S Which Are Thought to Belong to the Β-Subclass of The
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Aerobic Anoxygenic Photosynthesis Genes and Operons in Uncultured Bacteria in the Delaware River
Blackwell Science, LtdOxford, UKEMIEnvironmental Microbiology 1462-2912Society for Applied Microbiology and Blackwell Publishing Ltd, 200571218961908Original ArticleDelaware River AAP bacteriaL. A. Waidner and D. L. Kirchman Environmental Microbiology (2005) 7(12), 1896–1908 doi:10.1111/j.1462-2920.2005.00883.x Aerobic anoxygenic photosynthesis genes and operons in uncultured bacteria in the Delaware River Lisa A. Waidner and David L. Kirchman* AAP bacteria photosynthesize with the use of bacterio- University of Delaware, College of Marine Studies, 700 chlorophyll a (bchl a), but do not evolve oxygen (Yurkov Pilottown Road, Lewes, DE 19958, USA. and Beatty, 1998). A more thorough understanding of AAP bacteria is needed to elucidate their role in aquatic environments. Summary The diversity of marine AAP bacteria is often explored Photosynthesis genes and operons of aerobic anox- with the gene encoding the alpha subunit of the photosyn- ygenic photosynthetic (AAP) bacteria have been thetic reaction centre, puf M (Beja et al., 2002; Oz et al., examined in a variety of marine habitats, but genomic 2005; Schwalbach and Fuhrman, 2005). On the basis of information about freshwater AAP bacteria is lacking. puf M, AAP bacteria have been classified into two clusters The goal of this study was to examine photosynthesis of proteobacteria (Nagashima et al., 1997). One consists genes of AAP bacteria in the Delaware River. In a of a mixture of alpha-1 and alpha-2, beta- and gamma- fosmid library, we found two clones bearing photo- proteobacteria, referred to here as the ‘mixed cluster’ synthesis gene clusters with unique gene content and (Nagashima et al., 1997). The other cluster contains the organization. -
Cluster 1 Cluster 3 Cluster 2
5 9 Luteibacter yeojuensis strain SU11 (Ga0078639_1004, 2640590121) 7 0 Luteibacter rhizovicinus DSM 16549 (Ga0078601_1039, 2631914223) 4 7 Luteibacter sp. UNCMF366Tsu5.1 (FG06DRAFT_scaffold00001.1, 2595447474) 5 5 Dyella japonica UNC79MFTsu3.2 (N515DRAFT_scaffold00003.3, 2558296041) 4 8 100 Rhodanobacter sp. Root179 (Ga0124815_151, 2699823700) 9 4 Rhodanobacter sp. OR87 (RhoOR87DRAFT_scaffold_21.22, 2510416040) Dyella japonica DSM 16301 (Ga0078600_1041, 2640844523) Dyella sp. OK004 (Ga0066746_17, 2609553531) 9 9 9 3 Xanthomonas fuscans (007972314) 100 Xanthomonas axonopodis (078563083) 4 9 Xanthomonas oryzae pv. oryzae KACC10331 (NC_006834, 637633170) 100 100 Xanthomonas albilineans USA048 (Ga0078502_15, 2651125062) 5 6 Xanthomonas translucens XT123 (Ga0113452_1085, 2663222128) 6 5 Lysobacter enzymogenes ATCC 29487 (Ga0111606_103, 2678972498) 100 Rhizobacter sp. Root1221 (056656680) Rhizobacter sp. Root1221 (Ga0102088_103, 2644243628) 100 Aquabacterium sp. NJ1 (052162038) Aquabacterium sp. NJ1 (Ga0077486_101, 2634019136) Uliginosibacterium gangwonense DSM 18521 (B145DRAFT_scaffold_15.16, 2515877853) 9 6 9 7 Derxia lacustris (085315679) 8 7 Derxia gummosa DSM 723 (H566DRAFT_scaffold00003.3, 2529306053) 7 2 Ideonella sp. B508-1 (I73DRAFT_BADL01000387_1.387, 2553574224) Zoogloea sp. LCSB751 (079432982) PHB-accumulating bacterium (PHBDraf_Contig14, 2502333272) Thiobacillus sp. 65-1059 (OJW46643.1) 8 4 Dechloromonas aromatica RCB (NC_007298, 637680051) 8 4 7 7 Dechloromonas sp. JJ (JJ_JJcontig4, 2506671179) Dechloromonas RCB 100 Azoarcus -
Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor
Invitation for the public defense of my thesis Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic and biochemistry Physiology bacteria that use chlorate and/or nitrate as electron acceptor as electron nitrate and/or use chlorate that bacteria Physiology and biochemistry Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic hydrocarbon- degrading bacteria that bacteria that use chlorate and/or nitrate as electron acceptor use chlorate and/or nitrate as electron acceptor The public defense of my thesis will take place in the Aula of Wageningen University (Generall Faulkesweg 1, Wageningen) on December 18 2013 at 4:00 pm. This defense is followed by a reception in Café Carré (Vijzelstraat 2, Wageningen). Margreet J. Oosterkamp J. Margreet Paranimphs Ton van Gelder ([email protected]) Aura Widjaja Margreet J. Oosterkamp ([email protected]) Marjet Oosterkamp (911 W Springfield Ave Apt 19, Urbana, IL 61801, USA; [email protected]) Omslag met flap_MJOosterkamp.indd 1 25-11-2013 5:58:31 Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor Margreet J. Oosterkamp Thesis-MJOosterkamp.indd 1 25-11-2013 6:42:09 Thesis committee Thesis supervisor Prof. dr. ir. A. J. M. Stams Personal Chair at the Laboratory of Microbiology Wageningen University Thesis co-supervisors Dr. C. M. Plugge Assistant Professor at the Laboratory of Microbiology Wageningen University Dr. P. J. Schaap Assistant Professor at the Laboratory of Systems and Synthetic Biology Wageningen University Other members Prof. dr. L. Dijkhuizen, University of Groningen Prof. dr. H. J. Laanbroek, University of Utrecht Prof. -
Structure and Evolution of Chlorate Reduction Composite Transposons
RESEARCH ARTICLE Structure and Evolution of Chlorate Reduction Composite Transposons Iain C. Clark,a Ryan A. Melnyk,b Anna Engelbrektson,b John D. Coatesb Department of Civil and Environmental Engineeringa and Department of Plant and Microbial Biology,b University of California, Berkeley, California, USA ABSTRACT The genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. A newly isolated chlorate-reducing bacterium (Shewanella algae ACDC) and three previously isolated strains (Ideonella dechlora- tans, Pseudomonas sp. strain PK, and Dechloromarinus chlorophilus NSS) were genome sequenced and compared to published sequences (Alicycliphilus denitrificans BC plasmid pALIDE01 and Pseudomonas chloritidismutans AW-1). De novo assembly of genomes failed to join regions adjacent to genes involved in chlorate reduction, suggesting the presence of repeat regions. Using a bioinformatics approach and finishing PCRs to connect fragmented contigs, we discovered that chlorate reduction genes are flanked by insertion sequences, forming composite transposons in all four newly sequenced strains. These insertion sequences delineate regions with the potential to move horizontally and define a set of genes that may be important for chlorate reduction. In addition to core metabolic components, we have highlighted several such genes through comparative analysis and visualiza- tion. Phylogenetic analysis places chlorate reductase within a functionally diverse clade of type II dimethyl sulfoxide (DMSO) reductases, part of a larger family of enzymes with reactivity toward chlorate. Nucleotide-level forensics of regions surrounding chlorite dismutase (cld), as well as its phylogenetic clustering in a betaproteobacterial Cld clade, indicate that cld has been mobi- lized at least once from a perchlorate reducer to build chlorate respiration. -
Roseateles Depolymerans Gen. Nov., Sp. Nov., a New Bacteriochlorophyll A-Containing Obligate Aerobe Belonging to the P=Subclassof the Pro Teobacteria
International Journal of Systematic Bacteriology (1 999), 49,449-457 Printed in Great Britain Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the P=subclassof the Pro teobacteria Tetsushi Suyama,’ Toru Shigematsu,’ Shinichi Takaichit2 Yoshinobu Nodasakaf3Seizo F~jikawa,~Hiroyuki Hosoya,’ Yutaka Tokiwa,’ Takahiro Kanagawa’ and Satoshi Hanadal Author for correspondence : Tetsushi Suyama. Tel : + 8 1 298 54 659 1. Fax : + 8 1 298 54 6587. e-mail: [email protected] ~~ 1 National Institute of Strains 61AT(T = type strain) and 6IB2, the first bacteriochlorophyll (BChI) a- Bioscience and Human containing obligate aerobes to be classified in the /?-subclassof the Technology, 1-1 Higashi, Tsukuba, lbaraki Profeobacteria, were isolated from river water. The strains were originally 305-8566,Japan isolated as degraders of poly(hexamethy1ene carbonate) (PHC). The organisms * Biological Laboratory, can utilize PHC and some other biodegradable plastics. The strains grow only Nippon Medical School, under aerobic conditions. Good production of BChl a and carotenoid pigments Kawasaki 21 1-0063,Japan is achieved on PHC agar plates and an equivalent production is observed under 3.4 School of Dentistry3 and oligotrophic conditions on agar medium. Spectrometric results suggest that Institute of Low BChl a is present in light-harvesting complex I and the photochemical reaction Temperature Science4, Hokkaido University, centre. The main carotenoids are spirilloxanthin and its precursors. Analysis of Sapporo 060, Japan the 165 rRNA gene sequence indicated that the phylogenetic positions of the two strains are similar to each other and that their closest relatives are the genera Rubriwiwax, ldeonella and Leptothrix with similarities of 96.3, 962 and 96-1%, respectively. -
Biofilm Composition and Threshold Concentration for Growth Of
PUBLIC AND ENVIRONMENTAL HEALTH MICROBIOLOGY crossm Biofilm Composition and Threshold Concentration for Growth of Legionella pneumophila on Surfaces Exposed to Flowing Warm Tap Water without Disinfectant Downloaded from Dick van der Kooij,a Geo L. Bakker,b Ronald Italiaander,a Harm R. Veenendaal,a Bart A. Wullingsa KWR Watercycle Research Institute, Nieuwegein, the Netherlandsa; Vitens NV, Zwolle, the Netherlandsb ABSTRACT Legionella pneumophila in potable water installations poses a potential Received 1 October 2016 Accepted 13 health risk, but quantitative information about its replication in biofilms in relation http://aem.asm.org/ to water quality is scarce. Therefore, biofilm formation on the surfaces of glass and December 2016 Accepted manuscript posted online 6 chlorinated polyvinyl chloride (CPVC) in contact with tap water at 34 to 39°C was in- January 2017 vestigated under controlled hydraulic conditions in a model system inoculated with Citation van der Kooij D, Bakker GL, biofilm-grown L. pneumophila. The biofilm on glass (average steady-state concen- Italiaander R, Veenendaal HR, Wullings BA. tration, 23 Ϯ 9 pg ATP cmϪ2) exposed to treated aerobic groundwater (0.3 mg C 2017. Biofilm composition and threshold concentration for growth of Legionella Ϫ1 Ϫ1 liter ;1 g assimilable organic carbon [AOC] liter ) did not support growth of the pneumophila on surfaces exposed to flowing organism, which also disappeared from the biofilm on CPVC (49 Ϯ 9 pg ATP cmϪ2) warm tap water without disinfectant. Appl Ϫ2 Environ Microbiol 83:e02737-16. https:// after initial growth. L. pneumophila attained a level of 4.3 log CFU cm in the bio- on February 16, 2017 by guest doi.org/10.1128/AEM.02737-16. -
Malaysian Journal of Microbiology, Vol 13(2) June 2017, Pp
Malaysian Journal of Microbiology, Vol 13(2) June 2017, pp. 139-146 Malaysian Journal of Microbiology Published by Malaysian Society for Microbiology (In since 2011) Effect of biofertilizer on the diversity of nitrogen - fixing bacteria and total bacterial community in lowland paddy fields in Sukabumi West Java, Indonesia Masrukhin1, Iman Rusmana2*, Nisa Rachmania Mubarik3 1 Microbiology Study Program, Department of Biology, Bogor Agricultural University, Dramaga- Bogor 16680, West Java, Indonesia. 2,3Department of Biology, Faculty of Mathematic and Natural Sciences, Bogor Agricultural Univerisity, Dramaga- Bogor 16680, West Java, Indonesia. Email: [email protected] Received 18 August 2016; Received in revised form 23 September 2016; Accepted 9 November 2016 ABSTRACT Aims: Some of methanotrophic bacteria and nitrous oxide (N2O) reducing bacteria have been proven able to support the plant growth and increase productivity of paddy. However, the effect of application of the methanotrophics and N2O reducing bacteria as a biofertilizer to indigenous nitrogen-fixing bacteria and total bacterial community are still not well known yet. The aim of the study was to analyze the diversity of nitrogen-fixing bacteria and total bacterial communty in lowland paddy soils. Methodology and results: Soil samples were taken from lowland paddy fields in Pelabuhan Ratu, Sukabumi, West Java, Indonesia. There were two treatments applied to the paddy field i.e biofertilizer-treated field (biofertilizer with 50 kg/ha NPK) and control (250 kg/ha NPK fertilizer). There were nine different nifH bands which were successfully sequenced and most of them were identified as unculturable bacteria and three of them were closely related to Sphingomonas sp., Magnetospirillum sp. -
1 Possible Drivers in Endophyte Diversity and Transmission in The
Possible Drivers in Endophyte Diversity and Transmission in the Tomato Plant Bacterial Microbiome Thesis Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By Ana María Vázquez, B.S. Graduate Program in Plant Pathology The Ohio State University 2020 Thesis Committee Dr. María Soledad Benítez-Ponce, Advisor Dr. Christine Sprunger Dr. Jonathan M. Jacobs 1 Copyrighted by Ana María Vázquez 2020 2 Abstract It has been documented that beneficial plant-associated bacteria have contributed to disease suppression, growth promotion, and tolerance to abiotic stresses. Advances in high-throughput sequencing have allowed an increase in research regarding bacterial endophytes, which are microbes that colonize the interior of plants without causing disease. Practices associated with minimizing the use of off-farm resources, such as reduced tillage regimes and crop rotations, can cause shifts in plant-associated bacteria and its surrounding agroecosystem. Integrated crop–livestock systems are an option that can provide environmental benefits by implementing diverse cropping systems, incorporating perennial and legume forages and adding animal manure through grazing livestock. It has been found that crop-livestock systems can increase soil quality and fertility, reduce cost of herbicide use and improve sustainability, especially for farmers in poorer areas of the world. This work explores how crop-livestock systems that integrate chicken rotations can impact tomato plant growth, as well as soil and endophytic bacterial communities. Tomato plants were subjected to greenhouse and field studies where biomass was assessed, and bacterial communities were characterized through culture- dependent and -independent approaches. -
Metagenomic Profiling of Microbial Metal Interaction in Red Sea Deep-Anoxic Brine Pools
The American University in Cairo School of Sciences and Engineering Metagenomic Profiling of Microbial Metal Interaction in Red Sea Deep-Anoxic Brine Pools A Thesis Submitted to The Biotechnology Graduate Program in partial fulfillment of the requirements for the degree of Master of Science in Biotechnology By Mina Magdy Abdelsayed Hanna Under the supervision of Dr. Rania Siam Associate Professor, Chair-Biology Department The American University in Cairo Spring 2015 The American University in Cairo Metagenomic profiling of microbial metal interaction in Red Sea deep- anoxic brine pools A Thesis Submitted by Mina Magdy Abdelsayed Hanna To the Biotechnology Graduate Program Spring 2015 In partial fulfillment of the requirements for the degree of Master of Science in Biotechnology Has been approved by Dr. Rania Siam Thesis Committee Chair / Supervisor Associate Professor and Chair, Biology Department, AUC Dr. Ahmed Moustafa Thesis Committee Internal Examiner Associate Professor and Director, Biotechnology Graduate Program Biology Department, AUC Dr. Ramy Aziz Thesis Committee External Examiner Assistant Professor, Faculty of Pharmacy, Cairo University Dr. Andreas Kakarougkas Thesis Committee Moderator Assistant Professor, Biology Department, AUC ______________ ____________ ____________ ___________ Program Director Date Dean Date II DEDICATION This work is dedicated to my beloved mother and sister who always supported and encouraged me to fulfill my dreams and achieve more success in my life. This work is also dedicated to the soul of my father. III ACKNOWLEDGEMENTS I would like to express gratitude to Dr. Rania Siam, Associate Professor, Chair- Biology Department, and advisor of this thesis for her thoughtfulness, continuous support, encouragement and contribution to this work. -
Molecular Biological and Physiological Investigations of Heterotrophic Bacteria Associated with Marine Filamentous Cyanobacteria
Molecular Biological and Physiological Investigations of Heterotrophic Bacteria Associated with Marine Filamentous Cyanobacteria Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) dem Fachbereich Biologie / Chemie der Universität Bremen vorgelegt von Annina E. Hube Stade November 2009 1. Gutachter: Prof. Dr. Ulrich Fischer 2. Gutachter: PD Dr. Jens Harder Tag des Promotionskolloquiums: 16. Dezember 2009 2 Table of contents Table of contents Table of contents ........................................................................................................................ 3 List of abbreviations................................................................................................................... 4 Abstract ...................................................................................................................................... 5 Zusammenfassung...................................................................................................................... 7 1 Introduction ........................................................................................................................ 9 1.1 The Baltic Sea ............................................................................................................. 9 1.2 Bloom forming and benthic Baltic Sea cyanobacteria.............................................. 10 1.3 Cyanobacteria and heterotrophic bacteria................................................................. 12 1.4 Aerobic anoxygenic phototrophic -
Ideonella Sakaiensis Bacteria Pdf
Ideonella sakaiensis bacteria pdf Continue Ideonella sakaiensis Scientific classification Domain: Bacteria Phylum: Proteobacteria Class: Betaproteobacteria Order: Burkholderiales Family: Comamonadaceae Genus: Ideonella Species: I. sakaiensis Binomial name Ideonella sakaiensisYoshida et al. 2016 (1) Ideonella sakaiensis is a bacterium from the genus Ideonella and the Comamonadaceae family, capable of breaking and consuming plastic polyethylene terephtalat (PET) as the sole source of carbon and energy. The bacterium was originally isolated from a sediment sample taken outside a plastic bottle processing plant in Sakai, Japan. Discovery Ideonella sakaiensis was first identified in 2016 by a team of researchers led by Kohei Oda of the Kyoto Institute of Technology and Kenji Miamoto of Keio University after collecting a sample of PET-contaminated sediment near a plastic bottle processing plant in Japan. The bacterium was isolated from a consortium of microorganisms in a sample of sediments, including protozoa and yeast cells. It has been shown that the entire microbial community mineralizes 75% of degraded PET into carbon dioxide after it has been initially degraded and assimilated by I. sakaiensis. The characteristic of Ideonella sakaiensis is gram-negative, aerobic and rod-shaped. It does not form disputes. The cells are mottled and have one flagellum. I. sakaiensis also tests positive for oxidase and catalase. The bacterium grows in the pH range from 5.5 to 9.0 (optimally at temperatures of 7 to 7.5) and temperature from 15 to 42 degrees Celsius (optimally at 30-37 degrees Celsius). Colonies I. sakaiensis are colorless, smooth and round. Its size ranges from 0.6-0.8 microns wide and 1.2-1.5 microns in length. -
Appendix 1. New and Emended Taxa Described Since Publication of Volume One, Second Edition of the Systematics
188 THE REVISED ROAD MAP TO THE MANUAL Appendix 1. New and emended taxa described since publication of Volume One, Second Edition of the Systematics Acrocarpospora corrugata (Williams and Sharples 1976) Tamura et Basonyms and synonyms1 al. 2000a, 1170VP Bacillus thermodenitrificans (ex Klaushofer and Hollaus 1970) Man- Actinocorallia aurantiaca (Lavrova and Preobrazhenskaya 1975) achini et al. 2000, 1336VP Zhang et al. 2001, 381VP Blastomonas ursincola (Yurkov et al. 1997) Hiraishi et al. 2000a, VP 1117VP Actinocorallia glomerata (Itoh et al. 1996) Zhang et al. 2001, 381 Actinocorallia libanotica (Meyer 1981) Zhang et al. 2001, 381VP Cellulophaga uliginosa (ZoBell and Upham 1944) Bowman 2000, VP 1867VP Actinocorallia longicatena (Itoh et al. 1996) Zhang et al. 2001, 381 Dehalospirillum Scholz-Muramatsu et al. 2002, 1915VP (Effective Actinomadura viridilutea (Agre and Guzeva 1975) Zhang et al. VP publication: Scholz-Muramatsu et al., 1995) 2001, 381 Dehalospirillum multivorans Scholz-Muramatsu et al. 2002, 1915VP Agreia pratensis (Behrendt et al. 2002) Schumann et al. 2003, VP (Effective publication: Scholz-Muramatsu et al., 1995) 2043 Desulfotomaculum auripigmentum Newman et al. 2000, 1415VP (Ef- Alcanivorax jadensis (Bruns and Berthe-Corti 1999) Ferna´ndez- VP fective publication: Newman et al., 1997) Martı´nez et al. 2003, 337 Enterococcus porcinusVP Teixeira et al. 2001 pro synon. Enterococcus Alistipes putredinis (Weinberg et al. 1937) Rautio et al. 2003b, VP villorum Vancanneyt et al. 2001b, 1742VP De Graef et al., 2003 1701 (Effective publication: Rautio et al., 2003a) Hongia koreensis Lee et al. 2000d, 197VP Anaerococcus hydrogenalis (Ezaki et al. 1990) Ezaki et al. 2001, VP Mycobacterium bovis subsp. caprae (Aranaz et al.