DOCSLIB.ORG

UNIVERSITY of EMBU EDWARD NDERITU KARANJA Phd 2020

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

UNIVERSITY OF EMBU EDWARD NDERITU KARANJA PhD 2020 MICROBIAL COMMUNITY DIVERSITY AND STRUCTURE WITHIN ORGANIC AND CONVENTIONAL FARMING SYSTEMS IN CENTRAL HIGHLANDS OF KENYA EDWARD NDERITU KARANJA (MSc) A THESIS SUBMITTED IN PARTIAL FULFILLMENT FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN APPLIED MICROBIOLOGY IN THE UNIVERSITY OF EMBU NOVEMBER, 2020 DECLARATION This thesis is my original work and has not been presented for a degree in any other University Signature……………………………. Date………….……….. Edward Nderitu Karanja Department of Biological Science B801/147/2015 This thesis has been submitted for examination with our approval as the University Supervisors Signature……………………………. Date………….………. Prof. Romano Mwirichia Department of Biological science University of Embu (UoEm), Kenya Signature………. …………………………. Date………….…………. Dr. Andreas Fliessbach Department of Soil Science Research Institute of Organic Agriculture - FIBL, Switzerland i DEDICATION I dedicated to my family; my wife Anne Kelly Kambura, my children; Shawn Karanja, Melissa Wangithi, Joseph Munyuithia, Shayne Koome and Ann Wanjiku, my parents; Mr. Samuel Karanja and Mrs. Agnes Wangithi, my siblings, Ruth Wairimu, Juliet Muthoni, Alex Ngochi, James Karuma and Nelly Njoki. I appreciate the support you have accorded me during my studies. Your inspiration and backing in this journey made it easier to manage all challenges encountered. ii ACKNOWLEDGEMENT I express gratitude toward Almighty God for his mercies from the beginning of this long and thought-provoking journey. This was conducted in the framework of long-term systems comparison program, with financial support from Biovision Foundation, Coop Sustainability Fund, Liechtenstein Development Service (LED) and the Swiss Agency for Development and Cooperation (SDC). I acknowledge icipe core funding for the kind contribution provided by UK-Aid from UK Government, Swedish International Development Cooperation Agency, Swiss Agency for Development and Cooperation, Federal Democratic Republic of Ethiopia and the Kenyan Government. I recognize icipe (executing agency of the project in Kenya) for the opportunity to carry out my PhD study within the project. This work could not have been accomplished without the wise counsel, specialized intellect and research mentorship of Prof. Romano Mwirichia and Dr. Andreas Fliessbach on farming systems microbiome studies. I deeply appreciate my supervisors for their patience and for having confidence in me. Thank you for standing by me. My most sincere gratitude goes to Dr. Noah Adamtey, Dr. Komi Fiaboe, Dr. Chrysantus Tanga and Dr. Martha Musyoka for the help they accorded me as I assumed training and attended to my work obligations at icipe. Your presence made this research promising and the challenges encountered functional. In addition, no adjectives can define the appreciation I have for the support offered by the SysCom project team; the late Mr. Peter Owuor, Mr. Felix Matheri, Mr. James Karanja, Ms. Jane Makena and Ms. Felistus Mutua during field activities, field maintenance, data collection and soil sampling. I appreciate their intellectual ability as they ensured exact sampling and sample handling techniques were achieved for this research. I am greatly indebted to them. Particular recognition goes to Crop nutrition laboratory services and KALRO NARL Soil physics laboratory staff led by Mr. Edward Komba and Mr. John Mwangi for their support and during soil samples handling, extraction and analysis process. iii I would like to index incomparable indebtedness to my loving wife for her unending encouragement, patience and personal sacrifices through the process of accomplishing this achievement. I cannot thank her enough for being there for me. iv TABLE OF CONTENTS DECLARATION ......................................................................................................................... i DEDICATION ........................................................................................................................... ii ACKNOWLEDGEMENTS ...................................................................................................... iii TABLE OF CONTENTS ........................................................................................................... v LIST OF TABLES .................................................................................................................... ix LIST OF FIGURES .................................................................................................................... x LIST OF APPENDICES ......................................................................................................... xiv LIST OF ABBREVIATIONS AND ACRONYMS ................................................................. xv ABSTRACT ........................................................................................................................... xvii CHAPTER ONE: INTRODUCTION ..................................................................................... 1 1.1 General Introduction ............................................................................................................. 1 1.2 Statement of the problem ...................................................................................................... 2 1.3 Justification ........................................................................................................................... 3 1.4 Hypothesis ............................................................................................................................ 4 1.5 Objectives ............................................................................................................................. 4 1.5.1 General Objective .............................................................................................................. 4 1.5.2 Specific Objectives ............................................................................................................ 4 CHAPTER TWO: REVIEW OF LITERATURE ................................................................. 5 2.1 General background of farming systems .............................................................................. 5 2.2 Sustainable and conventional agricultural systems .............................................................. 6 2.3 Organic resources used in agro-ecosystems ......................................................................... 7 v 2.4 Long-term farming system comparison in the tropics .......................................................... 8 2.5 Soil microbial ecology .......................................................................................................... 9 2.6 Prokaryotic organisms in soil ecosystems .......................................................................... 11 2.7 Microbial ecology in farming systems ............................................................................... 13 2.8 Fungal communities in soil habitats ................................................................................... 14 2.9 Effect of land use on microbial diversity ........................................................................... 15 2.10 Use of molecular techniques in microbial ecology ……………………………………..15 CHAPTER THREE: MATERIALS AND METHODS ...................................................... 18 3.1 Study sites ........................................................................................................................... 18 3.2 Farming systems ................................................................................................................. 19 3.3 Soil sampling ...................................................................................................................... 25 3.4 Microbial community analysis ........................................................................................... 26 3.4.1 Total DNA extraction ...................................................................................................... 26 3.4.2 Total RNA Extraction ...................................................................................................... 27 3.4.3 Synthesis of cDNA from 16S rRNA ............................................................................... 27 3.4.4 16S rRNA amplicon library preparation and sequencing ................................................ 28 3.4.5 Prokaryotic bioinformatic sequence processing, taxonomic identification and statistical analysis………………………………………………………………………………….28 3.4.6 Fungal amplicon DNA library preparation and sequencing ............................................ 30 3.4.7 Fungal Sequence analysis ................................................................................................ 29 3.4.8 cDNA synthesis from mRNA, library construction and sequencing .............................. 31 3.4.9 Transcriptome sequence analysis .................................................................................... 32 vi CHAPTER FOUR: RESULTS .............................................................................................. 34 4.1 Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya…......……………………………………34 4.1.1 General sequence analysis .............................................................................................. 34 4.1.2 Diversity indices of soil prokaryotic communities ......................................................... 42 4.1.3 Soil
Recommended publications
  • Marsarchaeota Are an Aerobic Archaeal Lineage Abundant in Geothermal Iron Oxide Microbial Mats

    Marsarchaeota Are an Aerobic Archaeal Lineage Abundant in Geothermal Iron Oxide Microbial Mats

    Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Authors: Zackary J. Jay, Jacob P. Beam, Mansur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep This is a postprint of an article that originally appeared in Nature Microbiology on May 14, 2018. The final version can be found at https://dx.doi.org/10.1038/s41564-018-0163-1. Jay, Zackary J. , Jacob P. Beam, Mensur Dlakic, Douglas B. Rusch, Mark A. Kozubal, and William P. Inskeep. "Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats." Nature Microbiology 3, no. 6 (May 2018): 732-740. DOI: 10.1038/ s41564-018-0163-1. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats Zackary J. Jay1,4,7, Jacob P. Beam1,5,7, Mensur Dlakić2, Douglas B. Rusch3, Mark A. Kozubal1,6 and William P. Inskeep 1* The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and character- ization of a phylum-level archaeal lineage proposed and herein referred to as the ‘Marsarchaeota’, after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50–80 °C. Metagenomics, single-cell sequencing, enrichment culturing and in situ transcrip- tional analyses reveal their biogeochemical role as facultative aerobic chemoorganotrophs that may also mediate the reduction of Fe(III).
  • ARCHAEAL EVOLUTION Evolutionary Insights from the Vikings

    ARCHAEAL EVOLUTION Evolutionary Insights from the Vikings

    RESEARCH HIGHLIGHTS Nature Reviews Microbiology | Published online 16 Jan 2017; doi:10.1038/nrmicro.2016.198 ARCHAEAL EVOLUTION Evolutionary insights from the Vikings The emergence of the eukaryotic cell ASGARD — after the invisible the closest known homologue of during evolution gave rise to all com- ‘Gods of Asgard’ in Norse mythology. eukaryotic epsilon DNA polymerases primordial plex life forms on Earth, including The superphylum consists of the identified thus far. eukaryotic multicellular organisms such as ani- previously identified Lokiarchaeota Members of the ASGARD super- mals, plants and fungi. However, the and Thorarchaeota phyla, and the phylum were particularly enriched vesicular and origin of eukaryotes and their char- newly identified Odinarchaeota and for eukaryotic signature proteins trafficking acteristic structural complexity has Heimdallarchaeota phyla. Using that are involved in intracellular components remained a mystery. The most recent phylogenomics, they discovered trafficking and secretion. Several are derived insights into eukaryogenesis support a strong phylogenetic association proteins contained domain signatures the endosymbiotic theory, which between ASGARD lineages and of eukaryotic transport protein from our proposes that the first eukaryotic eukaryotes that placed the eukaryote particle (TRAPP) complexes, which archaeal cell arose from archaea through the lineage in close proximity to the are involved in transport from the ancestor acquisition of an alphaproteobacterial ASGARD superphylum. endoplasmic
  • Two Domains of Life, Not Three?

    Two Domains of Life, Not Three?

    Asgard Archaea Two domains of life, not three? A picture of visual interpretation of the Wagner’s opera Das Rheingold, a part of Richard Wagner’s Der Ring des Nibelungen Loki's Castle is a field of five active hydrothermal vents in the mid-Atlantic Ocean, located at 73 degrees north on the Mid-Atlantic Ridge between Greenland and Norway at a depth of 2,352 metres The vents were discovered in 2008 by a multinational scientific expedition of the university of Bergen, and are the most northerly black smokers to date. The five active chimneys of Loki's Castle are venting water as hot as 300 °C and sit on a vast mound of sulfide minerals. The vent field was given the name Loki's Castle as its shape reminded its discoverers of a fantasy castle. The reference is to the ancient Norse god of trickery, Loki. The top three feet (1 m) of a vent chimney almost 40 feet (12 m) tall at Loki's Castle in mid-July 2008. Visible at left is the arm of a remotely operated vehicle, reaching in to take fluid samples. Loki’s Castle Wents Loki's Castle - a field of five active hydrothermal vents in the mid-Atlantic Ocean - at 73 degrees north on the Mid-Atlantic Ridge - at a depth of 2,352 meters In Norse mythology, Loki is a cunning trickster who has the ability to change his shape and sex. Loki is represented as the companion of the great gods Odin and Thor. Preliminary observations have shown the warm area around the Loki's Castle vents to be alive with diverse and apparently unique microorganisms, unlike vent communities observed elsewhere.
  • Helarchaeota and Co-Occurring Sulfate-Reducing Bacteria in Subseafloor

    Helarchaeota and Co-Occurring Sulfate-Reducing Bacteria in Subseafloor

    www.nature.com/ismecomms ARTICLE OPEN Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica Margin ✉ Rui Zhao1 and Jennifer F. Biddle 1 © The Author(s) 2021 Deep sediments host many archaeal lineages, including the Asgard superphylum which contains lineages predicted to require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and the co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin. Phylogenetic analyses revealed three new metagenome-assembled genomes (MAGs) affiliating with Helarchaeota, each of which has three variants of the methyl-CoM reductase-like (MCR-like) complex that may enable them to oxidize short-chain alkanes anaerobically. These Helarchaeota have no multi-heme cytochromes but have Group 3b and Group 3c [NiFe] hydrogenases, and formate dehydrogenase, and therefore have the capacity to transfer the reducing equivalents (in the forms of hydrogen and formate) generated from alkane oxidation to external partners. We also recovered five MAGs of SRB affiliated with the class of Desulfobacteria, two of which showed relative abundances (represented by genome coverages) positively correlated with those of the three Helarchaeota. Genome analysis suggested that these SRB bacteria have the capacity of H2 and formate utilization and could facilitate electron transfers from other organisms by means of these reduced substances. Their co-occurrence and metabolic features suggest that Helarchaeota may metabolize synergistically with some SRB, and together exert an important influence on the carbon cycle by mitigating the hydrocarbon emission from sediments to the overlying ocean.
  • Quantum Chemical Cluster Modeling of Enzymatic Reactions Rong-Zhen

    Quantum Chemical Cluster Modeling of Enzymatic Reactions Rong-Zhen

    Quantum Chemical Cluster Modeling of Enzymatic Reactions Rong-Zhen Liao 1 Rong-Zhen Liao, Stockholm, 2010 ISBN 978-91-7447-129-8 Printed in Sweden by US-AB, Stockholm 2010 Distributor: Department of Organic Chemistry, Stockholm University 2 3 4 Abstract The Quantum chemical cluster approach has been shown to be quite powerful and efficient in the modeling of enzyme active sites and reaction mechanisms. In this thesis, the reaction mechanisms of several enzymes have been investigated using the hybrid density functional B3LYP. The enzymes studied include four dinuclear zinc enzymes, namely dihydroorotase, N-acyl-homoserine lactone hydrolase, RNase Z, and human renal dipeptidase, two trinuclear zinc enzymes, namely phospholipase C and nuclease P1, two tungstoenzymes, namely formaldehyde ferredoxin oxidoreductase and acetylene hydratase, aspartate α-decarboxylase, and mycolic acid cyclopropane synthase. The potential energy profiles for various mechanistic scenarios have been calculated and analyzed. The role of the metal ions as well as important active site residues has been discussed. In the cluster approach, the effects of the parts of the enzyme that are not explicitly included in the model are taken into account using implicit solvation methods. With aspartate α-decarboxylase as an example, systematic evaluation of the solvation effects with the increase of the model size has been performed. At a model size of 150-200 atoms, the solvation effects almost vanish and the choice of the dielectric constant becomes rather insignificant. For all six zinc-dependent enzymes studied, the di-zinc bridging hydroxide has been shown to be capable of performing nucleophilic attack on the substrate. In addition, one, two, or even all three zinc ions participate in the stabilization of the negative charge in the transition states and intermediates, thereby lowering the barriers.
  • Archaea and the Origin of Eukaryotes

    Archaea and the Origin of Eukaryotes

    REVIEWS Archaea and the origin of eukaryotes Laura Eme, Anja Spang, Jonathan Lombard, Courtney W. Stairs and Thijs J. G. Ettema Abstract | Woese and Fox’s 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor. Sister groups Two descendants that split The pioneering work by Carl Woese and colleagues In this Review, we discuss how culture- independent from the same node; the revealed that all cellular life could be divided into three genomics has transformed our understanding of descendants are each other’s major evolutionary lines (also called domains): the archaeal diversity and how this has influenced our closest relative.
  • Fermentation of Acetylene by an Obligate Anaerobe, Pelobacter Acetylenicus Sp

    Fermentation of Acetylene by an Obligate Anaerobe, Pelobacter Acetylenicus Sp

    Archives of Arch Microbiol (1985) 142: 295- 301 Microbiology Springer-Verlag 1985 Fermentation of acetylene by an obligate anaerobe, Pelobacter acetylenicus sp. nov. * Bernhard Schink Fakult/it ffir Biologie, Universit/it Konstanz, Postfach 5560, D-7750 Konstanz, Federal Republic of Germany Abstract. Four strains of strictly anaerobic Gram-negative tion reactions (Schink 1985a). No significant anaerobic rod-shaped non-sporeforming bacteria were enriched and degradation could be observed with ethylene (ethene), the isolated from marine and freshwater sediments with acety- most simple unsaturated hydrocarbon (Schink 1985 a, b). lene (ethine) as sole source of carbon and energy. Acetylene, It was reported recently that also acetylene can be metab- acetoin, ethanolamine, choline, 1,2-propanediol, and glyc- olized in the absence of molecular oxygen (Watanabe and erol were the only substrates utilized for growth, the latter de Guzman 1980). Enrichment cultures with acetylene as two only in the presence of small amounts of acetate. Sub- sole carbon source were obtained in mineral media with strates were fermented by disproportionation to acetate and sulfate as electron acceptor, and acetate could be identified ethanol or the respective higher acids and alcohols. No as an intermediary metabolite (Culbertson et al. 1981). How- cytochromes were detectable; the guanine plus cytosine ever, these enrichment cultures were difficult to maintain, content of the DNA was 57.1 _+ 0.2 tool%. Alcohol dehy- and the acetylene-degrading bacteria could not be identified drogenase, aldehyde dehydrogenase, phosphate acetyl- (C. W. Culbertson and R. S. Oremland, Abstr. 3rd Int. transferase, and acetate kinase were found in high activities Syrup.
  • S13568-020-0950-Y.Pdf

    S13568-020-0950-Y.Pdf

    Wang et al. AMB Expr (2020) 10:16 https://doi.org/10.1186/s13568-020-0950-y ORIGINAL ARTICLE Open Access Contrasting bacterial and archaeal distributions refecting diferent geochemical processes in a sediment core from the Pearl River Estuary Wenxiu Wang1, Jianchang Tao2, Haodong Liu2, Penghui Li2, Songze Chen1, Peng Wang1* and Chuanlun Zhang2,3* Abstract Microbial community structure and metabolic activities have profound impacts on biogeochemical processes in marine sediments. Functional bacteria such as nitrate- and sulfate-reducing bacteria respond to redox gradients by coupling specifc reactions amenable to relevant energy metabolisms. However, similar functional patterns have not been observed for sedimentary archaea (except for anaerobic methanotrophs and methanogens). We coupled taxo- nomic composition with comprehensive geochemical species to investigate the participation of distinct bacteria and archaea in sedimentary geochemical cycles in a sediment core (300 cm) from Pearl River Estuary (PRE). Geochemi- 2 13 cal properties (NO3−, dissolved Mn and Fe, SO4 +, NH4+; dissolved inorganic carbon (DIC), δ CDIC, dissolved organic 13 carbon (DOC), total organic carbon (TOC), δ CTOC, and fuorescent dissolved organic matter (FDOM)) exhibited strong depth variability of diferent trends. Bacterial 16S rRNA- and dsrB gene abundance decreased sharply with depth while archaeal and bathyarchaeotal 16S rRNA gene copies were relatively constant. This resulted in an increase in relative abundance of archaea from surface (11.6%) to bottom (42.8%). Network analysis showed that bacterial groups of 2 Desulfobacterales, Syntrophobacterales and Gammaproteobacteria were signifcantly (P < 0.0001) associated with SO4 − and dissolved Mn while archaeal groups of Bathyarchaeota, Group C3 and Marine Benthic Group D (MBGD) showed 13 close positive correlations (P < 0.0001) with NH4+, δ CTOC values and humic-like FDOM.
  • Microbial Community Composition and Functional Potential in Bothnian Sea Sediments Is Linked to Fe and S Dynamics and the Quality of Organic Matter

    Microbial Community Composition and Functional Potential in Bothnian Sea Sediments Is Linked to Fe and S Dynamics and the Quality of Organic Matter

    Limnol. Oceanogr. 65, 2020, S113–S133 © 2019 The Authors. Limnology and Oceanography published by Wiley Periodicals, Inc. on behalf of Association for the Sciences of Limnology and Oceanography. doi: 10.1002/lno.11371 Microbial community composition and functional potential in Bothnian Sea sediments is linked to Fe and S dynamics and the quality of organic matter Olivia Rasigraf ,1,2,3* Niels A. G. M. van Helmond,2,4 Jeroen Frank,1,5 Wytze K. Lenstra ,2,4 † Matthias Egger,4, Caroline P. Slomp,2,4 Mike S. M. Jetten1,2,5 1Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands 2Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands 3German Research Centre for Geosciences (GFZ), Geomicrobiology, Potsdam, Germany 4Department of Earth Sciences, Utrecht University, The Netherlands 5Soehngen Institute of Anaerobic Microbiology (SIAM), Radboud University Nijmegen, Nijmegen, The Netherlands Abstract The Bothnian Sea is an oligotrophic brackish basin characterized by low salinity and high concentrations of reactive iron, methane, and ammonium in its sediments, enabling the activity and interactions of many micro- bial guilds. Here, we studied the microbial network in these sediments by analyzing geochemical and microbial community depth profiles at one offshore and two near coastal sites. Analysis of 16S rRNA gene amplicons rev- ealed a distinct depth stratification of both archaeal and bacterial taxa. The microbial communities at the two near coastal sites were more similar to each other than the offshore site, which is likely due to differences in the quality and rate of organic matter degradation. The abundance of methanotrophic archaea of the ANME-2a clade was shown to be related to the presence of methane and varied with sediment iron content.
  • ATP-Dependent Substrate Reduction at an [Fe8s9] Double-Cubane Cluster

    ATP-Dependent Substrate Reduction at an [Fe8s9] Double-Cubane Cluster

    ATP-dependent substrate reduction at an [Fe8S9] double-cubane cluster Jae-Hun Jeounga and Holger Dobbeka,1 aInstitut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany Edited by Amy C. Rosenzweig, Northwestern University, Evanston, IL, and approved February 2, 2018 (received for review November 23, 2017) Chemically demanding reductive conversions in biology, such as the We have characterized the two components of a widespread reduction of dinitrogen to ammonia or the Birch-type reduction of system of the third type and find that the electron-accepting – aromatic compounds, depend on Fe/S-cluster containing ATPases. component features a double-cubane [Fe8S9]-cluster. This [Fe8S9]- These reductions are typically catalyzed by two-component systems, cluster, so far unknown to biology, catalyzes reductive reactions in which an Fe/S-cluster–containing ATPase energizes an electron to otherwise associated only with the complex iron–sulfur clusters reduce a metal site on the acceptor protein that drives the reductive of nitrogenases. Our results reveal several parallels between the reaction. Here, we show a two-component system featuring a double-cubane cluster-containing enzymes and nitrogenases μ double-cubane [Fe8S9]-cluster [{Fe4S4(SCys)3}2( 2-S)]. The double- and suggest that an unexplored biochemical reactivity space cubane–cluster-containing enzyme is capable of reducing small mol- may be hidden among the diverse ATP-dependent two-component − ecules, such as acetylene (C2H2), azide (N3 ), and hydrazine (N2H4). enzymes. We thus present a class of metalloenzymes akin in fold, metal clus- ters, and reactivity to nitrogenases. Results Distribution of Double-Cubane Cluster Protein-Like Proteins.
  • Metagenomic Analysis Reveals Large Potential for Carbon, Nitrogen and Sulfur Cycling in Coastal Methanic Sediments of the Bothnian Sea

    Metagenomic Analysis Reveals Large Potential for Carbon, Nitrogen and Sulfur Cycling in Coastal Methanic Sediments of the Bothnian Sea

    bioRxiv preprint doi: https://doi.org/10.1101/553131; this version posted February 18, 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. Metagenomic analysis reveals large potential for carbon, nitrogen and sulfur cycling in coastal methanic sediments of the Bothnian Sea Olivia Rasigraf1,2,*,§, Niels A.G.M. van Helmond3, Jeroen Frank1,4, Wytze K. Lenstra3, Matthias Egger3,#, Caroline P. Slomp2,3, Mike S.M. Jetten1,2,4 1 Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands 2 Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands 3 Department of Earth Sciences, Utrecht University, The Netherlands 4 Soehngen Institute of Anaerobic Microbiology (SIAM), Radboud University Nijmegen, Nijmegen, The Netherlands *current address: German Research Centre for Geosciences (GFZ), Section 3.7 Geomicrobiology, Potsdam, Germany #current address: The Ocean Cleanup, Rotterdam, The Netherlands §corresponding author: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/553131; this version posted February 18, 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 Abstract 2 3 The Bothnian Sea is an oligotrophic brackish basin characterized by low salinity and high 4 concentrations of reactive iron, methane and ammonium in the sediments potentially enabling an 5 intricate microbial network. Therefore, we analyzed and compared biogeochemical and microbial 6 profiles at one offshore and two near coastal sites in the Bothnian Sea. 16S rRNA amplicon 7 sequence analysis revealed stratification of both bacterial and archaeal taxa in accordance with 8 the geochemical gradients of iron, sulfate and methane.
  • Substratstereochemie Und Untersuchungen Zum Mechanismus Der 4-Hydroxybutyryl-Coa-Dehydratase Aus Clostridium Aminobutyricum

    Substratstereochemie Und Untersuchungen Zum Mechanismus Der 4-Hydroxybutyryl-Coa-Dehydratase Aus Clostridium Aminobutyricum

    Substratstereochemie und Untersuchungen zum Mechanismus der 4-Hydroxybutyryl-CoA-Dehydratase aus Clostridium aminobutyricum Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) dem Fachbereich Biologie der Philipps-Universität Marburg vorgelegt von Peter Friedrich aus Marburg/Lahn Marburg/Lahn 2008 Die Untersuchungen zur vorliegenden Arbeit wurden von November 2003 bis November 2008 am Fachbereich Biologie der Philipps-Universität Marburg unter der Leitung von Herrn Prof. Dr. W. Buckel durchgeführt. Vom Fachbereich Biologie der Philipps-Universität Marburg als Dissertation am angenommen. Erstgutachter: Prof. Dr. W. Buckel Zweitgutachter: Prof. Dr. R. Thauer Tag der mündlichen Prüfung: 18.12.2008 für meine Familie für Christine Die Ergebnisse dieser Dissertation sind in folgenden Publikationen veröffentlicht: Friedrich P, Darley DJ, Golding BT, Buckel W (2008) The complete stereochemistry of the enzymatic dehydration of 4-hydroxybutyryl coenzyme A to crotonyl coenzyme A. Angew. Chem. Int. Ed. Engl. 47:3254-3257. Der stereochemische Verlauf der enzymatischen Wassereliminierung von 4-Hydroxybutyryl-Coenzym A zu Crotonyl- Coenzym A. Angew. Chem. 120:3298-3301 Martins BM, Messerschmidt A, Friedrich P, Zhang J, Buckel W (2007) 4-Hydroxybutyryl- CoA dehydratase. In: Messerschmidt A (ed) Handbook of Metalloproteins Online Edition. John Wiley & Sons Ltd., Sussex, UK. Publisched online Dez 2007 weitere Veröffentlichungen: Scott R, Näser U, Friedrich P, Selmer T, Buckel W, Golding BT (2004) Stereochemistry of hydrogen