DOCSLIB.ORG

Denitrification and the Hypoxic Response in Obligate Aerobic Methane-Oxidizing Bacteria

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Denitrification and the Hypoxic Response in Obligate Aerobic Methane-Oxidizing Bacteria Denitrification and the hypoxic response in obligate aerobic methane-oxidizing bacteria By Kerim Dimitri Kits A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Microbiology and Biotechnology Department of Biological Sciences University of Alberta Kerim Dimitri Kits, 2016 Abstract Aerobic methanotrophic bacteria lessen the impact of the greenhouse gas methane (CH4) not only because they are a sink for atmospheric methane but also because they oxidize it before it is emitted to the atmospheric reservoir. Aerobic methanotrophs, unlike anaerobic methane oxidizing archaea, have a dual need for molecular oxygen (O2) for respiration and CH4 oxidation. Nevertheless, methanotrophs are highly abundant and active in environments that are extremely hypoxic and even anaerobic. While the O2 requirement in these organisms for CH4 oxidation is inflexible, recent genome sequencing efforts have uncovered the presence of putative denitrification genes in many aerobic methanotrophs. Being able to use two different terminal electron acceptors – hybrid respiration – would be massively advantageous to aerobic methanotrophs as it would allow them to halve their O2 requirement. But, the function of these genes that hint at an undiscovered respiratory anaerobic metabolism is unknown. Moreover, past work on pure cultures of aerobic methanotrophs ruled out the possibility that these organisms - denitrify. An organism that can couple CH4 oxidation to NO3 respiration so far does not exist in pure culture. So while the role of aerobic methanotrophs in the carbon cycle is appreciated, the hypoxic metabolism and contribution of these specialized microorganisms to the nitrogen cycle is not understood. Here we demonstrate using cultivation dependent approaches, microrespirometry, and whole genome, transcriptome, and proteome analysis that an aerobic - methanotroph – Methylomonas denitrificans FJG1 – couples CH4 oxidation to NO3 respiration - with N2O as the terminal product via the intermediates NO2 and NO. Whole transcriptome and proteome analysis reveals that respiratory nitrate (Nar, Nap), nitrite (Nir), and nitric oxide (Nor) reductases are expressed and upregulated at the transcript and protein levels under denitrifying conditions. Physiological analysis of denitrifying cultures of M. denitrificans FJG1 also confirms ii - that NO3 respiration is bioenergetically advantageous. We also confirm denitrification activity and upregulation of denitrification gene expression in another obligate methanotroph – Methylomicrobium album BG8 – and also show that this activity is supported by a diverse array of energy sources. Formaldehyde fermentation has been identified by others as an important adaptation of aerobic methanotrophs to hypoxia. We additionally illustrate here that M. denitrificans FJG1 can also ferment formaldehyde and that nitrate respiration and fermentation occur simultaneously during hypoxia. The work herein is a significant contribution to our knowledge of how aerobic methanotrophs affect greenhouse gas flux though CH4 oxidation in low O2 environments and through N2O production via denitrification. Preface This thesis is an original work by Kerim Kits and serves as a compendium of original research articles that are either currently published in peer reviewed journals or are currently in preparation for submission. The research objectives and background for these research articles are detailed in the opening chapter. The closing chapter – Chapter 5 – provides a synopsis of the conclusions, contributions, and major findings of this thesis and the articles contained within. The original research articles that contribute to this thesis have been reformatted from the original publication style and are as follows: Chapter 2: Kits, K. D., Klotz, M. G., and Stein, L. Y. (2015). Methane oxidation coupled to nitrate reduction under hypoxia by the Gammaproteobacterium Methylomonas denitrificans, sp. nov. type strain FJG1. Environ. Microbiol. 17, 3219–3232. doi:10.1111/1462-2920.12772. (in press) Chapter 3: Kits, K. D., Campbell, D. J., Rosana, A. R., and Stein, L. Y. (2015). Diverse electron sources support denitrification under hypoxia in the obligate methanotroph Methylomicrobium album strain BG8. Front. Microbiol. 6, 1072. doi:10.3389/fmicb.2015.01072. (in press) iii Chapter 4: Kits, K.D., Manuel, K., Liu, D., and Stein, L. Y. (2016). Simultaneous expression of denitrifying and fermentation pathways in the methanotroph, Methylomonas denitrificans FJG1. (in preparation) Additional original research articles in which the thesis author is the primary author but that do not contribute to the individual outlined chapters are included as appendices: Appendix A: Kits, K. D., Kalyuzhnaya, M. G., Klotz, M. G., Jetten, M. S. M., Op den Camp, H. J. M., Vuilleumier, S., et al. (2013). Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8. Genome Announc 1, e0017013–e00170– 13. doi:10.1128/genomeA.00170-13. (in press) Publications in which the thesis author was a co-author and not the primary author and are therefore not included in the thesis are: Stein, L. Y., F. Bringel, A. A. DiSpirito, S. Han, M. S. M. Jetten, M. G. Kalyuzhnaya, K. D. Kits, M. G. Klotz, H. J. M. O. den Camp, J. D. Semrau, S. Vuilleumier, D. C. Bruce, J. Cheng, K. W. Davenport, L. Goodwin, S. Han, L. Hauser, A. Lajus, M. L. Land, A. Lapidus, S. Lucas, C. Medigue, S. Pitluck, and T. Woyke. (2011). Genome sequence of the methanotrophic Alphaproteobacterium, Methylocystis sp. Rockwell (ATCC 49242). J. Bacteriol. 193, 2668– 2669. doi:10.1128/JB.00278-11. Boden, R., Cunliffe, M., Scanlan, J., Moussard, H., Kits, K. D., Klotz, M. G., et al. (2011). Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J. Bacteriol. 193, 7001–7002. doi:10.1128/JB.06267-11. Hamilton, R., Kits, K. D., Ramonovskaya, V. A., Rozova, O. N., Yurimoto, H., Iguchi, H., et al. (2015). Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. Genome Announc 3, e00515–15. doi:10.1128/genomeA.00515-15. Kozlowski, J. A., Kits, K. D., and Stein, L. Y. (2016a). Genome Sequence of Nitrosomonas iv communis Strain Nm2, a Mesophilic Ammonia-Oxidizing Bacterium Isolated from Mediterranean Soil. Genome Announc 4, e01541–15. doi:10.1128/genomeA.01541-15. Kozlowski, J. A., Kits, K. D., and Stein, L. Y. (2016b). Complete Genome Sequence of Nitrosomonas ureae Strain Nm10, an Oligotrophic Group 6a Nitrosomonad. Genome Announc 4, e00094–16. doi:10.1128/genomeA.00094-16. The contribution of the thesis author to the aforementioned published journal articles was as follows. For chapter 2, the thesis author performed all of the physiology, genome sequencing, transcriptome sequencing and all of the data analysis while Martin G. Klotz performed the phylogenetic analysis of the M. denitrificans FJG1 genome. The thesis author wrote the manuscript (Chapter 2) with input and guidance from M. G. Klotz and L. Y. Stein. For chapter 3, the thesis author performed all of the physiology, all of the data analysis, and a portion of the expression analysis while Albert R. R. Rosana finished the expression analysis. Chapter 3 was written by the thesis author with input from L. Y. Stein who also helped develop experimental design for this chapter. For chapter 4, the thesis author carried out the transcriptome sequencing and all data analysis, and Manuel Kleiner and Dan Liu performed the proteomics. In all cases, Lisa Y. Stein contributed guidance and editorial comments on written manuscripts. With regard to the publications in which the thesis author was a co-author and not a primary author, the contributions from the thesis author were as follows. The thesis author performed the main bioinformatics role, assembled, and closed genome sequences for Kozlowski et al., (2016a) and Kozlowski et al., (2016b). In all other co-authored original research articles, the author contributed to genome annotation. v Acknowledgements First, I would like to thank my supervisor – Dr. Lisa Stein. When I first started working in your lab, during my third undergraduate year, my CV was not that of a promising future research assistant or graduate student. You recognized something in me and you then played an enormous role in the development of my skills and interests as a then (very) junior scientist. Thank you for accepting me as a graduate student, thank you for providing me with funding and space to do research, and thank you for always giving me the independence to pursue my interests. Also, I have to thank you for always allowing and encouraging me to attend meetings and meet other scientists – these experiences gave me immeasurable maturity and perspective. I also have to levy a massive thank you to the other members of my graduate studies committee – Dr. Yan Boucher and Dr. George Owttrim. Thank you both so much for taking the time to read over my work and assessing my progress during our committee meetings. You were both valuable committee members and I am incredibly grateful for your suggestions, advice, and support. It is also important that I mention Dr. Martin Klotz, although Martin wasn’t officially part of my committee; Martin, your approach to critical thinking massively influenced me and ignited in me a true appreciation for exactitude of meaning, nomenclature, and logic. I have to recognize the contribution that other members of the University of Alberta had to my work. Thank you to the storeroom staff
Load more

Recommended publications
  • Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
    Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr.
    [Show full text]
  • Isolation and Characterisation of Methylocystis Spp. for Poly-3
    Rumah et al. AMB Expr (2021) 11:6 https://doi.org/10.1186/s13568-020-01159-4 ORIGINAL ARTICLE Open Access Isolation and characterisation of Methylocystis spp. for poly-3-hydroxybutyrate production using waste methane feedstocks Bashir L. Rumah† , Christopher E. Stead† , Benedict H. Claxton Stevens , Nigel P. Minton , Alexander Grosse‑Honebrink and Ying Zhang* Abstract Waste plastic and methane emissions are two anthropogenic by‑products exacerbating environmental pollution. Methane‑oxidizing bacteria (methanotrophs) hold the key to solving these problems simultaneously by utilising otherwise wasted methane gas as carbon source and accumulating the carbon as poly‑3‑hydroxybutyrate, a biode‑ gradable plastic polymer. Here we present the isolation and characterisation of two novel Methylocystis strains with the ability to produce up to 55.7 1.9% poly‑3‑hydroxybutyrate of cell dry weight when grown on methane from diferent waste sources such as landfll± and anaerobic digester gas. Methylocystis rosea BRCS1 isolated from a recrea‑ tional lake and Methylocystis parvus BRCS2 isolated from a bog were whole genome sequenced using PacBio and Illumina genome sequencing technologies. In addition to potassium nitrate, these strains were also shown to grow on ammonium chloride, glutamine and ornithine as nitrogen source. Growth of Methylocystis parvus BRCS2 on Nitrate Mineral Salt (NMS) media with 0.1% methanol vapor as carbon source was demonstrated. The genetic tractability by conjugation was also determined with conjugation efciencies up to 2.8 10–2 and 1.8 10–2 for Methylocystis rosea BRCS1 and Methylocystis parvus BRCS2 respectively using a plasmid with ColE1× origin of ×replication. Finally, we show that Methylocystis species can produce considerable amounts of poly‑3‑hydroxybutyrate on waste methane sources without impaired growth, a proof of concept which opens doors to their use in integrated bio‑facilities like landflls and anaerobic digesters.
    [Show full text]
  • Optimization and Characterization of the Growth Of
    OPTIMIZATION AND CHARACTERIZATION OF THE GROWTH OF THE PHOTOSYNTHETIC BACTERIUM BLASTOCHLORIS VIRIDIS AND A BRIEF SURVEY OF ITS POTENTIAL AS A REMEDIATIVE TOOL A Dissertation Submitted to the Graduate School of the University of Notre Dame in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Darcy Danielle LaClair, B.S. ___________________________________ Agnes E. Ostafin, Director Graduate Program in Chemical and Biomolecular Engineering Notre Dame, Indiana April 2006 OPTIMIZATION AND CHARACTERIZATION OF THE GROWTH OF THE PHOTOSYNTHETIC BACTERIUM BLASTOCHLORIS VIRIDIS AND A BRIEF SURVEY OF THEIR POTENTIAL AS A REMEDIATIVE TOOL Abstract by Darcy Danielle LaClair The growth of B. viridis was characterized in an undefined rich medium and a well-defined medium, which was later selected for further experimentation to insure repeatability. This medium presented a significant problem in obtaining either multigenerational or vigorous growth because of metabolic limitations; therefore optimization of the medium was undertaken. A primary requirement to obtain good growth was a shift in the pH of the medium from 6.9 to 5.9. Once this shift was made, it was possible to obtain growth in subsequent generations, and the media formulation was optimized. A response curve suggested optimum concentrations of 75 mM carbon, supplemented as sodium malate, 12.5 mM nitrogen, supplemented as ammonium sulfate, Darcy Danielle LaClair and 12.7 mM phosphate buffer. In addition, the vitamins p-Aminobenzoic acid, Thiamine, Biotin, B12, and Pantothenate were important to achieving good growth and good pigment formation. Exogenous carbon dioxide, added as 2.5 g sodium bicarbonate per liter media also enhanced growth and reduced the lag time.
    [Show full text]
  • Technologies for the Bioconversion of Methane Into More Valuable Products
    Revised manuscript_ COBIOT_2017 Technologies for the bioconversion of methane into more valuable products S. Cantera, R. Muñoz, R, Lebrero, J.C López, Y. Rodríguez, P A. García-Encina* Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain, Tel. +34 983186424, Fax: 983423013. [email protected] Abstract Methane, with a global warming potential twenty five times higher than that of CO2 is the second most important greenhouse gas emitted nowadays. Its bioconversion into microbial molecules with a high retail value in the industry offers a potential cost-efficient and environmentally friendly solution for mitigating anthropogenic diluted CH4-laden streams. Methane bio-refinery for the production of different compounds such as ectoine, feed proteins, biofuels, bioplastics and polysaccharides, apart from new bioproducts characteristic of methanotrophic bacteria, has been recently tested in discontinuous and continuous bioreactors with promising results. This review constitutes a critical discussion about the state-of-the-art of the potential and research niches of biotechnologies applied in a CH4 biorefinery approach. Keywords: CH4 bio-refinery, methane treatment, bio-products, industrial approach Graphical_abstract_COBIOT_2017 Highlights_COBIOT_2017 • Methanotrophs as a competitive platform for the generation of valuable products • CH4 emissions used as a feedstock in biorefinery reduces GHGs environmental impact • Current biotechnological limitations and potential improvements are reviewed • Environmental and economic analysis supports the feasibility of CH4 revalorization Manuscript_COBIOT_2017 Technologies for the bioconversion of methane into more valuable products S. Cantera, R. Muñoz, R, Lebrero, J.C López, Y. Rodríguez, P A. García-Encina* Department of Chemical Engineering and Environmental Technology, Valladolid University, Dr. Mergelina, s/n, Valladolid, Spain, Tel.
    [Show full text]
  • Characterizing Methanogen and Methanotroph Diversity, Abundance and Activity Within the Hampshire-Avon Catchment
    Characterizing methanogen and methanotroph diversity, abundance and activity within the Hampshire-Avon catchment A thesis submitted for the degree of PhD G. Leung Supervisors: Dr. C. Whitby, Prof. D. Nedwell (University of Essex) 1 Summary: Methane (CH4) is an important greenhouse gas and research into its production and oxidation by microbial communities is crucial in predicting their impact in future climate change. Here, potential rate measurements, quantitative real-time polymerase chain reactions (Q-PCR) of pmoA, mcrA genes and next generation sequencing, were applied to characterize methanogen and methanotroph community structure, abundance and activity in the Hampshire-Avon catchment, UK. Soil and river sediments were taken from sites across different underlying geologies based on their baseflow index (BFI); from low (chalk) to medium (greensand) to high BFI (clay). In general, methane oxidation potentials (MOP) and methane production potentials (MPP) were greater in river sediments compared to soils (particularly higher in clays). Sequence analysis identified Methanococcoides, Methanosarcina and Methanocorpusculum as candidates driving methanogenesis across all river geologies. Methylocystis was also found to predominate in all the river sediments and may be a key methane oxidiser. In soils microcosms, MOP doubled when temperature was increased from 4oC to 30oC (in greensand soils sampled in summer but not winter). In long-term in-situ field warming experiments, MOP was unaffected by temperature in the clay and chalk soils, whereas MOP increased by two-fold in the greensand soils. In both microcosms and field warming experiments pmoA abundance was unchanged. In soil microcosms amended with nitrogen (N) and phosphate (P), high N and low P concentrations had the greatest inhibition on methane oxidation in clay soils, whilst chalk and greensand soils were unaffected.
    [Show full text]
  • Evolution of Methanotrophy in the Beijerinckiaceae&Mdash
    The ISME Journal (2014) 8, 369–382 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis Ivica Tamas1, Angela V Smirnova1, Zhiguo He1,2 and Peter F Dunfield1 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada and 2Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT.
    [Show full text]
  • Rhodopseudomonas Viridis and Rhodopseudomonas Sulfoviridis to the Genus Blastochloris Gen
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1997, p. 217-219 Vol. 47, No. 1 0020-7713/97/$04.00+ 0 Copyright 0 1997, International Union of Microbiological Societies Transfer of the Bacteriochlorophyll &Containing Phototrophic Bacteria Rhodopseudomonas viridis and Rhodopseudomonas sulfoviridis to the Genus Blastochloris gen. nov. AKIRA HIMISHI* Department of Ecological Engineering, Toyohashi University of Technology, Toyohashi 441, and Laboratory of Environmental Biotechnology, Konishi Co., Tokyo 130, Japan The phylogenetic positions of the bacteriochlorophyll (BChl) b-producing budding phototrophic bacteria Rhodopseudomonas viridis and Rhodopseudomonas sulfoviridis were studied on the basis of 16s rRNA gene sequence information. These bacteria formed a tight cluster with the genus Rhodoplanes as a sister group within the alpha-2 subgroup of the Proteobacteria. Genomic DNA-DNA hybridization assays showed that R. viridis and R. sulfoviridis were closely related but were different species. Creation of the genus Blastochloris gen. nov. is proposed to accommodate these BChl b-producing species of phototrophic bacteria. In 1984 some species of the classically defined genus Rho- tion of the organisms. For Rhodopseudomonas sulfoviridis, the dopseudomonas were reclassified into new genera, including medium was supplemented with 10 mM glucose, 2 mM sodium the new genera Rhodobacter and Rhodopila, on the basis of sulfide (neutralized), and 2 mM thiosulfate. The medium was modern taxonomic criteria (17). In recent years, the taxonomy supplemented with 10 mM pyruvate (filter sterilized) for Rho- of the genus Rhodopseudomonas has been further reevaluated doplanes roseus. The organisms were grown at 30°C in screw- on the basis of increasing molecular and chemotaxonomic in- cap test tubes under anaerobic conditions in the light.
    [Show full text]
  • Methanotrophic Bacterial Biomass As Potential Mineral Feed Ingredients for Animals
    International Journal of Environmental Research and Public Health Article Methanotrophic Bacterial Biomass as Potential Mineral Feed Ingredients for Animals Agnieszka Ku´zniar 1,*, Karolina Furtak 2 , Kinga Włodarczyk 1, Zofia St˛epniewska 1 and Agnieszka Woli ´nska 1 1 Department of Biochemistry and Environmental Chemistry, The John Paul II Catholic University of Lublin, Konstantynów St. 1 I, 20-708 Lublin, Poland 2 Department of Agriculture Microbiology, Institute of Soil Sciences and Plant Cultivation State Research Institute, Czartoryskich St. 8, 24-100 Puławy, Poland * Correspondence: [email protected]; Tel.: +48-81-454-5461 Received: 14 June 2019; Accepted: 23 July 2019; Published: 26 July 2019 Abstract: Microorganisms play an important role in animal nutrition, as they can be used as a source of food or feed. The aim of the study was to determine the nutritional elements and fatty acids contained in the biomass of methanotrophic bacteria. Four bacterial consortia composed of Methylocystis and Methylosinus originating from Sphagnum flexuosum (Sp1), S. magellanicum (Sp2), S. fallax II (Sp3), S. magellanicum IV (Sp4), and one composed of Methylocaldum, Methylosinus, and Methylocystis that originated from coalbed rock (Sk108) were studied. Nutritional elements were determined using the flame atomic absorption spectroscopy technique after a biomass mineralization stage, whereas the fatty acid content was analyzed with the GC technique. Additionally, the growth of biomass and dynamics of methane consumption were monitored. It was found that the methanotrophic biomass 1 contained high concentrations of K, Mg, and Fe, i.e., approx. 9.6–19.1, 2.2–7.6, and 2.4–6.6 g kg− , respectively.
    [Show full text]
  • Seasonal and Ecohydrological Regulation of Active Microbial Populations Involved in DOC, CO2, and CH4 fluxes in Temperate Rainforest Soil
    The ISME Journal https://doi.org/10.1038/s41396-018-0334-3 ARTICLE Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil 1,2 2,3 1,2 4 5 David J. Levy-Booth ● Ian J. W. Giesbrecht ● Colleen T. E. Kellogg ● Thierry J. Heger ● David V. D’Amore ● 6 1 1 Patrick J. Keeling ● Steven J. Hallam ● William W. Mohn Received: 9 February 2018 / Revised: 12 October 2018 / Accepted: 3 December 2018 © The Author(s) 2019. This article is published with open access Abstract The Pacific coastal temperate rainforest (PCTR) is a global hot-spot for carbon cycling and export. Yet the influence of microorganisms on carbon cycling processes in PCTR soil is poorly characterized. We developed and tested a conceptual model of seasonal microbial carbon cycling in PCTR soil through integration of geochemistry, micro-meteorology, and eukaryotic and prokaryotic ribosomal amplicon (rRNA) sequencing from 216 soil DNA and RNA libraries. Soil moisture and pH increased during the wet season, with significant correlation to net CO2 flux in peat bog and net CH4 flux in bog 1234567890();,: 1234567890();,: forest soil. Fungal succession in these sites was characterized by the apparent turnover of Archaeorhizomycetes phylotypes accounting for 41% of ITS libraries. Anaerobic prokaryotes, including Syntrophobacteraceae and Methanomicrobia increased in rRNA libraries during the wet season. Putatively active populations of these phylotypes and their biogeochemical marker genes for sulfate and CH4 cycling, respectively, were positively correlated following rRNA and metatranscriptomic network analysis. The latter phylotype was positively correlated to CH4 fluxes (r = 0.46, p < 0.0001).
    [Show full text]
  • Microbial Degradation of Organic Micropollutants in Hyporheic Zone Sediments
    Microbial degradation of organic micropollutants in hyporheic zone sediments Dissertation To obtain the Academic Degree Doctor rerum naturalium (Dr. rer. nat.) Submitted to the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth by Cyrus Rutere Bayreuth, May 2020 This doctoral thesis was prepared at the Department of Ecological Microbiology – University of Bayreuth and AG Horn – Institute of Microbiology, Leibniz University Hannover, from August 2015 until April 2020, and was supervised by Prof. Dr. Marcus. A. Horn. This is a full reprint of the dissertation submitted to obtain the academic degree of Doctor of Natural Sciences (Dr. rer. nat.) and approved by the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth. Date of submission: 11. May 2020 Date of defense: 23. July 2020 Acting dean: Prof. Dr. Matthias Breuning Doctoral committee: Prof. Dr. Marcus. A. Horn (reviewer) Prof. Harold L. Drake, PhD (reviewer) Prof. Dr. Gerhard Rambold (chairman) Prof. Dr. Stefan Peiffer In the battle between the stream and the rock, the stream always wins, not through strength but by perseverance. Harriett Jackson Brown Jr. CONTENTS CONTENTS CONTENTS ............................................................................................................................ i FIGURES.............................................................................................................................. vi TABLES ..............................................................................................................................
    [Show full text]
  • Biological Conversion Process of Methane Into Methanol Using Mixed Culture Methanotrophic Bacteria Enriched from Activated Sludge System
    BIOLOGICAL CONVERSION PROCESS OF METHANE INTO METHANOL USING MIXED CULTURE METHANOTROPHIC BACTERIA ENRICHED FROM ACTIVATED SLUDGE SYSTEM Ahmed Mohamed AlSayed Mahmoud A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF APPLIED SCIENCE GRADUATE PROGRAM IN CIVIL ENGINEERING YORK UNIVERSITY, TORONTO, ONTARIO AUGUST 2017 © Ahmed AlSayed, 2017 Abstract Wastewater treatment plants contribute to the global warming phenomena not only by GHG emissions, but also, by consuming enormous amount of fossil fuel based energy. Therefore, methane bio-hydroxylation has attracted the attention as methanol is an efficient substitute for methane (GHG) due to its transportability and higher energy yield. This work is destined to investigate and optimize the factors affecting the microbial activity within methane bio-hydroxylation system using type I methanotrophs enriched from activated sludge system. The optimization resulted in a notable enhancement of the growth kinetics. The -1 attained maximum specific growth rate (µmax) (0.358 hr ) and maximum specific methane -1 biodegradation rate (qmax) (0.605 g-CH4,Total/g-DCW/hr ) were the highest reported in mixed cultures. Furthermore, the maximum methanol productivity achieved is comparable with pure cultures and equal to 2115±81 mg/L/day. Whereas, methanol concentration of 485±21 mg/L was attained which is two times higher than the reported using mixed culture. ii Dedication " Bountiful is your life, full and complete. Or so you think, until someone comes along and makes you realize what you have been missing all this time. Like a mirror that reflects what is absent rather than present, he shows you the void in your soul—the void you have resisted seeing.
    [Show full text]
  • Computational and Experimental Approaches for Evaluating the Genetic Basis of Mitochondrial Disorders
    Computational and Experimental Approaches For Evaluating the Genetic Basis of Mitochondrial Disorders The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. Lieber, Daniel Solomon. 2013. Computational and Experimental Citation Approaches For Evaluating the Genetic Basis of Mitochondrial Disorders. Doctoral dissertation, Harvard University. Accessed April 17, 2018 4:10:16 PM EDT Citable Link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11158264 This article was downloaded from Harvard University's DASH Terms of Use repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA (Article begins on next page) Computational and Experimental Approaches For Evaluating the Genetic Basis of Mitochondrial Disorders A dissertation presented by Daniel Solomon Lieber to The Committee on Higher Degrees in Systems Biology in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Systems Biology Harvard University Cambridge, Massachusetts April 2013 © 2013 - Daniel Solomon Lieber All rights reserved. Dissertation Adviser: Professor Vamsi K. Mootha Daniel Solomon Lieber Computational and Experimental Approaches For Evaluating the Genetic Basis of Mitochondrial Disorders Abstract Mitochondria are responsible for some of the cell’s most fundamental biological pathways and metabolic processes, including aerobic ATP production by the mitochondrial respiratory chain. In humans, mitochondrial dysfunction can lead to severe disorders of energy metabolism, which are collectively referred to as mitochondrial disorders and affect approximately 1:5,000 individuals. These disorders are clinically heterogeneous and can affect multiple organ systems, often within a single individual.
    [Show full text]