DOCSLIB.ORG

Phylogeny and Polyphasic Taxonomy of Caulobacter Species. Proposal of Maricaulis Gen

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

International Journal of Systematic Bacteriology (1 999), 49, 1053-1 073 Printed in Great Britain Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundirnonas and Caulobacter Wolf-Rainer Abraham,' Carsten StrOmpl,l Holger Meyer, Sabine Lindholst,l Edward R. B. Moore,' Ruprecht Christ,' Marc Vancanneyt,' B. J. Tindali,3 Antonio Bennasar,' John Smit4 and Michael Tesar' Author for correspondence: Wolf-Rainer Abraham. Tel: +49 531 6181 419. Fax: +49 531 6181 41 1. e-mail : [email protected] Gesellschaft fur The genus Caulobacter is composed of prosthecate bacteria often specialized Biotechnologische for oligotrophic environments. The taxonomy of Caulobacter has relied Forschung mbH, primarily upon morphological criteria: a strain that visually appeared to be a Mascheroder Weg 1, D- 38124 Braunschweig, member of the Caulobacter has generally been called one without Germany challenge. A polyphasic approach, comprising 165 rDNA sequencing, profiling Laboratorium voor restriction fragments of 165-235 rDNA interspacer regions, lipid analysis, Microbiologie, Universiteit immunological profiling and salt tolerance characterizations, was used Gent, Gent, Belgium to clarify the taxonomy of 76 strains of the genera Caulobacter, Deutsche Sammlung von Brevundimonas, Hyphomonas and Mycoplana. The described species of the Mikroorganismen und genus Caulobacter formed a paraphyletic group with Caulobacter henricii, Zellkulturen, Caulobacter fusiformis, Caulobacter vibrioides and Mycoplana segnis Braunschweig, Germany (Caulobacter segnis comb. nov.) belonging to Caulobacter sensu stricto. Dept of Microbiology and Caulobacter bacteroides (Brevundimonas bacteroides comb. nov.), C. henricii Immunology, University of subsp. aurantiacus (Brevundimonas aurantiaca comb. nov.), Caulobacter British Columbia, intermedius (Brevundimonas intermedia comb. nov.), Caulobacter Vancouver, British subvibrioides (Brevundimonas subvibrioides comb. nov.), C. subvibrioides Columbia, Canada subsp. albus (Brevundimonas alba comb. nov.), Caulobacter variabilis (Brevundimonas variabilis comb. nov.) and Mycoplana bullata belong to the genus Brevundimonas. The halophilic species Caulobacter maris and Caulobacter halobacteroides are different from these two genera and form the genus Maricaulis gen. nov. with Maricaulis maris as the type species. Caulobacter leidyia was observed to cluster with species of the genus Sphingomonas. Caulobacter crescentus is synonymous with C. vibrioides and C. halobacteroides is synonymous with Maricaulis maris as determined by these analyses and DNA-DNA hybridization. Biomarkers discerning these different genera were determined. The necessary recombinations have been proposed and a description of Maricaulis is presented. Keywords : Caulobacter, Brevundimonas, Maricaulis gen. nov., Mycoplana, Hyphomonas Abbreviations: DCI, desorption chemical ionization; FAB, fast atom bombardment; ISR, interspacer region; NFM, non-fat dry milk; SSCP, single-strand conformational polymorphism. The EMBL accession numbers for the 165 rDNA sequences reported in this paper are listed in Table 1. 00980 0 1999 IUMS Downloaded from www.microbiologyresearch.org by 1053 IP: 193.191.134.1 On: Thu, 03 Nov 2016 12:15:37 W.-R. Abraham and others INTRODUCTION Strain CB5 IT was obtained independently from the Caulobacter All-Russian Collection of Microorganisms (VKM B- The genus is composed of dimorphic, 1496T)and from J. T. Staley (= DSM 9893T). prosthecate bacteria. In these prokaryotes, repro- duction results in the separation of two cells that are Fatty acids of Caulobacter spp. were determined by morphologically and behaviourally different from each Carter & Schmidt (1976) and polar lipids have been other. One sibling is non-motile, sessile by virtue of analysed by various groups (Minnikin et al., 1973; adhesive material and prosthecate, possessing at least Wilkinson, 1969; Wilkinson & Bell, 1971 ; Andreev et one elongated, cylindrical appendage (a prostheca) al., 1986; Batrakov et al., 1996, 1997). Using 5s rRNA that is an outgrowth of the cell envelope, including the sequences, Stackebrandt et al. (1 988) determined the outer membrane, the peptidoglycan layer and the cell phylogenetic position of Caulobacter crescentus within membrane (Staley, 1968). The other sibling is the a-subclass of the Proteobacteria; similar results flagellated, bearing one polar flagellum, by which it is were reported two years later by Nikitin et al. (1990). motile. The mode of reproduction of the dimorphic Anast & Smit (1988) were the first to determine prosthecate bacteria is unique as a regular feature of a differences between freshwater and marine caulo- prokaryotic reproductive cycle. It is regarded as a bacteria on a large set of strains. In a pioneering study, reflection of an ecological programme helping to Stahl et al. (1992) sequenced the 16s rRNA of several disperse the population at each generation, thereby Caulobacter isolates. Although sequences of type minimizing competition for resources. strains of Caulobacter species were not included in this In each species studied so far, the motile cell grows less study and a strain wrongly labelled as Caulobacter actively than its prosthecate sibling. Progress toward subvibrioides was included (Sly et al., 1997), this study reproduction is initiated in the swarmers only after this revealed, for the first time, that Caulobacter actually period of motility. It is consistent with this devel- forms two different lineages, one comprising the opmental and reproductive habit that these bacteria freshwater and brackish water Caulobacter spp. and exhibit the physiological properties of oligotrophs the other comprising the marine forms. Stahl et al. (Poindexter, 198 1a, b) and, most importantly, the (1992) also showed that Brevundirnonas dirninuta tolerance of prolonged nutrient scarcity. Once isolated, (Segers et al., 1994) clusters within the group of individual strains may tolerate much higher nutrient freshwater Caulobacter spp. The 16s rDNA sequences concentrations than are useful for their enrichment of Mycoplana segnis and Mycoplana bullata (Yanagi & and isolation. All caulobacteria are oxybiotic and Yamasato, 1993) also fall in the freshwater grow in well-aerated cultures. CaulobacterlBrevundirPzonascluster and thus compli- cate the taxonomy further. Caulobacteria are ubiquitous in water. As typical aquatic bacteria, they may be second only to pseudo- As caulobacteria are ubiquitous in water samples and monads in the breadth of their distribution and are believed to play an important role in the carbon numbers (Lapteva, 1987). These two bacterial groups cycling within their habitats, the intent of the present together are presumed to be responsible for con- study was to evaluate the diversity of freshwater and siderable mineralization of dissolved organic material marine caulobacters using lipid analysis, immuno- in aquatic environments, whereby the oligotrophic logical profiling and 16s rRNA gene sequences to caulobacters are especially important when nutrient compare these results with physiological data. Because concentrations and ambient temperatures are low previous studies (Stahl et al., 1992) revealed a close (Staley et al., 1987). Practically any type of seawater ph ylogenetic distance be tween Caulobac ter , Hypho- contains Caulobacter (Jannasch & Jones, 1960; Anast rnonas jannaschiana, Mycoplana bullata, Mycoplana & Smit, 1988) and, further, MacRae & Smit (1991) segnis and B. dirninuta, strains of these genera were reported the ready detection of Caulobacter in highly also included in this study. aerobic activated sewage sludge. The first isolation of a Caulobacter sp. was reported by METHODS Loeffler (1 890). He noticed the unusually low nutrient requirements of the strain. He could not assign the Strains and culture conditions. The strains in this study were strain to a known taxon and named this ‘hochst obtained from the American Type Culture Collection merkwurdigen Organismus ’ ‘ Vibrio (?) spermato- (ATCC), the Deutsche Sammlung von Mikroorganismen .zoides’. Later, Henrici & Johnson (1935) described the und Zellkulturen (DSMZ ; DSM strains), the Laboratorium genus Caulobacter with Caulobacter vibrioides as the voor Microbiologie, Universiteit Gent, Belgium (LMG strains), the All-Russian Collection of Microorganisms type species. Then, Poindexter (1964) enlarged the (VKM), from Ingo Fritz at the GBF (Brevundimonas sp. imonotypic genus considerably by describing nine B0.07 and BO.10) and from the Dept of Microbiology and species and two subspecies, and later added Caulo- Immunology at the University of British Columbia (CB, bacter variabilis (Poindexter, 1989). FWC and MCS strains). Table 1 shows the origin of the Henrici & Johnson (1935) did not isolate Caulobacter isolates. vibrioides and therefore a type strain was not named. All strains were grown in medium PYEM with the exception Poindexter (1964) proposed strain CB5 1 as the neotype of Caulobacter maris ATCC 1526gT, Caulobacter halo- strain of C. vibrioides (Poindexter & Lewis, 1966). bacteroides ATCC 15269T, Hyphomonas spp. and all Caulo- 1054 Downloaded from www.microbiologyresearch.orglnterna by tional Journal of Systematic Bacteriology 49 IP: 193.191.134.1 On: Thu, 03 Nov 2016 12:15:37 Phylogeny of caulobacteria Table 7. List of strains used in this study including their serum reactions and the accession numbers of the
Recommended publications
  • Accepted Manuscript

    Accepted Manuscript

    Effect of engineered environment on microbial community structure in biofilter and biofilm on reverse osmosis membrane Item Type Article Authors Jeong, Sanghyun; Cho, Kyungjin; Jeong, Dawoon; Lee, Seockheon; Leiknes, TorOve; Vigneswaran, Saravanamuthu; Bae, Hyokwan Citation Jeong S, Cho K, Jeong D, Lee S, Leiknes T, et al. (2017) Effect of engineered environment on microbial community structure in biofilter and biofilm on reverse osmosis membrane. Water Research. Available: http://dx.doi.org/10.1016/ j.watres.2017.07.064. Eprint version Post-print DOI 10.1016/j.watres.2017.07.064 Publisher Elsevier BV Journal Water Research Rights NOTICE: this is the author’s version of a work that was accepted for publication in Water Research. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Water Research, [, , (2017-07-25)] DOI: 10.1016/j.watres.2017.07.064 . © 2017. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ Download date 03/10/2021 04:43:40 Link to Item http://hdl.handle.net/10754/625270 Accepted Manuscript Effect of engineered environment on microbial community structure in biofilter and biofilm on reverse osmosis membrane Sanghyun Jeong, Kyungjin Cho, Dawoon Jeong, Seockheon Lee, TorOve Leiknes, Saravanamuthu Vigneswaran, Hyokwan Bae PII: S0043-1354(17)30637-1 DOI: 10.1016/j.watres.2017.07.064 Reference: WR 13107 To appear in: Water Research Received Date: 19 January 2017 Revised Date: 11 May 2017 Accepted Date: 24 July 2017 Please cite this article as: Jeong, S., Cho, K., Jeong, D., Lee, S., Leiknes, T., Vigneswaran, S., Bae, H., Effect of engineered environment on microbial community structure in biofilter and biofilm on reverse osmosis membrane, Water Research (2017), doi: 10.1016/j.watres.2017.07.064.
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event

    The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event

    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
  • Is It Essential to Sequence the Entire 16S Rrna Gene for Bacterial

    Is It Essential to Sequence the Entire 16S Rrna Gene for Bacterial

    » INSTRUMENTATION » Is it Essential to Sequence Introduction Bacterial Identification in the biopharmaceutical industry, especially in the Entire 16S rRNA Gene manufacturing facilities, is very important because an occurrence of a problematic microorganism in the final product could be harmful for the end user and detrimental to a company’s finances and reputation. for Bacterial Identification? Environmental Monitoring (EM) programs are the cornerstone of understanding the microbial ecology in a manufacturing facility and have become a regulatory requirement for most manufacturers. The EM program is a biological surveillance system which enables companies to quickly identify organisms which are transient or resident in their facilities before these organisms have an opportunity to contaminate a product. A properly executed EM program provides an early warning of potential contamination problems due to Sunhee Hong, PhD and equipment failure, inadequate cleaning, or deficiencies in staff hygiene Christine E. Farrance, PhD training, for example, so that problems can be corrected to prevent Charles River adulteration of the end product. The Food and Drug Administration (FDA) has published guidelines for the production of sterile drugs by aseptic processing which includes a section on EM programs, and the USP general information chapter “Microbiological Control and Monitoring of Aseptic Processing Environments” also contains detailed information regarding EM programs1. The EM program is only effective if the organisms recovered from the facility are accurately identified, so the information gathered can be used to understand the microbial control through tracking and trending and dictate appropriate remediation activities. There are several different options available for bacterial identification; however, the use of 16S rRNA gene sequences has been considered the most powerful and accurate tool, while conventional phenotypic methods often show major weaknesses2-5.
  • Rhodobacter Veldkampii, a New Species of Phototrophic Purple Nonsulfur Bacteria

    Rhodobacter Veldkampii, a New Species of Phototrophic Purple Nonsulfur Bacteria

    CORE Metadata, citation and similar papers at core.ac.uk Provided by OceanRep INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1985, p. 115-116 Vol. 35, No. 1 0020-7713/85/010115-02$02.OO/O Copyright 0 1985, International Union of Microbiological Societies Rhodobacter veldkampii, a New Species of Phototrophic Purple Nonsulfur Bacteria T. A. HANSEN’ AND J. F. IMHOFF2* Laboratory of Microbiology, University of Groningen, Haren, The Netherlands, and Institut fur Mikrobiologie, Rheinische Friedrich- Wilhelms- Universitat, 0-5300 Bonn, Federal Republic of Germany’ We describe a new species of purple nonsulfur bacteria, which has the ability to grow under photoauto- trophic growth conditions with sulfide as an electron donor and shows the characteristic properties of Rhodobacter species (i.e., ovoid to rod-shaped cells, vesicular internal photosynthetic membranes, bacterio- chlorophyll a and carotenoids of the spheroidene series as photosynthetic pigments). In its physiological properties this new species is particularly similar to the recently described species Rhodobacter adriaticus, but it shows enough differences compared with R. adriaticus and the other Rhodobacter species to be recognized as a separate species. In honor of Hans Veldkamp, a Dutch microbiologist, the name Rhodobacter veldkampii sp. nov. is proposed. During attempts to isolate freshwater strains of the pho- nonsulfur bacterium was isolated, which oxidized sulfide totrophic purple nonsulfur bacterium Rhodobacter suljidoph- during photoautotrophic growth to sulfate by using it as an ilus, Hansen (Ph.D. thesis, University of Groningen, Haren, electron donor for photosynthesis (3). The following descrip- The Netherlands, 1974) obtained two strains (strains 51T [T tion is based entirely on previously published data (1, 2, 6; = type strain] and 55) of a bacterium which tolerated rather Hansen, Ph.D.
  • Downloaded from the JGI’S Genome Portal

    Downloaded from the JGI’S Genome Portal

    bioRxiv preprint doi: https://doi.org/10.1101/427211; this version posted October 3, 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-ND 4.0 International license. 1 Title: Community structure of phototrophic co-cultures from extreme environments 2 Charles Brooke1, Morgan P. Connolly2, Javier A. Garcia3, Miranda Harmon-Smith4, 3 Nicole Shapiro4, Erik Hawley5, Michael Barton4, Susannah G. Tringe4, Tijana Glavina del 4 Rio4, David E. Culley6, Richard Castenholz7 and *Matthias Hess1, 4 5 6 1Systems Microbiology & Natural Products Laboratory, University of California, Davis, CA 7 2Microbiology Graduate Group, University of California, Davis, CA 8 3Biochemistry, Molecular, Cellular, and Developmental Biology Graduate Group, University of 9 California, Davis, CA 10 4DOE Joint Genome Institute, Walnut Creek, CA 11 5Bayer, Pittsburg, PA 12 6LifeMine, Cambridge, MA 13 7University of Oregon, Eugene, OR 14 15 16 *Corresponding author: Matthias Hess 17 University of California, Davis 18 1 Shields Ave 19 Davis, CA 95616, USA 20 P (530) 530-752-8809 21 F (530) 752-0175 22 [email protected] 23 24 1 bioRxiv preprint doi: https://doi.org/10.1101/427211; this version posted October 3, 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-ND 4.0 International license. 25 ABSTRACT 26 Cyanobacteria are found in most illuminated environments and are key players in global 27 carbon and nitrogen cycling.
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater

    Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater

    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
  • Microbiological Study in Petrol-Spiked Soil

    Microbiological Study in Petrol-Spiked Soil

    molecules Article Microbiological Study in Petrol-Spiked Soil Agata Borowik , Jadwiga Wyszkowska * and Jan Kucharski Department of Soil Science and Microbiology, University of Warmia and Mazury in Olsztyn, 10-727 Olsztyn, Poland; [email protected] (A.B.); [email protected] (J.K.) * Correspondence: [email protected] Abstract: The pollution of arable lands and water with petroleum-derived products is still a valid problem, mainly due the extensive works aimed to improve their production technology to reduce fuel consumption and protect engines. An example of the upgraded fuels is the BP 98 unleaded petrol with Active technology. A pot experiment was carried out in which Eutric Cambisol soil was polluted with petrol to determine its effect on the microbiological and biochemical properties of this soil. Analyses were carried out to determine soil microbiome composition—with the incubation and metagenomic methods, the activity of seven enzymes, and cocksfoot effect on hydrocarbon degradation. The following indices were determined: colony development index (CD); ecophysiological diversity index (EP); index of cocksfoot effect on soil microorganisms and enzymes (IFG); index of petrol effect on soil microorganisms and enzymes (IFP); index of the resistance of microorganisms, enzymes, and cocksfoot to soil pollution with petrol (RS); Shannon–Weaver’s index of bacterial taxa diversity (H); and Shannon–Weaver’s index of hydrocarbon degradation (IDH). The soil pollution with petrol was found to increase population numbers of bacteria and fungi, and Protebacteria phylum abundance as well as to decrease the abundance of Actinobacteria and Acidobacteria phyla. The cultivation of cocksfoot on the petrol-polluted soil had an especially beneficial effect mainly on the Citation: Borowik, A.; Wyszkowska, bacteria belonging to the Ramlibacter, Pseudoxanthomonas, Mycoplana, and Sphingobium genera.
  • Microbial Production and Consumption of Hydrocarbons in the Global Ocean

    Microbial Production and Consumption of Hydrocarbons in the Global Ocean

    ARTICLES https://doi.org/10.1038/s41564-020-00859-8 Microbial production and consumption of hydrocarbons in the global ocean Connor R. Love1,4, Eleanor C. Arrington1,4, Kelsey M. Gosselin1, Christopher M. Reddy2, Benjamin A. S. Van Mooy 2, Robert K. Nelson2 and David L. Valentine 3 ✉ Seeps, spills and other oil pollution introduce hydrocarbons into the ocean. Marine cyanobacteria also produce hydrocarbons from fatty acids, but little is known about the size and turnover of this cyanobacterial hydrocarbon cycle. We report that cyano- bacteria in an oligotrophic gyre mainly produce n-pentadecane and that microbial hydrocarbon production exhibits stratifica- tion and diel cycling in the sunlit surface ocean. Using chemical and isotopic tracing we find that pentadecane production mainly occurs in the lower euphotic zone. Using a multifaceted approach, we estimate that the global flux of cyanobacteria-produced pentadecane exceeds total oil input in the ocean by 100- to 500-fold. We show that rapid pentadecane consumption sustains a population of pentadecane-degrading bacteria, and possibly archaea. Our findings characterize a microbial hydrocarbon cycle in the open ocean that dwarfs oil input. We hypothesize that cyanobacterial hydrocarbon production selectively primes the ocean’s microbiome with long-chain alkanes whereas degradation of other petroleum hydrocarbons is controlled by factors including proximity to petroleum seepage. ydrocarbons are released into the ocean via natural oil seeps total, we quantified alkane concentration in 441 particulate samples and industrial spills associated with extraction, transpor- (≥0.2 μm), mainly in triplicate (Methods, Supplementary Table 4 and 1 Htation and consumption of oil, totalling ~1.3 Tg per year .
  • The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro

    The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro

    FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities.
  • Investigation of the Biosynthesis of Bacterial Natural Products

    Investigation of the Biosynthesis of Bacterial Natural Products

    Investigation of the biosynthesis of bacterial natural products Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften vorgelegt beim Fachbereich für Biowissenschaften (15) der Johann Wolfgang Goethe-Universität in Frankfurt am Main von Sebastian Winfried Fuchs aus Hanau (2013) (D 30) vom Fachbereich für Biowissenschaften (15) der Johann Wolfgang Goethe-Universität als Dissertation angenommen. Dekanin: Professorin Anna Starzinski-Powitz Gutachter: Professor Dr. Helge B. Bode, Professor Dr. Eckhard Boles, Professor Dr. Christian Hertweck Datum der Disputation: 16.12.2013 ii Danksagung Danksagung Meinen Eltern und Großeltern möchte ich meinen herzlichen Dank für ihre Unterstützung ausdrücken. Herrn Professor Dr. Helge B. Bode und der gesamten Arbeitsgruppe danke ich für die überaus freundliche und motivierende Arbeitsatmosphäre, und die Unterstützung, die mir im Laufe der Zeit von Euch zugekommen ist. Herrn Professor Dr. Helge B. Bode möchte ich besonders für die Möglichkeit zur Bearbeitung der hierin beschriebenen Projekte danken. Herrn Professor Dr. Eckhard Boles danke ich für die Übernahme des Zweitgutachtens zu dieser Arbeit. Herrn Professor Dr. Michael Karas möchte ich für die Möglichkeit zur Nutzung der MALDI- Massenspektrometer danken. Herrn Dr. Thorsten Jaskolla möchte ich für seine freundliche Unterstützung danken, die mir das Feld der Massenspektrometrie näher gebracht hat. Weiterhin möchte ich meinen Freunden für unsere gemeinsamen Erlebnisse danken. iii Table of contents Table of contents Danksagung ..............................................................................................................................
  • Regulation of Bacterial Photosynthesis Genes by the Small Noncoding RNA Pcrz

    Regulation of Bacterial Photosynthesis Genes by the Small Noncoding RNA Pcrz

    Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ Nils N. Mank, Bork A. Berghoff, Yannick N. Hermanns, and Gabriele Klug1 Institut für Mikrobiologie und Molekularbiologie, Universität Giessen, D-35392 Giessen, Germany Edited by Caroline S. Harwood, University of Washington, Seattle, WA, and approved August 10, 2012 (received for review April 27, 2012) The small RNA PcrZ (photosynthesis control RNA Z) of the faculta- and induces transcription of photosynthesis genes at very low tive phototrophic bacterium Rhodobacter sphaeroides is induced oxygen tension or in the absence of oxygen (5, 10–13). Further- upon a drop of oxygen tension with similar kinetics to those of more, the FnrL protein activates some photosynthesis genes at genes for components of photosynthetic complexes. High expres- low oxygen tension (13) and the PpaA regulator activates some sion of PcrZ depends on PrrA, the response regulator of the PrrB/ photosynthesis genes under aerobic conditions (14). More re- cently CryB, a member of a newly described cryptochrome family PrrA two-component system with a central role in redox regula- R. sphaeroides (15), was shown to affect expression of photosynthesis genes in tion in . In addition the FnrL protein, an activator of R. sphaeroides and to interact with AppA (16, 17). Remarkably, some photosynthesis genes at low oxygen tension, is involved in the different signaling pathways for control of photosynthesis redox-dependent expression of this small (s)RNA. Overexpression genes are also interconnected, e.g., the appA gene is controlled of full-length PcrZ in R. sphaeroides affects expression of a small by PrrA (18, 19) and a PpsR binding site is located in the ppaA subset of genes, most of them with a function in photosynthesis.
  • Hyphal Proteobacteria, Hirschia Baltica Gen. Nov. , Sp. Nov

    Hyphal Proteobacteria, Hirschia Baltica Gen. Nov. , Sp. Nov

    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Oct. 1990, p. 443451 Vol. 40. No. 4 0020-7713/9O/040443-O9$02.00/0 Copyright 0 1990, International Union of Microbiological Societies Taxonomic and Phylogenetic Studies on a New Taxon of Budding, Hyphal Proteobacteria, Hirschia baltica gen. nov. , sp. nov. HEINZ SCHLESNER," CHRISTINA BARTELS, MANUEL SITTIG, MATTHIAS DORSCH, AND ERKO STACKEBRANDTT Institut fur Allgemeine Mikrobiologie, Christian-Albrecht-Universitat, 2300 Kiel, Federal Republic of Germany Four strains of budding, hyphal bacteria, which had very similar chemotaxonomic properties, were isolated from the Baltic Sea. The results of DNA-DNA hybridization experiments, indicated that three of the new isolates were closely related, while the fourth was only moderately related to the other three. Sequence signature and higher-order structural detail analyses of the 16s rRNA of strain IFAM 141gT (T = type strain) indicated that this isolate is related to the alpha subclass of the class Proteobacteriu. Although our isolates resemble members of the genera Hyphomicrobium and Hyphomonas in morphology, assignment to either of these genera was excluded on the basis of their markedly lower DNA guanine-plus-cytosine contents. We propose that these organisms should be placed in a new genus, Hirschiu baltica is the type species of this genus, and the type strain of H. bdtica is strain IFAM 1418 (= DSM 5838). Since the first description of a hyphal, budding bacterium, no1 and formamide were tested at concentrations of 0.02 and Hyphomicrobium vulgare (53), only the following additional 0.1% (vol/vol). Utilization of nitrogen sources was tested in genera having this morphological type have been formally M9 medium containing glucose as the carbon source.