015. This article is published with open access at Springerlink.com Abstract We evaluated movement of fish, especially Misgurnus spp. (loach), in paddy fields and irrigation ponds by conducting an inventory of d13C and d15N of fish, potential food sources, and soil organic matter in two irrigation pond–paddy field systems in Korea. The pond–paddy systems differ with respect to the presence or the absence of a ridge between the paddy field and the irrigation pond and also whether or not livestock are present in their watersheds. The ridge prevents the free movement of fish between paddy field and irrigation pond habitats in one of the pond–paddy watersheds, but not in the other watershed. We found differences in loach d13C and d15N inhabiting the paddy fields compared to those in loach d13C and d15Nin the irrigation ponds. In irrigation ponds, loach d13C was lower in September (average -27.9 and -27.7 %) compared to July (average -26.2 and -26.3 %) in the watershed with a ridge (station 1) and without a ridge (station 6), respectively. Loach d13C in irrigation ponds in September was similar to loach d13C in the paddy field in July at both sampling sites, indicating loach might have moved into irrigation pond from paddy field. Loach d15N in the watershed with livestock was significantly higher (average 18.2 %) in the irrigation ponds than loach d15N in the watershed with no livestock present (average 11.3 %), probably reflecting higher anthropogenic nitrogen inputs from livestock. -
An Integrated Study on Microbial Community in Anaerobic Digestion Systems
An Integrated Study on Microbial Community in Anaerobic Digestion Systems DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Yueh-Fen Li Graduate Program in Environmental Science The Ohio State University 2013 Dissertation Committee: Dr. Zhongtang Yu, Advisor Dr. Brian Ahmer Dr. Richard Dick Dr. Olli Tuovinen Copyrighted by Yueh-Fen Li 2013 Abstract Anaerobic digestion (AD) is an attractive microbiological technology for both waste treatment and energy production. Microorganisms are the driving force for the whole transformation process in anaerobic digesters. However, the microbial community underpinning the AD process remains poorly understood, especially with respect to community composition and dynamics in response to variations in feedstocks and operations. The overall objective was to better understand the microbiology driving anaerobic digestion processes by systematically investigating the diversity, composition and succession of microbial communities, both bacterial and archaeal, in anaerobic digesters of different designs, fed different feedstocks, and operated under different conditions. The first two studies focused on propionate-degrading bacteria with an emphasis on syntrophic propionate-oxidizing bacteria. Propionate is one of the most important intermediates and has great influence on AD stability in AD systems because it is inhibitory to methanogens and it can only be metabolized through syntrophic propionate- oxidizing acetogenesis under methanogenic conditions. In the first study (chapter 3), primers specific to the propionate-CoA transferase gene (pct) were designed and used to construct clone libraries, which were sequenced and analyzed to investigate the diversity and distribution of propionate-utilizing bacteria present in the granular and the liquid portions of samples collected from four digesters of different designs, fed different ii feedstocks, and operated at different temperatures. -
EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated -
Marine Sediments Illuminate Chlamydiae Diversity and Evolution
Supplementary Information for: Marine sediments illuminate Chlamydiae diversity and evolution Jennah E. Dharamshi1, Daniel Tamarit1†, Laura Eme1†, Courtney Stairs1, Joran Martijn1, Felix Homa1, Steffen L. Jørgensen2, Anja Spang1,3, Thijs J. G. Ettema1,4* 1 Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden 2 Department of Earth Science, Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway 3 Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, NL-1790 AB Den Burg, The Netherlands 4 Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands. † These authors contributed equally * Correspondence to: Thijs J. G. Ettema, Email: [email protected] Supplementary Information Supplementary Discussions ............................................................................................................................ 3 1. Evolutionary relationships within the Chlamydiae phylum ............................................................................. 3 2. Insights into the evolution of pathogenicity in Chlamydiaceae ...................................................................... 8 3. Secretion systems and flagella in Chlamydiae .............................................................................................. 13 4. Phylogenetic diversity of chlamydial nucleotide transporters. .................................................................... -
A Case Study of Weatherfish (Misgurnus Fossilis)
www.nature.com/scientificreports OPEN The role of detritivory as a feeding tactic in a harsh environment – a case study of weatherfsh Received: 31 July 2018 Accepted: 28 May 2019 (Misgurnus fossilis) Published: xx xx xxxx Kacper Pyrzanowski 1, Grzegorz Zięba 1, Małgorzata Dukowska1, Carl Smith1,2,3 & Mirosław Przybylski1 The weatherfsh (Misgurnus fossilis) is a species that is tolerant of unfavourable environmental conditions and can survive low dissolved oxygen concentrations and high water temperatures. Although this species occurs across almost the whole of Europe, and is protected in many countries, relatively little is known regarding its ecology. To determine the diet of weatherfsh, 120 individuals from an artifcial drainage canal in central Poland were collected in two seasons (spring and late summer) with contrasting abiotic condition (oxygen concentration, water temperature and transparency). Analysis of gut fullness showed that weatherfsh consumed a greater quantity of food in spring (0.92 ± 0.90) compared with summer (0.20 ± 0.26). Contrary to other cobitid taxa, weatherfsh fed actively during daytime in both seasons. An estimate of the importance of each dietary component indicated that the most important food categories were chironomids, copepods, Asellus aquaticus and detritus. SIMPER analysis indicated that these four categories together constituted over 65.8% of cumulative dissimilarity in the diet between seasons. Additionally, trophic niche breadth difered signifcantly between seasons. The study demonstrated that the weatherfsh is an opportunistic feeder, consuming large quantities of detritus despite possessing a gut morphology that is atypical of a detritivore. The quantity of detritus in the gut of weatherfsh was positively associated with fsh total length and varied seasonally, with a greater quantity of detritus in the diet in late summer. -
Microbial Diversity of Soda Lake Habitats
Microbial Diversity of Soda Lake Habitats Von der Gemeinsamen Naturwissenschaftlichen Fakultät der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Susanne Baumgarte aus Fritzlar 1. Referent: Prof. Dr. K. N. Timmis 2. Referent: Prof. Dr. E. Stackebrandt eingereicht am: 26.08.2002 mündliche Prüfung (Disputation) am: 10.01.2003 2003 Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Gemeinsamen Naturwissenschaftlichen Fakultät, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Baumgarte, S., Moore, E. R. & Tindall, B. J. (2001). Re-examining the 16S rDNA sequence of Halomonas salina. International Journal of Systematic and Evolutionary Microbiology 51: 51-53. Tagungsbeiträge Baumgarte, S., Mau, M., Bennasar, A., Moore, E. R., Tindall, B. J. & Timmis, K. N. (1999). Archaeal diversity in soda lake habitats. (Vortrag). Jahrestagung der VAAM, Göttingen. Baumgarte, S., Tindall, B. J., Mau, M., Bennasar, A., Timmis, K. N. & Moore, E. R. (1998). Bacterial and archaeal diversity in an African soda lake. (Poster). Körber Symposium on Molecular and Microsensor Studies of Microbial Communities, Bremen. II Contents 1. Introduction............................................................................................................... 1 1.1. The soda lake environment ................................................................................. -
Invasive Species and Your Business Join Us in Protecting Minnesota Waters | Sell Only Low-Risk Species and Help to Prevent Releases and Escapes
INVASIVE SPECIES AND YOUR BUSINESS JOIN US IN PROTECTING MINNESOTA WATERS | SELL ONLY LOW-RISK SPECIES AND HELP TO PREVENT RELEASES AND ESCAPES The invasive plants and animals pictured here have been documented in the pet and aquarium trades and are illegal to possess or sell in Minnesota. Invasive species are non-native species that present risks to Minnesota’s fish, wildlife and plant communities, water quality and recreation or human health. Please note, this is not a complete list of species that are illegal to possess or sell. DO NOT OFFER THESE SPECIES FOR SALE AT YOUR BUSINESS! AQUATIC PLANTS Visit dnr.state.mn.us/invasives/pet-and-aquarium-businesses.html for a complete list. Indian swampweed, dwarf hygrophila Giant salvinia Brittle naiad (Hygrophila polysperma) (Salvinia molesta) (Najas minor) Hydrilla Water soldier, water aloe (Hydrilla verticillata) (Stratiotes aloides) Please remind your customers not to release aquarium pets and plants into the wild! Remember: It is illegal to release most non-native animals and plants into a free-living state in Minnesota. PHOTO CREDITS Indian swampweed, dwarf hygrophila – U.S. Geological Survey Giant salvinia – Vic Ramey, UF/IFAS Center for Aquatic and Invasive Plants Brittle naiad – Mark Warman Hydrilla – L. Gettys, UF/IFAS Center for Aquatic and Invasive Plants DO NOT OFFER THESE SPECIES FOR SALE AT YOUR BUSINESS! FISH, CRAYFISH AND INVERTEBRATES Visit dnr.state.mn.us/invasives/pet-and-aquarium-businesses.html for a complete list. Oriental weatherfish, pond loach, dojo loach Western mosquitofish *Eastern mosquitofish (Misgurnus anguillicaudataus) (Gambusia affinis) (Gambusia holbrooki) Stone moroko Northern snakehead *Nile perch, Victoria perch, African snook (Pseudorasbora parva) (Channa argus), *Channa spp. -
Abricot (M) Meruňka
aberace aberration amorfní amorphous, shapeless abnormita abnormality, abnormity amortizér shock absorber, shock-absorber abort abortion amur amur abortivní abortive, undeveloped amur bílý grass carp, white amur abortivní mitóza abortive mitosis amur černý black carp absolutní plodnost absolute fertility anadromní ryby anadromous fish acentrická inverze acentric inversion anafázický anaphasic acentrický acentric anafázický pohyb anaphase number acentrický chromozóm acentric analog analogue chromosome aneuploid aneuploid adaptér k rychlé výměně splávku float aneuploidie aneuploidy adaptor anisomagie anisogamy adheze adhesion anofeles anopheles, anopheles mosquito aditiva additives anténní splávek antenna float aditivní účinek additive effect antibiotika antibiotics afinita affinity antigen antigen aglutinace agglutination antikinker antikink device achromatická figura achromatic figure antimutagen antimutagene achromatický achromatic antimutagenní antimutagenic achromazie achromasie apomiktický apomictic akce action archiplasma archiplasm, archoplasm akce prutu v dolním konci butt action arktický arctic akce prutu ve špičce tip action artefakt artefa akcesorní accessory asociace jader nuclear association akcesorní chromozóm accessory aster aster chromosome, B chromosome asymetrický bivalent skew bivalent aklimatizace ryb acclimatization of fish asynapse asynapse, asyndesis akrocentrický acrocentric atavismus atavism aktivace activation atavistický atavistic aktivita activity aterina Bleekerova flathead silverside akutní příznak acute symptom