DOCSLIB.ORG

View (Win32) V1.5.2 (Copyright Roderic D.M

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
View (Win32) V1.5.2 (Copyright Roderic D.M UNIVERSITY OF CINCINNATI Date:___________________ I, _________________________________________________________, hereby submit this work as part of the requirements for the degree of: in: It is entitled: This work and its defense approved by: Chair: _______________________________ _______________________________ _______________________________ _______________________________ _______________________________ Identification and Characterization of Bacterial Communities in Warm Groundwater Aquifers By Ian Laseke B.S. University of Cincinnati, Cincinnati, OH 45268 THESIS Submitted in partial fulfillment of the requirements for the M.S. Degree in Environmental Engineering In the College of Engineering in University of Cincinnati Cincinnati, Ohio 2006 ii ABSTRACT In Peoria, Arizona during the autumn season of 2002, two young children died from Primary amoebic meningoencephalitis (PAM) infections. Naegleria fowleri, was detected in the residual water from household pipes and sinks and was linked to the cause of PAM infections that resulted in the death of both children. In this study, we tested the same groundwater in Peoria, Arizona that was suspected to be contaminated by N. fowleri, for the presence of N. fowleri. Results of the study indicated the presence of N. fowleri in 12 samples. Five samples were analyzed for bacterial communities, of which three were PCR positive for N. fowleri. Analysis of bacterial communities present in the Peoria groundwater samples indicated the presence of β-proteobacteria such as Caldimonas manganoxidans, Leptothrix species, Aquabacterium species and bacteria of other genus such as Chloroflexus, Cytophaga, Flexibacter, Halochromatium, Meiothermus, Nitrospira, Nocardia, Rasbo bacterium, and Thermus. iii iv ACKNOWLEDGEMENT I feel grateful to the following people, without whom this thesis would not have been possible: Dr. Daniel B. Oerther, advisor; Dr. Sandhya Parshionikar, mentor and friend; My lab-mates, especially Kai Zhang, Mau-Yi Wu, Ting Lu, Rob Smith, and Pascal E. Saikaly, for their assistance in learning molecular biology. v TABLE OF CONTENTS Abstract…………………………………………………………………………………...iii Acknowledgement………………………………………………………………………...v Table of Contents…………………………………………………………………………vi Introduction……………………………………………………………………………….1 Methods and Materials…………………………………………………………………....5 Results……………………………………………………………………………………13 Validate Assay for N. fowleri…………………………………………………….13 Validate N. fowleri Assay in Environment……...…………………………….....17 Discussion………………………………………………………………………………..19 Validate Assay for E. coli O157:H7…………………………………………..…20 Validate E. coli O157:H7 in Environment…………………………………….....22 Identification of Predominant Bacterial Populations in Environment…………...22 Summary of Species Related to Sequences…………………………………...…28 Phylogenetic Analysis………………………………………………………...….40 Appendix…………………………………………………………………………...…….52 Tables………………………………………………………………………….…53 References……………………………………………………………………………..…73 vi INTRODUCTION General water microbiology More than 70 percent of the earth’s surface consists of water, both fresh and salt water. Oceans, seas, and certain inland lakes make up the marine habitats that contain salt concentrations of 3.5 percent and higher. Ponds, streams, lakes, rivers, and underground aquifers make up the freshwater habitats, which is only 2 percent of the total water on the planet (40). Several chemical and physical factors influence the microbial populations present in water environments. In fresh and salt waters there are various microorganisms found naturally, while other microorganisms can infiltrate into these waters from soil, industrial or domestic processes, and other contaminating events. Groundwater generally has good overall quality with little color, turbidity, and low numbers of microorganisms. However, groundwater may have high concentrations of dissolved minerals. On the other hand, surface waters contain large numbers of microorganisms and originate from streams, ponds, rivers, lakes, and shallow wells. Groundwater and surface water can be infiltrated and contaminated by potentially pathogenic bacteria, viruses, protozoa, and amoebae originating from raw wastewater, which is one of the greatest threats to the quality of water supplies (40). 1 A variety of bacteria, viruses, and protozoa cause waterborne infectious diseases and are a large source of illness and death worldwide, especially in developing countries lacking water treatment technology (40). There are very rigid water quality standards in developed countries, which limit the spread of waterborne diseases. In the United States, the Environmental Protection Agency (EPA) enforces the Clean Water Act and the Safe Drinking Water Act (SDWA) to ensure high quality of drinking water. Control of drinking water quality was given to the federal EPA in 1974, when congress passed the SDWA. Over the years, namely 1986 and 1996, congress has passed amendments to the SDWA. A federal regulation used to improve the microbiological quality of drinking water is the Total Coliform Rule. This regulation sets a maximum contaminant level for fecal coliform bacteria, E. coli, and total coliform bacteria in treated drinking water. To protect the quality of surface water the Surface Water Treatment Rule and the Enhanced Surface Water Treatment Rule focus on Legionella, Giardia, enteric viruses, heterotrophic bacteria plate count, and Cryptosporidium spores. Disinfection and other specific treatment technology are proposed by the EPA by this rule in order to achieve the reduction of these microorganisms (22). For groundwater protection there are currently three programs run by the EPA: 1) the Wellhead Protection Program (WPP) was designed to reduce the threat to the quality of groundwater used for public drinking water by identifying and managing recharge areas to specific wells or well fields, 2) the Source Water Assessment and Protection Program, which was created by the 1996 Amendments to the SDWA of 1974, builds on the 2 Wellhead Protection Program approach to protecting groundwater, 3) the Comprehensive State Groundwater Protection Programs establish a partnership between the EPA and the states, Native American tribes, and local governments to achieve a more efficient, coherent, and comprehensive approach to protecting the nation's groundwater resources. Specific water microbiology Microorganisms come from three domains of life: Bacteria, Archaea, and Eukarya. While no human pathogens have been identified from the domain of Archaea, there are a number of Bacteria and Eukaryotes capable of harming humans. Fecal contamination can occasionally introduce bacterial and protozoan (belonging to Eukarya) pathogens in drinking water in the United States. Infection of the free living amoeba Naegleria fowleri caused the death of two five-year old children in October 2002 from PAM (3). N. fowleri was discovered in the residual water from household pipes and sinks and linked to the cause of PAM infections that resulted in the death of both children (18). A total of 24 people in the United States have died by infection from N. fowleri during the period of 1989 to 2000 (6). Due to difficulties in detecting an uncommon infectious agent such as N. fowleri, many cases of infection are fatal. Amphotericin B, an anti-microbial agent, can be administered and is effective at eliminating the infection and allowing for a complete medical recovery of the infected individual if the identification of N. fowleri occurs quickly (3, 19). 3 The amoeboflagellate genus Naegleria contains pathogenic and nonpathogenic species, and most species are morphologically indistinguishable requiring molecular methods to define and identify members of the genus. The Naegleria isolates that cause PAM were given species status and named N. fowleri, after Malcolm Fowler who first recognized the disease in Australia (8, 19). N. fowleri is often isolated from warm soil and stagnant water up to 45oC, with cysts surviving temperatures up to 46oC, and is found with large quantities of fecal coliform bacteria as reported in the James River watershed, Virginia (8). The three life stages of N. fowleri include cysts, trophozoites, and flagellates. By entering the body through the mucous membranes of the nose, trophozoites infect humans and animals by traveling to the central nervous system where they cause PAM (8). Problem Statement The purpose of this study was to determine the presence of N. fowleri in the potable water supply from warm water aquifers in Peoria, Arizona where two children died from PAM. In a previous investigation a free living amoeba, N. fowleri, was discovered in the residual water from household pipes and sinks and linked to the cause of PAM infections that resulted in the death of both children. It was suspected that the probable vector of infection was the potable water supply from warm water aquifers in the area. Another goal of this study was to characterize the bacterial communities that were associated with N. fowleri. PCR assays and sequencing were used to detect N. fowleri, bacterial pathogens, and predominant bacterial populations from groundwater samples. 4 METHODS AND MATERIALS Samples Eschericha coli O157:H7 cultivation For the cultivation of Eschericha coli (E. coli) strains K12 and O157:H7, the pure cultures were grown in Luria Bertani (LB) medium (see Table 1 for a list of media and components). The medium was sterilized by autoclaving at 121oC for an amount of time dependent on the volume. The cultures were grown overnight (12-16 hours)
Load more

Recommended publications
  • Community Structure and Function of High-Temperature Chlorophototrophic Microbial Mats Inhabiting Diverse Geothermal Environments
    ORIGINAL RESEARCH ARTICLE published: 03 June 2013 doi: 10.3389/fmicb.2013.00106 Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments Christian G. Klatt 1,2†,William P.Inskeep 1,2*, Markus J. Herrgard 3, Zackary J. Jay 1,2, Douglas B. Rusch4, Susannah G.Tringe 5, M. Niki Parenteau 6,7, David M. Ward 1,2, Sarah M. Boomer 8, Donald A. Bryant 9,10 and Scott R. Miller 11 1 Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA 2 Thermal Biology Institute, Montana State University, Bozeman, MT, USA 3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark 4 Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA 5 Department of Energy Joint Genome Institute, Walnut Creek, CA, USA 6 Search for Extraterrestrial Intelligence Institute, Mountain View, CA, USA 7 National Aeronautics and Space Administration Ames Research Center, Mountain View, CA, USA 8 Western Oregon University, Monmouth, OR, USA 9 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA 10 Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA 11 Department of Biological Sciences, University of Montana, Missoula, MT, USA Edited by: Six phototrophic microbial mat communities from different geothermal springs (YNP) were Martin G. Klotz, University of North studied using metagenome sequencing and geochemical analyses. The primary goals of Carolina at Charlotte, USA this work were to determine differences in community composition of high-temperature Reviewed by: Andreas Teske, University of North phototrophic mats distributed across theYellowstone geothermal ecosystem, and to iden- Carolina at Chapel Hill, USA tify metabolic attributes of predominant organisms present in these communities that may Jesse Dillon, California State correlate with environmental attributes important in niche differentiation.
    [Show full text]
  • The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
    life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment.
    [Show full text]
  • BBA - Bioenergetics 1860 (2019) 461–468
    BBA - Bioenergetics 1860 (2019) 461–468 Contents lists available at ScienceDirect BBA - Bioenergetics journal homepage: www.elsevier.com/locate/bbabio Phospholipid distributions in purple phototrophic bacteria and LH1-RC core complexes T S. Nagatsumaa, K. Gotoua, T. Yamashitaa, L.-J. Yub, J.-R. Shenb, M.T. Madiganc, Y. Kimurad, ⁎ Z.-Y. Wang-Otomoa, a Faculty of Science, Ibaraki University, Mito 310-8512, Japan b Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan c Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, USA d Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan ARTICLE INFO ABSTRACT Keywords: In contrast to plants, algae and cyanobacteria that contain glycolipids as the major lipid components in their Thermochromatium tepidum photosynthetic membranes, phospholipids are the dominant lipids in the membranes of anoxygenic purple Light-harvesting phototrophic bacteria. Although the phospholipid compositions in whole cells or membranes are known for a Reaction center limited number of the purple bacteria, little is known about the phospholipids associated with individual Antenna complex photosynthetic complexes. In this study, we investigated the phospholipid distributions in both membranes and Cardiolipin the light-harvesting 1-reaction center (LH1-RC) complexes purified from several purple sulfur and nonsulfur bacteria. 31P NMR was used for determining the phospholipid compositions and inductively coupled plasma atomic emission spectroscopy was used for measuring the total phosphorous contents. Combining these two techniques, we could determine the numbers of specific phospholipids in the purified LH1-RC complexes. A total of approximate 20–30 phospholipids per LH1-RC were detected as the tightly bound lipids in all species.
    [Show full text]
  • Diversity of Anoxygenic Phototrophs in Contrasting Extreme Environments
    ÓäÎ ÛiÀÃÌÞÊvÊÝÞ}iVÊ* ÌÌÀ« ÃÊÊ ÌÀ>ÃÌ}Ê ÝÌÀiiÊ ÛÀiÌà -ICHAEL4-ADIGAN \$EBORAH/*UNG\%LIZABETH!+ARR 7-ATTHEW3ATTLEY\,AURIE!!CHENBACH\-ARCEL4*VANDER-EER $EPARTMENTOF-ICROBIOLOGY 3OUTHERN)LLINOIS5NIVERSITY #ARBONDALE $EPARTMENTOF-ICROBIOLOGY /HIO3TATE5NIVERSITY #OLUMBUS $EPARTMENTOF-ARINE"IOGEOCHEMISTRYAND4OXICOLOGY .ETHERLANDS)NSTITUTEFOR3EA2ESEARCH.)/: $EN"URG 4EXEL 4HE.ETHERLANDS #ORRESPONDING!UTHOR $EPARTMENTOF-ICROBIOLOGY 3OUTHERN)LLINOIS5NIVERSITY #ARBONDALE ), 0HONE&AX% MAILMADIGAN MICROSIUEDU Óä{ "/ ,Ê ""9Ê Ê " -/,9Ê Ê9 "7-/" Ê /" Ê*, -/, /ÊÊ 4HISCHAPTERDESCRIBESTHEGENERALPROPERTIESOFSEVERALANOXYGENICPHOTOTROPHICBACTERIAISOLATEDFROMEXTREMEENVIRONMENTS 4HESEINCLUDEPURPLEANDGREENSULFURBACTERIAFROM9ELLOWSTONEAND.EW:EALANDHOTSPRINGS ASWELLASPURPLENONSULFUR BACTERIAFROMAPERMANENTLYFROZEN!NTARCTICLAKE4HECOLLECTIVEPROPERTIESOFTHESEEXTREMOPHILICBACTERIAHAVEYIELDEDNEW INSIGHTSINTOTHEADAPTATIONSNECESSARYTOCARRYOUTPHOTOSYNTHESISINCONSTANTLYHOTORCOLDENVIRONMENTS iÞÊ7À`à Ì>ÀVÌVÊ ÀÞÊ6>iÞà ÀL>VÕÕÊ­ ÀLÕ®Ê Ìi«`Õ «ÕÀ«iÊL>VÌiÀ> , `viÀ>ÝÊ>Ì>ÀVÌVÕà ,ÃiyiÝÕÃÊë° / iÀV À>ÌÕÊÌi«`Õ Diversity of Anoxygenic Phototrophs 205 1.0 INTRODUCTION Antarctic purple bacteria were enriched using standard Anoxygenic phototrophic bacteria inhabit a variety liquid enrichment methods (Madigan 1988) from the of extreme environments, including thermal, polar, water column of Lake Fryxell, a permanently frozen lake hypersaline, acidic, and alkaline aquatic and terrestrial in the Taylor Valley, McMurdo Dry Valleys, Antarctica habitats (Madigan 2003). Typically, one finds
    [Show full text]
  • Anoxygenic Phototrophic Bacterial Diversity Within Wastewater Stabilization Plant During ‘Red Water’ Phenomenon
    Int. J. Environ. Sci. Technol. (2013) 10:837–846 DOI 10.1007/s13762-012-0163-2 ORIGINAL PAPER Anoxygenic phototrophic bacterial diversity within wastewater stabilization plant during ‘red water’ phenomenon A. Belila • I. Fazaa • A. Hassen • A. Ghrabi Received: 22 November 2011 / Revised: 2 October 2012 / Accepted: 21 October 2012 / Published online: 13 February 2013 Ó Islamic Azad University (IAU) 2013 Abstract The molecular diversity of the purple photo- Introduction synthetic bacteria was assessed during temporal pigmen- tation changes in four interconnected wastewater Wastewater stabilization ponds (WSPs) are an extremely stabilization ponds treating domestic wastewater by dena- effective, natural form of wastewater treatment. They turant gel gradient electrophoresis method applying pufM combine simplicity, robustness, low cost, and a very high gene. Results revealed high phylogenetic diversity of the degree of disinfection. WSPs are usually designed as one or purple phototrophic anoxygenic bacteria community char- more series of anaerobic, facultative, and maturation acterized by the presence of the purple non-sulfur, purple ponds. Their low operation and maintenance costs have sulfur, and purple aerobic photosynthetic anoxygenic bac- made them a popular choice for wastewater treatment, teria. This phototrophic bacterial assemblage was domi- particularly in developing countries since there is little nated by the purple non-sulfur bacteria group (59.3 %) need for specialized skills to operate the system. One of the with six different genera followed by the purple sulfur major problems which can cause malfunction of the WSP community (27.8 %) with four genera and finally 12.9 % is the massive growth of purple color producing bacteria of the pufM gene sequences were assigned throughout the (Belila et al.
    [Show full text]
  • Abiotic and Biotic Influences on Travertine Formation at Mammoth
    Sedimentology (2011) 58, 170–219 doi: 10.1111/j.1365-3091.2010.01209.x Hot-spring Systems Geobiology: abiotic and biotic influences on travertine formation at Mammoth Hot Springs, Yellowstone National Park, USA BRUCE W. FOUKE Departments of Geology, Microbiology, and Institute for Genomic Biology, University of Illinois Urbana-Champaign, 1301 West Green Street, Urbana, IL 61801, USA and Thermal Biology Institute, Montana State University, Leon Johnson Hall, Bozeman, MT 59717, USA (E-mail: [email protected]) Associate Editor – Jim Best ABSTRACT Multiple abiotic and biotic factors combine in nature to influence the formation of calcium carbonate limestone deposits. Systems Geobiology studies of how micro-organisms respond to, or sometimes even control, the coupled effects of environmental change and mineralization will permit more accurate interpretation of the fossil record of ancient microbial life. Mammoth Hot Springs in Yellowstone National Park, USA, serves as a natural laboratory for tracking how the dynamic interplay of physical, chemical and biological factors come together to form hot-spring limestone (called ‘travertine’). Systematic downstream correlations occur at Mammoth Hot Springs between travertine deposition (geomorphology, crystalline structure and geochemistry), microbial communities (mat morphology, pigmentation, and phylogenetic and metabolic diversity) and spring-water conditions (temperature, pH, geochemistry and flow). Field-based microscale and mesoscale experimentation indicates that microbes directly influence travertine growth rate and crystalline structure. At the macroscale, time-lapse field photography and numerical modelling suggest that travertine terrace geomorphology is influenced strongly by hydrology, heat dispersion and geochemistry. These results from Mammoth Hot Springs allow establishment of a conceptual framework across broad spatial and temporal scales in which to track how multiple geological and biological factors combine to control CaCO3 crystal precipitation and the resulting formation of travertine deposits.
    [Show full text]
  • Phaeobacterium Nitratireducens Gen. Nov., Sp. Nov., a Phototrophic
    International Journal of Systematic and Evolutionary Microbiology (2015), 65, 2357–2364 DOI 10.1099/ijs.0.000263 Phaeobacterium nitratireducens gen. nov., sp. nov., a phototrophic gammaproteobacterium isolated from a mangrove forest sediment sample Nupur,1 Naga Radha Srinivas Tanuku,2 Takaichi Shinichi3 and Anil Kumar Pinnaka1 Correspondence 1Microbial Type Culture Collection and Gene Bank, CSIR – Institute of Microbial Technology, Anil Kumar Pinnaka Sector 39A, Chandigarh – 160 036, India [email protected] 2CSIR – National Institute of Oceanography, Regional Centre, 176, Lawsons Bay Colony, Visakhapatnam – 530017, India 3Nippon Medical School, Department of Biology, Kosugi-cho, Nakahara, Kawasaki 211-0063, Japan A novel brown-coloured, Gram-negative-staining, rod-shaped, motile, phototrophic, purple sulfur bacterium, designated strain AK40T, was isolated in pure culture from a sediment sample collected from Coringa mangrove forest, India. Strain AK40T contained bacteriochlorophyll a and carotenoids of the rhodopin series as major photosynthetic pigments. Strain AK40T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically and did not utilize sulfide or thiosulfate as electron donors. Thiamine and riboflavin were required for growth. The dominant fatty acids were C12 : 0,C16 : 0, C18 : 1v7c and summed feature 3 (C16 : 1v7c and/or iso-C15 : 0 2-OH). The polar lipid profile of strain AK40T was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and eight unidentified lipids. Q-10 was the predominant respiratory quinone. The DNA G+C content of strain AK40T was 65.5 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represented a member of the family Chromatiaceae within the class Gammaproteobacteria.
    [Show full text]
  • Modern Topics in the Phototrophic Prokaryotes, DOI 10.1007/978-3-319-46261-5 482 Index
    Index A Candidatus Thermochlorobacter Acaryochloris marina, 15 aerophilum, 115–117 Acidic habitats, 447 Chloracidobacterium thermophilum, Acidicophilic phototrophic bacteria, 447–448 113–115 Acidiphilium rubrum, 117 metagenomic and metatranscriptomic Acidobacteria, 89, 90, 97, 112, 113, 123, 164 analysis, 112 Acidophiles, 469–470 types, 112 Adenosine A2a receptor (A2aR), 405 Alka(e)ne production, 381–382 Aerobic anoxygenic phototrophic bacteria Alkaline soda lakes. See Alkaliphilic (AAPB), 117 phototrophic bacteria Aerobic anoxygenic phototrophs (AAP), Alkaliphiles, 470 311, 312 Alkaliphilic phototrophic bacteria apparatus, photosynthetic, 208 Big Soda Lake, 457 BChl a, 194 Böddi-szék Soda Lake in Ungary, 458 carbon metabolic pathways, 201–203 brackish water and seawater salinities, 449 carotenoid, 195 halophilic purple sulfur bacterium, 449 characteristics, 198 harbor massive developments, 449 distribution and enumeration, 195–197 Mono Lake, 458 LH1 and LH2 complexes, 209 pH values, 448 morphology, 200 soap lakes, 456–457 photosynthetic electron transport chain, soda lakes, 448 209, 210 Kulunda Steppe (Altai Krai), 451 photosynthetic pigments Mongolian, 451 BChl a synthesis, 205–207 Transbaikal Region, 452 carotenoids, 207, 208 Wadi el-Natrun, 452–456 phylogenetic conundrums, 197, 199 sulfur-oxidizing chemotrophic PNSB, 195 bacteria, 449 toxic heavy metal(loid) oxides, 203–205 Allophycocyanin, 98, 101 zooplankton grazing, 201 Alphaproteobacteria, 449 Aerobic anoxygenic purple bacteria (AAPB) Alphaproteobacteria, purple nonsulfur alkaline,
    [Show full text]
  • Phylogenetic Relationships Among the Chromatiaceae, Their
    International Journal of Systematic Bacteriology (1998), 48, 11 29-1 143 Printed in Great Britain Phylogenetic relationships among the Chromatiaceae, their taxonomic reclassification and description of the new genera Allochromatium, Halochromatium, Isochromatium, Marichromatiurn , Thiococcus, Thiohalocapsa and Thermochromatium Johannes F. Imhoff, Jorg Wing and Ralf Petri Author for correspondence: Johannes F. Imhoff. Tel: +49 431 697 3850. Fax: +49 431 565876. e-mail : jimhoff(n ifm.uni-kiel.de lnstitut fur Meereskunde Sequences of the 16s rDNA from all available type strains of Chromatium an der Universitat Kiel, species have been determined and were compared to those of other Abteilung Marine Mikrobiologie, Chromatiaceae, a few selected Ectothiorhodospiraceae and Escherichia coli. Dusternbrooker Weg 20, The clear separation of Ectothiorhodospiraceae and Chromatiaceae is D-24105 Kiel, Germany confirmed. Most significantly the sequence comparison revealed a genetic divergence between Chromatium species originated from freshwater sources and those of truly marine and halophilic nature. Major phylogenetic branches of the Chromatiaceae contain (i)marine and halophilic species, (ii)freshwater Chromatium species together with Thiocystis species and (iii)species of the genera Thiocapsa and Amoebobacter as recently reclassified [Guyoneaud, R. & 6 other authors (1998). lnt J Syst Bacteriol48, 957-9641, namely Thiocapsa roseopersicina, Thiocapsa pendens (formerly Amoebobacter pendens), Thiocapsa rosea (formerly Amoebobacter roseus), Amoebobacter purpureus and Thiolamprovum pedioforme (formerly Amoebobacter pedioformis). The genetic relationships between the species and groups are not in congruence with the current classification of the Chromatiaceae and a reclassification is proposed on the basis of 16s rDNA sequence similarity supported by selected phenotypic properties. The proposed changes include the transfers of Chromatium minus and Chromatium violascens to Thiocystis minor comb.
    [Show full text]
  • Characterization of Purple Sulfur Bacteria from the South Andros
    Blackwell Science, LtdOxford, UKEMIEnvironmental Microbiology 1462-2912Society for Applied Microbiology and Blackwell Publishing Ltd, 2005Original ArticlePhototrophic bacteria in the South Andros Black HoleR. A. Herbert et al. Environmental Microbiology (2005) doi:10.1111/j.1462-2920.2005.00815.x Characterization of purple sulfur bacteria from the South Andros Black Hole cave system: highlights taxonomic problems for ecological studies among the genera Allochromatium and Thiocapsa Rodney A. Herbert,1* Anthony Ranchou-Peyruse,2 lems within these genera. These inconsistencies may Robert Duran,2 Rémy Guyoneaud2 and have implications for microbiologists studying the Stephanie Schwabe3 ecology of anoxygenic phototrophs. For ecologists 1Division of Environmental and Applied Biology, Biological studying the functioning of an ecosystem it may not Sciences Institute, University of Dundee, Dundee DD1 be particularily important to know whether a specific 4HN, Scotland. isolate belongs to one species or another. However, 2Laboratoire d’Ecologie Moléculaire-Microbiologie, if one wants to study the role of different populations EA3525, IBEAS, Université de Pau, BP1155, 64013 Pau, within a particular functional group then the species France. concept is important. This study demonstrates that 3Rob Palmer Blue Holes Foundation, 5 Longtitude Lane, further work is still required on the taxonomy of Charleston, SC 29401, USA. purple sulfur bacteria in order that microbial ecolo- gists are able to accurately identify a population/ species isolated from hitherto undescribed aquatic Summary ecosystems. A dense 1 m thick layer of phototrophic purple sulfur bacteria is present at the pycnocline (17.8 m depth) in Introduction the meromictic South Andros Black Hole cave system (Bahamas). Two purple sulfur bacteria present in sam- Phototrophic purple sulfur bacteria are widely distributed ples collected from this layer have been identified as in nature where oxygen is either absent or present at low belonging to the family Chromatiaceae.
    [Show full text]
  • A Comparative Look at Structural Variation Among RC–LH1 'Core'
    Photosynthesis Research https://doi.org/10.1007/s11120-020-00758-3 REVIEW A comparative look at structural variation among RC–LH1 ‘Core’ complexes present in anoxygenic phototrophic bacteria Alastair T. Gardiner1,2 · Tu C. Nguyen‑Phan1 · Richard J. Cogdell1 Received: 26 March 2020 / Accepted: 10 May 2020 © The Author(s) 2020 Abstract All purple photosynthetic bacteria contain RC–LH1 ‘Core’ complexes. The structure of this complex from Rhodobacter sphaeroides, Rhodopseudomonas palustris and Thermochromatium tepidum has been solved using X-ray crystallography. Recently, the application of single particle cryo-EM has revolutionised structural biology and the structure of the RC–LH1 ‘Core’ complex from Blastochloris viridis has been solved using this technique, as well as the complex from the non-purple Chlorofexi species, Roseifexus castenholzii. It is apparent that these structures are variations on a theme, although with a greater degree of structural diversity within them than previously thought. Furthermore, it has recently been discovered that the only phototrophic representative from the phylum Gemmatimonadetes, Gemmatimonas phototrophica, also contains a RC–LH1 ‘Core’ complex. At present only a low-resolution EM-projection map exists but this shows that the Gemmatimonas phototrophica complex contains a double LH1 ring. This short review compares these diferent structures and looks at the functional signifcance of these variations from two main standpoints: energy transfer and quinone exchange. Keywords Purple photosynthetic bacteria
    [Show full text]
  • Rhodobacter Sphaeroides and Escherichia Coli
    Assembly of modified and non-native proteins in Rhodobacter sphaeroides and Escherichia coli Katie Jane Grayson A thesis submitted for the degree of Doctor of Philosophy at the University of Sheffield Department of Molecular Biology and Biotechnology September 2015 Summary Photosynthesis is a highly efficient and productive process that converts solar energy into chemical energy. Much of the visible and near-infrared radiation falling on the surface of the Earth is not absorbed by photosynthesising organisms, which occupy particular spectral niches depending on the absorption of the particular pigments they synthesise. For synthetic biology applications it would be worthwhile to design and construct bacteria that could utilise a greater range of wavelengths than naturally-evolved photosynthetic bacteria. Although the incorporation of synthetic chromophores to complement native light-harvesting proteins is promising, the approach generally involves in vitro reassembly. In order to create tailor-made light harvesting antennas in vivo, we must make use of the toolbox of proteins and pigments available in nature, or create synthetic elements that are able to be created by the host organism. To investigate the possibility of creating artificial light-harvesting antennas in vivo, the yellow fluorescent protein, YFP, was incorporated as a chromophore into the photosynthetic apparatus of the purple photosynthetic bacterium Rhodobacter (Rba.) sphaeroides. It is shown that energy absorbed by YFP can transfer to the native reaction centre and LH1 proteins, sufficient to enhance the photosynthetic growth rate in a Rba. sphaeroides carotenoidless mutant. The light-driven proton pump, proteorhodopsin (PR), also has potential to augment the proton motive force in Rba.
    [Show full text]