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Pseudomonas Trautweiniana Sp University of Plymouth PEARL https://pearl.plymouth.ac.uk 04 University of Plymouth Research Theses 01 Research Theses Main Collection 2017 Taxonomy, physiology and biochemistry of the sulfur Bacteria Hutt, Lee Philip http://hdl.handle.net/10026.1/8612 University of Plymouth All content in PEARL is protected by copyright law. Author manuscripts are made available in accordance with publisher policies. Please cite only the published version using the details provided on the item record or document. In the absence of an open licence (e.g. Creative Commons), permissions for further reuse of content should be sought from the publisher or author. Copyright statement This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with its author and that no quotation from the thesis and no information derived from it may be published without the author’s prior consent. I II Taxonomy, physiology and biochemistry of the sulfur Bacteria By Lee Philip Hutt A thesis submitted to Plymouth University in partial fulfilment for the degree of DOCTOR OF PHILOSOPHY School of Biological Sciences, Faculty of Science and Technology July 2016 III Thesis Abstract Inorganic sulfur-oxidising Bacteria are present throughout the Proteobacteria and inhabit all environments of Earth. Despite these facts they are still poorly understood in terms of taxonomy, physiology, biochemistry and genetics. Using phylogenetic and chemotaxonomic analysis two species that were erroneously classified as Thiobacillus trautweinii spp. in 1921 and 1934 are in fact novel chemolithoheterotrophic species for which the names Pseudomonas trautweiniana sp. nov. and Achromobacter starkeyanus sp. nov. are proposed, respectively. These species were found to oxidise thiosulfate in a “fortuitous” manor when grown in continuous culture and increases in maximum theoretical growth yield (YMAX) and maximum specific growth rate (μMAX) were observed. Cytochrome c linked thiosulfate-dependent ATP production was confirmed in both species, confirming “true” chemolithoheterotrophy. Evidence is presented that the ATP concentration governs the benefits of chemolithoheterotrophy. There were significant changes in enzyme activities, including enzymes of the TCA cycle that might be affecting amino acid synthesis. This is strong evidence that chemolithoheterotrophy gives a strong physiological boost and evolutionary advantage over strictly heterotrophic species. An autotrophic species that was historically placed in Thiobacillus was also shown to be a novel species for which the name Thermithiobacillus parkerianus sp. nov. is proposed. The enzyme profiles of Thermithiobacillus parkerianus differed significantly between different inorganic sulfur growth substrates and was the first time all TCA cycle enzymes were assayed in a member of the Acidithiobacillia. The properties of thiosulfate dehydrogenase varied significantly between Pseudomonas sp. Strain T, Achromobacter sp. Strain B and Thermithiobacillus sp. ParkerM both in terms of optimal parameters and the effect of inhibitors. This evidence adds to the increasing body of work indicating there to be at least two thiosulfate dehydrogenases present in the Bacteria. IV List of abbreviations α Bunsen coefficient ε Molar extinction coefficient λ Wavelength μ Specific growth rate μMAX Maximum specific growth rate Ax Absorbance at x nm ADP Adenosine 5ˈ-Diphosphate AMP Adenosine 5ˈ-Monophosphate ATP Adenosine 5ˈ-Triphosphate BLAST Basic local alignment search tool BSA Bovine serum albumin CFE Cell-free Extract Cyt Cytochrome D Dilution rate DCPIP 2,6-Dichlorophenolindophenol DNA Deoxyribonucleic acid e- Electron EC number Enzyme Commission number EBS E-Basal Salts EDTA Ethylenediamine tetraacetic acid ETC Electron transport chain g Earth’s gravitational acceleration at sea level h hours K Kelvin m Maintenance energy coefficient ms Maintenance energy coefficient with respect to substrate V M Molar Mol Mole Mol% Molar percentage NAD+ Nicotinamide adenine dinucleotide (oxidised form) NADH Nicotinamide adenine dinucleotide (reduced form) NADP+ Nicotinamide adenine dinucleotide phosphate (oxidised form) NADPH Nicotinamide adenine dinucleotide phosphate (reduced form) N.D. Not detected NEM N-ethylmaleimide N.G. No growth ODx Optical density at x nm PBS Phosphate Buffered Saline PCA Perchloric acid pCMB p-chloromercuribenzoic acid PCR Polymerase chain reaction PGA 3-phosphoglycerate PSO Paracoccus sulfur oxidation SEM Standard Error of the Mean q Specific rate of substrate uptake RNA Ribonucleic acid RPM Revolutions per minute S4I Tetrasulfur intermediate T Type strain TCA Tricarboxylic acid TEM Transmission electron microscopy TOMES Thiosulfate-oxidising multi-enzyme system UV Ultraviolet VI V Rate of reaction VMAX Maximum rate of reaction v/v Volume to volume w/v Weight to volume x Dry weight of biomass Y Yield Y MAX Maximum yield VII List of contents List of Tables…………………………………………...……………………………XIX List of Figures………………………………………………………………...………XXIII Acknowledgements……………………………………………………………….XXXV Author’s declaration……………………………..………………...……………….XXXVI Presentations and conferences attended……………………….…………………..XXXVII Chapter 1 Introduction………………………………………………….……………….1 1.1 The Biogeochemical sulfur cycle………………………………………………......….2 1.2 Inorganic sulfur compounds…………………………………………...……………..13 1.2.1 Thiosulfate……………………………………………………………...……….….13 1.2.2 Polythionates………………………………………………………………..……...15 1.2.3 Sulfide and elemental sulfur………………………………………………………..18 1.2.4 Sulfate…………………………………………………………….…………...……18 1.3 Inorganic sulfur compound metabolism………………………………….……....…..19 1.3.1 Chemolithoautotrophy…………………………………………………….....……..19 1.3.1.1 The Kelly-Friedrich pathway…………………………………………..………...19 VIII 1.3.1.2 The Kelly-Trudinger pathway…………………………………………..……..…21 1.3.1.3 Other pathways……………………………………………………………..….…31 1.3.2 Chemolithoheterotrophy and mixotrophy……...……………………………..……31 Chapter 2 Materials and methods……………………..…………………..……39 2.1 Chemicals…………………………………………………..……...…………………40 2.2 Culture media…………………………………………………………………..…….40 2.2.1 Basal media…………………………………………………………………….....40 2.2.2 Trace metal solution…………………………………………………..…………....41 2.2.3 Vitamin solution………………………………………………………………..…41 2.2.4 Nutrient broth…………………………………………………………...………….42 2.3 Maintenance of bacterial strains…………………………………………………..….42 2.3.1 Pseudomonas spp. ………………………………………………..……………..…42 2.3.2 Achromobacter spp. …………………………………………………...…...……...42 2.3.3 Thermithiobacillus spp. ……………………………………………………....……43 2.4 Batch culture experiments……………………………………………………….…...43 2.4.1 Heterotrophic batch culture……………………………………………………...…43 IX 2.4.2 Autotrophic batch culture…………………………………………………………..44 2.4.3 Optimal growth temperature……………………………………………………….44 2.4.4 Optimal growth pH…………………………………………………………………44 2.5 Continuous culture experiments……………………………………………..…….....45 2.6 Growth kinetics…………………………………………………………………...….46 2.6.1 Batch growth kinetics………………………………………………..………..……46 2.6.1.1 Determination of yields (Y)…………………………...………………….46 2.6.1.2 Determination of specific growth rate (μ)………….………….………...47 2.6.1.3 Determination of specific rate of substrate uptake (q)…………….…….47 2.6.2 Chemostat kinetics……………………………………………………….……...…47 2.6.2.1 Determination of steady state yields (Y)……………….………….……...47 2.6.2.2 Determination of maximum theoretical growth yield (YMAX)………….…48 2.6.2.3 Determination of maintenance energy coefficient (ms)…………..……....48 2.6.3.4 Determination of maximum specific growth rate (μMAX)……………...…48 2.7 Analytical methods………………………………………………………………..…49 2.7.1 Determination of biomass……………………………………………………….....49 2.7.2 Determination of glucose………………………………………………………..…52 2.7.3 Determination of succinate…………………………………………………………52 2.7.4 Determination of thiosulfate, tetrathionate and trithionate………………………...52 X 2.7.5 Determination of ammonium………………………………………………………53 2.7.6 Determination of phosphates……………………………………………………….53 2.7.7 Determination of guanine plus cytosine genomic DNA content…………………...53 2.7.8 Ubiquinone extraction and analysis………………………………………………..53 2.7.9. Determination of cellular fatty acid methyl esters………………………………...54 2.7.10 Determination of total protein………………………………………………….…55 2.7.11 Oxygen uptake by whole cells…………………………………………………….55 2.7.12 Cytochrome spectra……………………………………………………………….55 2.7.13 Determination of cellular ATP and ADP…………………………………………56 2.8 Preparation of cell-free extracts…………………………………………………..…56 2.8.1 Harvesting cells………………………………………………………………..….56 2.8.2 Disruption of cell…………………………………………………………………56 2.9 Enzyme assays………………………………………………….………………….....57 2.9.1 Inorganic sulfur metabolism………………………………………………………57 2.9.1.1 Thiosulfate dehydrogenase (EC 1.8.2.2)………………………………..57 2.9.1.2 Sulfite dehydrogenase (EC 1.8.2.1), thiocyanate dehydrogenase and trithionate hydrolase (EC 3.12.1.1)……………………………………………..58 2.9.1.3 Tetrathionate hydrolase (EC 3.12.1.B1)……………………………….…58 2.9.1.4 Sulfur oxygenase (EC 1.13.11.55)……………………………………….58 XI 2.9.1.5 Sulfur dioxygenase (EC EC 1.13.11.18)…………………………………59 2.9.2 TCA cycle enzymes………………………………………………………………..59 2.9.2.1 Citrate synthase (EC 4.1.3.7)…………………………………………….59 2.9.2.2 Aconitase (EC 4.2.1.3)………………………………………………….60 2.9.2.3 Isocitrate dehydrogenase (EC 1.1.1.41)…………………….…………....60 2.9.2.4 α-ketoglutarate dehydrogenase (EC 1.2.4.2)………………………….….61 2.9.2.5 Succinyl-CoA synthetase (EC 6.2.1.5)……………………………..…….61 2.9.2.6 Succinate dehydrogenase (EC 1.3.99.1)…………………………….....…61 2.9.2.7 Fumarase (EC 4.2.1.2)……………………………………………..…..…62
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