DOCSLIB.ORG

Enrichment and Physiological Characterization of a Novel Comammox Nitrospira Indicates Ammonium Inhibition of Complete Nitrifica

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Enrichment and Physiological Characterization of a Novel Comammox Nitrospira Indicates Ammonium Inhibition of Complete Nitrifica 1 Supplementary Information for: 2 3 Enrichment and physiological characterization of a novel comammox 4 Nitrospira indicates ammonium inhibition of complete nitrification. 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 Supplemental figures and tables 26 27 A B 4 4 ammonium nitrite nitrate 3 3 2 2 1 1 Load (mmol/day) Concentration (mM) 0 0 0 200 400 600 800 1000 1200 0 200 400 600 800 1000 1200 28 Time (days) Time (days) 29 Figure S1. Substrate loading (A) and apparent substrate concentrations (B) in the bioreactor system during 30 the enrichment period. Symbols indicate ammonium (squares), nitrite (circles) and nitrate (triangles). Lin eage I Nitrospira Lineage II Nitrospira Total Nitrospira 100 80 60 40 Enrichment percentage (%) 20 0 18 33 39 Operation time (months) 31 32 Figure S2. Relative abundance of sublineage I and II Nitrospira bacteria in the bioreactor system over the 33 enrichment period. Sublineage abundances were normalized in relation to the relative abundance of the 34 total Nitrospira population in the enrichment culture. 100 100 80 80 80 80 80 79 76 75 75 75 74 73 71 72 71 71 72 74 74 71 71 70 71 71 70 71 71 70 71 71 71 73 70 70 70 70 70 Nitrospira sp. SG-bin1 95 80 100 86 86 86 86 85 77 76 76 75 74 74 72 72 72 72 72 74 75 71 71 71 71 71 71 71 71 71 71 71 72 73 70 70 70 70 70 Ca. Nitrospira nitrificans 90 80 86 100 95 94 92 92 77 76 76 76 74 74 71 72 72 71 72 74 75 71 71 71 71 71 71 71 71 71 71 70 71 72 70 69 69 69 70 Nitrospira sp. CG24B 80 86 95 100 95 91 91 77 76 76 76 74 74 71 72 71 71 71 74 74 71 71 71 71 71 70 71 71 71 71 70 71 72 70 69 70 69 70 Nitrospira sp. RSF5 85 80 86 94 95 100 91 91 77 76 76 76 74 74 71 72 71 71 71 74 74 71 71 70 71 71 71 71 71 71 71 70 71 72 69 69 69 69 70 Nitrospira sp. RSF1 80 80 86 92 91 91 100 93 77 76 76 76 74 74 71 72 71 71 72 74 74 71 71 71 71 71 71 71 71 71 71 70 71 72 69 69 69 69 70 Nitrospira sp. RSF12 75 79 85 92 91 91 93 100 77 76 76 76 74 74 71 72 71 71 72 74 74 71 71 71 71 71 70 71 71 71 71 70 71 72 69 69 70 69 70 Nitrospira sp. RSF9 70 76 77 77 77 77 77 77 100 75 74 74 73 73 71 71 71 71 71 73 74 70 70 70 70 70 70 70 70 70 70 70 70 72 69 69 69 70 70 Ca. Nitrospira kreftii 75 76 76 76 76 76 76 75 100 85 85 73 72 71 71 71 71 72 73 73 71 70 70 70 71 70 70 70 71 71 70 71 72 69 69 69 69 69 Nitrospira sp. UBA5698 75 76 76 76 76 76 76 74 85 100 94 72 72 70 71 71 71 71 72 72 71 70 70 70 70 70 70 70 70 70 70 71 72 69 69 69 69 69 Ca. Nitrospira nitrosa 75 75 76 76 76 76 76 74 85 94 100 72 72 71 71 71 71 71 72 73 70 70 70 70 70 70 70 70 70 70 70 71 72 69 69 69 69 69 Nitrospira sp. UW-LDO-01 74 74 74 74 74 74 74 73 73 72 72 100 95 73 73 73 72 74 77 77 72 72 71 72 72 72 72 72 72 72 71 72 74 70 70 70 70 70 Nitrospira sp. SG-bin2 73 74 74 74 74 74 74 73 72 72 72 95 100 72 72 73 72 74 77 77 72 72 71 72 72 71 72 72 72 72 71 72 73 70 70 70 70 70 Nitrospira sp. ST-bin4 71 72 71 71 71 71 71 71 71 70 71 73 72 100 86 88 88 72 72 73 73 73 72 72 72 71 72 72 72 72 72 72 73 70 70 71 71 72 Nitrospira lenta 72 72 72 72 72 72 72 71 71 71 71 73 72 86 100 88 89 71 72 74 73 72 72 72 71 72 72 72 72 72 71 72 74 71 70 71 71 71 Nitrospira sp. ST-bin5 71 72 72 71 71 71 71 71 71 71 71 73 73 88 88 100 98 71 72 73 72 72 72 72 72 72 72 72 72 72 71 72 73 70 70 70 70 71 Nitrospira sp. CG24D 71 72 71 71 71 71 71 71 71 71 71 72 72 88 89 98 100 71 72 73 72 72 72 72 72 72 72 72 72 72 71 72 74 70 70 70 71 71 Nitrospira sp. RSF13 72 72 72 71 71 72 72 71 72 71 71 74 74 72 71 71 71 100 74 73 71 71 70 70 70 70 70 71 71 71 71 72 73 70 69 70 70 70 Nitrospira inopinata 74 74 74 74 74 74 74 73 73 72 72 77 77 72 72 72 72 74 100 76 72 72 71 71 71 71 72 71 71 72 72 72 74 70 70 70 70 70 Nitrospira sp. UBA2082 74 75 75 74 74 74 74 74 73 72 73 77 77 73 74 73 73 73 76 100 72 72 72 72 72 72 73 74 73 73 72 72 75 70 70 70 70 71 Nitrospira sp. RCA 71 71 71 71 71 71 71 70 71 71 70 72 72 73 73 72 72 71 72 72 100 99 78 79 78 78 80 81 82 81 72 73 73 71 70 70 71 71 Nitrospira sp. Baikal-G1 71 71 71 71 71 71 71 70 70 70 70 72 72 73 72 72 72 71 72 72 99 100 78 78 78 78 79 81 81 81 72 72 72 70 70 70 71 71 Nitrospira sp. BD2 70 71 71 71 70 71 71 70 70 70 70 71 71 72 72 72 72 70 71 72 78 78 100 79 79 80 81 83 83 82 71 72 72 70 70 70 70 70 Nitrospira sp. CG24E 71 71 71 71 71 71 71 70 70 70 70 72 72 72 72 72 72 70 71 72 79 78 79 100 81 81 83 82 82 82 71 72 71 70 69 70 70 70 Nitrospira sp. RSF3 71 71 71 71 71 71 71 70 71 70 70 72 72 72 71 72 72 70 71 72 78 78 79 81 100 92 82 83 82 83 71 72 71 70 70 70 70 70 Nitrospira sp. CG24A 70 71 71 70 71 71 70 70 70 70 70 72 71 71 72 72 72 70 71 72 78 78 80 81 92 100 83 83 83 83 71 72 71 70 69 70 70 70 Nitrospira sp. RSF6 71 71 71 71 71 71 71 70 70 70 70 72 72 72 72 72 72 70 72 73 80 79 81 83 82 83 100 85 85 85 72 72 72 70 70 70 70 70 Nitrospira sp. RSF7 71 71 71 71 71 71 71 70 70 70 70 72 72 72 72 72 72 71 71 74 81 81 83 82 83 83 85 100 89 89 72 73 72 70 70 70 71 71 Nitrospira sp. RCB 70 71 71 71 71 71 71 70 71 70 70 72 72 72 72 72 72 71 71 73 82 81 83 82 82 83 85 89 100 97 71 73 72 70 70 70 70 71 Nitrospira sp. palsa 1315 71 71 71 71 71 71 71 70 71 70 70 72 72 72 72 72 72 71 72 73 81 81 82 82 83 83 85 89 97 100 72 73 72 70 70 70 70 71 Nitrospira sp. palsa 1310 71 71 70 70 70 70 70 70 70 70 70 71 71 72 71 71 71 71 72 72 72 72 71 71 71 71 72 72 71 72 100 75 73 70 70 70 70 70 Nitrospira japonica 71 72 71 71 71 71 71 70 71 71 71 72 72 72 72 72 72 72 72 72 73 72 72 72 72 72 72 73 73 73 75 100 74 71 70 70 70 71 Nitrospira sp.
Load more

Recommended publications
  • 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]
  • 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]
  • Diversification and Niche Adaptations of Nitrospina-Like Bacteria in The
    The ISME Journal (2016) 10, 1383–1399 OPEN © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Diversification and niche adaptations of Nitrospina- like bacteria in the polyextreme interfaces of Red Sea brines David Kamanda Ngugi1, Jochen Blom2, Ramunas Stepanauskas3 and Ulrich Stingl1 1Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia; 2Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany and 3Bigelow Laboratories for Ocean Sciences, East Boothbay, ME 04544-0380, USA Nitrite-oxidizing bacteria (NOB) of the genus Nitrospina have exclusively been found in marine environments. In the brine–seawater interface layer of Atlantis II Deep (Red Sea), Nitrospina-like bacteria constitute up to one-third of the bacterial 16S ribosomal RNA (rRNA) gene sequences. This is much higher compared with that reported in other marine habitats (~10% of all bacteria), and was unexpected because no NOB culture has been observed to grow above 4.0% salinity, presumably due to the low net energy gained from their metabolism that is insufficient for both growth and osmoregulation. Using phylogenetics, single-cell genomics and metagenomic fragment recruitment approaches, we document here that these Nitrospina-like bacteria, designated as Candidatus Nitromaritima RS, are not only highly diverged from the type species Nitrospina gracilis (pairwise genome identity of 69%) but are also ubiquitous in the deeper, highly saline interface layers (up to 11.2% salinity) with temperatures of up to 52 °C. Comparative pan-genome analyses revealed that less than half of the predicted proteome of Ca. Nitromaritima RS is shared with N.
    [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]
  • Wuchter Et Al., 2006; Tists Ever Since the Hallmark Publication by Winogradsky (1890) Mincer Et Al., 2007)
    PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher's version. For additional information about this publication click this link. http://hdl.handle.net/2066/111469 Please be advised that this information was generated on 2021-09-30 and may be subject to change. 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.
    [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]
  • Activity and Ecophysiology of Nitrite-Oxidizing Bacteria in Natural
    Activity and ecophysiology of nitrite-oxidizing bacteria in natural and engineered habitats Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften im Department Biologie der Universität Hamburg vorgelegt von Boris Nowka aus Bremen Hamburg 2014 Contents List of abbreviations 2 Chapter I Introduction 4 Chapter II Natural distribution of Nitrospira lineage I and II 16 and differentiation of two new isolates from activated sludge by morphological and physiological features Chapter III Comparative oxidation kinetics of nitrite-oxidizing 40 bacteria: nitrite availability as key factor for niche differentiation Chapter IV Summary 61 References 66 Appendix List of publications 81 Supplementary information 82 Acknowledgments 85 List of abbreviations °C degree Celsius % percentage µl microliter µm micrometer AOA ammonia-oxidizing archaea AOB ammonia-oxidizing bacteria BCA bicinchoninic acid BLAST Basic Local Alignment Search Tool bp base pairs CDS coding sequence cm centimeter DAPI 4',6-diamidino-2-phenylindole DGGE denaturing gradient gel electrophoresis DNA deoxyribonucleic acid DO dissolved oxygen EM electron microscopy EPS extracellular polymeric substances Fig. figure FISH fluorescence in situ hybridization fmol femtomole g gram h hour HPLC high-performance liquid chromatography l liter mM millimolar min minute nm nanometer NOB nitrite-oxidizing bacteria NXR nitrite oxidoreductase PCR polymerase chain reaction RAS recirculation aquaculture system 2 RFLP restriction fragment length polymorphism rpm revolutions per minute rRNA ribosomal ribonucleic acid s second SEM scanning electron microscope SMP soluble microbial products Tab. table TEM transmission electron microscope v volume WWTP wastewater treatment plant 3 Chapter I Introduction The nitrogen cycle The nitrogen cycle (Fig. 1.1) is a key process for life on earth. In the atmosphere and in natural waters nitrogen (N) exists mainly as dinitrogen gas (N2).
    [Show full text]
  • Niche Differentiation of Ammonia and Nitrite Oxidizers Along a Salinity Gradient from the Pearl River Estuary to the South China
    1 Niche differentiation of ammonia and nitrite oxidizers along a salinity gradient 2 from the Pearl River estuary to the South China Sea 3 4 Lei Hou1,2,†, Xiabing Xie1,†, Xianhui Wan1, Shuh-Ji Kao1,2, Nianzhi Jiao1,2, Yao Zhang1,2 5 1State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China 6 2College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China 7 8 Correspondence to: Yao Zhang ([email protected]) 9 †Contributed equally 10 1 1 Abstract 2 The niche differentiation of ammonia and nitrite oxidizers are controversial because they display 3 disparate patterns in estuarine, coastal, and oceanic regimes. We analyzed diversity and abundance of 4 ammonia-oxidizing archaea (AOA) and β-proteobacteria (AOB), nitrite-oxidizing bacteria (NOB), and 5 nitrification rates to identify their niche differentiation along a salinity gradient from the Pearl River 6 estuary to the South China Sea. AOA were generally more abundant than β-AOB; however, AOB more 7 clearly attached to particles compared with AOA in the upper reaches of the Pearl River estuary. The 8 NOB Nitrospira had higher abundances in the upper and middle reaches of the Pearl River estuary, 9 while Nitrospina was dominant in the lower estuary. In addition, AOB and Nitrospira could be more 10 active than AOA and Nitrospina since significantly positive correlations were observed between their 11 gene abundance and the nitrification rate in the Pearl River estuary. There is a significant positive 12 correlation between ammonia and nitrite oxidizer abundances in the hypoxic waters of the estuary, 13 suggesting a possible coupling through metabolic interactions between them.
    [Show full text]
  • Genomic and Kinetic Analysis of Novel Nitrospinae Enriched by Cell Sorting
    The ISME Journal (2021) 15:732–745 https://doi.org/10.1038/s41396-020-00809-6 ARTICLE Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting 1 1,2 3,4 1 5 Anna J. Mueller ● Man-Young Jung ● Cameron R. Strachan ● Craig W. Herbold ● Rasmus H. Kirkegaard ● 1,5,6 1,6 Michael Wagner ● Holger Daims Received: 29 May 2020 / Revised: 23 September 2020 / Accepted: 5 October 2020 / Published online: 16 October 2020 © The Author(s) 2020. This article is published with open access Abstract Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related 1234567890();,: 1234567890();,: to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense.
    [Show full text]
  • 9 Microbial Life in Terrestrial Permafrost: Methanogenesis and Nitrification in Gelisols As Potentials for Exobiological Processes
    9 Microbial Life in Terrestrial Permafrost: Methanogenesis and Nitrification in Gelisols as Potentials for Exobiological Processes Dirk Wagner, Eva Spieck, Eberhard Bock and Eva-Maria Pfeiffer The comparability of environmental and climatic conditions of the early Mars and Earth is of special interest for the actual research in astrobiology. Martian surface and terrestrial permafrost areas show similar morphological structures, which suggests that their development is based on comparable processes. Soil microbial investigations of adaptation strategies of microorganisms from terrestrial permafrost in combination with environmental, geochemical and physical analyses give insights into early stages of life on Earth. The extreme conditions in terrestrial permafrost soils can help to un- derstand the evolution of life on early Mars and help searching for possible niches of life on present Mars or in other extraterrestrial permafrost habitats [1, 2]. 9.1 Permafrost Soils and Active Layer In polar regions huge layers of frozen ground are formed - termed permafrost - which are defined as the thermal condition, in which soils and sediments remain at or below 0 °C for two or more years in succession. Terrestrial permafrost, which underlay more than 20% of the world‘s land area, is above all controlled by climatic factors and char- acterized by extreme terrain condition and landforms. On Earth the permafrost thick- ness can reach several hundreds of meters, e.g., in East Siberia (Central Yakutia) about 600-800 m. During the relatively short period of arctic/antarctic summer only the surface zone of permafrost sediments thaws. This uppermost part of the permafrost (active layer) includes the so called Gelisols [3], which contains permafrost in the upper 100 cm soil depth.
    [Show full text]
  • Enrichment and Physiological Characterization of a Novel Comammox Nitrospira Indicates Ammonium Inhibition of Complete Nitrifica
    The ISME Journal (2021) 15:1010–1024 https://doi.org/10.1038/s41396-020-00827-4 ARTICLE Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification 1,3 1 1,2 1,2 1 Dimitra Sakoula ● Hanna Koch ● Jeroen Frank ● Mike S. M. Jetten ● Maartje A. H. J. van Kessel ● Sebastian Lücker 1 Received: 5 June 2020 / Revised: 27 October 2020 / Accepted: 30 October 2020 / Published online: 13 November 2020 © The Author(s) 2020. This article is published with open access Abstract The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Additionally, most available genomic information is derived from metagenomic sequencing and high-quality genomes of Nitrospira in general are 1234567890();,: 1234567890();,: limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named “Candidatus Nitrospira kreftii”, and performed a detailed genomic and physiological characterization. The complete genome of “Ca.N. kreftii” allowed reconstruction of its basic metabolic traits. Similar to Nitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (Km(app)_NH3 ≈ 0.040 ± 0.01 µM), but a higher nitrite affinity (Km(app)_NO2- = 12.5 ± 4.0 µM), indicating an adaptation to highly oligotrophic environments. Furthermore, we observed partial inhibition of ammonia oxidation at ammonium concentrations as low as 25 µM.
    [Show full text]
  • Comparison of Bacterial and Archaeal Communities from Different Habitats of the Hypogenic Molnár János Cave of the Buda Thermal Karst System (Hungary)
    D. Anda, G. Krett, J. Makk, K. Márialigeti, J. Mádl-Szőnyi, and A. K. Borsodi. Comparison of bacterial and archaeal communities from different habitats of the hypogenic Molnár János Cave of the Buda Thermal Karst System (Hungary). Journal of Cave and Karst Studies, v. 79, no. 2, p. 113-121. DOI: 10.4311/2015MB0134 COmpARISON OF BACTERIAL AND ARchAEAL COmmUNITIES FROM DIFFERENT HABITATS OF THE HYPOGENIC MOLNÁR JÁNOS CAVE OF THE BUDA ThERMAL KARST SYSTEM (HUNGARY) Dóra Anda1, Gergely Krett1, Judit Makk1, Károly Márialigeti1, Judit Mádl-Szőnyi2, and Andrea K. Borsodi1, C Abstract The Molnár János Cave is part of the northern discharge area of the Buda Thermal Karst System, and is the largest active thermal water cave in the capital of Hungary. To compare the prokaryotic communities, reddish-brown cave wall biofilm, black biogeochemical layers, and thermal water samples from the phreatic mixing zone of the cave were sub- jected to three investigative approaches, scanning electron microscopy, cultivation, and molecular cloning. According to the SEM images, multilayer network structures were observed in the biofilm formed by iron-accumulating filamentous bacteria and mineral crystals. Cultivated strains belonging to Aeromonadaceae and Enterobacteriaceae were charac- teristic from both water and subaqueous biofilm samples. The most abundant molecular clones were representatives of the phylum Chloroflexi in the reddish-brown biofilm, the class Gammaproteobacteria in the black biogeochemical layer, and Thiobacillus (Betaproteobacteria) in the thermal water samples. The reddish-brown biofilm and black biogeochemi- cal layer’s bacterial communities proved to be somewhat more diverse than that of the thermal water. The archaeal 16S rRNA gene clone libraries were dominated by thermophilic ammonia-oxidizer Nitrosopumilus and Nitrososphaera phy- lotypes in all three habitats.
    [Show full text]