DOCSLIB.ORG

Brown MR 2019.Pdf

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Virus Dynamics and their Interactions with Microbial Communities and Ecosystem Functions in Engineered Systems. A thesis submitted to Newcastle University in partial fulfilment of the requirements for the degree of Doctor of Philosophy in the Faculty of Science, Agriculture and Engineering. Author: Mathew Robert Brown Supervisor: Professor Tom Curtis Co-Supervisor: Dr Russell Davenport 2019 Declaration I hereby certify that this work is my own, except where otherwise acknowledged, and that it has not been submitted for a degree at this, or any other, institution. Mathew Robert Brown Abstract Climate change, population growth and increasingly strict environmental regulation means the global water industry is currently facing an unprecedented coincidence of challenges (Palmer, 2010). Better microbial ecology could significantly contribute, since explicitly engineering and maintaining efficient and functionally stable microbial communities would allow existing assets to be optimised and their robustness improved. Given its role in natural systems viral infection could be an important, yet overlooked, factor. Here we attempt to address this lacuna, particularly within activated sludge systems. To facilitate this process we developed, optimised and validated a flow cytometry method, allowing rapid (relative to other methods), accurate and highly reproducible quantification of total free viruses in activated sludge samples (mixed liquor (ML)). Its use spatially identified viruses are highly abundant, with concentrations ranging from 0.59 - 5.14 × 109 viruses mL-1 across 25 activated sludge plants. Subsequently we applied this method to ML collected from one full- and twelve replicate lab-scale activated sludge systems respectively. At both scales viruses in the ML were shown to be both abundant and temporally/spatiotemporally dynamic, thus ever present across activated sludge systems. Through statistical inference they were shown to be associated (positively) with total host (bacterial) abundance, with microbial community structure and with a systems function (the + removal of COD and NH4 -N from influent wastewaters), whilst exogenous factors, particularly those involved in adsorption processes, played an important role in their dynamics. Evidence of predator-prey dynamics between a subset of measured viruses and a key functional group (ammonia oxidising bacteria (AOB)) within the full-scale system is also presented, whilst a detailed examination of all garnered abundances highlights the relative abundance of viruses, as reported in marine systems, declined with increasing host density. Finally preliminary metagenomic data shows wastewater viromes are largely phylogenetically and functionally uncharacterised, yet relative abundances of known viruses vary throughout the wastewater treatment stream. Considering the evidence presented viruses appear to play a more central role in the dynamics of activated sludge systems than hitherto realised and thus should be considered more frequently when assessing the key factors governing bacterial abundance, community composition and functional stability. Table of Contents CHAPTER 1 1 INTRODUCTION 1 1.1. Background 3 1.2 Viruses in Wastewater Treatment Processes 7 1.2.1. The Role of Bacteriophages in Wastewater Treatment: Interactions with Microbial Community composition 8 1.2.2 The Role of Bacteriophages in Wastewater Treatment: Interactions with food web processes and biogeochemical cycles 12 1.2.3 The Role of Bacteriophages in Wastewater Treatment: Can they influence process performance? 13 1.3 Insights from Natural Systems 15 1.3.1 Expanding the Spatial and Temporal Resolution of Viral Studies 15 1.3.2 Identifying True Viral Diversity 16 1.3.3 Elucidating who infects whom 17 1.4 Aims and Objectives 17 CHAPTER 2 19 FLOW CYTOMETRIC QUANTIFICATION OF VIRUSES IN ACTIVATED SLUDGE 19 2.1. Introduction 21 2.2. Materials and Methods 22 2.2.1. Protocol Optimisation 22 2.2.2. Fluorescent Staining and FCM Analysis 24 2.2.3. Virus Recovery Efficiency 24 2.2.4. Virus abundance at a suite of AS WWTP’s 25 2.2.5. Comparison of FCM and TEM counts 25 2.2.6. Statistical Analyses 26 2.3. Results 26 2.3.1. Optimisation of Protocol for AS Virus Enumeration by FCM 26 2.3.2. Virus Recovery and Enumeration Efficiency 28 2.3.3. Virus Abundance in Full Scale Activated Sludge WWTP’s 28 2.3.4. FCM vs. TEM 30 2.4. Discussion 31 2.5. Conclusions 34 2.6. Acknowledgments 34 CHAPTER 3 35 COUPLED VIRUS-BACTERIA INTERACTIONS AND ECOSYSTEM FUNCTION IN AN ENGINEERED MICROBIAL SYSTEM 35 I 3.1. Introduction 37 3.2. Materials and Methods 39 3.2.1. Sample Collection 39 3.2.2. Analytical Methods 39 3.2.3. Molecular Methods 39 3.2.4. Statistical Analysis 41 3.3. Results 44 3.3.1. Bioreactor Performance and Abiotic Conditions 44 3.3.2. Temporal Abundance Dynamics of Viruses and Bacteria 45 3.3.3. Virus Interactions with Biotic and Abiotic Conditions 47 3.3.4. Virus Interactions with Bacteria Community Structure 48 3.3.5. Virus interactions with community function 49 3.4. Discussion 50 3.5. Acknowledgements 54 CHAPTER 4 55 VIRUS - BACTERIA INTERACTIONS, SYNCHRONICITY AND ECOSYSTEM FUNCTION IN REPLICATE ENGINEERED MICROBIAL SYSTEMS 55 4.1. Introduction 57 4.2. Materials and Methods 58 4.2.1. Reactor Set Up 58 4.2.2. CSTR Operational Conditions 59 4.2.3. Sample Collection and Storage 59 4.2.4. Analytical Methods 59 4.2.5. Molecular Methods 60 4.2.6. Statistical Analysis 62 4.3. Results 66 4.3.1. Functional performance and Abiotic Conditions 66 4.3.2. Spatiotemporal Dynamics of Virus, Bacterial and AOB Abundances 67 4.3.3. Spatiotemporal Interactions 68 4.3.4. Similarity and Synchronicity of CSTR’s (day 62 - 204) 72 4.4. Discussion 75 4.5. Acknowledgements 78 CHAPTER 5 79 EVIDENCE OF PREDATOR-PREY DYNAMICS BETWEEN BACTERIOPHAGE AND AMMONIA OXIDISING BACTERIA IN AN ENGINEERED MICROBIAL SYSTEM 79 5.1. Introduction 81 II 5.2. Materials and Methods 82 5.2.1. Sample Collection 82 5.2.2. Flow Cytometry Analysis 82 5.2.3. DNA Extraction qPCR 82 5.2.4. Statistical Analysis 83 5.2.5. Theory 83 5.3. Results and Discussion 84 5.4. Acknowledgements 86 CHAPTER 6 89 A WASTEWATER PERSPECTIVE ON VIRAL AND MICROBIAL ABUNDANCES AND VIRUS-MICROBE RATIOS 89 6.1 Introduction 91 6.2 Materials and Methods 92 6.2.1 Sample Collection 92 6.2.2 Flow Cytometry Analysis 92 6.2.3 DNA Extraction qPCR 92 6.2.4 Statistical Analysis 93 6.3 Results and Discussion 93 6.4 Acknowledgements 96 CHAPTER 7 97 PRELIMINEARY METAGENOMIC CHARACTERISATION OF WASTEWATER VIRUSES 97 7.1 Introduction 99 7.2 Materials and Methods 100 7.2.1 Sample Collection 100 7.2.2 Sample Processing 100 7.2.3 Prophage Induction 101 7.2.4 Molecular Methods 101 7.2.5 Bioinformatics 101 7.3 Results and Discussion 103 7.3.1 General Characteristics of the Wastewater Viromes 103 7.3.2 Phylogenetic and Functional Profiles of Nucleotide Sequences 103 7.3.3 Phylogenetic Profiles of Assembled Protein Sequences 105 7.3.4 Mined Viral-like Genomes 106 7.3.5 Comparison of Wastewater Viromes 106 7.4 Preliminary Conclusions and Recommendations 107 7.5 Acknowledgements 108 III CHAPTER 8 109 GENERAL DISCUSSION AND CONCLUDING REMARKS 109 8.1 Rationale 111 8.2 Synopsis of results 111 8.3 Caveats 114 8.4 Conclusions 115 CHAPTER 9 117 FUTURE WORK 117 CHAPTER 10 125 REFERENCES 125 APPENDIX I 163 AN INTRODUCTION TO WASTEWATER TREATMENT 163 I.1. Introduction 165 I.2. Biological Secondary Treatment 165 I.3. The Activated Sludge Process 166 APPENDIX II 169 AN INTRODUCTION TO BACTERIOPHAGES 169 II.1. What is a phage?! 171 II.2. The Phage Infection Cycle 171 II.3. Phage Life Cycles 173 APPENDIX III 175 SUPPLEMENTARY INFORMATION - COUPLED VIRUS-BACTERIA INTERACTIONS AND ECOSYSTEM FUNCTION IN AN ENGINEERED MICROBIAL SYSTEM 175 III.1. Supplementary Methods 177 III.2. Supplementary Results 178 III.2.1. Bioreactor performance and abiotic conditions 178 III.2.2. Virus interactions with biotic and abiotic conditions 182 III.2.3. Virus interactions with bacteria community structure 185 APPENDIX IV 187 SUPPLEMENTARY INFORMATION - VIRUS - BACTERIA INTERACTIONS, SYNCHRONICITY AND ECOSYSTEM FUNCTION IN REPLICATE ENGINEERED MICROBIAL SYSTEMS 187 IV.1. Supplementary Results 189 APPENDIX V 203 SUPPLEMENTARY INFORMATION - EVIDENCE OF PREDATOR-PREY DYNAMICS BETWEEN BACTERIOPHAGE AND AMMONIA OXIDISING BACTERIA IN AN ENGINEERED MICROBIAL SYSTEM 203 V.1. Supplementary Theory 205 IV V.1.1. Extension of LV Equations 205 V.1.2. More complex models 205 V.1.3. AOB Mortality and Growth 206 APPENDIX VI 207 SUPPLEMENTARY INFORMATION - A WASTEWATER PERSPECTIVE ON VIRAL AND MICROBIAL ABUNDANCES AND VIRUS-MICROBE RATIOS 207 VI.1. Supplementary Results 209 APPENDIX VII 211 SUPPLEMENTARY INFORMATION - PRELIMINARY METAGENOMIC CHARACTERISATION OF WASTEWATER VIRUSES 211 VII.1. Supplementary Methods 213 VII.2. Supplementary Results 214 V VI List of Figures CHAPTER 1 Figure 1. 1. Possible scenarios for temporal changes in host abundance as a consequence of viral infection, (A – D) described in the text. 9 CHAPTER 2 Figure 2. 1. Effect of dispersants (A) and sonication time (B) on FCM virus abundance. Main bars indicate mean virus abundance across triplicates, whilst error bars indicate standard deviation across triplicates. * Significantly different from controls at the 0.05 level. 27 Figure 2. 2. Effect of DNase treatment (A), stain type and dilution (B) and incubation temperature (C) on FCM virus abundance. Main bars indicate mean virus abundance across triplicates, whilst error bars indicate standard deviation across triplicates. * Significantly different from other treatments at the 0.05 level. 27 Figure 2. 3. FCM density plots (A – C) and histograms (D – F) of AS samples taken from Tudhoe Mill WWTP stained with SG I (A and D), SG (B and E) and SG II (C and F), all at a 0.5 × 10-4 dilution of commercial stock.
Recommended publications
  • Knowles2020 Naturecomm.Pdf

    Knowles2020 Naturecomm.Pdf

    ARTICLE https://doi.org/10.1038/s41467-020-18078-4 OPEN Temperate infection in a virus–host system previously known for virulent dynamics ✉ Ben Knowles 1 , Juan A. Bonachela 2, Michael J. Behrenfeld3, Karen G. Bondoc 1, B. B. Cael4, Craig A. Carlson5, Nick Cieslik1, Ben Diaz1, Heidi L. Fuchs 1, Jason R. Graff3, Juris A. Grasis 6, Kimberly H. Halsey 7, Liti Haramaty1, Christopher T. Johns1, Frank Natale1, Jozef I. Nissimov8, Brittany Schieler1, Kimberlee Thamatrakoln 1, T. Frede Thingstad9, Selina Våge9, Cliff Watkins1, ✉ Toby K. Westberry 3 & Kay D. Bidle 1 1234567890():,; The blooming cosmopolitan coccolithophore Emiliania huxleyi and its viruses (EhVs) are a model for density-dependent virulent dynamics. EhVs commonly exhibit rapid viral repro- duction and drive host death in high-density laboratory cultures and mesocosms that simulate blooms. Here we show that this system exhibits physiology-dependent temperate dynamics at environmentally relevant E. huxleyi host densities rather than virulent dynamics, with viruses switching from a long-term non-lethal temperate phase in healthy hosts to a lethal lytic stage as host cells become physiologically stressed. Using this system as a model for temperate infection dynamics, we present a template to diagnose temperate infection in other virus–host systems by integrating experimental, theoretical, and environmental approaches. Finding temperate dynamics in such an established virulent host–virus model system indicates that temperateness may be more pervasive than previously considered, and that the role of viruses in bloom formation and decline may be governed by host physiology rather than by host–virus densities. 1 Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ 08901, USA.
  • Elisabeth Mendes Martins De Moura Diversidade De Vírus DNA

    Elisabeth Mendes Martins De Moura Diversidade De Vírus DNA

    Elisabeth Mendes Martins de Moura Diversidade de vírus DNA autóctones e alóctones de mananciais e de esgoto da região metropolitana de São Paulo Tese apresentada ao Programa de Pós- Graduação em Microbiologia do Instituto de Ciências Biomédicas da Universidade de São Paulo, para obtenção do Titulo de Doutor em Ciências. Área de concentração: Microbiologia Orienta: Prof (a). Dr (a). Dolores Ursula Mehnert versão original São Paulo 2017 RESUMO MOURA, E. M. M. Diversidade de vírus DNA autóctones e alóctones de mananciais e de esgoto da região metropolitana de São Paulo. 2017. 134f. Tese (Doutorado em Microbiologia) - Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, 2017. A água doce no Brasil, assim como o seu consumo é extremamente importante para as diversas atividades criadas pelo ser humano. Por esta razão o consumo deste bem é muito grande e consequentemente, provocando o seu impacto. Os mananciais são normalmente usados para abastecimento doméstico, comercial, industrial e outros fins. Os estudos na área de ecologia de micro-organismos nos ecossistemas aquáticos (mananciais) e em esgotos vêm sendo realizados com mais intensidade nos últimos anos. Nas últimas décadas foi introduzido o conceito de virioplâncton com base na abundância e diversidade de partículas virais presentes no ambiente aquático. O virioplâncton influencia muitos processos ecológicos e biogeoquímicos, como ciclagem de nutriente, taxa de sedimentação de partículas, diversidade e distribuição de espécies de algas e bactérias, controle de florações de fitoplâncton e transferência genética horizontal. Os estudos nesta área da virologia molecular ainda estão muito restritos no país, bem como muito pouco se conhece sobre a diversidade viral na água no Brasil.
  • Multiple Origins of Prokaryotic and Eukaryotic Single-Stranded DNA Viruses from Bacterial and Archaeal Plasmids

    Multiple Origins of Prokaryotic and Eukaryotic Single-Stranded DNA Viruses from Bacterial and Archaeal Plasmids

    ARTICLE https://doi.org/10.1038/s41467-019-11433-0 OPEN Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids Darius Kazlauskas 1, Arvind Varsani 2,3, Eugene V. Koonin 4 & Mart Krupovic 5 Single-stranded (ss) DNA viruses are a major component of the earth virome. In particular, the circular, Rep-encoding ssDNA (CRESS-DNA) viruses show high diversity and abundance 1234567890():,; in various habitats. By combining sequence similarity network and phylogenetic analyses of the replication proteins (Rep) belonging to the HUH endonuclease superfamily, we show that the replication machinery of the CRESS-DNA viruses evolved, on three independent occa- sions, from the Reps of bacterial rolling circle-replicating plasmids. The CRESS-DNA viruses emerged via recombination between such plasmids and cDNA copies of capsid genes of eukaryotic positive-sense RNA viruses. Similarly, the rep genes of prokaryotic DNA viruses appear to have evolved from HUH endonuclease genes of various bacterial and archaeal plasmids. Our findings also suggest that eukaryotic polyomaviruses and papillomaviruses with dsDNA genomes have evolved via parvoviruses from CRESS-DNA viruses. Collectively, our results shed light on the complex evolutionary history of a major class of viruses revealing its polyphyletic origins. 1 Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania. 2 The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA. 3 Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, 7700 Cape Town, South Africa.
  • Discovering Viral Genomes in Human Metagenomic Data by Predicting

    Discovering Viral Genomes in Human Metagenomic Data by Predicting

    www.nature.com/scientificreports OPEN Discovering viral genomes in human metagenomic data by predicting unknown protein Received: 10 May 2017 Accepted: 28 November 2017 families Published online: 08 January 2018 Mauricio Barrientos-Somarribas1, David N. Messina 2, Christian Pou1, Fredrik Lysholm1,3, Annelie Bjerkner4, Tobias Allander4, Björn Andersson 1 & Erik L. L. Sonnhammer2 Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identifcation is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of flters to extract bona fde protein families. We applied this method to 17 virus-enriched libraries originating from human nasopharyngeal aspirates, serum, feces, and cerebrospinal fuid samples. This resulted in 32 predicted putative novel gene families. Some families showed detectable homology to sequences in metagenomics datasets and protein databases after reannotation. Notably, one predicted family matches an ORF from the highly variable Torque Teno virus (TTV). Furthermore, follow-up from a predicted ORFan resulted in the complete reconstruction of a novel circular genome. Its organisation suggests that it most likely corresponds to a novel bacteriophage in the microviridae family, hence it was named bacteriophage HFM. Characterization of the human virome is crucial for our understanding of the role of the microbiome in health and disease. Te shif from culture-based methods to metagenomics in recent years, combined with the devel- opment of virus particle enrichment protocols, has made it possible to efciently study the entire fora of human viruses and bacteriophages associated with the human microbiome.
  • Cell Size Homeostasis and Optimal Viral Strategies

    Cell Size Homeostasis and Optimal Viral Strategies

    CELL SIZE HOMEOSTASIS AND OPTIMAL VIRAL STRATEGIES FOR HOST EXPLOITATION by Cesar Augusto Vargas-Garcia A dissertation submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Electrical and Computer Engineering Fall 2017 c 2017 Cesar Augusto Vargas-Garcia All Rights Reserved ACKNOWLEDGEMENTS I want to thank my advisor Abhyudai Singh. He discovered my professional potential and helped me to achieve this important goal in my life. I am grateful to the Dean, the Faculty, and the Staff of the Department of Electrical and Computer Engineering for providing their assistance and support through the years of my Ph.D. program. I want to thank also my co-advisor and friend, Dr. Ryan Zurakowski. He gave me the opportunity to start and enjoy this field. Also he encouraged me to be resilient in pursuing my degree in the hard days. I want to thank to professor and close friend Henry Arguello for all his support and advice through this years. I also want to thank my wife and daughter, Neyla Johanna and Victoria for their support and encouragement during my studies. They provided me the home to rest after every hard day. My students and alma-mater group HDSP gave me the motivation and encour- agement to make the best effort in my research. They have been my friends and part of my family during this time. I appreciate their collaboration and company in this part of my life. Special thanks to my friends and colleagues Mohammad Soltani and Khem Ghusinga for their support, friendship and collaborations in uncountable and exciting projects which are nowadays the core of my research.
  • Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula

    Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula

    fmicb-10-01014 May 10, 2019 Time: 14:46 # 1 ORIGINAL RESEARCH published: 14 May 2019 doi: 10.3389/fmicb.2019.01014 Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula Tomás Alarcón-Schumacher1,2†, Sergio Guajardo-Leiva1†, Josefa Antón3 and Beatriz Díez1,4* 1 Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile, 2 Max Planck Institute for Marine Microbiology, Bremen, Germany, 3 Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain, 4 Center for Climate and Resilience Research (CR2), University of Chile, Santiago, Chile In Antarctic coastal waters where nutrient limitations are low, viruses are expected to play a major role in the regulation of bloom events. Despite this, research in viral identification and dynamics is scarce, with limited information available for the Southern Ocean (SO). This study presents an integrative-omics approach, comparing variation in the viral and microbial active communities on two contrasting sample conditions from Edited by: a diatom-dominated phytoplankton bloom occurring in Chile Bay in the West Antarctic David Velazquez, Autonomous University of Madrid, Peninsula (WAP) in the summer of 2014. The known viral community, initially dominated Spain by Myoviridae family (∼82% of the total assigned reads), changed to become dominated Reviewed by: by Phycodnaviridae (∼90%), while viral activity was predominantly driven by dsDNA Carole Anne Llewellyn, ∼ ∼ Swansea University, United Kingdom members of the Phycodnaviridae ( 50%) and diatom infecting ssRNA viruses ( 38%), Márcio Silva de Souza, becoming more significant as chlorophyll a increased. A genomic and phylogenetic Fundação Universidade Federal do characterization allowed the identification of a new viral lineage within the Myoviridae Rio Grande, Brazil family.
  • Seasonal Determinations of Algal Virus Decay Rates Reveal Overwintering in a Temperate Freshwater Pond

    Seasonal Determinations of Algal Virus Decay Rates Reveal Overwintering in a Temperate Freshwater Pond

    The ISME Journal (2016) 10, 1602–1612 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Seasonal determinations of algal virus decay rates reveal overwintering in a temperate freshwater pond Andrew M Long1 and Steven M Short1,2 1Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada and 2Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada To address questions about algal virus persistence (i.e., continued existence) in the environment, rates of decay of infectivity for two viruses that infect Chlorella-like algae, ATCV-1 and CVM-1, and a virus that infects the prymnesiophyte Chrysochromulina parva, CpV-BQ1, were estimated from in situ incubations in a temperate, seasonally frozen pond. A series of experiments were conducted to estimate rates of decay of infectivity in all four seasons with incubations lasting 21 days in spring, summer and autumn, and 126 days in winter. Decay rates observed across this study were relatively low compared with previous estimates obtained for other algal viruses, and ranged from 0.012 to 11% h− 1. Overall, the virus CpV-BQ1 decayed most rapidly whereas ATCV-1 decayed most slowly, but for all viruses the highest decay rates were observed during the summer and the lowest were observed during the winter. Furthermore, the winter incubations revealed the ability of each virus to overwinter under ice as ATCV-1, CVM-1 and CpV-BQ1 retained up to 48%, 19% and 9% of their infectivity after 126 days, respectively. The observed resilience of algal viruses in a seasonally frozen freshwater pond provides a mechanism that can support the maintenance of viral seed banks in nature.
  • Extended Evaluation of Viral Diversity in Lake Baikal Through Metagenomics

    Extended Evaluation of Viral Diversity in Lake Baikal Through Metagenomics

    microorganisms Article Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics Tatyana V. Butina 1,* , Yurij S. Bukin 1,*, Ivan S. Petrushin 1 , Alexey E. Tupikin 2, Marsel R. Kabilov 2 and Sergey I. Belikov 1 1 Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya Str., 3, 664033 Irkutsk, Russia; [email protected] (I.S.P.); [email protected] (S.I.B.) 2 Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; [email protected] (A.E.T.); [email protected] (M.R.K.) * Correspondence: [email protected] (T.V.B.); [email protected] (Y.S.B.) Abstract: Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake’s viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake. There was a strict distinction of viral communities in areas with different environmental conditions. Comparative analysis with other freshwater lakes revealed the highest similarity of Baikal viromes with those of the Asian lakes Soyang and Biwa. Analysis of new data, together with previ- ously published data allowed us to get a deeper insight into the diversity and functional potential of Baikal viruses; however, the true diversity of Baikal viruses in the lake ecosystem remains still un- Citation: Butina, T.V.; Bukin, Y.S.; Petrushin, I.S.; Tupikin, A.E.; Kabilov, known.
  • Evaluation of a Potential Bacteriophage Cocktail for the Control of Shiga-Toxin Producing Escherichia Coli in Food

    Evaluation of a Potential Bacteriophage Cocktail for the Control of Shiga-Toxin Producing Escherichia Coli in Food

    fmicb-11-01801 July 23, 2020 Time: 17:24 # 1 ORIGINAL RESEARCH published: 24 July 2020 doi: 10.3389/fmicb.2020.01801 Evaluation of a Potential Bacteriophage Cocktail for the Control of Shiga-Toxin Producing Escherichia coli in Food Nicola Mangieri, Claudia Picozzi*, Riccardo Cocuzzi and Roberto Foschino Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy Shiga-toxin producing Escherichia coli (STEC) are important foodborne pathogens involved in gastrointestinal diseases. Furthermore, the recurrent use of antibiotics to treat different bacterial infections in animals has increased the spread of antibiotic-resistant bacteria, including E. coli, in foods of animal origin. The use of bacteriophages for the control of these microorganisms is therefore regarded as a valid alternative, especially considering the numerous advantages (high specificity, self-replicating, self-limiting, harmless to humans, animals, and plants). This study aimed to isolate bacteriophages Edited by: Lin Lin, active on STEC strains and to set up a suspension of viral particles that can be potentially Jiangsu University, China used to control STEC food contamination. Thirty-one STEC of different serogroups Reviewed by: (O26; O157; O111; O113; O145; O23, O76, O86, O91, O103, O104, O121, O128, Kim Stanford, Alberta Ministry of Agriculture and O139) were investigated for their antibiotic resistance profile and sensitivity to phage and Forestry, Canada attack. Ten percent of strains exhibited a high multi-resistance profile, whereas ampicillin Nancy Ann Strockbine, was the most effective antibiotic by inhibiting 65% of tested bacteria. On the other Centers for Disease Control and Prevention (CDC), United States side, a total of 20 phages were isolated from feces, sewage, and bedding material of *Correspondence: cattle.
  • Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil

    Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil

    viruses Article Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil Rafaela S. Fontenele 1,2, Cristiano Lacorte 2, Natalia S. Lamas 2, Kara Schmidlin 1, Arvind Varsani 1,3,* and Simone G. Ribeiro 2,* 1 The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA 2 Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF 70770-017, Brazil 3 Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa * Correspondence: [email protected] (A.V.); [email protected] (S.G.R.); Tel.: +1-480-727-2093 (A.V.); +55-61-3448-4666/3448-4703 (S.G.R.) Received: 14 June 2019; Accepted: 31 July 2019; Published: 2 August 2019 Abstract: Capybaras (Hydrochoerus hydrochaeris), the world’s largest rodents, are distributed throughout South America. These wild herbivores are commonly found near water bodies and are well adapted to rural and urban areas. There is limited information on the viruses circulating through capybaras. This study aimed to expand the knowledge on the viral diversity associated with capybaras by sampling their faeces. Using a viral metagenomics approach, we identified diverse single-stranded DNA viruses in the capybara faeces sampled in the Distrito Federal, Brazil. A total of 148 complete genomes of viruses in the Microviridae family were identified. In addition, 14 genomoviruses (family Genomoviridae), a novel cyclovirus (family Circoviridae), and a smacovirus (family Smacoviridae) were identified. Also, 37 diverse viruses that cannot be assigned to known families and more broadly referred to as unclassified circular replication associated protein encoding single-stranded (CRESS) DNA viruses were identified.
  • Evidence Supporting a Viral Origin of the Eukaryotic Nucleus

    Evidence Supporting a Viral Origin of the Eukaryotic Nucleus

    bioRxiv preprint doi: https://doi.org/10.1101/679175; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Evidence supporting a viral origin of the eukaryotic nucleus 2 3 4 Dr Philip JL Bell 5 Microbiogen Pty Ltd 6 Correspondence should be addressed to Email [email protected] 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Keywords: Viral eukaryogenesis, nucleus, eukaryote origin, viral factory, mRNA capping, phylogeny 26 27 1 bioRxiv preprint doi: https://doi.org/10.1101/679175; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 28 Abstract 29 30 The defining feature of the eukaryotic cell is the possession of a nucleus that uncouples transcription 31 from translation. This uncoupling of transcription from translation depends on a complex process 32 employing hundreds of eukaryotic specific genes acting in concert and requires the 7- 33 methylguanylate (m7G) cap to prime eukaryotic mRNA for splicing, nuclear export, and cytoplasmic 34 translation. The origin of this complex system is currently a paradox since it is not found or needed 35 in prokaryotic cells which lack nuclei, yet it was apparently present and fully functional in the Last 36 Eukaryotic Common Ancestor (LECA).
  • Ab Komplet 6.07.2018

    Ab Komplet 6.07.2018

    CONTENTS 1. Welcome addresses 2 2. Introduction 3 3. Acknowledgements 10 4. General information 11 5. Scientific program 16 6. Abstracts – oral presentations 27 7. Abstracts – poster sessions 99 8. Participants 419 1 EMBO Workshop Viruses of Microbes 2018 09 – 13 July 2018 | Wrocław, Poland 1. WELCOME ADDRESSES Welcome to the Viruses of Microbes 2018 EMBO Workshop! We are happy to welcome you to Wrocław for the 5th meeting of the Viruses of Microbes series. This series was launched in the year 2010 in Paris, and was continued in Brussels (2012), Zurich (2014), and Liverpool (2016). This year our meeting is co-organized by two partner institutions: the University of Wrocław and the Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences. The conference venue (University of Wrocław, Uniwersytecka 7-10, Building D) is located in the heart of Wrocław, within the old, historic part of the city. This creates an opportunity to experience the over 1000-year history of the city, combined with its current positive energy. The Viruses of Microbes community is constantly growing. More and more researchers are joining it, and they represent more and more countries worldwide. Our goal for this meeting was to create a true global platform for networking and exchanging ideas. We are most happy to welcome representatives of so many countries and continents. To accommodate the diversity and expertise of the scientists and practitioners gathered by VoM2018, the leading theme of this conference is “Biodiversity and Future Application”. With the help of your contribution, this theme was developed into a program covering a wide range of topics with the strongest practical aspect.