DOCSLIB.ORG

Downloaded from the NCBI Genbank Database (13/05/2019) and The

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Downloaded from the NCBI Genbank Database (13/05/2019) and The bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.136465; this version posted June 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 Enrichment and physiological characterization of a novel comammox 2 Nitrospira indicates ammonium inhibition of complete nitrification 3 4 Running title: Enrichment of an ammonium-sensitive comammox Nitrospira. 5 6 Author names: 7 Dimitra Sakoula1,#,*, Hanna Koch1, Jeroen Frank1,2, Mike SM Jetten1,2, Maartje AHJ van Kessel1, Sebastian 8 Lücker1,*. 9 10 Author affiliations: 11 1Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the 12 Netherlands. 13 2Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ 14 Nijmegen, the Netherlands. 15 #Present address: Division of Microbial Ecology, Center for Microbiology and Environmental Systems 16 Science, University of Vienna, Althanstraße 14, 1090, Vienna, Austria. 17 18 Corresponding authors: 19 Dimitra Sakoula, Division of Microbial Ecology, Center for Microbiology and Environmental Systems 20 Science, University of Vienna, Althanstraße 14, 1090, Vienna, Austria; phone: +43 1 4277 91201, mail: 21 [email protected] 22 23 Sebastian Lücker, Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 24 AJ Nijmegen, the Netherlands; phone: +31 24 3652618, mail: [email protected]. 25 26 Conflict of interest: 27 The authors declare no conflicts of interest. 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.136465; this version posted June 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 28 Abstract 29 The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation 30 (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be 31 performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural 32 and engineered ecosystems, information on their physiological properties is scarce due to the limited 33 number of cultured representatives. Furthermore, most available genomic information is derived from 34 metagenomic sequencing and high-quality genomes of Nitrospira in general are limited. In this study, we 35 obtained a high (90%) enrichment of a novel comammox species, tentatively named “Candidatus Nitrospira 36 kreftii”, and performed a detailed genomic and physiological characterization. The complete genome of “Ca. 37 N. kreftii” allowed reconstruction of its basic metabolic traits. Similar to Nitrospira inopinata, the enrichment 38 culture exhibited a very high ammonia affinity (Km(app)_NH3 » 0.036 µM), but a higher nitrite affinity 39 (Km(app)_NO2- » 13.8 µM), indicating an adaptation to highly oligotrophic environments. Counterintuitively for 40 a nitrifying microorganism, we also observed an inhibition of ammonia oxidation at ammonium 41 concentrations as low as 25 µM. This substrate inhibition of “Ca. N. kreftii” indicate that differences in 42 ammonium tolerance rather than affinity can be a niche determining factor for different comammox 43 Nitrospira. 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.136465; this version posted June 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 44 Introduction 45 Nitrification, the biological oxidation of ammonia to nitrate via nitrite, is a critical process within the global 46 biogeochemical nitrogen cycle. The nitrification process is of great biotechnological relevance since it fuels 47 the reductive part of the nitrogen cycle and is widely employed in drinking and wastewater treatment 48 systems for the efficient removal of excess ammonium. Traditionally, nitrification was considered to be a 49 two-step process catalyzed by two functionally distinct microbial guilds. According to this paradigm, 50 ammonia-oxidizing prokaryotes first oxidize ammonia to nitrite and subsequently nitrite-oxidizing bacteria 51 (NOB) are responsible for the conversion of nitrite to nitrate. While this dogma has been challenged by the 52 theoretical prediction of complete ammonia oxidation (comammox) (1, 2), it was the discovery of 53 comammox Nitrospira that has drastically altered our perception of nitrification (3-5). 54 All comammox organisms described to date are affiliated with Nitrospira sublineage II and can be further 55 divided into clade A and B based on phylogeny of the ammonia monooxygenase, the enzyme catalyzing 56 the first step of ammonia oxidation (4). Comammox Nitrospira were identified mainly via metagenomic 57 sequencing in various natural and engineered ecosystems, indicating their widespread occurrence and key 58 role in nitrogen cycling (6-15). This ubiquitous abundance of comammox Nitrospira has raised many 59 questions regarding their ecophysiology and potential biotechnological applicability. In order to provide the 60 necessary answers, in-depth understanding of the comammox physiology is required. So far, the sole 61 physiological data available was obtained from Nitrospira inopinata, the only existing pure culture of a 62 comammox bacterium (4). The extremely low apparent half saturation constant (Km(app)) for ammonia and 63 the high growth yield reported for N. inopinata indicate an adaptation to nutrient-limited environments (16) 64 and corroborate the predicted comammox lifestyle (1). 65 A general adaptation of comammox Nitrospira to oligotrophic environments is suggested by their presence 66 mainly in ecosystems with low ammonium loads. However, limited physiological data can highly bias our 67 perception of the ecophysiology of certain microbial groups and kinetic parameters might vary between 68 different comammox species. This was for instance recently observed for ammonia-oxidizing archaea 69 (AOA) and bacteria (AOB), where especially terrestrial AOA were found to have lower ammonia affinities 70 than previously assumed based on the extremely low Km reported for the marine AOA Nitrosopumilus 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.136465; this version posted June 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 71 maritimus (16, 17). For comammox Nitrospira, though, the lack of pure cultures or high enrichments 72 hampers the thorough understanding of the ecophysiology of these intriguing microorganisms. 73 In this study, we describe the enrichment of a novel comammox Nitrospira species in a continuous 74 membrane bioreactor system and provide genome-derived insights into its metabolic potential. 75 Furthermore, we report the ammonia- and nitrite-oxidation kinetics of this comammox organism, including 76 an apparent inhibition by ammonium concentrations as low as 25 µM, findings that provide crucial insights 77 into the niche partitioning factors of different comammox Nitrospira 78 79 Materials and Methods 80 81 Enrichment and reactor operation 82 A 7 L continuous membrane bioreactor (Applikon, Delft, The Netherlands), with a working volume of 5 L 83 was inoculated with biomass (300 mL) from a hypoxic enrichment culture described previously, which 84 contained two distinct comammox Nitrospira species (3). The bioreactor was operated for 39 months at 85 room temperature (RT) with moderate stirring (200 rpm). The pH of the culture was constantly monitored 86 by a pH electrode connected to an ADI1020 biocontroller (Applikon, Delft, The Netherlands) and maintained 87 at 7.5 by the automatic supply of a 1M KHCO3 solution. Dissolved oxygen was kept at 50% by providing 10 88 mL/min of a 1:1 mixture of Argon/CO2 (95%/5% v/v) and air through a metal tube with a porous sparger. 89 After 450 days of operation a bleed was installed, removing 100 to 300 mL biomass per day. 90 1 L of sterile NOB mineral salts medium (18) was supplied to the reactor per day. The medium was 91 supplemented with 1 mL of a trace element stock solution composed of NTA (15 g/L), ZnSO4⋅7H2O (0.43 92 g/L), CoCl2⋅6H2O (0.24 g/L), MnCl2⋅4H2O (0.99 g/L), CuSO4⋅5H2O (0.25 g/L), Na2MoO4⋅2H2O (0.22 g/L), 93 NiCl2⋅6H2O (0.19 g/L), NaSeO4·10H2O (0.021 g/L), H3BO4 (0.014 g/L), CeCl·6H2O (0.24 g/L) and 1 ml of 94 an iron stock solution composed of NTA (10 g/L) and FeSO4 (5 g/L). Initially, ammonium, nitrite and nitrate 95 (increasing from 80/0/50 to 250/20/500 µM NH4Cl/NaNO2/NaNO3, respectively) were supplied via the 96 medium. After 60 days of operation, ammonium was supplied as the sole substrate and the concentration 97 was slowly increased to a final concentration of 2.5 mM NH4Cl. Liquid samples from the bioreactor were 98 collected regularly for the determination of ammonium, nitrite and nitrate concentrations. 4 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.08.136465; this version posted June 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 99 Analytical methods 100 Ammonium concentrations were measured colorimetrically via a modified orthophatal-dialdehyde assay 101 (detection limit 10 µM) (19). Nitrite concentrations were determined by the sulfanilamide reaction (detection 102 limit 5 µM) (20). Nitrate was measured by converting it into nitric oxide at 95°C using a saturated solution 103 of VCl3 in HCl, which was subsequently measured using a nitric oxide analyzer (detection limit 1 µM; 104 NOA280i, GE Analytical Instruments, Manchester, UK).
Load more

Recommended publications
  • Metaproteomics Reveals Differential Modes of Metabolic Coupling Among Ubiquitous Oxygen Minimum Zone Microbes
    Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes Alyse K. Hawleya, Heather M. Brewerb, Angela D. Norbeckb, Ljiljana Paša-Tolicb, and Steven J. Hallama,c,d,1 aDepartment of Microbiology and Immunology, cGraduate Program in Bioinformatics, and dGenome Sciences and Technology Training Program, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; and bBiological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 Edited by Edward F. DeLong, Massachusetts Institute of Technology, Cambridge, MA, and approved June 10, 2014 (received for review November 26, 2013) Marine oxygen minimum zones (OMZs) are intrinsic water column transformations in nonsulfidic OMZs, providing evidence for features arising from respiratory oxygen demand during organic a cryptic sulfur cycle with the potential to drive inorganic carbon matter degradation in stratified waters. Currently OMZs are expand- fixation processes (13). Indeed, many of the key microbial players ing due to global climate change with resulting feedback on marine implicated in nitrogen and sulfur transformations in OMZs, in- ecosystem function. Here we use metaproteomics to chart spatial cluding Thaumarchaeota, Nitrospina, Nitrospira, Planctomycetes, and temporal patterns of gene expression along defined redox and SUP05/ARCTIC96BD-19 Gammaproteobacteria have the gradients in a seasonally stratified fjord to better understand metabolic potential for inorganic carbon fixation (14–19), and
    [Show full text]
  • Metabolic Versatility of the Nitrite-Oxidizing Bacterium Nitrospira
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185504; this version posted July 4, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira 2 marina and its proteomic response to oxygen-limited conditions 3 Barbara Bayer1*, Mak A. Saito2, Matthew R. McIlvin2, Sebastian Lücker3, Dawn M. Moran2, 4 Thomas S. Lankiewicz1, Christopher L. Dupont4, and Alyson E. Santoro1* 5 6 1 Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, 7 CA, USA 8 2 Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, 9 Woods Hole, MA, USA 10 3 Department of Microbiology, IWWR, Radboud University, Nijmegen, The Netherlands 11 4 J. Craig Venter Institute, La Jolla, CA, USA 12 13 *Correspondence: 14 Barbara Bayer, Department of Ecology, Evolution and Marine Biology, University of California, 15 Santa Barbara, CA, USA. E-mail: [email protected] 16 Alyson E. Santoro, Department of Ecology, Evolution and Marine Biology, University of 17 California, Santa Barbara, CA, USA. E-mail: [email protected] 18 19 Running title: Genome and proteome of Nitrospira marina 20 21 Competing Interests: The authors declare that they have no conflict of interest. 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185504; this version posted July 4, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • Being Aquifex Aeolicus: Untangling a Hyperthermophile's Checkered Past
    GBE Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past Robert J.M. Eveleigh1,2, Conor J. Meehan1,2,JohnM.Archibald1, and Robert G. Beiko2,* 1Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada 2Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada *Corresponding author: E-mail: [email protected]. Accepted: November 22, 2013 Abstract Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyper- thermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic analyses focused on Aquifex aeolicus identified Thermotogae and Downloaded from Aquificae either as successive early branches or sisters in a rooted bacterial phylogeny, but many phylogenies and cellular traits have suggested a stronger affiliation with the Epsilonproteobacteria. Different scenarios for the evolution of the Aquificae yield different phylogenetic predictions. Here, we outline these scenarios and consider the fit of the available data, including three sequenced Aquificae genomes, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the Epsilonproteobacteria have the strongest affinities with the three Aquificae analyzed. However, this pattern is shown by only a http://gbe.oxfordjournals.org/ minority of encoded proteins, and the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class Deltaproteobacteria also show strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: Most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, whereas a wide range of metabolic and cellular processes strongly supported the link between Aquificae and Epsilonproteobacteria.
    [Show full text]
  • High Functional Diversity Among Nitrospira Populations That Dominate Rotating Biological Contactor Microbial Communities in a Municipal Wastewater Treatment Plant
    The ISME Journal (2020) 14:1857–1872 https://doi.org/10.1038/s41396-020-0650-2 ARTICLE High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant 1 1 1 1 1 2 Emilie Spasov ● Jackson M. Tsuji ● Laura A. Hug ● Andrew C. Doxey ● Laura A. Sauder ● Wayne J. Parker ● Josh D. Neufeld 1 Received: 18 October 2019 / Revised: 3 March 2020 / Accepted: 30 March 2020 / Published online: 24 April 2020 © The Author(s) 2020. This article is published with open access Abstract Nitrification, the oxidation of ammonia to nitrate via nitrite, is an important process in municipal wastewater treatment plants (WWTPs). Members of the Nitrospira genus that contribute to complete ammonia oxidation (comammox) have only recently been discovered and their relevance to engineered water treatment systems is poorly understood. This study investigated distributions of Nitrospira, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in biofilm samples collected from tertiary rotating biological contactors (RBCs) of a municipal WWTP in Guelph, Ontario, 1234567890();,: 1234567890();,: Canada. Using quantitative PCR (qPCR), 16S rRNA gene sequencing, and metagenomics, our results demonstrate that Nitrospira species strongly dominate RBC biofilm samples and that comammox Nitrospira outnumber all other nitrifiers. Genome bins recovered from assembled metagenomes reveal multiple populations of comammox Nitrospira with distinct spatial and temporal distributions, including several taxa that are distinct from previously characterized Nitrospira members. Diverse functional profiles imply a high level of niche heterogeneity among comammox Nitrospira, in contrast to the sole detected AOA representative that was previously cultivated and characterized from the same RBC biofilm.
    [Show full text]
  • Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights Into the Origin and Distribution of Nitrogen Fixation Across Bacteria and Archaea
    microorganisms Article Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea Amrit Koirala 1 and Volker S. Brözel 1,2,* 1 Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA; [email protected] 2 Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa * Correspondence: [email protected]; Tel.: +1-605-688-6144 Abstract: The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico predic- tion of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocu- Citation: Koirala, A.; Brözel, V.S. mented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes Phylogeny of Nitrogenase Structural and Assembly Components Reveals are currently supported by biochemical evidence of diazotrophy.
    [Show full text]
  • Environmental and Anthropogenic Controls Over Bacterial Communities in Wetland Soils
    Environmental and anthropogenic controls over bacterial communities in wetland soils Wyatt H. Hartmana,1, Curtis J. Richardsona, Rytas Vilgalysb, and Gregory L. Brulandc aDuke University Wetland Center, Nicholas School of the Environment, Duke University, Durham, NC 27708; bBiology Department, Duke University, Durham, NC 27708; and cDepartment of Natural Resources and Environmental Management, University of Hawai’i at Ma៮noa, Honolulu, HI 96822 Communicated by William L. Chameides, Duke University, Durham, NC, September 29, 2008 (received for review October 12, 2007) Soil bacteria regulate wetland biogeochemical processes, yet little specific phylogenetic groups of microbes affected by restoration is known about controls over their distribution and abundance. have not yet been determined in either of these systems. Eu- Bacteria in North Carolina swamps and bogs differ greatly from trophication and productivity gradients appear to be the primary Florida Everglades fens, where communities studied were unex- determinants of microbial community composition in freshwater pectedly similar along a nutrient enrichment gradient. Bacterial aquatic ecosystems (17, 18). To capture the range of likely composition and diversity corresponded strongly with soil pH, land controls over uncultured bacterial communities across freshwa- use, and restoration status, but less to nutrient concentrations, and ter wetland types, we chose sites representing a range of soil not with wetland type or soil carbon. Surprisingly, wetland resto- chemistry and land uses, including reference wetlands, agricul- ration decreased bacterial diversity, a response opposite to that in tural and restored wetlands, and sites along a nutrient enrich- terrestrial ecosystems. Community level patterns were underlain ment gradient. by responses of a few taxa, especially the Acidobacteria and The sites we selected represented a range of land uses Proteobacteria, suggesting promise for bacterial indicators of res- encompassing natural, disturbed, and restored conditions across toration and trophic status.
    [Show full text]
  • The Ecology of the Chloroflexi in Full-Scale Activated Sludge 2 Wastewater Treatment Plants
    bioRxiv preprint doi: https://doi.org/10.1101/335752; this version posted May 31, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 The ecology of the Chloroflexi in full-scale activated sludge 2 wastewater treatment plants 3 Marta Nierychlo1, Aleksandra Miłobędzka2,3, Francesca Petriglieri1, Bianca 4 McIlroy1, Per Halkjær Nielsen1, and Simon Jon McIlroy1§* 5 1Center for Microbial Communities, Department of Chemistry and Bioscience, 6 Aalborg University, Aalborg, Denmark 7 2Microbial Ecology and Environmental Biotechnology Department, Institute of 8 Botany, Faculty of Biology, University of Warsaw; Biological and Chemical 9 Research Centre, Żwirki i Wigury 101, Warsaw 02-089, Poland 10 3Department of Biology, Faculty of Building Services, Hydro and Environmental 11 Engineering, Warsaw University of Technology, 00-653 Warsaw, Poland 12 * Corresponding author: Simon Jon McIlroy, Center for Microbial Communities, 13 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 14 DK-9220 Aalborg, Denmark; Tel.: +45 9940 3573; Fax: +45 9814 1808; Email: 15 [email protected] 16 § Present address: Australian Centre for Ecogenomics, University of Queensland, 17 Australia 1 bioRxiv preprint doi: https://doi.org/10.1101/335752; this version posted May 31, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.
    [Show full text]
  • Long Solids Retention Times and Attached Growth Phase Favor Prevalence of Comammox 2 Bacteria in Nitrogen Removal Systems
    bioRxiv preprint doi: https://doi.org/10.1101/696351; this version posted July 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Long solids retention times and attached growth phase favor prevalence of comammox 2 bacteria in nitrogen removal systems. 3 4 Irmarie Cotto1, Zihan Dai2, Linxuan Huo1, Christopher L. Anderson1, Katherine J. Vilardi1, Umer 5 Ijaz2, Wendell Khunjar3, Christopher Wilson4, Haydee De Clippeleir5, Kevin Gilmore6, Erika 6 Bailey7, Ameet J. Pinto1*. 7 8 1 Department of Civil and Environmental Engineering, Northeastern University. 9 2 School of Engineering, University of Glasgow. 10 3 Hazen and Sawyer, Inc. 11 4 Hampton Roads Sanitation District. 12 5 DC Water. 13 6 Department of Civil and Environmental Engineering, Bucknell University. 14 7 City of Raleigh Public Utilities. 15 16 *corresponding author: [email protected] 17 18 Keywords: comammox bacteria, nitrification, solids retention time, qPCR, metagenomics 19 20 21 22 Highlights 23 • Clade A comammox bacteria were detected in wastewater nitrogen removal systems. 24 • New qPCR assay targeting the amoB gene of clade A comammox bacteria was developed. 25 • Comammox bacteria are prevalent in mainstream conventional and simultaneous 26 nitrification-denitrification systems with long solids retention times (>10 days). 27 • Comammox bacteria were not detected in sidestream partial nitrification-anammox 28 systems included in this study. 1 bioRxiv preprint doi: https://doi.org/10.1101/696351; this version posted July 29, 2019.
    [Show full text]
  • BEING Aquifex Aeolicus: UNTANGLING a HYPERTHERMOPHILE‘S CHECKERED PAST
    BEING Aquifex aeolicus: UNTANGLING A HYPERTHERMOPHILE‘S CHECKERED PAST by Robert J.M. Eveleigh Submitted in partial fulfillment of the requirements for the degree of Master of Science at Dalhousie University Halifax, Nova Scotia December 2011 © Copyright by Robert J.M. Eveleigh, 2011 DALHOUSIE UNIVERSITY DEPARTMENT OF COMPUTATIONAL BIOLOGY AND BIOINFORMATICS The undersigned hereby certify that they have read and recommend to the Faculty of Graduate Studies for acceptance a thesis entitled ―BEING Aquifex aeolicus: UNTANGLING A HYPERTHERMOPHILE‘S CHECKERED PAST‖ by Robert J.M. Eveleigh in partial fulfillment of the requirements for the degree of Master of Science. Dated: December 13, 2011 Co-Supervisors: _________________________________ _________________________________ Readers: _________________________________ ii DALHOUSIE UNIVERSITY DATE: December 13, 2011 AUTHOR: Robert J.M. Eveleigh TITLE: BEING Aquifex aeolicus: UNTANGLING A HYPERTHERMOPHILE‘S CHECKERED PAST DEPARTMENT OR SCHOOL: Department of Computational Biology and Bioinformatics DEGREE: MSc CONVOCATION: May YEAR: 2012 Permission is herewith granted to Dalhousie University to circulate and to have copied for non-commercial purposes, at its discretion, the above title upon the request of individuals or institutions. I understand that my thesis will be electronically available to the public. The author reserves other publication rights, and neither the thesis nor extensive extracts from it may be printed or otherwise reproduced without the author‘s written permission. The author attests that permission has been obtained for the use of any copyrighted material appearing in the thesis (other than the brief excerpts requiring only proper acknowledgement in scholarly writing), and that all such use is clearly acknowledged. _______________________________ Signature of Author iii TABLE OF CONTENTS List of Tables ....................................................................................................................
    [Show full text]
  • A Novel Marine Nitrite-Oxidizing Nitrospira Species from Dutch Coastal North Sea Water
    ORIGINAL RESEARCH ARTICLE published: 18 March 2013 doi: 10.3389/fmicb.2013.00060 A novel marine nitrite-oxidizing Nitrospira species from Dutch coastal North Sea water Suzanne C. M. Haaijer1*, Ke Ji 1, Laura van Niftrik1, Alexander Hoischen 2, Daan Speth1, MikeS.M.Jetten1, Jaap S. Sinninghe Damsté3 and Huub J. M. Op den Camp1 1 Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands 2 Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Nijmegen, Nijmegen, Netherlands 3 Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Texel, Netherlands Edited by: Marine microorganisms are important for the global nitrogen cycle, but marine nitrifiers, Boran Kartal, Radboud University, especially aerobic nitrite oxidizers, remain largely unexplored. To increase the number Netherlands of cultured representatives of marine nitrite-oxidizing bacteria (NOB), a bioreactor Reviewed by: cultivation approach was adopted to first enrich nitrifiers and ultimately nitrite oxidizers Eva Spieck, University of Hamburg, Germany from Dutch coastal North Sea water. With solely ammonia as the substrate an active Luis A. Sayavedra-Soto, Oregon State nitrifying community consisting of novel marine Nitrosomonas aerobic ammonia oxidizers University, USA (ammonia-oxidizing bacteria) and Nitrospina and Nitrospira NOB was obtained which *Correspondence: converted a maximum of 2 mmol of ammonia per liter per day. Switching the feed of the Suzanne C. M. Haaijer, Department of culture to nitrite as a sole substrate resulted in a Nitrospira NOB dominated community Microbiology, Institute for Water and Wetland Research, Radboud (approximately 80% of the total microbial community based on fluorescence in situ University Nijmegen, hybridization and metagenomic data) converting a maximum of 3 mmol of nitrite per liter Heyendaalseweg 135, Nijmegen, per day.
    [Show full text]
  • 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
    [Show full text]
  • Phototrophic Methane Oxidation in a Member of the Chloroflexi Phylum
    bioRxiv preprint doi: https://doi.org/10.1101/531582; this version posted January 26, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Phototrophic Methane Oxidation in a Member of the Chloroflexi Phylum Lewis M. Ward1,2, Patrick M. Shih3,4, James Hemp5, Takeshi Kakegawa6, Woodward W. Fischer7, Shawn E. McGlynn2,8,9 1. Department of Earth & Planetary Sciences, Harvard University, Cambridge, MA USA. 2. Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan. 3. Department of Plant Biology, University of California, Davis, Davis, CA USA. 4. Department of Energy, Joint BioEnergy Institute, Emeryville, CA USA. 5. School of Medicine, University of Utah, Salt Lake City, UT USA. 6. Department of Geosciences, Tohoku University, Sendai City, Japan 7. Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA USA. 8. Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, Wako-shi Japan 9. Blue Marble Space Institute of Science, Seattle, WA, USA Abstract: Biological methane cycling plays an important role in Earth’s climate and the global carbon cycle, with biological methane oxidation (methanotrophy) modulating methane release from numerous environments including soils, sediments, and water columns. Methanotrophy is typically coupled to aerobic respiration or anaerobically via the reduction of sulfate, nitrate, or metal oxides, and while the possibility of coupling methane oxidation to phototrophy (photomethanotrophy) has been proposed, no organism has ever been described that is capable of this metabolism.
    [Show full text]