Copper-Induced Stimulation of Nitrification in Biological Rapid Sand Filters for Drinking Water Production by Proliferation of Nitrosomonas Spp
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CUED Phd and Mphil Thesis Classes
High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice. -
General Introduction
Physiological Characteristics and Genomic Properties of Nitrosomonas mobilis Isolated from Nitrifying Granule of Wastewater Treatment Bioreactor December 2016 Soe Myat Thandar ソー ミャット サンダー Physiological Characteristics and Genomic Properties of Nitrosomonas mobilis Isolated from Nitrifying Granule of Wastewater Treatment Bioreactor December 2016 Waseda University Graduate School of Advanced Science and Engineering Department of Life Science and Medical Bioscience Research on Environmental Biotechnology Soe Myat Thandar ソー ミャット サンダー Contents Abbreviations ................................................................................................................... i Chapter 1-General introduction .................................................................................... 1 1.1. Nitrification and wastewater treatment system .......................................................... 3 1.2. Important of Nitrosomonas mobilis ........................................................................... 8 1.3. Objectives and outlines of this study ....................................................................... 12 1.4. Reference.................................................................................................................. 12 Chapter 2- Physiological characteristics of Nitrosomonas mobilis Ms1 ................... 17 2.1. Introduction .............................................................................................................. 19 2.2. Material and methods .............................................................................................. -
APP201895 APP201895__Appli
APPLICATION FORM DETERMINATION Determine if an organism is a new organism under the Hazardous Substances and New Organisms Act 1996 Send by post to: Environmental Protection Authority, Private Bag 63002, Wellington 6140 OR email to: [email protected] Application number APP201895 Applicant Neil Pritchard Key contact NPN Ltd www.epa.govt.nz 2 Application to determine if an organism is a new organism Important This application form is used to determine if an organism is a new organism. If you need help to complete this form, please look at our website (www.epa.govt.nz) or email us at [email protected]. This application form will be made publicly available so any confidential information must be collated in a separate labelled appendix. The fee for this application can be found on our website at www.epa.govt.nz. This form was approved on 1 May 2012. May 2012 EPA0159 3 Application to determine if an organism is a new organism 1. Information about the new organism What is the name of the new organism? Briefly describe the biology of the organism. Is it a genetically modified organism? Pseudomonas monteilii Kingdom: Bacteria Phylum: Proteobacteria Class: Gamma Proteobacteria Order: Pseudomonadales Family: Pseudomonadaceae Genus: Pseudomonas Species: Pseudomonas monteilii Elomari et al., 1997 Binomial name: Pseudomonas monteilii Elomari et al., 1997. Pseudomonas monteilii is a Gram-negative, rod- shaped, motile bacterium isolated from human bronchial aspirate (Elomari et al 1997). They are incapable of liquefing gelatin. They grow at 10°C but not at 41°C, produce fluorescent pigments, catalase, and cytochrome oxidase, and possesse the arginine dihydrolase system. -
Comparison of Physiology and Genome-Wide Expression in Two Nitrosomonas Spp
Comparison of physiology and genome-wide expression in two Nitrosomonas spp. under batch cultivation By Mohammad Ghashghavi A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science In Microbiology and Biotechnology Department of Biological Sciences University of Alberta © Mohammad Ghashghavi, 2014 Abstract: Ammonia oxidizing bacteria (AOB) play a central role in the nitrogen cycle by oxidizing ammonia to nitrite. Nitrosomonas europaea ATCC 19718 has been the single most studied AOB that has contributed to our understanding of chemolithotrophic ammonia oxidation. As a closely related species, Nitrosomonas eutropha C91 has also been extensively studied. Both of these bacteria are involved in wastewater treatment systems and play a crucial part in major losses of ammonium-based fertilizers globally. Although comparative genome analysis studies have been done before, change in genome-wide expression between closely related organisms are scarce. In this study, we compared these two organisms through physiology and transcriptomic experiments during exponential and early stationary growth phase. We found that under batch cultivation, N. europaea produces more N2O while N. eutropha consumes more nitrite. From transcriptomic analysis, we also found that there are selections of motility genes that are highly expressed in N. eutropha during early stationary growth phase and such observation was completely absent in N. europaea. Lastly, principle homologous genes that have been well studied had different patterns of expression in these strains. This study not only gives us a better understanding regarding physiology and genome-wide expression of these two AOB, it also opens a wide array of opportunities to further our knowledge in understanding other closely related species with regards to their evolution, physiology and niche preference. -
WWW-VERSION (Without Papers) in This Online Version of the Thesis, Paper I-IV Are Not Included but Can Be Obtained from Electronic Article Databases E.G
Downloaded from orbit.dtu.dk on: Sep 27, 2021 Discovery and description of complete ammonium oxidizers in groundwater-fed rapid sand filters Palomo, Alejandro Publication date: 2017 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Palomo, A. (2017). Discovery and description of complete ammonium oxidizers in groundwater-fed rapid sand filters. Department of Environmental Engineering, Technical University of Denmark (DTU). General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Discovery and description of complete ammonium oxidizers in groundwater-fed rapid sand filters Alejandro Palomo-González PhD Thesis June 2017 DTU Environment Department of Environmental Engineering Technical University of Denmark Alejandro Palomo-González Discovery and description of complete ammonium oxidizers in ground- water-fed rapid sand filters PhD Thesis, June 2017 The synopsis part of this thesis is available as a pdf-file for download from the DTU research database ORBIT: http://www.orbit.dtu.dk. -
Nitrification 31
NITROGEN IN SOILS/Nitrification 31 See also: Eutrophication; Greenhouse Gas Emis- Powlson DS (1993) Understanding the soil nitrogen cycle. sions; Isotopes in Soil and Plant Investigations; Soil Use and Management 9: 86–94. Nitrogen in Soils: Cycle; Nitrification; Plant Uptake; Powlson DS (1999) Fate of nitrogen from manufactured Symbiotic Fixation; Pollution: Groundwater fertilizers in agriculture. In: Wilson WS, Ball AS, and Hinton RH (eds) Managing Risks of Nitrates to Humans Further Reading and the Environment, pp. 42–57. Cambridge: Royal Society of Chemistry. Addiscott TM, Whitmore AP, and Powlson DS (1991) Powlson DS (1997) Integrating agricultural nutrient man- Farming, Fertilizers and the Nitrate Problem. Wallingford: agement with environmental objectives – current state CAB International. and future prospects. Proceedings No. 402. York: The Benjamin N (2000) Nitrates in the human diet – good or Fertiliser Society. bad? Annales de Zootechnologie 49: 207–216. Powlson DS, Hart PBS, Poulton PR, Johnston AE, and Catt JA et al. (1998) Strategies to decrease nitrate leaching Jenkinson DS (1986) Recovery of 15N-labelled fertilizer in the Brimstone Farm experiment, Oxfordshire, UK, applied in autumn to winter wheat at four sites in eastern 1988–1993: the effects of winter cover crops and England. Journal of Agricultural Science, Cambridge unfertilized grass leys. Plant and Soil 203: 57–69. 107: 611–620. Cheney K (1990) Effect of nitrogen fertilizer rate on soil Recous S, Fresnau C, Faurie G, and Mary B (1988) The fate nitrate nitrogen content after harvesting winter wheat. of labelled 15N urea and ammonium nitrate applied to a Journal of Agricultural Science, Cambridge 114: winter wheat crop. -
Ammonia Oxidizers in a Grazing Land with a History of Poultry
AMMONIA OXIDIZERS IN A GRAZING LAND WITH A HISTORY OF POULTRY LITTER APPLICATION by ABHA MUNDEPI (Under the Direction of Mussie Y. Habteselassie) ABSTRACT Poultry litter (PL) is widely applied on grazing lands in Georgia, but it is not clear how it affects the function and community structure of ammonia-oxidizing bacteria (AOB) and archaea (AOA). In 2009, soil samples were collected from plots that received PL for 15 years at 8 Mg ha-1 annually and those plots were resampled in 2013 after 2 years of PL stoppage, with the objective of examining the long-term impacts of PL and its legacy effects on AOB and AOA. In 2009, the abundance of AOB and AOA were significantly higher in PL treated soils (6.98 and 7.06 log copies g soil-1 for AOB and AOA, respectively) than controls plots that received equivalent amount of nitrogen (N) in the form of urea ammonium nitrate (6.39 and 6.53 log copies g soil-1 for AOB and AOA, respectively). In 2013, AOB abundance decreased significantly in response to the discontinuation of PL application. We used dicyandiamide to separate the roles of AOB and AOA in nitrification in PL and CL (no N added) soils. At early stage of incubation, AOA dominated nitrification in both PL and unamended CL, accounting for ≥70% of nitrification potential (NP). With time, AOB contribution to NP grew in PL, accounting for ≥50% at high ammonium level. We designed a laboratory study to examine how AOB and AOA respond to elevated levels of Zinc (Zn) and Copper (Cu). -
Nitrosomonas Stercoris Sp. Nov., a Chemoautotrophic Ammonia-Oxidizing Bacterium Tolerant of High Ammonium Isolated from Composted Cattle Manure
Microbes Environ. Vol. 30, No. 3, 221-227, 2015 https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME15072 Nitrosomonas stercoris sp. nov., a Chemoautotrophic Ammonia-Oxidizing Bacterium Tolerant of High Ammonium Isolated from Composted Cattle Manure TATSUNORI NAKAGAWA1* and REIJI TAKAHASHI1 1College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252–0880, Japan (Received February 4, 2014—Accepted May 18, 2015—Published online July 4, 2015) Among ammonia-oxidizing bacteria, Nitrosomonas eutropha-like microbes are distributed in strongly eutrophic environments such as wastewater treatment plants and animal manure. In the present study, we isolated an ammonia-oxidizing bacterium tolerant of high ammonium levels, designated strain KYUHI-ST, from composted cattle manure. Unlike the other known Nitrosomonas species, this isolate grew at 1,000 mM ammonium. Phylogenetic analyses based on 16S rRNA and amoA genes indicated that the isolate belonged to the genus Nitrosomonas and formed a unique cluster with the uncultured ammonia oxidizers found in wastewater systems and animal manure composts, suggesting that these ammonia oxidizers contributed to removing higher concentrations of ammonia in strongly eutrophic environments. Based on the physiological and phylogenetic data presented here, we propose and call for the validation of the provisional taxonomic assignment Nitrosomonas stercoris, with strain KYUHI-S as the type strain (type strain KYUHI-ST = NBRC 110753T = ATCC BAA-2718T). Key words: high ammonium-tolerant, cattle manure, ammonia-oxidizing bacteria, compost, Nitrosomonas stercoris Chemoautotrophic ammonia-oxidizing bacteria (AOB) that phylogenetically related to Nitrosomonas europaea and oxidize ammonium to nitrite are found not only in natural Nitrosomonas eutropha are involved in the conversion of ecosystems such as soils, sediment, freshwater, and marine ammonia to nitrite within manure composts (18, 22, 36–38). -
Complete Nitrification by Nitrospira Bacteria Holger Daims1, Elena V
ARTICLE doi:10.1038/nature16461 Complete nitrification by Nitrospira bacteria Holger Daims1, Elena V. Lebedeva2, Petra Pjevac1, Ping Han1, Craig Herbold1, Mads Albertsen3, Nico Jehmlich4, Marton Palatinszky1, Julia Vierheilig1, Alexandr Bulaev2, Rasmus H. Kirkegaard3, Martin von Bergen4,5, Thomas Rattei6, Bernd Bendinger7, Per H. Nielsen3 & Michael Wagner1 Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly expressed during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira- contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities. Nitrification is catalysed by ammonia-oxidizing -
Microbial Nitrogen Metabolism in Chloraminated Drinking Water
bioRxiv preprint doi: https://doi.org/10.1101/655316; this version posted June 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Microbial Nitrogen Metabolism in Chloraminated Drinking Water 2 Reservoirs 3 4 Sarah C Potgietera, Zihan Daic, Stefanus N Ventera, Makhosazana Sigudud and Ameet J 5 Pintob* 6 7 a Rand Water Chair in Water Microbiology, Department of Microbiology and Plant 8 Pathology, University of Pretoria, South Africa 9 b Department of Civil and Environmental Engineering, Northeastern University, Boston, USA 10 c College of Science and Engineering, School of Engineering, University of Glasgow, UK 11 d Scientific Services, Rand Water, Vereeniging, South Africa 12 13 *corresponding author: Dr Ameet J Pinto 14 Email address: [email protected] 15 16 17 18 19 20 21 22 23 24 25 bioRxiv preprint doi: https://doi.org/10.1101/655316; this version posted June 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 26 Abstract 27 Nitrification is a common concern in chloraminated drinking water distribution systems. The 28 addition of ammonia promotes the growth of nitrifying organisms, causing the depletion of 29 chloramine residuals and resulting in operational problems for many drinking water utilities. 30 Therefore, a comprehensive understanding of the microbially mediated processes behind 31 nitrogen metabolism together with chemical water quality data, may allow water utilities to 32 better address the undesirable effects caused by nitrification. -
Application of Hierarchical Oligonucleotide Primer Extension (HOPE) to Assess Relative Abundances of Ammonia- and Nitrite-Oxidiz
Scarascia et al. BMC Microbiology (2017) 17:85 DOI 10.1186/s12866-017-0998-2 RESEARCH ARTICLE Open Access Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria Giantommaso Scarascia, Hong Cheng, Moustapha Harb and Pei-Ying Hong* Abstract Background: Establishing an optimal proportion of nitrifying microbial populations, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), complete nitrite oxidizers (comammox) and ammonia-oxidizing archaea (AOA), is important for ensuring the efficiency of nitrification in water treatment systems. Hierarchical oligonucleotide primer extension (HOPE), previously developed to rapidly quantify relative abundances of specific microbial groups of interest, was applied in this study to track the abundances of the important nitrifying bacterial populations. Results: The method was tested against biomass obtained from a laboratory-scale biofilm-based trickling reactor, and the findings were validated against those obtained by 16S rRNA gene-based amplicon sequencing. Our findings indicated a good correlation between the relative abundance of nitrifying bacterial populations obtained using both HOPE and amplicon sequencing. HOPE showed a significant increase in the relative abundance of AOB, specifically Nitrosomonas, with increasing ammonium content and shock loading (p < 0.001). In contrast, Nitrosospira remained stable in its relative abundance against the total community throughout the operational phases. There was a corresponding significant decrease in the relative abundance of NOB, specifically Nitrospira and those affiliated to comammox, during the shock loading. Based on the relative abundance of AOB and NOB (including commamox) obtained from HOPE, it was determined that the optimal ratio of AOB against NOB ranged from 0.2 to 2.5 during stable reactor performance. -
Microbial Diversity and Evidence of Sulfur- and Ammonium-Based Chemolithotrophy in Movile Cave
The ISME Journal (2009) 3, 1093–1104 & 2009 International Society for Microbial Ecology All rights reserved 1751-7362/09 $32.00 www.nature.com/ismej ORIGINAL ARTICLE Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave Yin Chen1,5, Liqin Wu2,5, Rich Boden1, Alexandra Hillebrand3, Deepak Kumaresan1, He´le`ne Moussard1, Mihai Baciu4, Yahai Lu2 and J Colin Murrell1 1Department of Biological Sciences, University of Warwick, Coventry, UK; 2College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; 3Institute of Speleology ‘Emil Racovita’, Bucharest, Romania and 4The Group of Underwater and Speleological Exploration, Bucharest, Romania Microbial diversity in Movile Cave (Romania) was studied using bacterial and archaeal 16S rRNA gene sequence and functional gene analyses, including ribulose-1,5-bisphosphate carboxylase/ oxygenase (RuBisCO), soxB (sulfate thioesterase/thiohydrolase) and amoA (ammonia monoox- ygenase). Sulfur oxidizers from both Gammaproteobacteria and Betaproteobacteria were detected in 16S rRNA, soxB and RuBisCO gene libraries. DNA-based stable-isotope probing analyses using 13 C-bicarbonate showed that Thiobacillus spp. were most active in assimilating CO2 and also implied that ammonia and nitrite oxidizers were active during incubations. Nitrosomonas spp. were detected in both 16S rRNA and amoA gene libraries from the ‘heavy’ DNA and sequences related to nitrite- oxidizing bacteria Nitrospira and Candidatus ‘Nitrotoga’ were also detected in the ‘heavy’ DNA, which suggests that ammonia/nitrite oxidation may be another major primary production process in this unique ecosystem. A significant number of sequences associated with known methylotrophs from the Betaproteobacteria were obtained, including Methylotenera, Methylophilus and Methylo- vorus, supporting the view that cycling of one-carbon compounds may be an important process within Movile Cave.