DOCSLIB.ORG

The Effects of Long-Term Exposure of an Artificially Assembled Microbial Community to Uranium Or Low Ph

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

MIAMI UNIVERSITY THE GRADUATE SCHOOL CERTIFICATE FOR APPROVING THE DISSERTATION We hereby approve the Dissertation of Ryann Michelle Brzoska Candidate for the Degree: Doctor of Philosophy ______________________________________ Dr. Annette Bollmann, Director ______________________________________ Dr. Mitchell F. Balish, Reader ______________________________________ Dr. Rachael M. Morgan-Kiss, Reader ______________________________________ Dr. Donald J. Ferguson ______________________________________ Dr. Melany C. Fisk Graduate School Representative ! ABSTRACT THE EFFECTS OF LONG-TERM EXPOSURE OF AN ARTIFICIALLY ASSEMBLED MICROBIAL COMMUNITY TO URANIUM OR LOW PH by Ryann Michelle Brzoska Uranium-contaminated environments contain microbial communities capable of immobilizing uranium. There is evidence that some bacterial communities are capable of immobilizing higher concentrations of uranium than individual species. However, the interactions between bacterial species contributing to increased uranium immobilization are not understood. Therefore, the goal of this study was to identify interactions between species in an artificial community and assess their influence on uranium immobilization. Bacterial species previously isolated from the uranium-contaminated subsurface at Oak Ridge, Tennessee, were characterized both individually and in a mixed community in the presence and absence of uranium or low pH. Growth of individual bacterial strains in the presence of uranium or low pH revealed two Sediminibacterium strains, Sediminibacterium spp. OR43 and OR53, with different degrees of tolerance towards uranium. The main physiological or genomic difference between the Sediminibacterium strains was the sensitivity of Sediminibacterium sp. OR43 to uranium concentrations ≥ 200 µM uranium. Sediminibacterium sp. OR53 was chosen along with Caulobacter sp. OR37, Ralstonia sp. OR214, and Rhodanobacter sp. OR444 to be a part of an artificially assembled community. The productivity of the community was assessed by monitoring the optical density and the abundance of each species in the community in the presence or absence of 200 µM uranium at pH 4.5 (pH4.5) or 7 (pH7) for 30 weeks (~300 generations). At pH7 and pH4.5, all strains were present, but the strain tolerant to the lowest pH, Ralstonia sp. OR214, was the most abundant. The presence of uranium selected for the uranium- tolerant strains, Sediminibacterium sp. OR53 and Caulobacter sp. OR37. Moreover, when a subculture of the consortium at pH 7 with uranium (pH7U) was transferred into pH7 without uranium, the uranium-sensitive strains did not recover. Re-isolated strains of Caulobacter spp. OR37 and Sediminibacterium spp. OR53 from the pH7U condition showed increased growth in coculture that did not correlate with an increase in uranium immobilization when compared to individual strains. Taken together, our results indicate that commensalistic and competitive interactions may develop between microbial species and impact growth and uranium immobilization, which are important for microbial communities considered for the purpose of bioremediation. THE EFFECTS OF LONG-TERM EXPOSURE OF AN ARTIFICIALLY ASSEMBLED MICROBIAL COMMUNITY TO URANIUM OR LOW PH A Dissertation Submitted to the Faculty of Miami University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Microbiology by Ryann Michelle Brzoska Miami University Oxford, OH 2015 Dissertation Director: Annette Bollmann, Ph.D. TABLE OF CONTENTS List of Tables iii List of Figures v Acknowledgements vii Introduction 1 Chapter 1. Physiological and genomic analysis of two novel Bacteroidetes strains Sediminibacterium spp. OR43 and OR53. 21 Chapter 2. The effects of uranium and low pH on the composition and productivity of an artificial community in a long-term growth experiment. 60 Chapter 3. Physiological and genomic comparison of strains re-isolated from an artificial community in the presence of uranium. 91 Summary 149 References 162 ! ! ! ii! LIST OF TABLES Table Page 1. Genome sequencing project information for Sediminibacterium spp. OR43 and OR53. 29 2. Differential physiological characteristics of strains Sediminibacterium spp. OR43 and OR53T in comparison with type strains of closely related species. 36 3. Fatty acid profiles of Sediminibacterium spp. OR43 and OR53 strains in comparison with type strains of closely related species. 38 4. Influence of the nitrate concentration (mM) in the medium on the growth -1 rate (day ) and maximum biomass (max OD600) of Sediminibacterium spp. OR43 and OR53 after two days. 40 5. Influence of the pH in the medium on the growth rate (day-1), maximum biomass (max OD600), and lag phase (days) of Sediminibacterium sp. OR43 after two days. 44 6. Influence of the pH in the medium on the growth rate (day-1), maximum biomass (max OD600), and lag phase (days) of Sediminibacterium sp. OR53 after two days. 45 7. Influence of the uranium concentration (µM) in the medium on the growth rate -1 (day ), maximum biomass (max OD600), and lag phase (days) of Sediminibacterium sp. OR43 after two days. 46 8. Influence of the uranium concentration (µM) in the medium on the growth rate -1 (day ), maximum biomass (max OD600), and lag phase (days) of Sediminibacterium sp. OR53 after two days. 47 9. Genome properties of Sediminibacterium spp. OR43 and OR53. 48 10. Number of genes associated with the general COG functional categories. 49 11. Presence (+) and absence (-) of genes involved in nitrate metabolism in Sediminibacterium spp. OR43 and OR53. 50 12. Enumeration of genes potentially involved in the adaptation to low pH in Sediminibacterium spp. OR43 and OR53. 52 13. Heavy metal resistance genes in the genome of Sediminibacterium sp. OR53. 53 14. Membrane associated phospholipid phosphatases in the genome of Sediminibacterium sp. OR53 and the percent identity (%) of orthologous sequences in Sediminibacterium spp. OR43, C3, and S. salmoneum. 56 ! iii! 15. Primers used for measuring the relative abundance of Caulobacter sp. OR37, Sediminibacterium sp. OR53, Ralstonia sp. OR214, and Rhodanobacter sp. OR444. 67 16. PCR conditions (temperature (°C)/time (s)) and validation of qPCR. 68 17. Maximum uranium concentration and minimum pH value in the MS medium that allowed growth of the bacterial species as pure cultures. 70 18. Influence of 0, 200, and 300 µM uranium on the growth rate (h-1) of the re-isolated and ancestral strains after two days of exposure. 104 19. Influence of 0, 200, and 300 µM uranium on the max OD600 of re-isolated and ancestral strains of Caulobacter spp. OR37 and Sediminibacterium spp. OR53 after two days of exposure. 105 20. Influence of 0, 200, and 300 µM uranium on the length of lag phase (hours) of the re-isolated and ancestral strains of Caulobacter spp. OR37 and Sediminibacterium spp. OR53 after two days of exposure. 106 21. Growth rate and maximum OD600 (biomass yield) of ancestral and re-isolated Caulobacter spp. OR37 and Sediminibacterium spp. OR53 as a coculture in the presence of 300 µM uranium. 110 22. Uranium concentration (µM) in the presence of re-isolated and ancestral strains of Caulobacter spp. OR37 and Sediminibacterium spp. OR53 either individually or in coculture after seven days exposure to 300 µM uranium. 111 23. Read mapping coverage of re-isolated strains to the ancestral genomes. 132 24. Genetic variations in the re-isolated strains of Sediminibacterium spp. OR53 compared to the ancestral strain. 133 25. Location of amino acid changes in re-isolated Sediminibacterium spp. OR53 strains. 134 26. Genetic variations in the re-isolated strains of Caulobacter spp. OR37 compared to the ancestral strain. 135 27. Location of amino acid changes in re-isolated Caulobacter spp. OR37 strains. 137 28. Positive effects (+) of the OD600 (growth) in cocultures of ancestral and re-isolated Caulobacter spp. OR37 and Sediminibacterium spp. OR53 in the presence of 300 µM uranium after two days. 139 ! iv! LIST OF FIGURES Figure Page 1. Uranium speciation as a function of pH. 2 2. The S-3 ponds and the surrounding contaminated areas at Oak Ridge. 6 3. Schematic of efflux transporters involved in heavy metal resistance. 11 4. Mechanisms used by bacteria for immobilizing uranium. 13 5. Maximum likelihood phylogenetic tree based on 16S rRNA gene sequences of Sediminibacterium spp. OR43 and OR53. 32 6. Transmission electron micrographs of (A) Sediminibacterium sp. OR43; and (B) Sediminibacterium sp. OR53. 34 7. Growth rate (day-1) of Sediminibacterium spp. OR43 and OR53 in the presence of (A) different pH values; and (B) uranium concentrations. 41 8. Influence of 0-200 µM uranium on the growth rates (h-1) and length of lag phase (h) of Caulobacter sp. OR37, Sediminibacterium sp. OR53, Ralstonia sp. OR214, and Rhodanobacter sp. OR444. 71 9. Influence of pH on the growth rate (h-1) of Caulobacter sp. OR37, Sediminibacterium sp. OR53, Ralstonia sp. OR214, and Rhodanobacter sp. OR444. 73 10. OD600 (as a measure of the total biomass) at the end of each week during the long- term growth experiment. 75 11. Relative abundance (%) of the 16S rRNA genes of Caulobacter sp. OR37, Sediminibacterium sp. OR53, Ralstonia sp. OR214, and Rhodanobacter sp. OR444 in the artificial community at (A) pH7; (B) pH7->pH 4.5; (C) pH4.5; and (D) pH4.5->pH7. 78 12. Relative abundance (%) of the 16S rRNA genes of Caulobacter sp. OR37, Sediminibacterium sp. OR53, Ralstonia sp. OR214, and Rhodanobacter sp. OR444 in the artificial community at (A) pH7; (B) pH7->pH7U; (C) pH7U; and (D) pH7U->pH7. 80 13. Relative abundance (%) of the 16S rRNA genes of Caulobacter sp. OR37, Sediminibacterium sp. OR53, Ralstonia sp. OR214, and Rhodanobacter sp. OR444 in the artificial community under all conditions at the beginning of the ! v! experiment (week 0), at week 12, and at the end of the experiment (week 30). 82 14. Concentration of uranium (µM) in medium at pH7U and pH7->pH7U communities of the long-term growth experiment. 85 15. Influence of 0, 200, and 300 µM uranium on the change in OD600 over time (growth) of the ancestral strains of Caulobacter sp. OR37 (OR37A) and Sediminibacterium sp. OR53 (OR53A) and the re-isolated (OR37 Is8, OR37 Is14, OR37 Is28, OR53 Is7, OR53 Is18, OR53 Is70) strains.
Recommended publications
  • Universidade Federal Do Rio Grande Do Sul Centro De Biotecnologia Programa De Pós-Graduação Em Biologia Celular E Molecular

    Universidade Federal Do Rio Grande Do Sul Centro De Biotecnologia Programa De Pós-Graduação Em Biologia Celular E Molecular

    UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL CENTRO DE BIOTECNOLOGIA PROGRAMA DE PÓS-GRADUAÇÃO EM BIOLOGIA CELULAR E MOLECULAR Caracterização Molecular do Microbioma Hospitalar por Sequenciamento de Alto Desempenho Tese de Doutorado Pabulo Henrique Rampelotto Porto Alegre 2019 UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL CENTRO DE BIOTECNOLOGIA PROGRAMA DE PÓS-GRADUAÇÃO EM BIOLOGIA CELULAR E MOLECULAR Caracterização Molecular do Microbioma Hospitalar por Sequenciamento de Alto Desempenho Tese submetida ao Programa de Pós-Graduação em Biologia Celular e Molecular da UFRGS, como requisito parcial para a obtenção do grau de Doutor em Ciências Pabulo Henrique Rampelotto Orientador: Dr. Rogério Margis Porto Alegre, Abril de 2019 Instituições e fontes financiadoras: Instituições: Laboratório de Genomas e Populações de Plantas (LGPP), Departamento de Biofísica, UFRGS – Porto Alegre/RS, Brasil. Neoprospecta Microbiome Technologies SA – Florianópolis/SC, Brasil. Hospital Universitário Polydoro Ernani de São Thiago, Universidade Federal de Santa Catarina (UFSC) – Florianópolis/SC, Brasil. Fontes financiadoras: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brasil. Agradecimentos Aos meus familiares, pelo suporte incondicional em todos os momentos de minha vida. Ao meu orientador Prof. Rogério Margis, pela oportunidade e confiança. Aos colegas de laboratório, pelo apoio e amizade. Ao Programa de Pós-Graduação em Biologia Celular e Molecular, por todo o suporte. Aos inúmeros autores e co-autores que participaram dos meus diversos projetos editoriais, pelas brilhantes discussões em temas tão fascinantes. Enfim, a todos que, de alguma forma, contribuíram para a realização deste trabalho. “A tarefa não é tanto ver aquilo que ninguém viu, mas pensar o que ninguém ainda pensou sobre aquilo que todo mundo vê” (Arthur Schopenhauer) SUMÁRIO LISTA DE ABREVIATURAS ..........................................................................................
  • Taxonomy JN869023

    Taxonomy JN869023

    Species that differentiate periods of high vs. low species richness in unattached communities Species Taxonomy JN869023 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 JN674641 Bacteria; Bacteroidetes; [Saprospirae]; [Saprospirales]; Chitinophagaceae; Sediminibacterium JN869030 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 U51104 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae; Limnohabitans JN868812 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae JN391888 Bacteria; Planctomycetes; Planctomycetia; Planctomycetales; Planctomycetaceae; Planctomyces HM856408 Bacteria; Planctomycetes; Phycisphaerae; Phycisphaerales GQ347385 Bacteria; Verrucomicrobia; [Methylacidiphilae]; Methylacidiphilales; LD19 GU305856 Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Pelagibacteraceae GQ340302 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales JN869125 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae New.ReferenceOTU470 Bacteria; Cyanobacteria; ML635J-21 JN679119 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae HM141858 Bacteria; Acidobacteria; Holophagae; Holophagales; Holophagaceae; Geothrix FQ659340 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; auto67_4W AY133074 Bacteria; Elusimicrobia; Elusimicrobia; Elusimicrobiales FJ800541 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; R4-41B JQ346769 Bacteria; Acidobacteria; [Chloracidobacteria]; RB41; Ellin6075
  • MIAMI UNIVERSITY the Graduate School

    MIAMI UNIVERSITY the Graduate School

    MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Steven Lindau Distelhorst Candidate for the Degree Doctor of Philosophy ______________________________________ Dr. Mitchell F. Balish, Director ______________________________________ Kelly Z. Abshire, Reader ______________________________________ Natosha L. Finley, Reader ______________________________________ Joseph M. Carlin, Reader ______________________________________ Jack C. Vaughn, Graduate School Representative ABSTRACT UNDERSTANDING VIRULENCE FACTORS OF MYCOPLASMA PENETRANS: ATTACHMENT ORGANELLE ORGANIZATION AND GENE EXPRESSION by Steven Lindau Distelhorst The ability to establish and maintain cell polarity plays an important role in cellular organization for both functional and morphological integrity in eukaryotic and prokaryotic organisms. Like eukaryotes, bacteria, including the genomically reduced species of the Mycoplasma genus, use an array of cytoskeletal proteins to generate and maintain cellular polarity. Some mycoplasmas, such as Mycoplasma penetrans, exhibit a distinct polarized structure, known as the attachment organelle (AO), which is used for attachment to host cells and motility. The M. penetrans AO, like AOs of other mycoplasmas, contains a cytoskeletal structure at the core, but lacks any homologs of identified AO core proteins of other investigated mycoplasmas. To characterize the composition of the M. penetrans AO cytoskeleton we purified the detergent-insoluble core material and examined
  • Mycoplasma Pneumoniae Terminal Organelle

    Mycoplasma Pneumoniae Terminal Organelle

    MYCOPLASMA PNEUMONIAE TERMINAL ORGANELLE DEVELOPMENT AND GLIDING MOTILITY by BENJAMIN MICHAEL HASSELBRING (Under the Direction of Duncan Charles Krause) ABSTRACT With a minimal genome containing less than 700 open reading frames and a cell volume < 10% of that of model prokaryotes, Mycoplasma pneumoniae is considered among the smallest and simplest organisms capable of self-replication. And yet, this unique wall-less bacterium exhibits a remarkable level of cellular complexity with a dynamic cytoskeleton and a morphological asymmetry highlighted by a polar, membrane-bound terminal organelle containing an elaborate macromolecular core. The M. pneumoniae terminal organelle functions in distinct, and seemingly disparate cellular processes that include cytadherence, cell division, and presumably gliding motility, as individual cells translocate over surfaces with the cell pole harboring the structure engaged as the leading end. While recent years have witnessed a dramatic increase in the knowledge of protein interactions required for core stability and adhesin trafficking, the mechanism of M. pneumoniae gliding has not been defined nor have interdependencies between the various terminal organelle functions been assessed. The studies presented in the current volume describe the first genetic and molecular investigations into the location, components, architecture, and regulation of the M. pneumoniae gliding machinery. The data indicate that cytadherence and gliding motility are separable properties, and identify a subset of M. pneumoniae proteins contributing directly to the latter process. Characterizations of novel gliding-deficient mutants confirm that the terminal organelle contains the molecular gliding machinery, revealing that with the loss of a single terminal organelle cytoskeletal element, protein P41, terminal organelles detach from the cell body but retain gliding function.
  • A Noval Investigation of Microbiome from Vermicomposting Liquid Produced by Thai Earthworm, Perionyx Sp

    A Noval Investigation of Microbiome from Vermicomposting Liquid Produced by Thai Earthworm, Perionyx Sp

    International Journal of Agricultural Technology 2021Vol. 17(4):1363-1372 Available online http://www.ijat-aatsea.com ISSN 2630-0192 (Online) A novel investigation of microbiome from vermicomposting liquid produced by Thai earthworm, Perionyx sp. 1 Kraisittipanit, R.1,2, Tancho, A.2,3, Aumtong, S.3 and Charerntantanakul, W.1* 1Program of Biotechnology, Faculty of Science, Maejo University, Chiang Mai, Thailand; 2Natural Farming Research and Development Center, Maejo University, Chiang Mai, Thailand; 3Faculty of Agricultural Production, Maejo University, Thailand. Kraisittipanit, R., Tancho, A., Aumtong, S. and Charerntantanakul, W. (2021). A noval investigation of microbiome from vermicomposting liquid produced by Thai earthworm, Perionyx sp. 1. International Journal of Agricultural Technology 17(4):1363-1372. Abstract The whole microbiota structure in vermicomposting liquid derived from Thai earthworm, Perionyx sp. 1 was estimated. It showed high richness microbial species and belongs to 127 species, separated in 3 fungal phyla (Ascomycota, Basidiomycota, Mucoromycota), 1 Actinomycetes and 16 bacterial phyla (Acidobacteria, Armatimonadetes, Bacteroidetes, Balneolaeota, Candidatus, Chloroflexi, Deinococcus, Fibrobacteres, Firmicutes, Gemmatimonadates, Ignavibacteriae, Nitrospirae, Planctomycetes, Proteobacteria, Tenericutes and Verrucomicrobia). The OTUs data analysis revealed the highest taxonomic abundant ratio in bacteria and fungi belong to Proteobacteria (70.20 %) and Ascomycota (5.96 %). The result confirmed that Perionyx sp. 1
  • Proposal of Vibrionimonas Magnilacihabitans Gen. Nov., Sp

    Proposal of Vibrionimonas Magnilacihabitans Gen. Nov., Sp

    Marquette University e-Publications@Marquette Civil and Environmental Engineering Faculty Civil and Environmental Engineering, Department Research and Publications of 2-1-2014 Proposal of Vibrionimonas magnilacihabitans gen. nov., sp. nov., a Curved Gram Negative Bacterium Isolated From Lake Michigan Water Richard A. Albert Marquette University, [email protected] Daniel Zitomer Marquette University, [email protected] Michael Dollhopf Marquette University, [email protected] Anne Schauer-Gimenez Marquette University Craig Struble Marquette University, [email protected] See next page for additional authors Accepted version. International Journal of Systematic and Evolutionary Microbiology, Vol. 64, No. 2 (February 2014): 613-620. DOI. © 2014 Society for General Microbiology. Used with permission. Authors Richard A. Albert, Daniel Zitomer, Michael Dollhopf, Anne Schauer-Gimenez, Craig Struble, Michael King, Sona Son, Stefan Langer, and Hans-Jürgen Busse This article is available at e-Publications@Marquette: https://epublications.marquette.edu/civengin_fac/8 NOT THE PUBLISHED VERSION; this is the author’s final, peer-reviewed manuscript. The published version may be accessed by following the link in the citation at the bottom of the page. Proposal of Vibrionimonas magnilacihabitans gen. nov., sp. nov., a Curved Gram-Stain-Negative Bacterium Isolated from Lake Water Richard A. Albert Water Quality Center, Marquette University, Milwaukee, WI Daniel Zitomer Water Quality Center, Marquette University, Milwaukee, WI Michael Dollhopf Water Quality Center, Marquette University, Milwaukee, WI A.E. Schauer-Gimenez Water Quality Center, Marquette University, Milwaukee, WI Craig Struble Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI International Journal of Systematic and Evolutionary Microbiology, Vol. 64, No. 2 (February 2014): pg.
  • ( 12 ) United States Patent

    ( 12 ) United States Patent

    US009956282B2 (12 ) United States Patent ( 10 ) Patent No. : US 9 ,956 , 282 B2 Cook et al. (45 ) Date of Patent: May 1 , 2018 ( 54 ) BACTERIAL COMPOSITIONS AND (58 ) Field of Classification Search METHODS OF USE THEREOF FOR None TREATMENT OF IMMUNE SYSTEM See application file for complete search history . DISORDERS ( 56 ) References Cited (71 ) Applicant : Seres Therapeutics , Inc. , Cambridge , U . S . PATENT DOCUMENTS MA (US ) 3 ,009 , 864 A 11 / 1961 Gordon - Aldterton et al . 3 , 228 , 838 A 1 / 1966 Rinfret (72 ) Inventors : David N . Cook , Brooklyn , NY (US ) ; 3 ,608 ,030 A 11/ 1971 Grant David Arthur Berry , Brookline, MA 4 ,077 , 227 A 3 / 1978 Larson 4 ,205 , 132 A 5 / 1980 Sandine (US ) ; Geoffrey von Maltzahn , Boston , 4 ,655 , 047 A 4 / 1987 Temple MA (US ) ; Matthew R . Henn , 4 ,689 ,226 A 8 / 1987 Nurmi Somerville , MA (US ) ; Han Zhang , 4 ,839 , 281 A 6 / 1989 Gorbach et al. Oakton , VA (US ); Brian Goodman , 5 , 196 , 205 A 3 / 1993 Borody 5 , 425 , 951 A 6 / 1995 Goodrich Boston , MA (US ) 5 ,436 , 002 A 7 / 1995 Payne 5 ,443 , 826 A 8 / 1995 Borody ( 73 ) Assignee : Seres Therapeutics , Inc. , Cambridge , 5 ,599 ,795 A 2 / 1997 McCann 5 . 648 , 206 A 7 / 1997 Goodrich MA (US ) 5 , 951 , 977 A 9 / 1999 Nisbet et al. 5 , 965 , 128 A 10 / 1999 Doyle et al. ( * ) Notice : Subject to any disclaimer , the term of this 6 ,589 , 771 B1 7 /2003 Marshall patent is extended or adjusted under 35 6 , 645 , 530 B1 . 11 /2003 Borody U .
  • International Journal of Systematic and Evolutionary Microbiology

    International Journal of Systematic and Evolutionary Microbiology

    International Journal of Systematic and Evolutionary Microbiology Mycoplasma tullyi sp. nov., isolated from penguins of the genus Spheniscus --Manuscript Draft-- Manuscript Number: IJSEM-D-17-00095R1 Full Title: Mycoplasma tullyi sp. nov., isolated from penguins of the genus Spheniscus Article Type: Note Section/Category: New taxa - other bacteria Keywords: Mollicutes Mycoplasma sp. nov. penguin Spheniscus humboldti Corresponding Author: Ana S. Ramirez, Ph.D. Universidad de Las Palmas de Garn Canaria Arucas, Las Palmas SPAIN First Author: Christine A. Yavari, PhD Order of Authors: Christine A. Yavari, PhD Ana S. Ramirez, Ph.D. Robin A. J. Nicholas, PhD Alan D. Radford, PhD Alistair C. Darby, PhD Janet M. Bradbury, PhD Manuscript Region of Origin: UNITED KINGDOM Abstract: A mycoplasma isolated from the liver of a dead Humboldt penguin (Spheniscus humboldti) and designated strain 56A97, was investigated to determine its taxonomic status. Complete 16S rRNA gene sequence analysis indicated that the organism was most closely related to M. gallisepticum and M. imitans (99.7 and 99.9% similarity, respectively). The average DNA-DNA hybridization (DDH) values between strain 56A97 and M. gallisepticum and M. imitans were 39.5% and 30%, respectively and the values for Genome-to Genome Distance Calculator (GGDC) gave a result of 29.10 and 23.50% respectively. The 16S-23S rRNA intergenic spacer was 72-73% similar to M. gallisepticum strains and 52.2% to M. imitans. A partial sequence of rpoB was 91.1- 92% similar to M. gallisepticum strains and 84.7 % to M. imitans. Colonies possessed a typical fried-egg appearance and electron micrographs revealed the lack of a cell wall and a nearly-spherical morphology, with an electron dense tip-like structure on some flask-shaped cells.
  • Determining Lineage-Specific Bacterial Growth Curves with a Novel

    Determining Lineage-Specific Bacterial Growth Curves with a Novel

    The ISME Journal (2018) 12:2640–2654 https://doi.org/10.1038/s41396-018-0213-y ARTICLE Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS) 1 2 3 2 1,4 3 Kasia Piwosz ● Tanja Shabarova ● Jürgen Tomasch ● Karel Šimek ● Karel Kopejtka ● Silke Kahl ● 3 1,4 Dietmar H. Pieper ● Michal Koblížek Received: 10 January 2018 / Revised: 1 June 2018 / Accepted: 9 June 2018 / Published online: 6 July 2018 © The Author(s) 2018. This article is published with open access Abstract The growth rate is a fundamental characteristic of bacterial species, determining its contributions to the microbial community and carbon flow. High-throughput sequencing can reveal bacterial diversity, but its quantitative inaccuracy precludes estimation of abundances and growth rates from the read numbers. Here, we overcame this limitation by normalizing Illumina-derived amplicon reads using an internal standard: a constant amount of Escherichia coli cells added to samples just before biomass collection. This approach made it possible to reconstruct growth curves for 319 individual OTUs during the 1234567890();,: 1234567890();,: grazer-removal experiment conducted in a freshwater reservoir Římov. The high resolution data signalize significant functional heterogeneity inside the commonly investigated bacterial groups. For instance, many Actinobacterial phylotypes, a group considered to harbor slow-growing defense specialists, grew rapidly upon grazers’ removal, demonstrating their considerable importance in carbon flow through food webs, while most Verrucomicrobial phylotypes were particle associated. Such differences indicate distinct life strategies and roles in food webs of specific bacterial phylotypes and groups. The impact of grazers on the specific growth rate distributions supports the hypothesis that bacterivory reduces competition and allows existence of diverse bacterial communities.
  • Moving Beyond Serovars

    Moving Beyond Serovars

    ABSTRACT Title of Document: MOLECULAR AND BIOINFORMATICS APPROACHES TO REDEFINE OUR UNDERSTANDING OF UREAPLASMAS: MOVING BEYOND SEROVARS Vanya Paralanov, Doctor of Philosophy, 2014 Directed By: Prof. Jonathan Dinman, Cell Biology and Molecular Genetics, University of Maryland College Park Prof. John I. Glass, Synthetic Biology, J. Craig Venter Institute Ureaplasma parvum and Ureaplasma urealyticum are sexually transmitted, opportunistic pathogens of the human urogenital tract. There are 14 known serovars of the two species. For decades, it has been postulated that virulence is related to serotype specificity. Understanding of the role of ureaplasmas in human diseases has been thwarted due to two major barriers: (1) lack of suitable diagnostic tests and (2) lack of genetic manipulation tools for the creation of mutants to study the role of potential pathogenicity factors. To address the first barrier we developed real-time quantitative PCRs (RT-qPCR) for the reliable differentiation of the two species and 14 serovars. We typed 1,061 ureaplasma clinical isolates and observed about 40% of isolates to be genetic mosaics, arising from the recombination of multiple serovars. Furthermore, comparative genome analysis of the 14 serovars and 5 clinical isolates showed that the mba gene, used for serotyping ureaplasmas was part of a large, phase variable gene system, and some serovars shown to express different MBA proteins also encode mba genes associated with other serovars. Together these data suggests that differential pathogenicity and clinical outcome of an ureaplasmal infection is most likely due to the presence or absence of potential pathogenicity factors in individual ureaplasma clinical isolates and/or patient to patient differences in terms of autoimmunity and microbiome.
  • Taibaiella Smilacinae Gen. Nov., Sp. Nov., an Endophytic Member of The

    Taibaiella Smilacinae Gen. Nov., Sp. Nov., an Endophytic Member of The

    International Journal of Systematic and Evolutionary Microbiology (2013), 63, 3769–3776 DOI 10.1099/ijs.0.051607-0 Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus Lei Zhang,1,2 Yang Wang,3 Linfang Wei,1 Yao Wang,1 Xihui Shen1 and Shiqing Li1,2 Correspondence 1State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Xihui Shen Northwest A&F University, Yangling, Shaanxi 712100, PR China [email protected] 2State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Northwest A&F University, Yangling, Shaanxi 712100, PR China 3Hubei Institute for Food and Drug Control, Wuhan 430072, PR China A light-yellow-coloured bacterium, designated strain PTJT-5T, was isolated from the stem of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. The novel isolate grew optimally at 25–28 6C and pH 6.0–7.0. Flexirubin-type pigments were produced. Cells were Gram-reaction-negative, strictly aerobic, rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTJT-5T was a member of the phylum Bacteroidetes, exhibiting the highest sequence similarity to Lacibacter cauensis NJ-8T (87.7 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 and iso-C17 : 0 3-OH.
  • Bacterial Community Analysis of Two Neighboring Freshwater Lakes Originating from One Lake

    Bacterial Community Analysis of Two Neighboring Freshwater Lakes Originating from One Lake

    Pol. J. Environ. Stud. Vol. 30, No. 1 (2021), 111-117 DOI: 10.15244/pjoes/119094 ONLINE PUBLICATION DATE: 2020-07-31 Original Research Bacterial Community Analysis of Two Neighboring Freshwater Lakes Originating from One Lake Dabin Guo1,2, Jiechao Liang1, Wei Chen1, Jian Wang1, Bin Ji1*, Shiyi Luo3 1Department of Water and Wastewater Engineering, School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065 2School of Environmental Science & Engineering, Huazhong University of Science and Technology, Wuhan 430074, China 3State Key Laboratory of Physical Chemistry of Solid Surfaces and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China Received: 20 January 2020 Accepted: 16 March 2020 Abstract Bacterial community compositions of two neighboring freshwater lakes (i.e. Inner Sand Lake and Sand Lake in Wuhan, China) originating from one lake were studied by triplicate sampling based on Illumina Miseq sequencing. The pollutant concentrations in Sand Lake were twice as in Inner Sand Lake generally. Proteobacteria mainly containing Betaproteobacteria and Alphaproteobacteria were most abundant in the two lakes. The most dramatic differences at phylum level were that Inner Sand Lake had a higher proportion of Bacteroidetes while Sand Lake had a higher proportion of Cyanobacteria. The eutrophic Sand Lake had more taxa as for Alpinimonas, Flavobacterium, Lautropia, Pelomonas, Pseudomonas, Sphingorhabdus, Candidatus Aquirestis and Vogesella. On the contrary, the oligotrophic Inner Sand Lake had more taxa as for Aeromonas, Bradyrhizobium, Fluviicola, Limnohabitans, Luteolibacter, Polynucleobacter, Pseudarcicella and Sediminibacterium. Correlation network analysis revealed that Pseudarcicella, Sediminibacterium, Luteolibacter, Aeromonas in fresh lakes were potential bacterial indicators of good-quality lakes. Conversely, Flavobacterium, Pseudomonas and Candidatus Aquirestis seemed to be bacterial indicators of bad-quality lakes.