DOCSLIB.ORG

Sulfur-Oxidizing Symbionts Without Canonical Genes for Autotrophic CO2 Fixation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Sulfur-Oxidizing Symbionts Without Canonical Genes for Autotrophic CO2 Fixation bioRxiv preprint doi: https://doi.org/10.1101/540435; this version posted February 5, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 Sulfur-oxidizing symbionts without canonical genes 2 for autotrophic CO2 fixation 3 Classification: Biological Sciences – Environmental Sciences 4 Brandon K. B. Seah*1,7, Chakkiath Paul Antony1,8, Bruno Huettel2, Jan Zarzycki3, 5 Lennart Schada von Borzyskowski3, Tobias J. Erb3, Angela Kouris4, Manuel Kleiner5, 6 Manuel Liebeke1, Nicole Dubilier1,6, Harald R. Gruber-Vodicka1 7 1 Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany 8 2 Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 9 10, 50829 Cologne, Germany 10 3 Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany 11 4 Energy Bioengineering and Geomicrobiology Group, University of Calgary, 2500 University Drive Northwest, 12 Calgary, Alberta T2N 1N4, Canada 13 5 Department of Plant and Microbial Biology, North Carolina State University, Raleigh 27695, North Carolina, 14 United States of America 15 6 MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany 16 7 Current address: Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, 17 Germany 18 8 Current address: Red Sea Research Center, Biological and Environmental Sciences and Engineering (BESE) 19 Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi 20 Arabia 21 * Corresponding author: Brandon K. B. Seah, Max Planck Institute for Developmental Biology, Max-Planck- 22 Ring 5, 72076 Tübingen, Germany; tel. +49 7071 601 1342; [email protected] / 23 [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/540435; this version posted February 5, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. 24 Abstract 25 Since the discovery of symbioses between sulfur-oxidizing (thiotrophic) bacteria and 26 invertebrates at hydrothermal vents over 40 years ago, it has been assumed that autotrophic 27 fixation of CO2 by the symbionts drives these nutritional associations. In this study, we 28 investigated Candidatus Kentron, the clade of symbionts hosted by Kentrophoros, a diverse 29 genus of ciliates which are found in marine coastal sediments around the world. Despite 30 being the main food source for their hosts, Kentron lack the key canonical genes for any of 31 the known pathways for autotrophic fixation, and have a carbon stable isotope fingerprint 32 unlike other thiotrophic symbionts from similar habitats. Our genomic and transcriptomic 33 analyses instead found metabolic features consistent with growth on organic carbon, 34 especially organic and amino acids, for which they have abundant uptake transporters. All 35 known thiotrophic symbionts have converged on using reduced sulfur to generate energy 36 lithotrophically, but they are diverse in their carbon sources. Some clades are obligate 37 autotrophs, while many are mixotrophs that can supplement autotrophic carbon fixation with 38 heterotrophic capabilities similar to those in Kentron. We have shown that Kentron are the 39 only thiotrophic symbionts that appear to be entirely heterotrophic, unlike all other 40 thiotrophic symbionts studied to date, which possess either the Calvin-Benson-Bassham or 41 reverse tricarboxylic acid cycles for autotrophy. 42 Keywords: meiofauna, ectosymbiont, Gammaproteobacteria, protist, lithoheterotrophy 2 bioRxiv preprint doi: https://doi.org/10.1101/540435; this version posted February 5, 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. 43 Significance Statement 44 Many animals and protists depend on symbiotic sulfur-oxidizing bacteria as their main food 45 source. These bacteria use energy from oxidizing inorganic sulfur compounds to make 46 biomass autotrophically from CO2, serving as primary producers for their hosts. Here we 47 describe apparently non-autotrophic sulfur symbionts called Kentron, associated with marine 48 ciliates. They lack genes for known autotrophic pathways, and have a carbon stable isotope 49 fingerprint heavier than other symbionts from similar habitats. Instead they have the potential 50 to oxidize sulfur to fuel the uptake of organic compounds for heterotrophic growth, a 51 metabolic mode called chemolithoheterotrophy that is not found in other symbioses. 52 Although several symbionts have heterotrophic features to supplement primary production, in 53 Kentron they appear to supplant it entirely. 3 bioRxiv preprint doi: https://doi.org/10.1101/540435; this version posted February 5, 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. 54 Introduction 55 Chemosynthetic symbioses between heterotrophic, eukaryotic hosts and bacteria that use the 56 oxidation of inorganic chemicals or methane to fuel growth are common in marine 57 environments. They occur in habitats ranging from deep sea vents and seeps, where they are 58 responsible for much of the primary production, to the shallow water interstitial, where the 59 hosts are often small and inconspicuous meiofauna. Among the energy sources for 60 chemosynthesis are reduced sulfur species like sulfide and thiosulfate, and such sulfur- 61 oxidizing (thiotrophic) symbioses have convergently evolved multiple times (1). They are 62 commonly interpreted as nutritional symbioses where the symbionts fix CO2 autotrophically 63 into biomass with the energy from sulfur oxidation and eventually serve as food for their 64 hosts (1, 2). Indeed, several host groups have become so completely dependent on their 65 symbionts for nutrition that they have reduced digestive systems. All sulfur-oxidizing 66 symbioses investigated thus far possess a primary thiotrophic symbiont with genes of either 67 the Calvin-Benson-Bassham (CBB) (3–10) or reverse tricarboxylic acid (rTCA) (11, 12) 68 cycles for CO2 fixation, and the different pathways may relate to different ecological niches 69 occupied by the symbioses (13). The symbionts of the vestimentiferan tubeworms are 70 additionally able to encode both the CBB and rTCA cycles, which may be active under 71 different environmental conditions (14–16). Beyond sulfur oxidation and carbon fixation, 72 several thiotrophic symbionts have additional metabolic capabilities such as the uptake of 73 organic carbon (17), the use of carbon monoxide (18) and hydrogen (19) as energy sources, 74 and the ability to fix inorganic nitrogen (4, 5). 75 The thiotrophic ectosymbionts of the ciliate genus Kentrophoros constitute a distinct clade of 76 Gammaproteobacteria named “Candidatus Kentron” (hereafter Kentron) (20). Kentron has 77 previously been shown to oxidize sulfide and fix CO2 (21), and to be consumed and digested 4 bioRxiv preprint doi: https://doi.org/10.1101/540435; this version posted February 5, 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. 78 by its hosts (21, 22). Unlike most ciliates, which consume their food at a specific location on 79 the cell that bears feeding structures composed of specialized cilia, Kentrophoros has only 80 vestiges of such cilia, and instead directly engulfs its symbionts along the entire cell body 81 (23), suggesting that Kentron bacteria are its main food source. 82 Given that all previous studies of thiotrophic symbionts, including Kentron, have 83 characterized them as autotrophic, we expected that the pathways of energy and carbon 84 metabolism used by Kentron would resemble those in other thiotrophic bacteria involved in 85 nutritional symbioses. In this study, we used metagenomic and transcriptomic analyses of 86 single host individuals to show that the Kentron clade lacks the canonical pathways of 87 autotrophic CO2 fixation. Based on a metabolic reconstruction of the core genome from 88 eleven Kentron phylotypes collected from three different sites, and results from direct protein 89 stable isotope fingerprinting, we propose that it is a lithoheterotrophic nutritional symbiont, 90 relying on assimilation of organic substrates rather than fixation of inorganic carbon to feed 91 its hosts. 92 Results 93 Symbiont genome assemblies have high coverage and 94 completeness, and represent eleven phylotypes 95 Genomes of Kentron symbionts were binned from 34 metagenome assemblies, each 96 corresponding to a single Kentrophoros host ciliate individual. These samples represented 12 97 host morphospecies from three different geographical locations: the Mediterranean, 98 Caribbean, and Baltic Seas (Supplementary Table 1). The symbiont genome assemblies
Load more

Recommended publications
  • Platyhelminthes, Nemertea, and "Aschelminthes" - A
    BIOLOGICAL SCIENCE FUNDAMENTALS AND SYSTEMATICS – Vol. III - Platyhelminthes, Nemertea, and "Aschelminthes" - A. Schmidt-Rhaesa PLATYHELMINTHES, NEMERTEA, AND “ASCHELMINTHES” A. Schmidt-Rhaesa University of Bielefeld, Germany Keywords: Platyhelminthes, Nemertea, Gnathifera, Gnathostomulida, Micrognathozoa, Rotifera, Acanthocephala, Cycliophora, Nemathelminthes, Gastrotricha, Nematoda, Nematomorpha, Priapulida, Kinorhyncha, Loricifera Contents 1. Introduction 2. General Morphology 3. Platyhelminthes, the Flatworms 4. Nemertea (Nemertini), the Ribbon Worms 5. “Aschelminthes” 5.1. Gnathifera 5.1.1. Gnathostomulida 5.1.2. Micrognathozoa (Limnognathia maerski) 5.1.3. Rotifera 5.1.4. Acanthocephala 5.1.5. Cycliophora (Symbion pandora) 5.2. Nemathelminthes 5.2.1. Gastrotricha 5.2.2. Nematoda, the Roundworms 5.2.3. Nematomorpha, the Horsehair Worms 5.2.4. Priapulida 5.2.5. Kinorhyncha 5.2.6. Loricifera Acknowledgements Glossary Bibliography Biographical Sketch Summary UNESCO – EOLSS This chapter provides information on several basal bilaterian groups: flatworms, nemerteans, Gnathifera,SAMPLE and Nemathelminthes. CHAPTERS These include species-rich taxa such as Nematoda and Platyhelminthes, and as taxa with few or even only one species, such as Micrognathozoa (Limnognathia maerski) and Cycliophora (Symbion pandora). All Acanthocephala and subgroups of Platyhelminthes and Nematoda, are parasites that often exhibit complex life cycles. Most of the taxa described are marine, but some have also invaded freshwater or the terrestrial environment. “Aschelminthes” are not a natural group, instead, two taxa have been recognized that were earlier summarized under this name. Gnathifera include taxa with a conspicuous jaw apparatus such as Gnathostomulida, Micrognathozoa, and Rotifera. Although they do not possess a jaw apparatus, Acanthocephala also belong to Gnathifera due to their epidermal structure. ©Encyclopedia of Life Support Systems (EOLSS) BIOLOGICAL SCIENCE FUNDAMENTALS AND SYSTEMATICS – Vol.
    [Show full text]
  • Wood-Eating Bivalves Daniel L
    The University of Maine DigitalCommons@UMaine University of Maine Office of Research and Special Collections Sponsored Programs: Grant Reports 1-27-2006 Evolution of Endosymbiosis in (xylotrophic) Wood-Eating Bivalves Daniel L. Distel Principal Investigator; University of Maine, Orono Follow this and additional works at: https://digitalcommons.library.umaine.edu/orsp_reports Part of the Marine Biology Commons Recommended Citation Distel, Daniel L., "Evolution of Endosymbiosis in (xylotrophic) Wood-Eating Bivalves" (2006). University of Maine Office of Research and Sponsored Programs: Grant Reports. 133. https://digitalcommons.library.umaine.edu/orsp_reports/133 This Open-Access Report is brought to you for free and open access by DigitalCommons@UMaine. It has been accepted for inclusion in University of Maine Office of Research and Sponsored Programs: Grant Reports by an authorized administrator of DigitalCommons@UMaine. For more information, please contact [email protected]. Annual Report: 0129117 Annual Report for Period:06/2004 - 06/2005 Submitted on: 01/27/2006 Principal Investigator: Distel, Daniel L. Award ID: 0129117 Organization: University of Maine Title: Evolution of Endosymbiosis in (xylotrophic) Wood-Eating Bivalves Project Participants Senior Personnel Name: Distel, Daniel Worked for more than 160 Hours: Yes Contribution to Project: Post-doc Graduate Student Name: Luyten, Yvette Worked for more than 160 Hours: Yes Contribution to Project: Graduate student participated in lab research with support from this grant. Name: Mamangkey, Gustaf Worked for more than 160 Hours: Yes Contribution to Project: Gustaf Mamangkey is a lecturer at the Tropical Marine Mollusc Programme, Faculty of Fisheries and Marine Sciences, Sam Ratulangi University,Jl. Kampus UNSRAT Bahu, Manado 95115,Indonesia.
    [Show full text]
  • Methylamine As a Nitrogen Source for Microorganisms from a Coastal Marine
    Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment Martin Tauberta,b, Carolina Grobb, Alexandra M. Howatb, Oliver J. Burnsc, Jennifer Pratscherb, Nico Jehmlichd, Martin von Bergend,e,f, Hans H. Richnowg, Yin Chenh,1, J. Colin Murrellb,1 aAquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany bSchool of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK cSchool of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK dDepartment of Molecular Systems Biology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany eInstitute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Brüderstraße 32, 04103 Leipzig, Germany fDepartment of Chemistry and Bioscience, University of Aalborg, Fredrik Bajers Vej 7H, 9220 Aalborg East, Denmark. gDepartment of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research – UFZ, Permoserstrasse 15, 04318 Leipzig, Germany hSchool of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK 1To whom correspondence should be addressed. J. Colin Murrell, Phone: +44 (0)1603 59 2959, Email: [email protected], and Yin Chen, Phone: +44 (0)24 76528976, Email: [email protected] Keywords: marine methylotrophs, 15N stable isotope probing, methylamine, metagenomics, metaproteomics Classification: BIOLOGICAL SCIENCES/Microbiology Short title: Methylamine as a Nitrogen Source for Marine Microbes This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as an ‘Accepted Article’, doi: 10.1111/1462-2920.13709 This article is protected by copyright.
    [Show full text]
  • Spongejaspis Sp-Associated Bacteria Producing Protease Inhibitor
    ORIGINAL ARTICLE Spongejaspis sp-Associated Bacteria Producing Protease Inhibitor DEDE MAHDIYAH1,2, ARIS TRI WAHYUDI3, WIDANARNI3, HELMIA FARIDA4 1 Sari Mulia University, Banjarmasin, Indonesia 2Doctoral Programm, Faculty of Medicine, Diponegoro University, Semarang, Indonesia 3Bogor Agricultural University, Bogor, Indonesia 4Faculty of Medicine, Diponegoro University, Semarang, Indonesia Correspondence to Dr. Dede Mahdiyah, Email :[email protected], Telp: +62-82250812565 ABSTRACT Background: Proteaseinhibitors are important in medicine, particularly in disabling proteases in the pathogenic processes of human diseases such as arthritis, cancer,HIV/AIDS and other infections. Sponges are excellent sources forbioactive compounds such as enzyme inhibitors, antiviral, antimicrobial. Aim: To explore sponge-associated bacteria as sources of protease inhibitors. Methods:This was an explorative descriptive study. Bacteria isolated from sponge Jaspis sp were screened using sea water complete and skim-milk double-layer plate. When the screening test positive, the activity of protease inhibitors was assessed using three substrates i.e proteinase-K, crude extract of protease (CEP) from Staphylococcus aureus, Pseudomonasaeruginosa, Enteropathogenic Escherichiacoli(EPEC) K11, and subtilisin. Optimum incubation time, temperature, and pH were determined to measure the activity ofthe protease inhibitors. Phenotypical characterization was performed using Gram and Microbact-kit. 16S-rRNA sequencing was done for identification. Results: Out of 136 isolates screened, three were positive for their potency as protease inhibitor producers, including oneGram-negative coccus and two Gram-positive cocci. The isolates showed protease inhibitor activity up to 90% toward the three substrates. The optimum time incubation toward three substratesranged 12-24 hours. The optimum temperatures for the three isolates were 30Co-60oC, 20o-30oC, and 30oC respectively.
    [Show full text]
  • Which Organisms Are Used for Anti-Biofouling Studies
    Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E.
    [Show full text]
  • Ecosystems Mario V
    Ecosystems Mario V. Balzan, Abed El Rahman Hassoun, Najet Aroua, Virginie Baldy, Magda Bou Dagher, Cristina Branquinho, Jean-Claude Dutay, Monia El Bour, Frédéric Médail, Meryem Mojtahid, et al. To cite this version: Mario V. Balzan, Abed El Rahman Hassoun, Najet Aroua, Virginie Baldy, Magda Bou Dagher, et al.. Ecosystems. Cramer W, Guiot J, Marini K. Climate and Environmental Change in the Mediterranean Basin -Current Situation and Risks for the Future, Union for the Mediterranean, Plan Bleu, UNEP/MAP, Marseille, France, pp.323-468, 2021, ISBN: 978-2-9577416-0-1. hal-03210122 HAL Id: hal-03210122 https://hal-amu.archives-ouvertes.fr/hal-03210122 Submitted on 28 Apr 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Climate and Environmental Change in the Mediterranean Basin – Current Situation and Risks for the Future First Mediterranean Assessment Report (MAR1) Chapter 4 Ecosystems Coordinating Lead Authors: Mario V. Balzan (Malta), Abed El Rahman Hassoun (Lebanon) Lead Authors: Najet Aroua (Algeria), Virginie Baldy (France), Magda Bou Dagher (Lebanon), Cristina Branquinho (Portugal), Jean-Claude Dutay (France), Monia El Bour (Tunisia), Frédéric Médail (France), Meryem Mojtahid (Morocco/France), Alejandra Morán-Ordóñez (Spain), Pier Paolo Roggero (Italy), Sergio Rossi Heras (Italy), Bertrand Schatz (France), Ioannis N.
    [Show full text]
  • Cyanobacterial Evolution During the Precambrian
    International Journal of Astrobiology 15 (3): 187–204 (2016) doi:10.1017/S1473550415000579 © Cambridge University Press 2016 This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited. Cyanobacterial evolution during the Precambrian Bettina E. Schirrmeister1, Patricia Sanchez-Baracaldo2 and David Wacey1,3 1School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen’s Road, Bristol BS8 1RJ, UK e-mail: [email protected] 2School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK 3Centre for Microscopy, Characterisation and Analysis, and ARC Centre of Excellence for Core to Crust Fluid Systems, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia Abstract: Life on Earth has existed for at least 3.5 billion years. Yet, relatively little is known of its evolution during the first two billion years, due to the scarceness and generally poor preservation of fossilized biological material. Cyanobacteria, formerly known as blue green algae were among the first crown Eubacteria to evolve and for more than 2.5 billion years they have strongly influenced Earth’s biosphere. Being the only organism where oxygenic photosynthesis has originated, they have oxygenated Earth’s atmosphere and hydrosphere, triggered the evolution of plants –being ancestral to chloroplasts– and enabled the evolution of complex life based on aerobic respiration. Having such a strong impact on early life, one might expect that the evolutionary success of this group may also have triggered further biosphere changes during early Earth history.
    [Show full text]
  • Metabarcoding Analysis on European Coastal Samples Reveals New
    1 A research a rticle submitted to Scientific Reports 2 3 Metabarcoding analysis on European coastal samples 4 reveals new molecular metazoan diversity 5 6 David López -Escardó 1, Jordi Paps 2, Colomban de Vargas 3,4 , Ramon Massana 5, Iñaki 7 Ruiz -Trillo 1,6,7* , Javier del Campo 1,8* 8 Supplementary Figure Legends and Table s 9 Fig. S 1: Box plot distribution of relative metazoan abundance compar ed with all 10 eukaryotes. Relative abundance of metazoans compared to all eukaryotes in (a) 11 different oxic pelagic fractions, (b) different sites and in ( c) different depths. Note that 12 data is provided from just one sample in the anoxic sediments. 13 Fig. S2: Rarefaction curves . Rarefaction curves calculated with vegan from the 14 samples divided (a) by template (RNA or DNA) or (b) by env ironment keepig as well 15 divided the samples from RNA ( discontinuous line) or DNA ( continuous line ). Both 16 plots show the rarefaction curve of all the samples. 17 Fig. S3: Jackknife clustering analysis of phylogenetic composition of the samples . 18 The chart repr esents the relative abundance within metazoan phyla in each sample. 19 Samples from extracellular DNA and the ones with less than 100 reads (DNA+RNA) 20 were removed from the analysis. Sample characteristics are expressed in colors. On 21 the right site there is th e legend. RNA and DNA are expressed in white and black 22 respectively. Picoplanktonic, nanoplanktonic, micromesoplanktonic samples and the 23 samples from the sediments are representedwith yellow, green, dark red and purple 24 respectively.
    [Show full text]
  • Thiomargarita Namibiensis Cells by Using Microelectrodes Heide N
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Nov. 2002, p. 5746–5749 Vol. 68, No. 11 0099-2240/02/$04.00ϩ0 DOI: 10.1128/AEM.68.11.5746–5749.2002 Copyright © 2002, American Society for Microbiology. All Rights Reserved. Uptake Rates of Oxygen and Sulfide Measured with Individual Thiomargarita namibiensis Cells by Using Microelectrodes Heide N. Schulz1,2* and Dirk de Beer1 Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany,1 and Section of Microbiology, University of California, Davis, Davis, California 956162 Received 25 March 2002/Accepted 31 July 2002 Gradients of oxygen and sulfide measured towards individual cells of the large nitrate-storing sulfur bacterium Thiomargarita namibiensis showed that in addition to nitrate oxygen is used for oxidation of sulfide. Stable gradients around the cells were found only if acetate was added to the medium at low concentrations. The sulfur bacterium Thiomargarita namibiensis is a close conclusions about their physiology by observing chemotactic relative of the filamentous sulfur bacteria of the genera Beg- behavior, as has been done successfully with Beggiatoa and giatoa and Thioploca. It was only recently discovered off the Thioploca filaments (5, 10). However, because of the large size Namibian coast in fluid sediments rich in organic matter and of Thiomargarita cells, they develop, around individual cells, sulfide (15). The large, spherical cells of Thiomargarita (diam- measurable gradients of oxygen and sulfide that can be used eter, 100 to 300 ␮m) are held together in a chain by mucus that for calculating uptake rates of oxygen and sulfide. Thus, the surrounds each cell (Fig. 1). Most of the cell volume is taken physiological reactions of individual cells to changes in oxygen up by a central vacuole in which nitrate is stored at concen- and sulfide concentrations can be directly observed by observ- trations of up to 800 mM.
    [Show full text]
  • Nanosims and Tissue Autoradiography Reveal Symbiont Carbon fixation and Organic Carbon Transfer to Giant Ciliate Host
    The ISME Journal (2018) 12:714–727 https://doi.org/10.1038/s41396-018-0069-1 ARTICLE NanoSIMS and tissue autoradiography reveal symbiont carbon fixation and organic carbon transfer to giant ciliate host 1 2 1 3 4 Jean-Marie Volland ● Arno Schintlmeister ● Helena Zambalos ● Siegfried Reipert ● Patricija Mozetič ● 1 4 2 1 Salvador Espada-Hinojosa ● Valentina Turk ● Michael Wagner ● Monika Bright Received: 23 February 2017 / Revised: 3 October 2017 / Accepted: 9 October 2017 / Published online: 9 February 2018 © The Author(s) 2018. This article is published with open access Abstract The giant colonial ciliate Zoothamnium niveum harbors a monolayer of the gammaproteobacteria Cand. Thiobios zoothamnicoli on its outer surface. Cultivation experiments revealed maximal growth and survival under steady flow of high oxygen and low sulfide concentrations. We aimed at directly demonstrating the sulfur-oxidizing, chemoautotrophic nature of the symbionts and at investigating putative carbon transfer from the symbiont to the ciliate host. We performed pulse-chase incubations with 14C- and 13C-labeled bicarbonate under varying environmental conditions. A combination of tissue autoradiography and nanoscale secondary ion mass spectrometry coupled with transmission electron microscopy was used to fi 1234567890();,: follow the fate of the radioactive and stable isotopes of carbon, respectively. We show that symbiont cells x substantial amounts of inorganic carbon in the presence of sulfide, but also (to a lesser degree) in the absence of sulfide by utilizing internally stored sulfur. Isotope labeling patterns point to translocation of organic carbon to the host through both release of these compounds and digestion of symbiont cells. The latter mechanism is also supported by ultracytochemical detection of acid phosphatase in lysosomes and in food vacuoles of ciliate cells.
    [Show full text]
  • The Evolutionary Pathways of Photoreceptors by Paul Nethercott
    The Evolutionary Pathways Of Photoreceptors By Paul Nethercott August 2014 www.CreationismOnline.com www.wikipedia.com Evolution Of Photoreceptors And Eyes Sorted By Phyletic Group Phylum Meaning Common name Eyes Species Acanthocephala Thorny headed worms Thorny‐headed worms None 756 Acoelomorpha Without gut Acoels None 1 Annelida Little ring Segmented worms Ocelli, Compound Eyes 17,000 Arthropoda Jointed foot Arthropods Ocelli, Compound Eyes 1,134,000 Brachiopoda Arm foot Lamp shells None 400 Bryozoa Moss animals Moss animals, sea mats None 5,000 Chaetognatha Longhair jaw Arrow worms Compound Eyes 100 Chordata With a cord Chordates Single Lense 100,000 Cnidaria Stinging nettle Coelenterates Ocelli, Single Lense 11,000 Ctenophora Comb bearer Comb jellies None 100 Cycliophora Wheel carrying Symbion None 3 Echinodermata Spiny skin Echinoderms Ocelli 7,000 Entoprocta Inside anus Goblet worm Ocelli 150 Gastrotricha Hair stomach Meiofauna Ocelli 690 Gnathostomulida Jaw orifice Jaw worms None 100 Hemichordata Half cord Acorn worms None 100 Kinorhyncha Motion snout Mud dragons Ocelli 150 Loricifera Corset bearer Brush heads None 122 Micrognathozoa Tiny jaw animals — None 1 Mollusca Soft Mollusks Ocelli 112,000 Nematoda Thread like Round worms Ocelli 100,000 Nematomorpha Thread form Horsehair worms None 320 Nemertea A sea nymph Ribbon worms Ocelli 1,200 Onychophora Claw bearer Velvet worms Ocelli 200 Orthonectida Straight swim None 20 Phoronida Zeus's mistress Horseshoe worms None 11 Placozoa Plate animals None 1 Platyhelminthes Flat worms Flat
    [Show full text]
  • TREATISE ONLINE Number 48
    TREATISE ONLINE Number 48 Part N, Revised, Volume 1, Chapter 31: Illustrated Glossary of the Bivalvia Joseph G. Carter, Peter J. Harries, Nikolaus Malchus, André F. Sartori, Laurie C. Anderson, Rüdiger Bieler, Arthur E. Bogan, Eugene V. Coan, John C. W. Cope, Simon M. Cragg, José R. García-March, Jørgen Hylleberg, Patricia Kelley, Karl Kleemann, Jiří Kříž, Christopher McRoberts, Paula M. Mikkelsen, John Pojeta, Jr., Peter W. Skelton, Ilya Tëmkin, Thomas Yancey, and Alexandra Zieritz 2012 Lawrence, Kansas, USA ISSN 2153-4012 (online) paleo.ku.edu/treatiseonline PART N, REVISED, VOLUME 1, CHAPTER 31: ILLUSTRATED GLOSSARY OF THE BIVALVIA JOSEPH G. CARTER,1 PETER J. HARRIES,2 NIKOLAUS MALCHUS,3 ANDRÉ F. SARTORI,4 LAURIE C. ANDERSON,5 RÜDIGER BIELER,6 ARTHUR E. BOGAN,7 EUGENE V. COAN,8 JOHN C. W. COPE,9 SIMON M. CRAgg,10 JOSÉ R. GARCÍA-MARCH,11 JØRGEN HYLLEBERG,12 PATRICIA KELLEY,13 KARL KLEEMAnn,14 JIřÍ KřÍž,15 CHRISTOPHER MCROBERTS,16 PAULA M. MIKKELSEN,17 JOHN POJETA, JR.,18 PETER W. SKELTON,19 ILYA TËMKIN,20 THOMAS YAncEY,21 and ALEXANDRA ZIERITZ22 [1University of North Carolina, Chapel Hill, USA, [email protected]; 2University of South Florida, Tampa, USA, [email protected], [email protected]; 3Institut Català de Paleontologia (ICP), Catalunya, Spain, [email protected], [email protected]; 4Field Museum of Natural History, Chicago, USA, [email protected]; 5South Dakota School of Mines and Technology, Rapid City, [email protected]; 6Field Museum of Natural History, Chicago, USA, [email protected]; 7North
    [Show full text]