Effect of Reclaimed Water Effluent on Bacterial Community Structure in the Typha Angustifolia L
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Optimization and Characterization of the Growth Of
OPTIMIZATION AND CHARACTERIZATION OF THE GROWTH OF THE PHOTOSYNTHETIC BACTERIUM BLASTOCHLORIS VIRIDIS AND A BRIEF SURVEY OF ITS POTENTIAL AS A REMEDIATIVE TOOL A Dissertation Submitted to the Graduate School of the University of Notre Dame in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Darcy Danielle LaClair, B.S. ___________________________________ Agnes E. Ostafin, Director Graduate Program in Chemical and Biomolecular Engineering Notre Dame, Indiana April 2006 OPTIMIZATION AND CHARACTERIZATION OF THE GROWTH OF THE PHOTOSYNTHETIC BACTERIUM BLASTOCHLORIS VIRIDIS AND A BRIEF SURVEY OF THEIR POTENTIAL AS A REMEDIATIVE TOOL Abstract by Darcy Danielle LaClair The growth of B. viridis was characterized in an undefined rich medium and a well-defined medium, which was later selected for further experimentation to insure repeatability. This medium presented a significant problem in obtaining either multigenerational or vigorous growth because of metabolic limitations; therefore optimization of the medium was undertaken. A primary requirement to obtain good growth was a shift in the pH of the medium from 6.9 to 5.9. Once this shift was made, it was possible to obtain growth in subsequent generations, and the media formulation was optimized. A response curve suggested optimum concentrations of 75 mM carbon, supplemented as sodium malate, 12.5 mM nitrogen, supplemented as ammonium sulfate, Darcy Danielle LaClair and 12.7 mM phosphate buffer. In addition, the vitamins p-Aminobenzoic acid, Thiamine, Biotin, B12, and Pantothenate were important to achieving good growth and good pigment formation. Exogenous carbon dioxide, added as 2.5 g sodium bicarbonate per liter media also enhanced growth and reduced the lag time. -
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). -
International Journal of Systematic and Evolutionary Microbiology
University of Plymouth PEARL https://pearl.plymouth.ac.uk 01 University of Plymouth Research Outputs University of Plymouth Research Outputs 2017-05-01 Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the 'Proteobacteria', and four new families within the orders Nitrosomonadales and Rhodocyclales Boden, R http://hdl.handle.net/10026.1/8740 10.1099/ijsem.0.001927 International Journal of Systematic and Evolutionary Microbiology All content in PEARL is protected by copyright law. Author manuscripts are made available in accordance with publisher policies. Please cite only the published version using the details provided on the item record or document. In the absence of an open licence (e.g. Creative Commons), permissions for further reuse of content should be sought from the publisher or author. International Journal of Systematic and Evolutionary Microbiology Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov. Transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the 'Proteobacteria', and 4 new families within the orders Nitrosomonadales and Rhodocyclales. --Manuscript Draft-- Manuscript Number: IJSEM-D-16-00980R2 Full Title: Reclassification of Thiobacillus aquaesulis (Wood & Kelly, -
Draft Genome Sequence of a Nitrate-Reducing, O-Phthalate Degrading Bacterium, Azoarcus Sp. Strain PA01T Madan Junghare1,2*, Yogita Patil2 and Bernhard Schink2
Junghare et al. Standards in Genomic Sciences (2015) 10:90 DOI 10.1186/s40793-015-0079-9 SHORT GENOME REPORT Open Access Draft genome sequence of a nitrate-reducing, o-phthalate degrading bacterium, Azoarcus sp. strain PA01T Madan Junghare1,2*, Yogita Patil2 and Bernhard Schink2 Abstract Azoarcus sp. strain PA01T belongs to the genus Azoarcus,ofthefamilyRhodocyclaceae within the class Betaproteobacteria. It is a facultatively anaerobic, mesophilic, non-motile, Gram-stain negative, non-spore-forming, short rod-shaped bacterium that was isolated from a wastewater treatment plant in Constance, Germany. It is of interest because of its ability to degrade o-phthalate and a wide variety of aromatic compounds with nitrate as an electron acceptor. Elucidation of the o-phthalate degradation pathway may help to improve the treatment of phthalate-containing wastes in the future. Here, we describe the features of this organism, together with the draft genome sequence information and annotation. The draft genome consists of 4 contigs with 3,908,301 bp and an overall G + C content of 66.08 %. Out of 3,712 total genes predicted, 3,625 genes code for proteins and 87 genes for RNAs. The majority of the protein-encoding genes (83.51 %) were assigned a putative function while those remaining were annotated as hypothetical proteins. Keywords: Azoarcus sp. strain PA01T, o-phthalate degradation, Rhodocyclaceae, Betaproteobacteria, anaerobic degradation, wastewater treatment plant, pollutant Introduction aromatic compounds found in fossil fuel [8], such as phen- Phthalic acid consists of a benzene ring to which two anthrene [9], fluorene [10] and fluoranthene [11]. carboxylic groups are attached. -
Riverine Bacterial Communities Reveal Environmental Disturbance Signatures Within the Betaproteobacteria and Verrucomicrobia
ORIGINAL RESEARCH published: 15 September 2016 doi: 10.3389/fmicb.2016.01441 Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia John Paul Balmonte *, Carol Arnosti, Sarah Underwood, Brent A. McKee and Andreas Teske Department of Marine Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA Riverine bacterial communities play an essential role in the biogeochemical coupling of terrestrial and marine environments, transforming elements and organic matter in their journey from land to sea. However, precisely due to the fact that rivers receive significant Edited by: terrestrial input, the distinction between resident freshwater taxa vs. land-derived James Cotner, microbes can often become ambiguous. Furthermore, ecosystem perturbations could University of Minnesota, USA introduce allochthonous microbial groups and reshape riverine bacterial communities. Reviewed by: Barbara J. Campbell, Using full- and partial-length 16S ribosomal RNA gene sequences, we analyzed the Clemson University, USA composition of bacterial communities in the Tar River of North Carolina from November Martin W. Hahn, 2010 to November 2011, during which a natural perturbation occurred: the inundation of University of Innsbruck, Austria the lower reaches of an otherwise drought-stricken river associated with Hurricane Irene, *Correspondence: John Paul Balmonte which passed over eastern North Carolina in late August 2011. This event provided the [email protected] opportunity to examine the microbiological, hydrological, and geochemical impacts of a disturbance, defined here as the large freshwater influx into the Tar River, superimposed Specialty section: This article was submitted to on seasonal changes or other ecosystem variability independent of the hurricane. Our Aquatic Microbiology, findings demonstrate that downstream communities are more taxonomically diverse a section of the journal Frontiers in Microbiology and temporally variable than their upstream counterparts. -
Anoxygenic Phototrophic Chloroflexota Member Uses a Type I Reaction Center
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.07.190934; this version posted July 7, 2020. 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. Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center Tsuji JM1*, Shaw NA1, Nagashima S2, Venkiteswaran JJ1,3, Schiff SL1, Hanada S2, Tank M2,4*, Neufeld JD1* 5 1University of Waterloo, 200 University Avenue West, Waterloo, Ontario, Canada, N2L 3G1 2Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo, Japan, 192-0397 3Wilfrid Laurier University, 75 University Avenue West, Waterloo, Ontario, Canada, N2L 3C5 4Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 10 Inhoffenstrasse 7B, 38124 Braunschweig, Germany *Corresponding authors: [email protected]; [email protected]; [email protected] Keywords: Chloroflexota; Chloroflexi; filamentous anoxygenic phototroph; boreal lakes; anoxygenic photoautotrophy; evolution of photosynthesis; enrichment cultivation bioRxiv preprint doi: https://doi.org/10.1101/2020.07.07.190934; this version posted July 7, 2020. 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. 15 Summary Chlorophyll-based phototrophy is performed using quinone and/or Fe-S type reaction centers1,2. Unlike oxygenic phototrophs, where both reaction center classes are used in tandem as Photosystem II and Photosystem I, anoxygenic phototrophs use only one class of reaction center, termed Type II (RCII) or Type I (RCI) reaction centers, separately for phototrophy3. -
Approches Moléculaires De La Diversité Microbienne De Deux Environnements Extrêmes : Les Sources Hydrothermales Profondes Et Les Réservoirs Pétroliers Erwan Corre
Approches moléculaires de la diversité microbienne de deux environnements extrêmes : les sources hydrothermales profondes et les réservoirs pétroliers Erwan Corre To cite this version: Erwan Corre. Approches moléculaires de la diversité microbienne de deux environnements extrêmes : les sources hydrothermales profondes et les réservoirs pétroliers. Biologie moléculaire. Université de Bretagne Occidentale, 2000. Français. tel-01115381 HAL Id: tel-01115381 https://hal.sorbonne-universite.fr/tel-01115381 Submitted on 12 Feb 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Avertissement Au vu de la législation sur les droits d'auteur, ce travail de thèse demeure la propriété de son auteur, et toute reproduction de cette oeuvre doit faire l'objet d'une autorisation de l'auteur. (cf Loi n°92-597; 1/07/1992. Journal Officiel, 2/07/1992) THESE présentée pour l'obtention du grade de Docteur de l'Université de Bretagne Occidentale (Mention Microbiologie) Erwan CORRE Approches moléculaires de la diversité microbienne de deux environnements extrêmes : les sources hydrothermales profondes et les réservoirs pétroliers Soutenue le Mercredi 2 Février 2000 devant le jury composé de : MM. P. CAUMETTE, Professeur, Université de Pau Examinateur M. -
Rugosibacter Aromaticivorans Gen. Nov., Sp. Nov., a Bacterium Within
NOTE Corteselli et al., Int J Syst Evol Microbiol 2014;67:311–318 DOI 10.1099/ijsem.0.001622 Rugosibacter aromaticivorans gen. nov., sp. nov., a bacterium within the family Rhodocyclaceae, isolated from contaminated soil, capable of degrading aromatic compounds Elizabeth M. Corteselli, Michael D. Aitken and David R. Singleton* Abstract A bacterial strain designated Ca6T was isolated from polycyclic aromatic hydrocarbon (PAH)-contaminated soil from the site of a former manufactured gas plant in Charlotte, NC, USA, and linked phylogenetically to the family Rhodocyclaceae of the class Betaproteobacteria. Its 16S rRNA gene sequence was highly similar to globally distributed environmental sequences, including those previously designated ‘Pyrene Group 1’ demonstrated to grow on the PAHs phenanthrene and pyrene by stable-isotope probing. The most closely related described relative was Sulfuritalea hydrogenivorans strain sk43HT (93.6 % 16S rRNA gene sequence identity). In addition to a limited number of organic acids, Ca6T was capable of growth on the monoaromatic compounds benzene and toluene, and the azaarene carbazole, as sole sources of carbon and energy. Growth on the PAHs phenanthrene and pyrene was also confirmed. Optimal growth was observed aerobically under mesophilic temperature, neutral pH and low salinity conditions. Major fatty acids present included summed feature 3 (C16 : 1!7c or C16 : 1 !6c) and C16 : 0. The DNA G+C content of the single chromosome was 55.14 mol% as determined by complete genome sequencing. Due to its distinct genetic and physiological properties, strain Ca6T is proposed as a member of a novel genus and species within the family Rhodocyclaceae, for which the name Rugosibacter aromaticivorans gen. -
Lateral Gene Transfer Challenges Principles of Microbial Systematics
Opinion Lateral gene transfer challenges principles of microbial systematics Eric Bapteste1 and Yan Boucher2 1 UPMC UMR 7138, 7 quai Saint-Bernard, Baˆ timent A, 4e`me e´ tage, 75005, Paris, France 2 Department of Civil and Environmental Engineering, MIT, Building 48–305, 77 Massachusetts Avenue, Cambridge, MA 02139, USA Evolutionists strive to learn about the natural historical As a result, the traditional TOL reconstruction project, process that gave rise to various taxa, while also as far as prokaryotic organisms are concerned, fell short. It attempting to classify them efficiently and make gener- is arguable whether debating the branching order in the alizations about them. The quantitative importance of TOL and looking for a unique nested hierarchy is a satis- lateral gene transfer inferred from genomic data, factory way to classify such microbes in the presence of although well acknowledged by microbiologists, is in lateral gene transfer. Instead, we propose alternative con- conflict with the conceptual foundations of the cepts to the traditional phylogenetic projects to deal with traditional phylogenetic system erected to achieve these microbial evolution and systematics: (i) a redefinition of goals. To provide a true account of microbial evolution, natural groups; (ii) the description of a new type of evol- we suggest developing an alternative conception of utionary unit originating from lateral gene transfer (LGT); natural groups and introduce a new notion – the com- and (iii) the realization of an interactive taxonomical data- posite evolutionary unit. Furthermore, we argue that a base (comprising overlapping groups) to progress towards comprehensive database containing overlapping taxo- a more natural classification. -
Draft Genome Sequence of a Nitrate-Reducing, O-Phthalate Degrading Bacterium, Azoarcus Sp. Strain PA01T Madan Junghare1,2*, Yogita Patil2 and Bernhard Schink2
Erschienen in: Standards in Genomic Sciences ; 10 (2015). - 90 http://dx.doi.org/10.1186/s40793-015-0079-9 Junghare et al. Standards in Genomic Sciences (2015) 10:90 DOI 10.1186/s40793-015-0079-9 SHORT GENOME REPORT Open Access Draft genome sequence of a nitrate-reducing, o-phthalate degrading bacterium, Azoarcus sp. strain PA01T Madan Junghare1,2*, Yogita Patil2 and Bernhard Schink2 Abstract Azoarcus sp. strain PA01T belongs to the genus Azoarcus,ofthefamilyRhodocyclaceae within the class Betaproteobacteria. It is a facultatively anaerobic, mesophilic, non-motile, Gram-stain negative, non-spore-forming, short rod-shaped bacterium that was isolated from a wastewater treatment plant in Constance, Germany. It is of interest because of its ability to degrade o-phthalate and a wide variety of aromatic compounds with nitrate as an electron acceptor. Elucidation of the o-phthalate degradation pathway may help to improve the treatment of phthalate-containing wastes in the future. Here, we describe the features of this organism, together with the draft genome sequence information and annotation. The draft genome consists of 4 contigs with 3,908,301 bp and an overall G + C content of 66.08 %. Out of 3,712 total genes predicted, 3,625 genes code for proteins and 87 genes for RNAs. The majority of the protein-encoding genes (83.51 %) were assigned a putative function while those remaining were annotated as hypothetical proteins. Keywords: Azoarcus sp. strain PA01T, o-phthalate degradation, Rhodocyclaceae, Betaproteobacteria, anaerobic degradation, wastewater treatment plant, pollutant Introduction aromatic compounds found in fossil fuel [8], such as phen- Phthalic acid consists of a benzene ring to which two anthrene [9], fluorene [10] and fluoranthene [11]. -
Rubrivivax Benzoatilyticus Sp. Nov., an Aromatic, Hydrocarbon-Degrading Purple Betaproteobacterium
International Journal of Systematic and Evolutionary Microbiology (2006), 56, 2157–2164 DOI 10.1099/ijs.0.64209-0 Rubrivivax benzoatilyticus sp. nov., an aromatic, hydrocarbon-degrading purple betaproteobacterium Ch. V. Ramana,1 Ch. Sasikala,2 K. Arunasri,2 P. Anil Kumar,2 T. N. R. Srinivas,2 S. Shivaji,3 P. Gupta,3 J. Su¨ling4 and J. F. Imhoff4 Correspondence 1Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Ch. V. Ramana PO Central University, Hyderabad 500 046, India [email protected] 2Environmental Microbial Biotechnology Laboratory, Center for Environment, Institute of or Science and Technology, J.N.T. University, Kukatpally, Hyderabad 500 072, India [email protected] 3Center for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India 4Leibniz-Institut fu¨r Meereswissenschaften, IFM-GEOMAR, Marine Mikrobiologie, Du¨sternbrooker Weg 20, 24105 Kiel, Germany A brown-coloured bacterium was isolated from photoheterotrophic (benzoate) enrichments of flooded paddy soil from Andhra Pradesh, India. On the basis of 16S rRNA gene sequence analysis, strain JA2T was shown to belong to the class Betaproteobacteria, related to Rubrivivax gelatinosus (99 % sequence similarity). Cells of strain JA2T are Gram-negative, motile rods with monopolar single flagella. The strain contained bacteriochlorophyll a and most probably the carotenoids spirilloxanthin and sphaeroidene, but did not have internal membrane structures. Intact cells had absorption maxima at 378, 488, 520, 590, 802 and 884 nm. No growth factors were required. Strain JA2T grew on benzoate, 2-aminobenzoate (anthranilate), 4-aminobenzoate, 4-hydroxy- benzoate, phthalate, phenylalanine, trans-cinnamate, benzamide, salicylate, cyclohexanone, cyclohexanol and cyclohexane-2-carboxylate as carbon sources and/or electron donors. -
Hidden Sources and Sinks of Fe(II) in the Sedimentary Biogeochemical Iron Cycle – the Role of Light
Hidden sources and sinks of Fe(II) in the sedimentary biogeochemical iron cycle – The role of light Dissertation der Mathematisch-Naturwissenschaftlichen Fakultät der Eberhard Karls Universität Tübingen zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) vorgelegt von M. Sc. Ulf Lüder aus Heidenheim an der Brenz Tübingen 2019 Gedruckt mit Genehmigung der Mathematisch-Naturwissenschaftlichen Fakultät der Eberhard Karls Universität Tübingen. Tag der mündlichen Qualifikation: 15.11.2019 Dekan: Prof. Dr. Wolfgang Rosenstiel 1. Berichterstatter: Prof. Dr. Andreas Kappler 2. Berichterstatter: Prof. Dr. Bo Barker Jørgensen Contents Summary ............................................................................................................................................... 1 Zusammenfassung............................................................................................................................. 3 Chapter 1: Introduction and objectives of this study ............................................................... 5 1.1 Abiotic Fe redox reactions ................................................................................................... 5 1.2 Microbially catalyzed Fe redox reactions .......................................................................... 6 1.3 Biogeochemical Fe cycling in freshwater and marine sediments ................................. 8 1.4 Field sites description ........................................................................................................