DOCSLIB.ORG

The Genome Sequence of the Giant Phototrophic

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Genome Sequence of the Giant Phototrophic Archives of Microbiology (2021) 203:97–105 https://doi.org/10.1007/s00203-020-02006-7 ORIGINAL PAPER The genome sequence of the giant phototrophic gammaproteobacterium Thiospirillum jenense gives insight into its physiological properties and phylogenetic relationships Johannes F. Imhof1 · Terrance E. Meyer2 · John A. Kyndt3 Received: 23 June 2020 / Revised: 21 July 2020 / Accepted: 24 July 2020 / Published online: 5 August 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020 Abstract In a conserved culture of the purple sulfur bacterium Thiospirillum jenense DSM216T, cells of this species were easily rec- ognized by cell morphology, large-size spirilla and visible fagellar tuft. The Tsp. jenense genome is 3.22 Mb in size and has a GC content of 48.7 mol%. It was readily identifed as a member of the Chromatiaceae by the complement of proteins in its genome. A whole genome comparison clearly placed Tsp. jenense near Thiorhodovibrio and Rhabdochromatium species and somewhat more distant from Thiohalocapsa and Halochromatium species. This relationship was also found with the sequences of the photosynthetic reaction center protein PufM. The genome sequence supported important properties of this bacterium: the presence of ribulose-bisphosphate carboxylase and enzymes of the Calvin cycle of autotrophic carbon diox- ide fxation but the absence of carboxysomes, an incomplete tricarboxylic acid cycle and the lack of malate dehydrogenase, the presence of a sulfur oxidation pathway including adenylylsulfate reductase (aprAB) but absence of assimilatory sulfate reduction, the presence of hydrogenase (hoxHMFYUFE), nitrogenase and a photosynthetic gene cluster (pufBALMC). The FixNOP type of cytochrome oxidase was notably lacking, which may be the reason that renders the cells highly sensitive to oxygen. Two minor phototrophic contaminants were found using metagenomic binning: one was identifed as a strain of Rhodopseudomonas palustris and the second one has an average nucleotide identity of 82% to the nearest neighbor Rho- doferax antarcticus. It should be considered as a new species of this genus and Rhodoferax jenense is proposed as the name. Keywords Thiospirillum jenense · Thiospirillum genome · Purple sulfur bacteria · Chromatiaceae · New Rhodoferax species Introduction for almost two centuries, especially during the early years of microbiology. The bacterium was found by Ehrenberg It was the immense size of the bacterium, its colored cul- (1838) in calm water of a cove in a small creek near Zie- tures, the content of highly refractive sulfur globules com- genhain (Jena, Germany), where it developed together bined with the active motility and phototactic behavior that with Chromatium okenii. He described this bacterium as made Thiospirillum jenense an interesting study object Ophidomonas jenensis with a cell width of 3.5–4.5 µm and a length of 30–40 up to 100 µm, a giant among bacteria. Cultures of Tsp. jenense are pastel-colored orange-brown Communicated by Erko Stackebrandt. and due to the size, even single cells can be recognized as * Johannes F. Imhof colored in the light microscope. In contrast to many other [email protected] bacteria, the large polar fagellar tuft of Tsp. jenense may be visible in the light microscope (Fig. 1) and already Ehren- 1 GEOMAR Helmholtz Centre for Ocean Research RU Marine Symbioses, Düsternbrooker Weg 20, 24105 Kiel, berg (1838) observed these fagella, for the frst time with a Germany living bacterium. The fagellar tuft pushes the cell forward, 2 Department of Biochemistry, University of Arizona, Tucson, but at reversal of direction it turns down over the cell and AZ, USA then draws it through the water (Buder 1915). It was also 3 College of Science and Technology, Bellevue University, Ehrenberg (1838) who reported on refractive inclusion bod- Bellevue, NE 68005, USA ies that were later recognized to be elemental sulfur globules Vol.:(0123456789)1 3 98 Archives of Microbiology (2021) 203:97–105 and a small bottle was smuggled from the eastern to the western part of Germany across the inner border which was at this time strictly closed. The Thiospirillum thrived for a while in a Winogradsky column set up with sewage sludge and eventually was brought into highly enriched and pure culture (Schlegel and Pfennig 1961). Pfennig discovered that it required the addition of vitamin B 12 and that it also was sensitive to the continuous bright lights in the laboratory and enjoyed a diurnal cycle of 16 h light and 8 h darkness. It would tolerate only 2–3 mM sulfde and had to be fed regularly to achieve dense populations in the cultures. Cultures of Tsp. jenense appear orange in color and the major carotenoids were identifed as lyco- pene and rhodopin (Schmidt 1963; Schmidt et al. 1965). Fig. 1 Brightfeld photomicrograph of Tsp. jenense DSM216 showing Thiospirillum sanguineum on the other hand is a marine intracellular elemental sulfur globules and a polar tuft of fagella. Bar bacterium and is rose-red in color (Paterek and Paynter indicates 10 µm (courtesy of N. Pfennig) 1988), which suggests that the carotenoids may be domi- nated by spirilloxanthin. Pfennig also continued studies on the phototactic behavior (van Niel 1932). The requirement of hydrogen sulfde as well and an impressive movie was produced that is still available as light for the development of Tsp. jenense and other purple online (Pfennig 1963). In this video, the phototactic move- sulfur bacteria was concluded by Buder (1919) from his eco- ment and the reversal of the fagella rotation upon light/dark logical observations on the development of these bacteria. stimuli were demonstrated. Also the collection of cells in a All of the early studies on metabolism, motility and pho- small light frame due to their phototactic response and the totactic responses of Tsp. jenense were made with material accumulation of the cells at light of specifc wavelength, in taken from the natural environment (Winogradsky 1888; particular at the absorption maxima of bacteriochlorophyll Buder 1915, 1919; Schlegel 1956; van Niel 1955). Although a, were observed (Pfennig 1963). However, after this short many attempts had been made in the early years, Tsp. jen- period of active research on this bacterium, for more than ense could not be grown in the laboratory, not even in crude fve decades the problems in cultivation of Tsp. jenense and cultures. It was Buder who was able to keep transient cul- later also the missing availability of cultures have disabled tures of Tsp. jenense according to the Winogradsky method further detailed studies. The original locations, where the (Winogradsky 1888; Buder 1915). The source for many Tsp. jenense was collected from no longer exist and there- years was a pond in Ostrau near Halle, where these bacte- fore, frozen cultures currently represent the only source to ria formed regular mass developments from April to July obtain data on this interesting bacterium. No sequence infor- (Schlegel and Pfennig 1961). This material formed the basis mation of this bacterium, even no 16S rRNA gene sequences, for studies on the photobiology of Tsp. jenense and Chroma- have been available so far. The data presented here for the tium okenii by H.G. Schlegel during his PhD studies in the frst time allow the phylogenetic alignment of Tsp. jenense lab of Johannes Buder (Schlegel 1956). The mechanism of with other purple sulfur bacteria and give insight into its photophobic tactic movements of Tsp. jenense, responsible genomic capability and physiological properties. Despite for the reversal of fagellar rotation upon entering dark zones the lack of pure cultures, bacteria resembling Thiospirillum or dim light, was shown by studies of Buder and Schlegel appear to be more widespread in nature and developments (Buder, 1915, 1919; Schlegel 1956) and demonstrated to be in anaerobic habitats including both marine and freshwater responsible for accumulation of the cells in the light. environments of spiral-shaped bacteria containing diferent Years later Schlegel and Pfennig (1961) in great detail carotenoids have been observed (Paterek and Paynter 1988; described enrichment conditions and culture media for the Briee et al. 2007; Caldwell and Tiedje 1975). This includes a growth of Tsp. jenense. Norbert Pfennig was successful in brackish pond in San Elijo Lagoon near La Jolla (California) the cultivation of Tsp. jenense and other large-cell Chro- were such a development of a pink-colored Thiospirillum matiaceae including Chromatium okenii and Allochroma- was observed and maintained as enrichment for a while in a tium warmingii. As he describes in his memoirs (Pfennig Winogradsky-type column by one of the authors (JFI). The 1993), he used the pond near Ostrau (in particular, well genome sequence of Tsp. jenense should stimulate the search known by H.-G. Schlegel who used material from the same for and the identifcation of other Thiospirillum and related pond during his PhD thesis, and at that time was head bacteria in nature, eventually leading to further isolation and of the Microbiology Institute in Göttingen) as a source characterization of other Thiospirillum species. 1 3 Archives of Microbiology (2021) 203:97–105 99 Materials and methods Metagenomic binning Cultures The sequencing reads were used to perform a metagen- omic binning using the Metagenomic Binning service Cultures of Thiospirillum jenense DSM 216T (Pfennig within PATRIC (Wattam et al. 2017). Paired-end reads 1112, strain Ostrau) were received by JFI from N. Pfen- were used as input and default parameters were used. Sets nig, who at this time (1991) worked at the University of of contig bins were constructed (hits against contigs that Konstanz. Living cultures were maintained for some years have less than fourfold coverage or are less than 400 bp in in the Institute for Microbiology at the University of Bonn length are removed). The contig pool was split into bins and in parallel the cultures were preserved immediately using reference genomes. Quality control of each bin was after transfer to Bonn and kept in liquid nitrogen.
Load more

Recommended publications
  • The Microbial Ecology of Sulfur Transformations in Oyster Pond, Woods Hole, Massachusetts
    University of New Hampshire University of New Hampshire Scholars' Repository Doctoral Dissertations Student Scholarship Spring 1970 THE MICROBIAL ECOLOGY OF SULFUR TRANSFORMATIONS IN OYSTER POND, WOODS HOLE, MASSACHUSETTS FRANK W. BARVENIK Follow this and additional works at: https://scholars.unh.edu/dissertation Recommended Citation BARVENIK, FRANK W., "THE MICROBIAL ECOLOGY OF SULFUR TRANSFORMATIONS IN OYSTER POND, WOODS HOLE, MASSACHUSETTS" (1970). Doctoral Dissertations. 933. https://scholars.unh.edu/dissertation/933 This Dissertation is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. 71-5863 BARVENIK, Frank W., 1943- | THE MICROBIAL ECOLOGY OF SULFUR TRANSFORMATIONS I IN OYSTER POND, WOODS HOLE, MASSACHUSETTS. f i University of New Hampshire, Ph.D., 1970 f Microbiology University Microfilms, Inc., Ann Arbor, Michigan THIS DISSERTATION HAS BEEN MICROFILMED EXACTLY AS RECEIVED THE MICROBIAL ECOLOGY OF SULFUR TRANSFORMATIONS IN OYSTER POND, WOODS HOLE, MASSACHUSETTS by FRANK W. BARVENIK B.A., University of Connecticut, 1965 A THESIS Submitted to the University of New Hampshire In Partial Fulfillment of The Requirements for the Degree of Doctor of Philosophy Graduate School Department of Microbiology June, 1970 This thesis has been examined and approved. C. __ _ Thesisis director, #£len2alen E. Jones, Prof. of Microbiology William R. Chesbro, Prof. of Microbiology ______ jawrence W. Slanetz, Prof. of M igroipiology IjHtVX 7 ~ _____ ___ _________________ Henri E. Gaudettfy, Asso. Prcff. of Geiology Sanuiel C.
    [Show full text]
  • 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 .
    [Show full text]
  • Int J Syst Evol Microbiol 67 1
    Author version : International Journal of Systematic and Evolutionary Microbiology, vol.67(6); 2017; 1949-1956 Imhoffiella gen. nov.. a marine phototrophic member of family Chromatiaceae including the description of Imhoffiella purpurea sp. nov. and the reclassification of Thiorhodococcus bheemlicus Anil Kumar et al. 2007 as Imhoffiella bheemlica comb. nov. Nupur1, Mohit Kumar Saini1, Pradeep Kumar Singh1, Suresh Korpole1, Naga Radha Srinivas Tanuku2, Shinichi Takaichi3 and Anil Kumar Pinnaka1* 1Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh – 160 036, INDIA 2CSIR-National Institute of Oceanography, Regional Centre, 176, Lawsons Bay Colony, Visakhapatnam-530017, INDIA 3Nippon Medical School, Department of Biology, Kyonan-cho, Musashino 180-0023, Japan Address for correspondence* Dr. P. Anil Kumar Microbial Type Culture Collection and Gene Bank, Institute of Microbial Technology (CSIR), Sector 39A, Chandigarh – 160 036, INDIA Email: [email protected] Telephone: 00-91-172-6665170 Running title Imhoffiella purpurea sp. nov. Subject category New taxa (Gammaproteobacteria) The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain AK35T is HF562219. A coccoid-shaped phototrophic purple sulfur bacterium was isolated from a coastal surface water sample collected from Visakhapatnam, India. Strain AK35T was Gram-negative, motile, purple colored, containing bacteriochlorophyll a and the carotenoid rhodopinal as major photosynthetic pigments. Strain AK35T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically. Strain AK35T was able to utilize sulfide and thiosulfate as electron donors. The main fatty acids present were identified as C16:0, C18:1 T 7c and C16:1 7c and/or iso-C15:0 2OH (Summed feature 3) were identified.
    [Show full text]
  • Coupled Reductive and Oxidative Sulfur Cycling in the Phototrophic Plate of a Meromictic Lake T
    Geobiology (2014), 12, 451–468 DOI: 10.1111/gbi.12092 Coupled reductive and oxidative sulfur cycling in the phototrophic plate of a meromictic lake T. L. HAMILTON,1 R. J. BOVEE,2 V. THIEL,3 S. R. SATTIN,2 W. MOHR,2 I. SCHAPERDOTH,1 K. VOGL,3 W. P. GILHOOLY III,4 T. W. LYONS,5 L. P. TOMSHO,3 S. C. SCHUSTER,3,6 J. OVERMANN,7 D. A. BRYANT,3,6,8 A. PEARSON2 AND J. L. MACALADY1 1Department of Geosciences, Penn State Astrobiology Research Center (PSARC), The Pennsylvania State University, University Park, PA, USA 2Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA 3Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA 4Department of Earth Sciences, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA 5Department of Earth Sciences, University of California, Riverside, CA, USA 6Singapore Center for Environmental Life Sciences Engineering, Nanyang Technological University, Nanyang, Singapore 7Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany 8Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA ABSTRACT Mahoney Lake represents an extreme meromictic model system and is a valuable site for examining the organisms and processes that sustain photic zone euxinia (PZE). A single population of purple sulfur bacte- ria (PSB) living in a dense phototrophic plate in the chemocline is responsible for most of the primary pro- duction in Mahoney Lake. Here, we present metagenomic data from this phototrophic plate – including the genome of the major PSB, as obtained from both a highly enriched culture and from the metagenomic data – as well as evidence for multiple other taxa that contribute to the oxidative sulfur cycle and to sulfate reduction.
    [Show full text]
  • Supporting Information
    Supporting Information Musat et al. 10.1073/pnas.0809329105 SI Text bottles at in situ light and temperature conditions for 4, 8, and Method Development and Testing. Before application to environ- 12 h. In situ light and temperature conditions were created in the mental samples, the HISH-SIMS procedure was tested using a laboratory based on multiple measurements of light intensities mixture of 2 bacterial cultures, E. coli, a gammaproteobacterium and temperature performed annually and seasonally in the grown on 13C-labeled glucose as sole carbon source, and Azo- chemocline of Lake Cadagno between 1994–2007 [e.g., (5–7), arcus sp., a betaproteobacterium grown without labeled sub- this study]. In situ temperature was maintained between 5 to 8 °C strate. The cultures were fixed and then mixed, filtered on using a mix of water and ice under light intensities of 10–20 ␮mol Ϫ Ϫ gold-palladium coated filters, and hybridized with a horseradish m 2 s 1 as previously described (5, 7). Subsamples were taken peroxidase (HRP)-labeled oligonucleotide probe targeting the for bulk measurements of nitrogen and carbon from all three 23S rRNA gene of the Gammaproteobacteria. Following the incubation time points and only from a 12-h incubation exper- deposition of fluorine-containing tyramides within the hybrid- iment for nanoSIMS analysis of single cells. Water samples for ized cells, filters were analyzed using nanoSIMS. In this way, only bulk measurements were filtered on 0.7 ␮m pore-size type GF/F a single nanoSIMS scan was required to quantify the incorpo- filters (Millipore). After freeze-drying and decalcifying with ration of 13C-glucose by individual cells and to identify these cells 37% hydrochloric acid, the GF/F filters were kept at room based on a signal conferred by rRNA-targeted oligonucleotide temperature until further processing.
    [Show full text]
  • This Article Was Published in an Elsevier Journal. the Attached Copy
    This article was published in an Elsevier journal. The attached copy is furnished to the author for non-commercial research and education use, including for instruction at the author’s institution, sharing with colleagues and providing to institution administration. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier’s archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright Author's personal copy Available online at www.sciencedirect.com Geochimica et Cosmochimica Acta 72 (2008) 1396–1414 www.elsevier.com/locate/gca Okenane, a biomarker for purple sulfur bacteria (Chromatiaceae), and other new carotenoid derivatives from the 1640 Ma Barney Creek Formation Jochen J. Brocks a,*, Philippe Schaeffer b a Research School of Earth Sciences and Centre for Macroevolution and Macroecology, The Australian National University, Canberra, ACT 0200, Australia b Laboratoire de Ge´ochimie Bio-organique, CNRS UMR 7177, Ecole Europe´enne de Chimie, Polyme`res et Mate´riaux, 25 rue Becquerel, 67200 Strasbourg, France Received 20 June 2007; accepted in revised form 12 December 2007; available online 23 December 2007 Abstract Carbonates of the 1640 million years (Ma) old Barney Creek Formation (BCF), McArthur Basin, Australia, contain more than 22 different C40 carotenoid derivatives including lycopane, c-carotane, b-carotane, chlorobactane, isorenieratane, b-iso- renieratane, renieratane, b-renierapurpurane, renierapurpurane and the monoaromatic carotenoid okenane.
    [Show full text]
  • Dark Aerobic Sulfide Oxidation by Anoxygenic Phototrophs in the Anoxic Waters 2 of Lake Cadagno 3 4 Jasmine S
    bioRxiv preprint doi: https://doi.org/10.1101/487272; this version posted December 6, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Dark aerobic sulfide oxidation by anoxygenic phototrophs in the anoxic waters 2 of Lake Cadagno 3 4 Jasmine S. Berg1,2*, Petra Pjevac3, Tobias Sommer4, Caroline R.T. Buckner1, Miriam Philippi1, Philipp F. 5 Hach1, Manuel Liebeke5, Moritz Holtappels6, Francesco Danza7,8, Mauro Tonolla7,8, Anupam Sengupta9, , 6 Carsten J. Schubert4, Jana Milucka1, Marcel M.M. Kuypers1 7 8 1Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany 9 2Institut de Minéralogie, Physique des Matériaux et Cosmochimie, Université Pierre et Marie Curie, CNRS UMR 10 7590, 4 Place Jussieu, 75252 Paris Cedex 05, France 11 3Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090 12 Vienna, Austria 13 4Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland 14 5Department of Symbiosis, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany 15 6Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Am Alten Hafen 26, 27568 16 Bremerhaven, Germany 17 7Laboratory of Applied Microbiology (LMA), Department for Environmental Constructions and Design (DACD), 18 University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, 6500 Bellinzona, 19 Switzerland 20 8Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland 21 9Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH 22 Zurich, 8093 Zurich, Switzerland.
    [Show full text]
  • Spatio-Temporal Distribution of Phototrophic Sulfur Bacteria in the Chemocline of Meromictic Lake Cadagno (Switzerland)
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by RERO DOC Digital Library FEMS Microbiology Ecology 43 (2003) 89^98 www.fems-microbiology.org Spatio-temporal distribution of phototrophic sulfur bacteria in the chemocline of meromictic Lake Cadagno (Switzerland) Mauro Tonolla a, Sandro Peduzzi a;b, Dittmar Hahn b;Ã, Ra¡aele Peduzzi a a Cantonal Institute of Microbiology, Microbial Ecology (University of Geneva), Via Giuseppe Bu⁄ 6, CH-6904 Lugano, Switzerland b Department of Chemical Engineering, New Jersey Institute of Technology (NJIT), and Department of Biological Sciences, Rutgers University, 101 Warren Street, Smith Hall 135, Newark, NJ 07102-1811, USA Received 24 May 2002; received in revised form 26 July 2002; accepted 30 July 2002 First published online 4 September 2002 Abstract In situ hybridization was used to study the spatio-temporal distribution of phototrophic sulfur bacteria in the permanent chemocline of meromictic Lake Cadagno, Switzerland. At all four sampling times during the year the numerically most important phototrophic sulfur bacteria in the chemocline were small-celled purple sulfur bacteria of two yet uncultured populations designated Dand F. Other small- celled purple sulfur bacteria (Amoebobacter purpureus and Lamprocystis roseopersicina) were found in numbers about one order of magnitude lower. These numbers were similar to those of large-celled purple sulfur bacteria (Chromatium okenii) and green sulfur bacteria that almost entirely consisted of Chlorobium phaeobacteroides. In March and June when low light intensities reached the chemocline, cell densities of all populations, with the exception of L. roseopersicina, were about one order of magnitude lower than in August and October when light intensities were much higher.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8,501,463 B2 Cox Et Al
    USOO85O1463B2 (12) United States Patent (10) Patent No.: US 8,501,463 B2 Cox et al. (45) Date of Patent: Aug. 6, 2013 (54) ANAEROBC PRODUCTION OF HYDROGEN (56) References Cited AND OTHER CHEMICAL PRODUCTS U.S. PATENT DOCUMENTS (75) Inventors: Marion E. Cox, Morgan Hill, CA (US); 5,350,685 A 9/1994 Taguchi et al. Laura M. Nondorf, Morgan Hill, CA 5,464,539 A 11/1995 Ueno et al. 6,090,266 A 7/2000 Roychowdhury (US); Steven M. Cox, Morgan Hill, CA 6,251,643 B1 6/2001 Hansen et al. (US) 6,299,774 B1 * 10/2001 Ainsworth et al. ........... 210,603 6,342,378 B1 1/2002 Zhang et al. (73) Assignee: Anaerobe Systems, Morgan Hill, CA 6,569,332 B2 * 5/2003 Ainsworth et al. ........... 210,603 2004/0050778 A1 3/2004 Noike et al. (US) 2004/O115782 A1 6/2004 Paterek (*) Notice: Subject to any disclaimer, the term of this FOREIGN PATENT DOCUMENTS patent is extended or adjusted under 35 WO WO-2006-119052 A2 11/2006 U.S.C. 154(b) by 1347 days. OTHER PUBLICATIONS (21) Appl. No.: 11/912,881 Liu et al., 2004. Effects of Culture and Medium Conditions on Hydro gen Production from Starch Using Anaerobic Bacteria. Journal of (22) PCT Fled: Apr. 27, 2006 Bioscience and Bioengineering, vol. 98, No. 4, pp. 251-256.* Zhang et al., Distributed Computer Control of Penicillin Fermenta (86) PCT NO.: PCT/US2OO6/O16332 tion Industrial Production. Proceedings of the IEEE International Conference on Industrial Technology, 1996, pp. 52-56.* S371 (c)(1), New Brunswick, an eppenforf Company, pp.
    [Show full text]
  • Chapter 3 Transposon Mutagenesis of Rhodobacter Sphaeroides
    Chapter 3 Transposon Mutagenesis of Rhodobacter sphaeroides Timothy D. Paustian and Robin S. Kurtz Department of Bacteriology University of Wisconsin–Madison Madison, Wisconsin 53706 (608) 263-4921, [email protected] Robin and Tim are associate faculty and coordinate the instructional labs for the Department of Bacteriology. Tim earned his B.S. in Biochemistry from the University of Wisconsin–Madison and Ph.D. from the Department of Bacteriology at UW–Madison. His interests include curriculum development, computer-aided instruction, and development of computer programs. Robin earned her B.S. and Ph.D. in Bacteriology from UW-Madison. Her interests include instructional lab development, curriculum improvement, and immunology. Robin and Tim have co-authored three lab manuals that are used in the introductory and advanced microbiology laboratories at UW–Madison. Reprinted from: Paustian, T. D., and R. S. Kurtz. 1994. Transposon mutagenesis of rhodobacter sphaeroides. Pages 45-61, in Tested studies for laboratory teaching, Volume 15 (C. A. Goldman, Editor). Proceedings of the 15th Workshop/Conference of the Association for Biology Laboratory Education (ABLE), 390 pages. - Copyright policy: http://www.zoo.utoronto.ca/able/volumes/copyright.htm Although the laboratory exercises in ABLE proceedings volumes have been tested and due consideration has been given to safety, individuals performing these exercises must assume all responsibility for risk. The Association for Biology Laboratory Education (ABLE) disclaims any liability with regards
    [Show full text]
  • Novel Magnetite-Producing Magnetotactic Bacteria Belonging to the Gammaproteobacteria
    The ISME Journal (2012) 6, 440–450 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE Novel magnetite-producing magnetotactic bacteria belonging to the Gammaproteobacteria Christopher T Lefe`vre1,4, Nathan Viloria1, Marian L Schmidt1,5, Miha´ly Po´sfai2, Richard B Frankel3 and Dennis A Bazylinski1 1School of Life Sciences, University of Nevada at Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, USA; 2Department of Earth and Environmental Sciences, University of Pannonia, Veszpre´m, Hungary and 3Department of Physics, California Polytechnic State University, San Luis Obispo, CA, USA Two novel magnetotactic bacteria (MTB) were isolated from sediment and water collected from the Badwater Basin, Death Valley National Park and southeastern shore of the Salton Sea, respectively, and were designated as strains BW-2 and SS-5, respectively. Both organisms are rod-shaped, biomineralize magnetite, and are motile by means of flagella. The strains grow chemolithoauto- trophically oxidizing thiosulfate and sulfide microaerobically as electron donors, with thiosulfate oxidized stoichiometrically to sulfate. They appear to utilize the Calvin–Benson–Bassham cycle for autotrophy based on ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity and the presence of partial sequences of RubisCO genes. Strains BW-2 and SS-5 biomineralize chains of octahedral magnetite crystals, although the crystals of SS-5 are elongated. Based on 16S rRNA gene sequences, both strains are phylogenetically affiliated with the Gammaproteobacteria class. Strain SS-5 belongs to the order Chromatiales; the cultured bacterium with the highest 16S rRNA gene sequence identity to SS-5 is Thiohalocapsa marina (93.0%).
    [Show full text]
  • Anoxygenic Photosynthesis and Dark Carbon Metabolism Under
    bioRxiv preprint doi: https://doi.org/10.1101/420927; this version posted September 18, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 2 3 Anoxygenic Photosynthesis and Dark Carbon Metabolism 4 under micro-oxic conditions in the Purple Sulfur Bacterium 5 “Thiodictyon syntrophicum“ nov. strain Cad16T 6 7 8 Samuel M Luedin 1 2 3*, Nicola Storelli 2, Francesco Danza 1 2, Samuele Roman 2 4, 9 Matthias Wittwer 3, Joël F Pothier 5 and Mauro Tonolla 1 2 4‡ 10 11 12 1 Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, 13 Geneva, Switzerland 14 2 Laboratory of Applied Microbiology, Department of Environment, Constructions and 15 Design, University of Applied Sciences of Southern Switzerland (SUPSI), Bellinzona, 16 Switzerland 17 3 Biology Division, Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland 18 4 Alpine Biology Center Foundation, via Mirasole 22a, Bellinzona, Switzerland 19 5 Environmental Genomics and System Biology Research Group, Institute of Natural 20 Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland 21 22 Corresponding Authors 23 *Samuel Luedin 24 [email protected] 25 ‡Prof. Mauro Tonolla 26 [email protected] 27 bioRxiv preprint doi: https://doi.org/10.1101/420927; this version posted September 18, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]