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Hyper Ammonia Producing Bacteria and Bacteriophages in the Rumen Microbiome

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Hyper Ammonia Producing Bacteria and Bacteriophages in the Rumen Microbiome STUDYING THE UNDERSTUDIED: HYPER AMMONIA PRODUCING BACTERIA AND BACTERIOPHAGES IN THE RUMEN MICROBIOME by Jessica Charlotte Abigail Friedersdorff A thesis submitted in partial fulfillment of the requirements for the degree of PhD in Biological Sciences Aberystwyth University 2020 Preface I. Mandatory Layout of Declaration/Statements Word Count of thesis: 62,288 DECLARATION This work has not previously been accepted in substance for any degree and is not being concurrently submitted in candidature for any degree. Candidate name Jessica Charlotte Abigail Friedersdorff Signature: Date 15/09/2020 STATEMENT 1 This thesis is the result of my own investigations, except where otherwise stated. Where *correction services have been used, the extent and nature of the correction is clearly marked in a footnote(s). Other sources are acknowledged by footnotes giving explicit references. A bibliography is appended. Signature: Date 15/09/2020 [*this refers to the extent to which the text has been corrected by others] STATEMENT 2 I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loan, and for the title and summary to be made available to outside organisations. Signature: Date 15/09/2020 NB: Candidates on whose behalf a bar on access (hard copy) has been approved by the University should use the following version of Statement 2: I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loans after expiry of a bar on access approved by Aberystwyth University. Signature: Date 15/09/2020 1 Preface II. Summary Candidate’s Surname/Family Name Friedersdorff Candidate’s Forenames (in full) Jessica Charlotte Abigail Candidate for the Degree of PhD Academic year the work submitted for examination 2020 Summary: Greenhouse gas emissions and feed efficiency in ruminant livestock are pertinent and important topics, ones which have not suffered from lack of attention as ample research has endeavoured to further our understanding of the complex rumen microbial ecosystem. Despite this, some populations remain understudied. This is the key motivation behind the studies herein, which contribute to the understanding of the niche bacterial population of hyper ammonia producers (HAP) and bacteriophages (viruses that infect bacteria). HAP species degrade amino acids and peptides for energy, in the process producing hydrogen, carbon dioxide, and excessive amounts of ammonia. Hydrogen and carbon dioxide feed into methane production by archaea present in the rumen, whilst excess ammonia is removed from the animal host. This makes the HAPs an ideal target for potential population control, but firstly it was imperative to better understand them. This study first characterised the ammonia production phenotypes of bacterial cultures, then compared their genomes and transcriptomes to identify a signature that indicates the HAP phenotype. The work presented here has demonstrated the complexity and variability underlying the seemingly simple HAP phenotype, warranting further investigation in future work and isolation of novel HAPs in order to better understand this group before controlling the population. Phage therapy is one approach to population control that has been relatively little explored to date in the rumen. Despite phages being abundant in the rumen, there were only five genomes available of phages isolated from rumen-associated samples. This study isolated and characterised a further five novel phages that infect Butyrivibrio fibrisolvens. While the work presented here did not identify phages active against HAPs, these five Butyrivibrio phages contribute valuable information about the structure and function of the rumen ecosystem. It is suggested that continuation of this line of enquiry in future work would complement ongoing research utilising metagenomics, metatranscriptomics and metaproteomics aimed at understanding and improving rumen efficiency. 2 Preface III. Funding Knowledge Economy Skills Scholarships (KESS 2) is a pan-Wales higher level skills initiative led by Bangor University on behalf of the HE sector in Wales. It is part funded by the Welsh Government’s European Social Fund (ESF) convergence programme for West Wales and the Valleys. The supporting company partner was Dr David Rooke, director of Dynamic Extractions LTD. 3 Preface IV. Contents I. MANDATORY LAYOUT OF DECLARATION/STATEMENTS ...................................... 1 II. SUMMARY ............................................................................................................................... 2 III. FUNDING ................................................................................................................................. 3 IV. CONTENTS .............................................................................................................................. 4 V. ACKNOWLEDGMENTS ...................................................................................................... 10 VI. LIST OF PUBLICATIONS ................................................................................................... 11 VII. FIGURE LEGENDS .............................................................................................................. 12 VIII. TABLE LEGENDS ................................................................................................................ 21 IX. ABBREVIATIONS ................................................................................................................ 24 X. ABSTRACT ............................................................................................................................ 25 1. BACKGROUND AND INTRODUCTION .......................................................................... 27 1.1. RUMINANTS AND THEIR IMPORTANCE ................................................................................. 27 1.2. STRUCTURE AND FUNCTION OF THE RUMINANT STOMACH ................................................ 27 1.2.1. The Rumen and its Specialised Function ........................................................................ 28 1.3. DIGESTION IN RUMINANTS .................................................................................................. 29 1.3.1. Feed and Diet ................................................................................................................... 29 1.3.2. Mechanical Digestion ...................................................................................................... 29 1.3.3. Fermentation .................................................................................................................... 30 1.3.4. Carbohydrate Metabolism ............................................................................................... 32 1.3.5. Nitrogen Metabolism ....................................................................................................... 32 1.3.5.1. Ammonia in the Rumen; Sources, Transport and Fate ........................................... 33 1.4. THE RUMEN MICROBIOME ................................................................................................... 36 1.4.1. Bacteria ............................................................................................................................ 36 1.4.1.1. Fibrolytic Bacteria .................................................................................................. 37 1.4.1.2. Proteolytic Bacteria ................................................................................................ 39 1.4.1.3. Deaminating Bacteria ............................................................................................. 40 1.4.1.4. Hyper Ammonia Producing (HAP) bacteria........................................................... 43 1.4.2. Archaea ............................................................................................................................ 50 1.4.3. Viruses ............................................................................................................................. 50 1.4.3.1. Bacteriophages ....................................................................................................... 50 1.4.3.2. Archaeal phages ..................................................................................................... 55 1.4.4. Fungi ................................................................................................................................ 55 1.4.5. Protozoa ........................................................................................................................... 55 4 Preface 1.4.6. Understanding the Rumen Microbiome .......................................................................... 56 1.5. FEED EFFICIENCY AND METHANE PRODUCTION IN THE RUMEN ......................................... 57 1.5.1. Methane Production in the Rumen .................................................................................. 58 1.5.2. Ammonia Production in the Rumen ................................................................................ 58 1.5.3. Methods Considered to Mitigate Methane Emissions and Increase Feed Efficiency ...... 59 1.6. AIMS AND OBJECTIVES ........................................................................................................ 61 2. MATERIALS AND METHODS ........................................................................................... 62 2.1. RUMEN FLUID .....................................................................................................................
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