The Aerobic Bacteria, Erythrobacter Longus and Roseobacter
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Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas Sp
microorganisms Article Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5 Karel Kopejtka 1 , Yonghui Zeng 1,2, David Kaftan 1,3 , Vadim Selyanin 1, Zdenko Gardian 3,4 , Jürgen Tomasch 5,† , Ruben Sommaruga 6 and Michal Koblížek 1,* 1 Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, 379 81 Tˇreboˇn,Czech Republic; [email protected] (K.K.); [email protected] (Y.Z.); [email protected] (D.K.); [email protected] (V.S.) 2 Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark 3 Faculty of Science, University of South Bohemia, 370 05 Ceskˇ é Budˇejovice,Czech Republic; [email protected] 4 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 Ceskˇ é Budˇejovice,Czech Republic 5 Research Group Microbial Communication, Technical University of Braunschweig, 38106 Braunschweig, Germany; [email protected] 6 Laboratory of Aquatic Photobiology and Plankton Ecology, Department of Ecology, University of Innsbruck, 6020 Innsbruck, Austria; [email protected] * Correspondence: [email protected] † Present Address: Department of Molecular Bacteriology, Helmholtz-Centre for Infection Research, 38106 Braunschweig, Germany. Abstract: An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 Citation: Kopejtka, K.; Zeng, Y.; (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Ty- Kaftan, D.; Selyanin, V.; Gardian, Z.; rolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic Tomasch, J.; Sommaruga, R.; Koblížek, analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas M. Characterization of the Aerobic and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Anoxygenic Phototrophic Bacterium Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). -
Article-Associated Bac- Teria and Colony Isolation in Soft Agar Medium for Bacteria Unable to Grow at the Air-Water Interface
Biogeosciences, 8, 1955–1970, 2011 www.biogeosciences.net/8/1955/2011/ Biogeosciences doi:10.5194/bg-8-1955-2011 © Author(s) 2011. CC Attribution 3.0 License. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea C. Jeanthon1,2, D. Boeuf1,2, O. Dahan1,2, F. Le Gall1,2, L. Garczarek1,2, E. M. Bendif1,2, and A.-C. Lehours3 1Observatoire Oceanologique´ de Roscoff, UMR7144, INSU-CNRS – Groupe Plancton Oceanique,´ 29680 Roscoff, France 2UPMC Univ Paris 06, UMR7144, Adaptation et Diversite´ en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France 3CNRS, UMR6023, Microorganismes: Genome´ et Environnement, Universite´ Blaise Pascal, 63177 Aubiere` Cedex, France Received: 21 April 2011 – Published in Biogeosciences Discuss.: 5 May 2011 Revised: 7 July 2011 – Accepted: 8 July 2011 – Published: 20 July 2011 Abstract. Aerobic anoxygenic phototrophic (AAP) bac- detected in the eastern basin, reflecting the highest diver- teria play significant roles in the bacterioplankton produc- sity of pufM transcripts observed in this ultra-oligotrophic tivity and biogeochemical cycles of the surface ocean. In region. To our knowledge, this is the first study to document this study, we applied both cultivation and mRNA-based extensively the diversity of AAP isolates and to unveil the ac- molecular methods to explore the diversity of AAP bacte- tive AAP community in an oligotrophic marine environment. ria along an oligotrophic gradient in the Mediterranean Sea By pointing out the discrepancies between culture-based and in early summer 2008. Colony-forming units obtained on molecular methods, this study highlights the existing gaps in three different agar media were screened for the production the understanding of the AAP bacteria ecology, especially in of bacteriochlorophyll-a (BChl-a), the light-harvesting pig- the Mediterranean Sea and likely globally. -
Downloaded from the NCBI Genome Portal (Table S1)
J. Microbiol. Biotechnol. 2021. 31(4): 601–609 https://doi.org/10.4014/jmb.2012.12054 Review Assessment of Erythrobacter Species Diversity through Pan-Genome Analysis with Newly Isolated Erythrobacter sp. 3-20A1M Sang-Hyeok Cho1, Yujin Jeong1, Eunju Lee1, So-Ra Ko3, Chi-Yong Ahn3, Hee-Mock Oh3, Byung-Kwan Cho1,2*, and Suhyung Cho1,2* 1Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea 2KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea 3Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pan- genome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. -
Investigating Bacterial Community Structure Over Temporal and Spatial Scales in the Northwest Atlantic Ocean
INVESTIGATING BACTERIAL COMMUNITY STRUCTURE OVER TEMPORAL AND SPATIAL SCALES IN THE NORTHWEST ATLANTIC OCEAN by Jackie Zorz Submitted in partial fulfilment of the requirements for the degree of Master of Science at Dalhousie University Halifax, Nova Scotia February 2016 © Copyright by Jackie Zorz, 2016 Table of Contents List of Tables ...................................................................................................................... v List of Figures ................................................................................................................... vii Abstract ............................................................................................................................... x List of Abbreviations and Symbols Used .......................................................................... xi Acknowledgements ........................................................................................................... xii Chapter 1: Introduction ....................................................................................................... 1 Chapter 2: Bacterial Community Structure of the Scotian Shelf ........................................ 5 2.0 Abstract ......................................................................................................................... 5 2.1 Introduction ................................................................................................................... 5 2.2 Materials and Methods ............................................................................................... -
Diversity of Aerobic Anoxygenic Phototrophs and Rhodopsin-Containing Bacteria in the Surface Microlayer, Water Column and Epilithic Biofilms of Lake Baikal
microorganisms Article Diversity of Aerobic Anoxygenic Phototrophs and Rhodopsin-Containing Bacteria in the Surface Microlayer, Water Column and Epilithic Biofilms of Lake Baikal Agnia Dmitrievna Galachyants 1,*, Andrey Yurjevich Krasnopeev 1 , Galina Vladimirovna Podlesnaya 1 , Sergey Anatoljevich Potapov 1 , Elena Viktorovna Sukhanova 1 , Irina Vasiljevna Tikhonova 1 , Ekaterina Andreevna Zimens 1, Marsel Rasimovich Kabilov 2 , Natalia Albertovna Zhuchenko 1, Anna Sergeevna Gorshkova 1, Maria Yurjevna Suslova 1 and Olga Ivanovna Belykh 1,* 1 Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; [email protected] (A.Y.K.); [email protected] (G.V.P.); [email protected] (S.A.P.); [email protected] (E.V.S.); [email protected] (I.V.T.); [email protected] (E.A.Z.); [email protected] (N.A.Z.); [email protected] (A.S.G.); [email protected] (M.Y.S.) 2 Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia; [email protected] * Correspondence: [email protected] (A.D.G.); [email protected] (O.I.B.); Citation: Galachyants, A.D.; Tel.: +73-952-425-415 (A.D.G. & O.I.B.) Krasnopeev, A.Y.; Podlesnaya, G.V.; Potapov, S.A.; Sukhanova, E.V.; Abstract: The diversity of aerobic anoxygenic phototrophs (AAPs) and rhodopsin-containing bac- Tikhonova, I.V.; Zimens, E.A.; teria in the surface microlayer, water column, and epilithic biofilms of Lake Baikal was studied for Kabilov, M.R.; Zhuchenko, N.A.; the first time, employing pufM and rhodopsin genes, and compared to 16S rRNA diversity. -
Evolutionary) Change: Breathing New Life Into Microbiology GARY J
JOURNAL OF BACTERIOLOGY, Jan. 1994, p. 1-6 Vol. 176, No. 1 0021-9193/94/$04.00+ Copyright 1994, American Society for Microbiology MINIREVIEW The Winds of (Evolutionary) Change: Breathing New Life into Microbiology GARY J. OLSEN,'* CARL R. WOESE,1 AND ROSS OVERBEEK2 Department ofMicrobiology, University of Illinois, Urbana, Illinois 61801, and Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439-48012 Of all the spectacular changes that have transformed biology a bacterium"' (28). The problem with and the pernicious over the last several decades, the least touted, but ultimately nature of this dichotomy lay in the fact that the prokaryote was one of the most profound is that now under way in microbiol- initially defined negatively, in cytological terms. In other ogy. It is not simply that we are coming to see microbiology per words, prokaryotes lacked this or that feature characteristic of se in a new light but that we are coming to appreciate the the eukaryotic cell: even oil drops, or coacervates, could fit central roles microorganisms play in shaping the past and such a negative definition. Any virtue in the prokaryote- present environments of Earth and the nature of all life on this eukaryote dichotomy lay in what it could contribute to an planet. Because each organism is the product of its history, a understanding of the eukaryote, which might have evolved knowledge of phylogenetic relationships-of common evolu- through "prokaryotic" stages. With repetition (as catechism) tionary histories-is essential to understanding the nature of the prokaryote-eukaryote dichotomy served only to make any organism. -
Chitinases in the Tree of Life Ecological, Kinetic and Structural Studies of Archaeal and Marine Bacterial Chitinases
Chitinases in the tree of life Ecological, kinetic and structural studies of archaeal and marine bacterial chitinases. Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel vorgelegt von Tim Staufenberger Kiel, 2012 Referent: Prof. Dr. Johannes F. Imhoff Koreferent: Prof. Dr. Peter Schönheit Tag der mündlichen Prüfung: 13. April 2012 Zum Druck genehmigt: 13. April 2012 gez. Prof. Dr. Lutz Kipp, Dekan Eidesstattliche Erklärung Ich versichere an Eides statt, dass ich bis zum heutigen Tage weder an der Christian- Albrechts-Universität zu Kiel noch an einer anderen Hochschule ein Promotionsverfahren endgültig nicht bestanden habe oder mich in einem entsprechenden Verfahren befinde. Wei- terhin versichere ich an Eides statt, dass ich die Inanspruchnahme fremder Hilfen aufgeführt habe, sowie, dass ich die wörtlich oder inhaltlich aus anderen Quellen entnommenen Stellen als solche gekennzeichnet habe. Dies Abhandlung ist nach Inhalt und Form meine eigene Ar- beit, abgesehen von der Beratung durch meinen Betreuer. Die Arbeit wurde unter Einhaltung der Regeln guter wissenschaftlicher Praxis der Deutschen Forschungsgemeinschaft verfasst. Kiel, (Datum) Tim Staufenberger Ein Teil der während der Doktorarbeit erzielten Ergebnisse ist in den folgenden Artikeln veröffentlicht worden beziehungsweise wird zur Veröffentlichung eingereicht: Staufenberger, T., Imhoff, J.F. and Labes, A. First crenarchaeal chitinase found in Sulfolobus tokodaii. Microbiological Research, 2011 Staufenberger, T., Labes, A. and Imhoff, J.F. First expression of the chitinase from Halobac- terium salinarum in a mesohaline expression system Staufenberger, T., Labes, A. and Imhoff, J.F. Screening for chitinases - Combining molecular and cultivation techniques Staufenberger, T., Gärtner, A., Klokman, V., Heindl, H., Wiese, J., Labes, A. -
Staleya Guttiformis Gen. Nov., Sp. Nov. and Sulfitobacter Brevis Sp. Nov., Α-3-Proteobacteria from Hypersaline, Heliothermal and Meromictic Antarctic Ekho Lake
International Journal of Systematic and Evolutionary Microbiology (2000), 50, 303–313 Printed in Great Britain Staleya guttiformis gen. nov., sp. nov. and Sulfitobacter brevis sp. nov., α-3-Proteobacteria from hypersaline, heliothermal and meromictic antarctic Ekho Lake Matthias Labrenz,1 B. J. Tindall,2 Paul A. Lawson,3 Matthew D. Collins,3 Peter Schumann4 and Peter Hirsch1 Author for correspondence: Peter Hirsch. Tel: 49 431 880 4340. Fax: 49 431 880 2194. e-mail: phirsch!ifam.uni-kiel.de 1 Institut fu$ r Allgemeine Two Gram-negative, aerobic, pointed and budding bacteria were isolated from Mikrobiologie, Universita$ t various depths of hypersaline, heliothermal and meromictic Ekho Lake Kiel, D-24118 Kiel, Germany (Vestfold Hills, East Antarctica). 16S rRNA gene sequence comparisons show the isolates to be phylogenetically close to the genera Sulfitobacter and 2 DSMZ – Deutsche Sammlung von Roseobacter. Cells can be motile and contain storage granules. Sulfite addition Mikroorganismen und does not stimulate growth. Isolate EL-38T can produce bacteriochlorophyll a Zellkulturen GmbH, and has a weak requirement for sodium ions; polar lipids include D-38124 Braunschweig, Germany phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified amino lipid, but not diphosphatidylgycerol. The dominant fatty 3 Department of Food Science and Technology, acid is 18:1ω7c; other characteristic fatty acids are 3-OH 10:0, 3-OH 14:1, 16:0, University of Reading, 18:0, 18:2 and 19:1. The DNA base composition is 55<0–56<3 mol% GMC. Isolate Reading RG6 6AP, UK EL-162T has an absolute requirement for sodium ions. Diphosphatidylglycerol, 4 DSMZ – Deutsche phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an Sammlung von unidentified amino lipid are present in the polar lipids. -
Bacterial Diversity Associated with the Tunic of the Model Chordate Ciona Intestinalis
The ISME Journal (2014) 8, 309–320 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE Bacterial diversity associated with the tunic of the model chordate Ciona intestinalis Leah C Blasiak1, Stephen H Zinder2, Daniel H Buckley3 and Russell T Hill1 1Institute of Marine and Environmental Technology (IMET), University of Maryland Center for Environmental Science, Baltimore, MD, USA; 2Department of Microbiology, Cornell University, Ithaca, NY, USA and 3Department of Crop and Soil Sciences, Cornell University, Ithaca, NY, USA The sea squirt Ciona intestinalis is a well-studied model organism in developmental biology, yet little is known about its associated bacterial community. In this study, a combination of 454 pyrosequencing of 16S ribosomal RNA genes, catalyzed reporter deposition-fluorescence in situ hybridization and bacterial culture were used to characterize the bacteria living inside and on the exterior coating, or tunic, of C. intestinalis adults. The 454 sequencing data set demonstrated that the tunic bacterial community structure is different from that of the surrounding seawater. The observed tunic bacterial consortium contained a shared community of o10 abundant bacterial phylotypes across three individuals. Culture experiments yielded four bacterial strains that were also dominant groups in the 454 sequencing data set, including novel representatives of the classes Alphaproteobacteria and Flavobacteria. The relatively simple bacterial community and availability of dominant community members in culture make C. intestinalis a promising system in which to investigate functional interactions between host-associated microbiota and the development of host innate immunity. The ISME Journal (2014) 8, 309–320; doi:10.1038/ismej.2013.156; published online 19 September 2013 Subject Category: Microbe-microbe and microbe-host interactions Keywords: 16S rRNA gene; microbiome; tunicate; ascidian; symbiont; CARD-FISH Introduction C. -
Complete Genome Sequence of the Marine Carbazole-Degrading Bacterium Erythrobacter Sp
Complete Genome Sequence of the Marine Carbazole-Degrading Bacterium Erythrobacter sp. Strain KY5 著者 Felipe Vejarano, Chiho Suzuki-Minakuchi, Yoshiyuki Ohtsubo, Masataka Tsuda, Kazunori Okada, Hideaki Nojiria journal or Microbiology Resource Announcements publication title volume 7 number 8 page range e00935-18 year 2018-08-30 URL http://hdl.handle.net/10097/00125641 doi: 10.1128/MRA.00935-18 Creative Commons : 表示 http://creativecommons.org/licenses/by/3.0/deed.ja GENOME SEQUENCES crossm Complete Genome Sequence of the Marine Carbazole- Degrading Bacterium Erythrobacter sp. Strain KY5 Downloaded from Felipe Vejarano,a Chiho Suzuki-Minakuchi,a,b Yoshiyuki Ohtsubo,c Masataka Tsuda,c Kazunori Okada,a Hideaki Nojiria,b aBiotechnology Research Center, The University of Tokyo, Tokyo, Japan bCollaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan cGraduate School of Life Sciences, Tohoku University, Sendai, Japan ABSTRACT We determined the complete genome sequence of Erythrobacter sp. http://mra.asm.org/ strain KY5, a bacterium isolated from Tokyo Bay and capable of degrading carbazole. The genome consists of a 3.3-Mb circular chromosome that carries the gene clusters involved in carbazole degradation and biosynthesis of the photosynthetic apparatus of aerobic anoxygenic phototrophic bacteria. n recent years, bacterial strains capable of degrading carbazole, a carcinogenic and Imutagenic nitrogen-containing aromatic contaminant in fossil fuels (1–3), have been isolated from marine environments (4–8). While the nucleotide sequences of the on August 29, 2019 at TOHOKU UNIVERSITY carbazole-degradative car gene clusters have been determined, no complete genome sequences of these marine isolates have been obtained to date. -
Biodegradation of Poly(Ethylene Terephthalate) by Marine Bacteria, and Strategies for Its Enhancement
Biodegradation of poly(ethylene terephthalate) by marine bacteria, and strategies for its enhancement Submitted in total fulfillment of the requirements for the degree of Doctor of Philosophy by Hayden Webb Environmental and Biotechnology Centre Faculty of Life and Social Sciences Swinburne University of Technology May 2012 ___________________________________________________________________ Abstract Plastic accumulation, particularly in the world’s oceans is of increasing environmental concern. One of the major components of plastic waste is poly(ethylene terephthalate) (PET), a polymer frequently used in many applications, including textiles and food packaging. The current methods of disposal of PET waste, landfill, incineration and recycling, each have inherent drawbacks and limitations, and as such there is a need for efficient and cost-effective alternative. Biodegradation is an attractive option for environmentally friendly and efficient disposal of plastic waste. To date, no protocol has yet been developed to feasibly dispose of PET by biodegradation con a commercial scale. The current works aims to investigate the potential of PET biodegradation as a plastic disposal procedure by providing fundamental knowledge of biodegradation processes, and to develop strategies for improving biodegradation efficiency. PET samples were incubated in marine bacterial community enrichment cultures, and the dynamics of the polymer – bacterial interactions traced. Modifications to polymer surfaces were monitored using a variety of surface characterisation techniques, including atomic force microscopy (AFM), x-ray photoelectron spectroscopy (XPS) and infrared microspectroscopy using Synchrotron radiation. Taxonomic members of the bacterial enrichment cultures that developed in the presence of PET were recovered and identified via 16S rRNA gene sequencing. Marine bacteria were shown to possess the ability to degrade PET surfaces. -
Photosynthesis Is Widely Distributed Among Proteobacteria As Demonstrated by the Phylogeny of Puflm Reaction Center Proteins
fmicb-08-02679 January 20, 2018 Time: 16:46 # 1 ORIGINAL RESEARCH published: 23 January 2018 doi: 10.3389/fmicb.2017.02679 Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of PufLM Reaction Center Proteins Johannes F. Imhoff1*, Tanja Rahn1, Sven Künzel2 and Sven C. Neulinger3 1 Research Unit Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany, 2 Max Planck Institute for Evolutionary Biology, Plön, Germany, 3 omics2view.consulting GbR, Kiel, Germany Two different photosystems for performing bacteriochlorophyll-mediated photosynthetic energy conversion are employed in different bacterial phyla. Those bacteria employing a photosystem II type of photosynthetic apparatus include the phototrophic purple bacteria (Proteobacteria), Gemmatimonas and Chloroflexus with their photosynthetic relatives. The proteins of the photosynthetic reaction center PufL and PufM are essential components and are common to all bacteria with a type-II photosynthetic apparatus, including the anaerobic as well as the aerobic phototrophic Proteobacteria. Edited by: Therefore, PufL and PufM proteins and their genes are perfect tools to evaluate the Marina G. Kalyuzhanaya, phylogeny of the photosynthetic apparatus and to study the diversity of the bacteria San Diego State University, United States employing this photosystem in nature. Almost complete pufLM gene sequences and Reviewed by: the derived protein sequences from 152 type strains and 45 additional strains of Nikolai Ravin, phototrophic Proteobacteria employing photosystem II were compared. The results Research Center for Biotechnology (RAS), Russia give interesting and comprehensive insights into the phylogeny of the photosynthetic Ivan A. Berg, apparatus and clearly define Chromatiales, Rhodobacterales, Sphingomonadales as Universität Münster, Germany major groups distinct from other Alphaproteobacteria, from Betaproteobacteria and from *Correspondence: Caulobacterales (Brevundimonas subvibrioides).