DOCSLIB.ORG

Analysis of Environmental Bacteria Capable of Utilizing Reduced

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Analysis of Environmental Bacteria Capable of Utilizing Reduced ANALYSIS OF ENVIRONMENTAL BACTERIA CAPABLE OF UTILIZING REDUCED PHOSPHORUS COMPOUNDS ____________ A Thesis Presented to the Faculty of California State University, Chico ____________ In Partial Fulfillment of the Requirements for the Degree Master of Science in Biological Sciences ____________ by Brandee L. Stone Summer 2011 ANALYSIS OF ENVIRONMENTAL BACTERIA CAPABLE OF UTILIZING REDUCED PHOSPHORUS COMPOUNDS A Thesis by Brandee L. Stone Summer 2011 APPROVED BY THE DEAN OF GRADUATE STUDIES AND VICE PROVOST FOR RESEARCH: Eun K. Park, Ph.D. APPROVED BY THE GRADUATE ADVISORY COMMITTEE: !"#$%#&'()**"$+,#&*"-.(,#/'0($'1"'' Andrea K. White, Ph.D., Chair Graduate Coordinator Daniel D. Clark, Ph.D. Patricia L. Edelmann, Ph.D. Larry F. Hanne, Ph.D. Gordon V. Wolfe, Ph.D. ACKNOWLEDGEMENTS A thesis, though bearing a single author, is never a solo project. Without the support of the faculty (past and present in biology and chemistry) I never would have made it to the beginning of a Masters program. Without their continued support, I never would have made it to the end. Thank you Dr. Dan Clark, Dr. Patricia Edelmann, Dr. Larry Hanne, and Dr. Gordon Wolfe for your extensive support including guidance on developing experiments, data analysis, and reviews of this thesis. Thank you to past and present members of the Microbial Biochemistry Research Group, especially Dr. Larry Kirk, for your interest, questions, and suggestions. A huge thank you to Dr. Colleen Hatfield for your guidance and the very often swift kicks to get me back on track. Thank you Dr. Andrea White for taking a chance on a (sometimes) misguided undergraduate. Without you, this thesis would have been authored by another. Thank you Dr. William W. Metcalf for the control strains used in this study. Thank you Jeremy Ault and Jared Stockwell for your help with the PCR experiments. Finally, thank you to my friends and family. You never stopped cheering, pushing, and understanding. Support was received through the California State University, Chico Graduate Equity Fellowship. This work was funded by the Faculty-Student Collaborative Research Seed Grant from the California State University Program for Education and Research in Biotechnology (CSUPERB). iii TABLE OF CONTENTS PAGE Acknowledgements ....................................................................................... iii List of Tables ................................................................................................. vi List of Figures ................................................................................................ vii List of Nomenclature ...................................................................................... ix Abstract ......................................................................................................... x CHAPTER I. Introduction .................................................................................. 1 Molecular and Biochemical Characterization of Reduced Phosphorus Oxidation Pathways .................................... 4 Questions .......................................................................... 9 II. Materials and Methods ................................................................. 11 Media and Growth Conditions ........................................... 11 Most Probable Number for Reduced Phosphorus Oxidizing Bacteria ........................................................... 12 Genetic Analyses for htxA and ptxD .................................. 19 III. Results ......................................................................................... 24 Most Probable Number for Reduced Phosphorus Oxidizing Bacteria ........................................................... 24 Genetic Analyses for htxA and ptxD .................................. 32 IV. Discussion .................................................................................... 47 Most Probable Number for Reduced Phosphorus Oxidizing Bacteria ........................................................... 47 Genetic Analyses for htxA and ptxD .................................. 52 iv PAGE References .................................................................................................... 61 Appendix A. Percent similarities for 16s, ptxD, and htxA .................................. 67 v LIST OF TABLES TABLE PAGE 1. Locations of sample sites in Glenn and Butte County, California ........ 14 2. Soil properties from the Soil Data Mart database for 12 natural environmental sites in Butte and Glenn County showing these are typical (i.e. not extreme) sites .................................................. 16 3. Primers and expected product size for amplified htxA and ptxD products ......................................................................................... 21 4. Substrate ranges, hybridization, and PCR for ptxD and htxA of 19 isolates ..................................................................................... 34 vi LIST OF FIGURES FIGURE PAGE 1. Structure, oxidation states, and abbreviations of reduced P compounds used or referenced in this study ................................ 2 2. Diagram showing the traditional P cycle ............................................ 3 3. Operons, loci, and substrates specific to each involved in the catalysis of reduced P compounds in P. stutzeri WM88, A. faecalis WM2072, X. flavus WM2814, and E. coli B ..................... 6 4. Biochemical pathway for HtxA and PtxD as characterized in P. stutzeri WM88 .............................................................................. 7 5. Location of MPN sites in Glenn and Butte County, California ............ 15 6. Diagram of MPN experimental setup ................................................. 19 7. MPN/g soil for sample Soil1 ............................................................... 25 8. The average MPN/g for 12 aquatic and terrestrial sites shows the number of bacteria capable of oxidizing Hpt, Pt, or AEpn are comparable to the MPN/g with Pi as the sole P source ................ 26 9. MPN/g sediment or soil slurry for 12 samples collected during summer (A) or winter (B) .............................................................. 28 10. MPN/g for reduced P oxidizing bacteria in each of the 12 aquatic (Sed) and terrestrial (Soil) sites arranged by most pristine (Sed1, mountain stream) to least pristine (Sed8, extensive urban and agricultural run-off) ...................................................... 30 11. Ratio of MPN capable of growth on Hpt, Pt, and AEpn expressed as a percentage of Pi (defined as 100%) ...................................... 31 12. Average MPN/g sediment or soil slurry for paired sites .................... 32 13. 16S rRNA identifications of 19 reduced P oxidizing bacteria ............. 35 vii 14. Hybridization for P. stutzeri WM88 ptxD ............................................ 37 15. Hybridization for htxA ......................................................................... 37 16. A 1% TAE agarose gel stained with ethidium bromide for htxA PCR products for all isolates ........................................................ 38 17. A 1% TAE agarose gel stained with ethidium bromide for A. faecalis WM2072 ptxD PCR products for all isolates.................... 39 18. A 1% TAE agarose gel stained with ethidium bromide for P. stutzeri WM88 ptxD PCR products for all isolates ........................ 40 19. A 1% TAE agarose gel stained with ethidium bromide for X. flavus WM2814 ptxD PCR products for all isolates ...................... 41 20. A 1% TAE agarose gel stained with ethidium bromide for X. flavus WM2814 ptxD PCR products for all isolates ...................... 42 21. Phylogenetic tree of ptxD amino acid sequences obtained from !"#$%&'()*+&"*,-./*0#+#1#!"!*2!""*34#+#1#!"*5'('()6*'(* Methods) and sequencing BS isolate ptxD PCR products ............ 43 22. 16S rRNA phylogenetic tree for bacteria possessing a ptxD ortholog (see Fig. 21) ................................................................... 45 23. A more accurate P cycle .................................................................... 60 viii LIST OF NOMENCLATURE P Phosphorus. Refers to any molecule or compound containing phosphorus. Pi Phosphate. Inorganic phosphorus compound. Oxidation state +5. Hpt Hypophosphite. Inorganic reduced phosphorus compound. Oxidation state +1. Pt Phosphite. Inorganic reduced phosphorus compound. Oxidation state +3. AEpn Aminoethylphosphonate. Organic reduced phosphorus compound. Oxidation state +3. PH3 Phosphine. Fully reduced phosphorus compound. Oxidation state -3. htxA Gene encoding a 2-oxoglutarate-dependent hypophosphite dioxygenase. Responsible for the oxidation of hypophosphite to phosphite. ptxD Gene encoding an NAD-dependent phosphite dehydrogenase. Responsible for the oxidation of phosphite to phosphate. RPO Reduced phosphorus oxidation RPOB Reduced phosphorus oxidizing bacteria ix ABSTRACT ANALYSIS OF ENVIRONMENTAL BACTERIA CAPABLE OF UTILIZING REDUCED PHOSPHORUS COMPOUNDS by Brandee L. Stone Master of Science in Biological Sciences California State University, Chico Summer 2011 Although bacterial metabolic pathways to oxidize the reduced phosphorus compounds hypophosphite and phosphite have been characterized, bacterial reduced phosphorus oxidation in the environment and the impact of this activity on P biogeochemistry has largely been overlooked. In this study, I attempted to answer two of the basic questions in this field: (1) how abundant are culturable reduced phosphorus oxidizing bacteria
Load more

Recommended publications
  • Azorhizobium Doebereinerae Sp. Nov
    ARTICLE IN PRESS Systematic and Applied Microbiology 29 (2006) 197–206 www.elsevier.de/syapm Azorhizobium doebereinerae sp. Nov. Microsymbiont of Sesbania virgata (Caz.) Pers.$ Fa´tima Maria de Souza Moreiraa,Ã, Leonardo Cruzb,Se´rgio Miana de Fariac, Terence Marshd, Esperanza Martı´nez-Romeroe,Fa´bio de Oliveira Pedrosab, Rosa Maria Pitardc, J. Peter W. Youngf aDepto. Cieˆncia do solo, Universidade Federal de Lavras, C.P. 3037 , 37 200–000, Lavras, MG, Brazil bUniversidade Federal do Parana´, C.P. 19046, 81513-990, PR, Brazil cEmbrapa Agrobiologia, antiga estrada Rio, Sa˜o Paulo km 47, 23 851-970, Serope´dica, RJ, Brazil dCenter for Microbial Ecology, Michigan State University, MI 48824, USA eCentro de Investigacio´n sobre Fijacio´n de Nitro´geno, Universidad Nacional Auto´noma de Mexico, Apdo Postal 565-A, Cuernavaca, Mor, Me´xico fDepartment of Biology, University of York, PO Box 373, York YO10 5YW, UK Received 18 August 2005 Abstract Thirty-four rhizobium strains were isolated from root nodules of the fast-growing woody native species Sesbania virgata in different regions of southeast Brazil (Minas Gerais and Rio de Janeiro States). These isolates had cultural characteristics on YMA quite similar to Azorhizobium caulinodans (alkalinization, scant extracellular polysaccharide production, fast or intermediate growth rate). They exhibited a high similarity of phenotypic and genotypic characteristics among themselves and to a lesser extent with A. caulinodans. DNA:DNA hybridization and 16SrRNA sequences support their inclusion in the genus Azorhizobium, but not in the species A. caulinodans. The name A. doebereinerae is proposed, with isolate UFLA1-100 ( ¼ BR5401, ¼ LMG9993 ¼ SEMIA 6401) as the type strain.
    [Show full text]
  • Xanthobacter Flavus, a New Species of Nitrogen-Fixing Hydrogen Bacteria
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Oct. 1979, p. 283-287 Vol. 29, No. 4 0020-7713/79/04-0283/05$02.00/0 Xanthobacter flavus, a New Species of Nitrogen-Fixing Hydrogen Bacteria K. A. MALIK AND D. CLAUS Deutsche Sammlung von Mikroorganismen, Gesellschaft fur Biotechnologische Forschung mbH, D-3400 Gottingen, Federal Republic of Germany Mycobacterium flavum strain 301 (= Deutsche Sammlung von Mikroorganis- men 338), a hydrogen-utilizing bacterium, is capable of fixing molecular nitrogen and resembles other nitrogen-fixing hydrogen bacteria. However, it is clearly different in many characters from other strains of M. flavum (Orla-Jensen) Jensen (syn.: Micro bacterium flavum Orla-Jensen). It does resemble strains of Xantho- bacter Wiegel et al. with respect to cell wall composition, production of carotenoid pigments, carbon source utilization pattern, and deoxyribonucleic acid (DNA) base composition (69 mol% guanine + cytosine). Strain 301 is here regarded as belonging to a new and distinct species, for which the name Xanthobacter flauus is proposed. Strain 301 is the type strain of this species. X. flavus differs from Xanthobacter autotrophicus, the only other species in this genus to date, in several respects, and the DNA-DNA hybridization between X. flavus and X. autotrophicus is only 25%. In 1961 Federov and Kalininskaya (13) iso- Tsukamura (24) showed that unlike most rap- lated an aerobic, nitrogen-fixing bacterium idly growing mycobacteria, strain 301 has no (strain 301) from turf podzol soils and identified mycobactin. Mycobacteria are usually gram pos- it according to Krasil’nikov’s scheme (18) as a itive and strongly acid fast, but strain 301 is member of Mycobacterium flavum (Orla-Jen- gram variable and weakly acid fast.
    [Show full text]
  • Bacterial Metabolism of Methylated Amines and Identification of Novel Methylotrophs in Movile Cave
    The ISME Journal (2015) 9, 195–206 & 2015 International Society for Microbial Ecology All rights reserved 1751-7362/15 www.nature.com/ismej ORIGINAL ARTICLE Bacterial metabolism of methylated amines and identification of novel methylotrophs in Movile Cave Daniela Wischer1, Deepak Kumaresan1,4, Antonia Johnston1, Myriam El Khawand1, Jason Stephenson2, Alexandra M Hillebrand-Voiculescu3, Yin Chen2 and J Colin Murrell1 1School of Environmental Sciences, University of East Anglia, Norwich, UK; 2School of Life Sciences, University of Warwick, Coventry, UK and 3Department of Biospeleology and Karst Edaphobiology, Emil Racovit¸a˘ Institute of Speleology, Bucharest, Romania Movile Cave, Romania, is an unusual underground ecosystem that has been sealed off from the outside world for several million years and is sustained by non-phototrophic carbon fixation. Methane and sulfur-oxidising bacteria are the main primary producers, supporting a complex food web that includes bacteria, fungi and cave-adapted invertebrates. A range of methylotrophic bacteria in Movile Cave grow on one-carbon compounds including methylated amines, which are produced via decomposition of organic-rich microbial mats. The role of methylated amines as a carbon and nitrogen source for bacteria in Movile Cave was investigated using a combination of cultivation studies and DNA stable isotope probing (DNA-SIP) using 13C-monomethylamine (MMA). Two newly developed primer sets targeting the gene for gamma-glutamylmethylamide synthetase (gmaS), the first enzyme of the recently-discovered indirect MMA-oxidation pathway, were applied in functional gene probing. SIP experiments revealed that the obligate methylotroph Methylotenera mobilis is one of the dominant MMA utilisers in the cave. DNA-SIP experiments also showed that a new facultative methylotroph isolated in this study, Catellibacterium sp.
    [Show full text]
  • Research Collection
    Research Collection Doctoral Thesis Development and application of molecular tools to investigate microbial alkaline phosphatase genes in soil Author(s): Ragot, Sabine A. Publication Date: 2016 Permanent Link: https://doi.org/10.3929/ethz-a-010630685 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO.23284 DEVELOPMENT AND APPLICATION OF MOLECULAR TOOLS TO INVESTIGATE MICROBIAL ALKALINE PHOSPHATASE GENES IN SOIL A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) presented by SABINE ANNE RAGOT Master of Science UZH in Biology born on 25.02.1987 citizen of Fribourg, FR accepted on the recommendation of Prof. Dr. Emmanuel Frossard, examiner PD Dr. Else Katrin Bünemann-König, co-examiner Prof. Dr. Michael Kertesz, co-examiner Dr. Claude Plassard, co-examiner 2016 Sabine Anne Ragot: Development and application of molecular tools to investigate microbial alkaline phosphatase genes in soil, c 2016 ⃝ ABSTRACT Phosphatase enzymes play an important role in soil phosphorus cycling by hydrolyzing organic phosphorus to orthophosphate, which can be taken up by plants and microorgan- isms. PhoD and PhoX alkaline phosphatases and AcpA acid phosphatase are produced by microorganisms in response to phosphorus limitation in the environment. In this thesis, the current knowledge of the prevalence of phoD and phoX in the environment and of their taxonomic distribution was assessed, and new molecular tools were developed to target the phoD and phoX alkaline phosphatase genes in soil microorganisms.
    [Show full text]
  • Identification of Nitrogen-Fixing Hydrogen Bacterium Strain N34 and Its Oxygen-Resistant Segregant Strain
    Agric. Biol Chem., 49 (6), 1703-1709, 1985 1703 Identification of Nitrogen-fixing Hydrogen Bacterium Strain N34 and Its Oxygen-resistant Segregant Strain, Y38 Yoshihiro Nakamura, Takashi Yamanobeand Jiro Ooyama Fermentation Research Institute, Tsukuba Science City, Ibaraki 305, Japan Received October 29, 1984 A hydrogen bacterium strain, N34, and its oxygen-resistant segregant strain, Y38, were subjected to a taxonomical study. Since both strains were capable of N2-fixation, N2-fixing facultative hydrogen autotrophs listed in "Bergey's Manual of Systematic Bacteriology" were used for comparison. Both strains produced a water-insoluble carotenoid pigment, zeaxanthin di- rhamnoside, indicating that both should be classified into the genus Xanthobacter. Then, the differential characteristics of the two species of the genus Xanthobacter, X. autotrophicus and X. flavus, were investigated as to both strains. The vitamin requirement, the sensitivity to oxygen under autotrophic conditions, the inducibility of hydrogenase, the substrate range of carbohydrates and N2-fixing growth characteristics of both strains were almost completely opposite to those of X. flavus. Moreover, both strains coincided exactly with X. autotrophicus in morphological and other physiological characteristics. From these results both strains were identified as Xanthobacter auto trophicus. In 1971, Ooyama isolated a nitrogen-fixing strain N34 and its nitrogen-fixing growth on hydrogen bacterium from oily soil in a nor- manyorganic compounds,culture conditions thern district
    [Show full text]
  • Diversity of Culturable Aerobic Denitrifying Bacteria in the Sediment, Water and Biofilms in Liangshui River of Beijing, China
    This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. Diversity of culturable aerobic denitrifying bacteria in the sediment, water and biofilms in Liangshui River of Beijing, China Lv, Pengyi; Luo, Jinxue; Zhuang, Xuliang; Zhang, Dongqing; Huang, Zhanbin; Bai, Zhihui 2017 Lv, P., Luo, J., Zhuang, X., Zhang, D., Huang, Z., & Bai, Z. (2017). Diversity of culturable aerobic denitrifying bacteria in the sediment, water and biofilms in Liangshui River of Beijing, China. Scientific Reports, 7, 10032‑. https://hdl.handle.net/10356/87899 https://doi.org/10.1038/s41598‑017‑09556‑9 © 2017 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Te images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Downloaded on 07 Oct 2021 12:22:55 SGT www.nature.com/scientificreports OPEN Diversity of culturable aerobic denitrifying bacteria in the sediment, water and bioflms in Received: 2 February 2017 Accepted: 24 July 2017 Liangshui River of Beijing, China Published: xx xx xxxx Pengyi Lv1,2, Jinxue Luo2, Xuliang Zhuang2,3, Dongqing Zhang4, Zhanbin Huang1 & Zhihui Bai 2,3 Aerobic denitrifcation is a process reducing the nitrate into gaseous nitrogen forms in the presence of oxygen gas, which makes the nitrifcation and denitrifcation performed simultaneously.
    [Show full text]
  • Extreme Environments and High-Level Bacterial Tellurite Resistance
    microorganisms Review Extreme Environments and High-Level Bacterial Tellurite Resistance Chris Maltman 1,* and Vladimir Yurkov 2 1 Department of Biology, Slippery Rock University, Slippery Rock, PA 16001, USA 2 Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; [email protected] * Correspondence: [email protected]; Tel.: +724-738-4963 Received: 28 October 2019; Accepted: 20 November 2019; Published: 22 November 2019 Abstract: Bacteria have long been known to possess resistance to the highly toxic oxyanion tellurite, most commonly though reduction to elemental tellurium. However, the majority of research has focused on the impact of this compound on microbes, namely E. coli, which have a very low level of resistance. Very little has been done regarding bacteria on the other end of the spectrum, with three to four orders of magnitude greater resistance than E. coli. With more focus on ecologically-friendly methods of pollutant removal, the use of bacteria for tellurite remediation, and possibly recovery, further highlights the importance of better understanding the effect on microbes, and approaches for resistance/reduction. The goal of this review is to compile current research on bacterial tellurite resistance, with a focus on high-level resistance by bacteria inhabiting extreme environments. Keywords: tellurite; tellurite resistance; extreme environments; metalloids; bioremediation; biometallurgy 1. Introduction Microorganisms possess a wide range of extraordinary abilities, from the production of bioactive molecules [1] to resistance to and transformation of highly toxic compounds [2–5]. Of great interest are bacteria which can convert the deleterious oxyanion tellurite to elemental tellurium (Te) through reduction. Currently, research into bacterial interactions with tellurite has been lagging behind investigation of the oxyanions of other metals such as nickel (Ni), molybdenum (Mo), tungsten (W), iron (Fe), and cobalt (Co).
    [Show full text]
  • Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas Sp
    microorganisms Article Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1 Dong Liang 1,† , Changyixin Xiao 1,† , Fuping Song 2, Haitao Li 1 , Rongmei Liu 1,* and Jiguo Gao 1,* 1 College of Life Science, Northeast Agricultural University, Harbin 150038, China; [email protected] (D.L.); [email protected] (C.X.); [email protected] (H.L.) 2 State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; [email protected] * Correspondence: [email protected] (R.L.); [email protected] (J.G.); Tel.: +86-133-5999-0992 (J.G.) † These authors contributed equally to this work. Abstract: The genus Pseudomonas is widely recognized for its potential for environmental reme- diation and plant growth promotion. Pseudomonas sp. DY-1 was isolated from the agricultural soil contaminated five years by prometryne, it manifested an outstanding prometryne degradation efficiency and an untapped potential for plant resistance improvement. Thus, it is meaningful to comprehend the genetic background for strain DY-1. The whole genome sequence of this strain revealed a series of environment adaptive and plant beneficial genes which involved in environmen- tal stress response, heavy metal or metalloid resistance, nitrate dissimilatory reduction, riboflavin synthesis, and iron acquisition. Detailed analyses presented the potential of strain DY-1 for degrad- ing various organic compounds via a homogenized pathway or the protocatechuate and catechol branches of the β-ketoadipate pathway. In addition, heterologous expression, and high efficiency Citation: Liang, D.; Xiao, C.; Song, F.; liquid chromatography (HPLC) confirmed that prometryne could be oxidized by a Baeyer-Villiger Li, H.; Liu, R.; Gao, J.
    [Show full text]
  • Characterisation of Pseudomonas Spp. Isolated from Foods
    07.QXD 9-03-2007 15:08 Pagina 39 Annals of Microbiology, 57 (1) 39-47 (2007) Characterisation of Pseudomonas spp. isolated from foods Laura FRANZETTI*, Mauro SCARPELLINI Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, sezione Microbiologia Agraria Alimentare Ecologica, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy Received 30 June 2006 / Accepted 27 December 2006 Abstract - Putative Pseudomonas spp. (102 isolates) from different foods were first characterised by API 20NE and then tested for some enzymatic activities (lipase and lecithinase production, starch hydrolysis and proteolytic activity). However subsequent molecular tests did not always confirm the results obtained, thus highlighting the limits of API 20NE. Instead RFLP ITS1 and the sequencing of 16S rRNA gene grouped the isolates into 6 clusters: Pseudomonas fluorescens (cluster I), Pseudomonas fragi (cluster II and V) Pseudomonas migulae (cluster III), Pseudomonas aeruginosa (cluster IV) and Pseudomonas chicorii (cluster VI). The pectinolytic activity was typical of species isolated from vegetable products, especially Pseudomonas fluorescens. Instead Pseudomonas fragi, predominantly isolated from meat was characterised by proteolytic and lipolytic activities. Key words: Pseudomonas fluorescens, enzymatic activity, ITS1. INTRODUCTION the most frequently found species, however the species dis- tribution within the food ecosystem remains relatively The genus Pseudomonas is the most heterogeneous and unknown (Arnaut-Rollier et al., 1999). The principal micro- ecologically significant group of known bacteria, and bial population of many vegetables in the field consists of includes Gram-negative motile aerobic rods that are wide- species of the genus Pseudomonas, especially the fluores- spread throughout nature and characterised by elevated cent forms.
    [Show full text]
  • Evolution of Methanotrophy in the Beijerinckiaceae&Mdash
    The ISME Journal (2014) 8, 369–382 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis Ivica Tamas1, Angela V Smirnova1, Zhiguo He1,2 and Peter F Dunfield1 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada and 2Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT.
    [Show full text]
  • Aquatic Microbial Ecology 80:15
    The following supplement accompanies the article Isolates as models to study bacterial ecophysiology and biogeochemistry Åke Hagström*, Farooq Azam, Carlo Berg, Ulla Li Zweifel *Corresponding author: [email protected] Aquatic Microbial Ecology 80: 15–27 (2017) Supplementary Materials & Methods The bacteria characterized in this study were collected from sites at three different sea areas; the Northern Baltic Sea (63°30’N, 19°48’E), Northwest Mediterranean Sea (43°41'N, 7°19'E) and Southern California Bight (32°53'N, 117°15'W). Seawater was spread onto Zobell agar plates or marine agar plates (DIFCO) and incubated at in situ temperature. Colonies were picked and plate- purified before being frozen in liquid medium with 20% glycerol. The collection represents aerobic heterotrophic bacteria from pelagic waters. Bacteria were grown in media according to their physiological needs of salinity. Isolates from the Baltic Sea were grown on Zobell media (ZoBELL, 1941) (800 ml filtered seawater from the Baltic, 200 ml Milli-Q water, 5g Bacto-peptone, 1g Bacto-yeast extract). Isolates from the Mediterranean Sea and the Southern California Bight were grown on marine agar or marine broth (DIFCO laboratories). The optimal temperature for growth was determined by growing each isolate in 4ml of appropriate media at 5, 10, 15, 20, 25, 30, 35, 40, 45 and 50o C with gentle shaking. Growth was measured by an increase in absorbance at 550nm. Statistical analyses The influence of temperature, geographical origin and taxonomic affiliation on growth rates was assessed by a two-way analysis of variance (ANOVA) in R (http://www.r-project.org/) and the “car” package.
    [Show full text]
  • CGM-18-001 Perseus Report Update Bacterial Taxonomy Final Errata
    report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly. These lists of bacteria originate from 2011, when COGEM petitioned a research project to evaluate the classifications of bacteria in the former GMO regulation and to supplement this list with bacteria that have been classified by other governmental organizations.
    [Show full text]