DOCSLIB.ORG

Testing Different Membrane Filters for 16S Rrna Gene-Based Metabarcoding in Karstic Springs

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Testing Different Membrane Filters for 16S Rrna Gene-Based Metabarcoding in Karstic Springs water Article Testing Different Membrane Filters for 16S rRNA Gene-Based Metabarcoding in Karstic Springs Oana Teodora Moldovan 1,* , Andreea Baricz 2,3,4,*, Edina Szekeres 2,3,4, Marius Kenesz 1, 5 5 6 Marial Alexandra Hoaghia , Erika Andrea Levei , Ionut, Cornel Mirea , Ruxandra Năstase-Bucur 1 , Traian Brad 1 , Iulia Chiciudean 2,3 and Horia Leonard Banciu 2,3 1 Emil Racovitza Institute of Speleology, Cluj Department, Clinicilor 5, 400006 Cluj-Napoca, Romania; [email protected] (M.K.); [email protected] (R.N.-B.); [email protected] (T.B.) 2 Department of Molecular Biology and Biotechnology, Babes, -Bolyai University, 400000 Cluj-Napoca, Romania; [email protected] (E.S.); [email protected] (I.C.); [email protected] (H.L.B.) 3 Centre for Systems Biology, Biodiversity and Bioresources, Babes, -Bolyai University, 400000 Cluj-Napoca, Romania 4 National Institute of Research and Development for Biological Sciences, Institute of Biological Research, 400015 Cluj-Napoca, Romania 5 National Institute for Research and Development of Optoelectronics Bucharest INOE 2000, Research Institute for Analytical Instrumentation Subsidiary, 400293 Cluj-Napoca, Romania; [email protected] (M.A.H.); [email protected] (E.A.L.) 6 Emil Racovitza Institute of Speleology, Calea 13 Septembrie 13, 050711 Bucures, ti, Romania; [email protected] * Correspondence: [email protected] (O.T.M.); [email protected] (A.B.) Received: 8 October 2020; Accepted: 29 November 2020; Published: 3 December 2020 Abstract: Introduction: Karstic springs are used worldwide by rural communities as sources of fresh water for humans and livestock. In Romania, one-third of the population has no direct access to a public water supply. The present study is part of a country-wide project to develop simple, quick and cheap methods for seasonal environmental and microbiological monitoring of karstic springs used as drinking water by rural populations. Critical steps for monitoring workflow consist of evaluating water quality and selecting suitable membrane filters to efficiently capture environmental DNA for further microbial diversity estimation using 16S rRNA gene-based metabarcoding. Methods: Several commercial membrane filters of different compositions and pore sizes were tested on the water sampled from three karstic springs in Romania, followed by water chemistry and whole community 16S rRNA gene-based metabarcoding analysis. Results: We found that different types of applied membrane filters provide varying recovery in diversity and abundance of both overall and pathogenic bacteria. Conclusions: The result of the experiment with different filters shows that mixed cellulose ester, cellulose acetate, and nitrate membranes of 0.20 and 0.22 µm are the best for amplicon-based metabarcoding monitoring of karst springs. Keywords: spring water; karst; 16S rRNA gene; membrane filters; metabarcoding; pathogenic bacteria 1. Introduction A recent review [1] considered the main environmental drivers for 21st century global trends regarding freshwater availability. Changes in freshwater availability not only impact regional food supplies, human and ecosystem health and energy generation but also cause social unrest [1]. Half of the world’s population use groundwater for domestic needs [2], and groundwater provides 38% of the global consumptive irrigation water demand [3]. Yet groundwater monitoring and management are challenging tasks for the vastness and unseen distribution of these freshwater sources, mainly found Water 2020, 12, 3400; doi:10.3390/w12123400 www.mdpi.com/journal/water Water 2020, 12, 3400 2 of 16 in soluble rocks such as limestones and dolomites. The high demand for food, in conjunction with climate change, has resulted in economic and social hardships already reported in many parts of the world and are foreseen to accelerate the depletion of available groundwater sources used for drinking and agriculture [4]. The 2006–2017 Eurostat survey (published in 2020, [5]) shows that 5 out of 12 European countries have less than 90% of households connected to a public water supply, with Romania ranked at the lowest percentage of 67.5%. One cause of this shortcoming might be the sparse distribution of houses in most rural areas that makes access to a public water supply problematic if not impossible. Small rural populations use local sources of water that are not under the monitoring programs of water agencies. Usually, such small local sources that come from porous karstic rocks are prone to periods of low or no flow or a combination of low flow and a concentration of contaminants [6]. The primary sources of contamination in small rural localities are from livestock, septic tanks, mining activities in the area and the use of chemicals in agricultural practices [7]. Environmental DNA (eDNA) metabarcoding was proposed as a viable alternative for freshwater quality assessment [8] as it quickly and sensitively reveals the taxonomic inventory of eukaryotic [9,10] or prokaryotic communities [11]. Recently, eDNA metabarcoding has proven to be a useful tool to detect waterborne pathogens in rural surface freshwater impacted by faecal pollution [12] and antibiotic-contaminated groundwater [13]. Surprisingly, little information exists on the microbiological quality of groundwater sources that are used as drinking water in rural areas worldwide. In most, if not all, of the cases, the detection of Escherichia coli as a representative of coliform bacteria is the only microbiological test to check the potential for waterborne diseases [14]. This approach is unable to detect other dangerous bacteria, including pathogenic or opportunistic species bearing antibiotic resistance traits [15]. In this light, eDNA metabarcoding appears to be a novel and feasible approach to assess the microbial diversity of groundwater sources for drinking water in rural areas. For rural populations that use spring water as their main source of fresh water, our purpose was to test and propose tools and protocols for seasonal water quality monitoring [16]. Within the framework of this country-wide project, we performed a survey on the physicochemical and microbiological characteristics of selected karst springs to establish a fast and cost-effective monitoring protocol. We aimed to evaluate the most suitable membrane filter type and filtration strategy to efficiently recover environmental DNA (eDNA) for further fast and accurate whole community diversity assessment using 16S rRNA gene-based metabarcoding. 2. Materials and Methods 2.1. Sampling and Sample Preparation Three springs were chosen for their ease of access from Cluj-Napoca (Romania), the headquarters of logistics and the authors. Banpotoc, Băit, a (Baita) and Rapolt, el (Rapoltel) springs are located in the Apuseni Mountains in northwestern Romania (Figure1). These springs are the only sources of water used by the local populations as drinking water resources for human and livestock consumption and are not included in the national or local water monitoring programs. In September 2019, samples of spring water were collected from each of the three springs in sterile polyethylene bottles. Bottles were rinsed three times with the sample water and kept refrigerated at 4 ◦C until chemical analysis. Five liters of water were filtered under aseptic conditions using a vacuum pump and a filtering device, composed of a glass filter holder and a funnel, attached to a collecting Kitasato flask. Nine different types of membrane filters with different pore sizes were tested for their efficiency in retaining biomass that sourced for eDNA from karstic spring water (Table1). After filtration, each membrane was cut into small pieces and kept in a sterile Petri dish at 20 C until − ◦ eDNA extraction. Water 2020, 12, 3400 3 of 16 Water 2020, 12, x FOR PEER REVIEW 3 of 15 FigureFigure 1.1. ((aa)) TheThe locationlocation of the three tested karstic karstic sp springsrings in in Romania Romania and and photos photos taken taken during during the the samplingsampling campaigncampaign ((((bb)) == Baita, ( c)) = Banpotoc,Banpotoc, (d (d) )== Rapoltel).Rapoltel). TableTable 1.1. The tested membrane filters filters for metabarcoding metabarcoding in in karstic karstic spring spring water. water. Membrane Porosity Fabric Producer Porosity Sterile * Price ** MembraneCode Code Fabric Producer (µm) Sterile * Price ** (µm) PESPES polyethersulfonepolyethersulfone MilliporeMillipore 0.220.22 sterilizedsterilized High High PVDF polyvinylidene fluoride Millipore 0.22 sterilized High PVDF polyvinylidene fluoride Millipore 0.22 sterilized High NC cellulose nitrate Macherey-Nagel 0.20 sterilized Low NYLONNC nyloncellulose nitrate FioroniMacherey-Nagel 0.22 0.20 sterilizedsterilized Low Low MCE_aNYLON mixed cellulosenylon ester FioroniFioroni 0.220.22 sterilesterilized Low Low MCE_bMCE_a mixedmixed cellulose cellulose ester ester WhatmanFioroni 0.200.22 sterilesterile MediumLow S-PakMCE_b mixedmixed cellulose cellulose ester ester MerckWhatman 0.200.20 sterilesterile Medium Low PSR009S-Pak cellulosemixed acetate cellulose and nitrate ester NahitaMerck 0.220.20 sterilizedsterile Low Low PSR010 cellulose acetate and nitrate Nahita 0.45 sterilized Low PSR009 cellulose acetate and nitrate Nahita 0.22 sterilized Low * We termedPSR010 ‘sterile’ thosecellulose membrane acetate filters and provided nitrate sterile byNahita the manufacturer 0.45 and ‘sterilized’sterilized those membraneLow filters provided non-sterile and further steam-sterilized at 121 ◦C for 20
Load more

Recommended publications
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • 1 Supplementary Information Ugly Ducklings – the Dark Side of Plastic
    Supplementary Information Ugly ducklings – The dark side of plastic materials in contact with potable water Lisa Neu1,2, Carola Bänziger1, Caitlin R. Proctor1,2, Ya Zhang3, Wen-Tso Liu3, Frederik Hammes1,* 1 Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland 2 Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland 3 Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, USA Table of contents Table S1 Exemplary online blog entries on biofouling in bath toys Figure S1 Images of all examined bath toys Figure S2 Additional images of bath toy biofilms by OCT Figure S3 Additional images on biofilm composition by SEM Figure S4 Number of bacteria and proportion of intact cells in bath toy biofilms Table S2 Classification of shared OTUs between bath toys Table S3 Shared and ‘core’ communities in bath toys from single households Table S4 Richness and diversity Figure S5 Classification of abundant OTUs in real bath toy biofilms Table S5 Comparison of most abundant OTUs in control bath toy biofilms Figure S6 Fungal community composition in bath toy biofilms Table S6 Conventional plating results for indicator bacteria and groups Table S7 Bioavailability of migrating carbon from control bath toys’ material Water chemistry Method and results (Table S8) Table S9 Settings for Amplification PCR and Index PCR reactions 1 Table S1: Exemplary online blog entries on biofouling inside bath toys Issue - What is the slime? Link Rub-a-dub-dub, https://www.babble.com/baby/whats-in-the-tub/ what’s in the tub? What’s the black stuff http://blogs.babycenter.com/momstories/whats-the-black- in your squeeze toys? stuff-in-your-squeeze-toys/ Friday Find: NBC’s http://www.bebravekeepgoing.com/2010/03/friday-find-nbcs- Today Show segment: today-show-segment-do.html Do bath toys carry germs? Yuck.
    [Show full text]
  • Study on Diversity of Endophytic Bacterial Communities in Seeds of Hybrid Maize and Their Parental Lines
    Study on diversity of endophytic bacterial communities in seeds of hybrid maize and their parental lines Yang Liu, Shan Zuo, Liwen Xu, Yuanyuan Zou & Wei Song Archives of Microbiology ISSN 0302-8933 Volume 194 Number 12 Arch Microbiol (2012) 194:1001-1012 DOI 10.1007/s00203-012-0836-8 1 23 Your article is protected by copyright and all rights are held exclusively by Springer- Verlag. This e-offprint is for personal use only and shall not be self-archived in electronic repositories. If you wish to self-archive your work, please use the accepted author’s version for posting to your own website or your institution’s repository. You may further deposit the accepted author’s version on a funder’s repository at a funder’s request, provided it is not made publicly available until 12 months after publication. 1 23 Author's personal copy Arch Microbiol (2012) 194:1001–1012 DOI 10.1007/s00203-012-0836-8 ORIGINAL PAPER Study on diversity of endophytic bacterial communities in seeds of hybrid maize and their parental lines Yang Liu • Shan Zuo • Liwen Xu • Yuanyuan Zou • Wei Song Received: 29 August 2011 / Revised: 23 May 2012 / Accepted: 30 July 2012 / Published online: 15 August 2012 Ó Springer-Verlag 2012 Abstract The seeds of plants are carriers of a variety of bacterium Acinetobacter (9.26 %) was also the second beneficial bacteria and pathogens. Using the non-culture dominant bacterium of its male parent. In the hybrid methods of building 16S rDNA libraries, we investigated Jingdan 28, the second dominant bacterium Pseudomonas the endophytic bacterial communities of seeds of four (12.78 %) was also the second dominant bacterium of its hybrid maize offspring and their respective parents.
    [Show full text]
  • Differential Depth Distribution of Microbial Function and Putative Symbionts Through Sediment-Hosted Aquifers in the Deep Terrestrial Subsurface
    ARTICLES https://doi.org/10.1038/s41564-017-0098-y Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface Alexander J. Probst1,5,7, Bethany Ladd2,7, Jessica K. Jarett3, David E. Geller-McGrath1, Christian M. K. Sieber1,3, Joanne B. Emerson1,6, Karthik Anantharaman1, Brian C. Thomas1, Rex R. Malmstrom3, Michaela Stieglmeier4, Andreas Klingl4, Tanja Woyke 3, M. Cathryn Ryan 2* and Jillian F. Banfield 1* An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome- resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep- branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.
    [Show full text]
  • Revealing the Full Biosphere Structure and Versatile Metabolic Functions In
    Chen et al. Genome Biology (2021) 22:207 https://doi.org/10.1186/s13059-021-02408-w RESEARCH Open Access Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep Ping Chen1†, Hui Zhou1,2†, Yanyan Huang3,4†, Zhe Xie5†, Mengjie Zhang1,2†, Yuli Wei5, Jia Li1,2, Yuewei Ma3, Min Luo5, Wenmian Ding3, Junwei Cao5, Tao Jiang1,2, Peng Nan3*, Jiasong Fang5* and Xuan Li1,2* * Correspondence: nanpeng@fudan. edu.cn; [email protected]; lixuan@ Abstract sippe.ac.cn †Ping Chen, Hui Zhou, Yanyan Background: The full biosphere structure and functional exploration of the microbial Huang, Zhe Xie and Mengjie Zhang communities of the Challenger Deep of the Mariana Trench, the deepest known contributed equally to this work. hadal zone on Earth, lag far behind that of other marine realms. 3Ministry of Education Key Laboratory for Biodiversity Science Results: We adopt a deep metagenomics approach to investigate the microbiome and Ecological Engineering, School in the sediment of Challenger Deep, Mariana Trench. We construct 178 of Life Sciences, Fudan University, Shanghai, China metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are 5Shanghai Engineering Research reported from hadal sediment for the first time. Based on the MAGs, we find the Center of Hadal Science and microbial community functions are marked by enrichment and prevalence of Technology, College of Marine Sciences, Shanghai Ocean mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is University, Shanghai, China found to be dominated by six fungal groups that are characterized for the first time 1CAS-Key Laboratory of Synthetic in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute reduction, and hydrogen sulfide oxidation pathways.
    [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]
  • (Antarctica) Glacial, Basal, and Accretion Ice
    CHARACTERIZATION OF ORGANISMS IN VOSTOK (ANTARCTICA) GLACIAL, BASAL, AND ACCRETION ICE Colby J. Gura A Thesis Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE December 2019 Committee: Scott O. Rogers, Advisor Helen Michaels Paul Morris © 2019 Colby Gura All Rights Reserved iii ABSTRACT Scott O. Rogers, Advisor Chapter 1: Lake Vostok is named for the nearby Vostok Station located at 78°28’S, 106°48’E and at an elevation of 3,488 m. The lake is covered by a glacier that is approximately 4 km thick and comprised of 4 different types of ice: meteoric, basal, type 1 accretion ice, and type 2 accretion ice. Six samples were derived from the glacial, basal, and accretion ice of the 5G ice core (depths of 2,149 m; 3,501 m; 3,520 m; 3,540 m; 3,569 m; and 3,585 m) and prepared through several processes. The RNA and DNA were extracted from ultracentrifugally concentrated meltwater samples. From the extracted RNA, cDNA was synthesized so the samples could be further manipulated. Both the cDNA and the DNA were amplified through polymerase chain reaction. Ion Torrent primers were attached to the DNA and cDNA and then prepared to be sequenced. Following sequencing the sequences were analyzed using BLAST. Python and Biopython were then used to collect more data and organize the data for manual curation and analysis. Chapter 2: As a result of the glacier and its geographic location, Lake Vostok is an extreme and unique environment that is often compared to Jupiter’s ice-covered moon, Europa.
    [Show full text]
  • The Bacterial Sulfur Cycle in Expanding Dysoxic and Euxinic Marine Waters
    Environmental Microbiology (2020) 00(00), 00–00 doi:10.1111/1462-2920.15265 Special Issue Article The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters Daan M. van Vliet ,1 F.A. Bastiaan von Meijenfeldt,2 bacteria, and discuss the probable involvement of Bas E. Dutilh,2 Laura Villanueva,3 uncultivated SAR324 and BS-GSO2 bacteria in sulfur Jaap S. Sinninghe Damsté,3,4 Alfons J.M. Stams1,5 oxidation. Uncultivated Marinimicrobia bacteria with and Irene Sánchez-Andrea 1* a presumed organoheterotrophic metabolism are 1Laboratory of Microbiology, Wageningen University and abundant in DMW. Like SRB, they may use specific Research, Stippeneng 4, 6708WE, Wageningen, molybdoenzymes to conserve energy from the oxida- Netherlands. tion, reduction or disproportionation of sulfur cycle 2Theoretical Biology and Bioinformatics, Science for intermediates such as S0 and thiosulfate, produced Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, from the oxidation of sulfide. We expect that tailored Netherlands. sampling methods and a renewed focus on cultiva- 3Department of Marine Microbiology and tion will yield deeper insight into sulfur-cycling bacte- Biogeochemistry, Royal Netherlands Institute for Sea ria in DMW. Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, ’t Horntje (Texel), Netherlands. Introduction 4Department of Earth Sciences, Faculty of Geosciences, Oxygen deficiency is a rather common phenomenon in Utrecht University, Princetonlaan 8A, 3584 CB, Utrecht, marine waters caused by microbial aerobic respiration Netherlands. coupled to the degradation of organic matter, combined 5Centre of Biological Engineering, University of Minho, with insufficient supply of oxygen through water circulation Campus de Gualtar, 4710-057 Braga, Portugal. or diffusion (Canfield et al., 2005).
    [Show full text]
  • Aerobic Anoxygenic Photosynthesis Genes and Operons in Uncultured Bacteria in the Delaware River
    Blackwell Science, LtdOxford, UKEMIEnvironmental Microbiology 1462-2912Society for Applied Microbiology and Blackwell Publishing Ltd, 200571218961908Original ArticleDelaware River AAP bacteriaL. A. Waidner and D. L. Kirchman Environmental Microbiology (2005) 7(12), 1896–1908 doi:10.1111/j.1462-2920.2005.00883.x Aerobic anoxygenic photosynthesis genes and operons in uncultured bacteria in the Delaware River Lisa A. Waidner and David L. Kirchman* AAP bacteria photosynthesize with the use of bacterio- University of Delaware, College of Marine Studies, 700 chlorophyll a (bchl a), but do not evolve oxygen (Yurkov Pilottown Road, Lewes, DE 19958, USA. and Beatty, 1998). A more thorough understanding of AAP bacteria is needed to elucidate their role in aquatic environments. Summary The diversity of marine AAP bacteria is often explored Photosynthesis genes and operons of aerobic anox- with the gene encoding the alpha subunit of the photosyn- ygenic photosynthetic (AAP) bacteria have been thetic reaction centre, puf M (Beja et al., 2002; Oz et al., examined in a variety of marine habitats, but genomic 2005; Schwalbach and Fuhrman, 2005). On the basis of information about freshwater AAP bacteria is lacking. puf M, AAP bacteria have been classified into two clusters The goal of this study was to examine photosynthesis of proteobacteria (Nagashima et al., 1997). One consists genes of AAP bacteria in the Delaware River. In a of a mixture of alpha-1 and alpha-2, beta- and gamma- fosmid library, we found two clones bearing photo- proteobacteria, referred to here as the ‘mixed cluster’ synthesis gene clusters with unique gene content and (Nagashima et al., 1997). The other cluster contains the organization.
    [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]
  • Single Cell Analyses Reveal Contrasting Life Strategies of the Two Main Nitrifiers in the Ocean
    Aalborg Universitet Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean Kitzinger, Katharina; Marchant, Hannah K.; Bristow, Laura A.; Herbold, Craig W.; Padilla, Cory C.; Kidane, Abiel T.; Littmann, Sten; Daims, Holger; Pjevac, Petra; Stewart, Frank J.; Wagner, Michael; Kuypers, Marcel M.M. Published in: Nature Communications DOI (link to publication from Publisher): 10.1038/s41467-020-14542-3 Creative Commons License CC BY 4.0 Publication date: 2020 Document Version Publisher's PDF, also known as Version of record Link to publication from Aalborg University Citation for published version (APA): Kitzinger, K., Marchant, H. K., Bristow, L. A., Herbold, C. W., Padilla, C. C., Kidane, A. T., Littmann, S., Daims, H., Pjevac, P., Stewart, F. J., Wagner, M., & Kuypers, M. M. M. (2020). Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean. Nature Communications, 11(1), [767]. https://doi.org/10.1038/s41467-020-14542-3 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. ? Users may download and print one copy of any publication from the public portal for the purpose of private study or research. ? You may not further distribute the material or use it for any profit-making activity or commercial gain ? You may freely distribute the URL identifying the publication in the public portal ? ARTICLE https://doi.org/10.1038/s41467-020-14542-3 OPEN Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean Katharina Kitzinger 1,2*, Hannah K.
    [Show full text]
  • Roseateles Depolymerans Gen. Nov., Sp. Nov., a New Bacteriochlorophyll A-Containing Obligate Aerobe Belonging to the P=Subclassof the Pro Teobacteria
    International Journal of Systematic Bacteriology (1 999), 49,449-457 Printed in Great Britain Roseateles depolymerans gen. nov., sp. nov., a new bacteriochlorophyll a-containing obligate aerobe belonging to the P=subclassof the Pro teobacteria Tetsushi Suyama,’ Toru Shigematsu,’ Shinichi Takaichit2 Yoshinobu Nodasakaf3Seizo F~jikawa,~Hiroyuki Hosoya,’ Yutaka Tokiwa,’ Takahiro Kanagawa’ and Satoshi Hanadal Author for correspondence : Tetsushi Suyama. Tel : + 8 1 298 54 659 1. Fax : + 8 1 298 54 6587. e-mail: [email protected] ~~ 1 National Institute of Strains 61AT(T = type strain) and 6IB2, the first bacteriochlorophyll (BChI) a- Bioscience and Human containing obligate aerobes to be classified in the /?-subclassof the Technology, 1-1 Higashi, Tsukuba, lbaraki Profeobacteria, were isolated from river water. The strains were originally 305-8566,Japan isolated as degraders of poly(hexamethy1ene carbonate) (PHC). The organisms * Biological Laboratory, can utilize PHC and some other biodegradable plastics. The strains grow only Nippon Medical School, under aerobic conditions. Good production of BChl a and carotenoid pigments Kawasaki 21 1-0063,Japan is achieved on PHC agar plates and an equivalent production is observed under 3.4 School of Dentistry3 and oligotrophic conditions on agar medium. Spectrometric results suggest that Institute of Low BChl a is present in light-harvesting complex I and the photochemical reaction Temperature Science4, Hokkaido University, centre. The main carotenoids are spirilloxanthin and its precursors. Analysis of Sapporo 060, Japan the 165 rRNA gene sequence indicated that the phylogenetic positions of the two strains are similar to each other and that their closest relatives are the genera Rubriwiwax, ldeonella and Leptothrix with similarities of 96.3, 962 and 96-1%, respectively.
    [Show full text]