DOCSLIB.ORG

Spectro-Microscopic Studies of Microbial Selenium and Iron Reduction in a Metal Contaminated Aquifer

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Spectro-Microscopic Studies of Microbial Selenium and Iron Reduction in a Metal Contaminated Aquifer Spectro-Microscopic Studies of Microbial Selenium and Iron Reduction in a Metal Contaminated Aquifer By Sirine Constance Fakra A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Earth and Planetary Science in the GRADUATE DIVISION of the UNIVERSITY OF CALIFORNIA, BERKELEY Committee in charge: Professor Jillian F. Banfield, Chair Professor James Bishop Professor Céline Pallud Spring 2015 Spectro-Microscopic Studies of Microbial Selenium and Iron Reduction in a Metal Contaminated Aquifer © 2015 By Sirine Constance Fakra Abstract Spectro-microscopic studies of microbial selenium and iron reduction in a metal contaminated aquifer by Sirine C. Fakra Doctor of Philosophy in Earth and Planetary Science University of California, Berkeley Professor Jillian F. Banfield, Chair Redox-sensitive metal contaminants in subsurface environments can be reduced enzymatically or indirectly by microbial activity to convert them from soluble mobile (toxic) to comparatively insoluble, relatively immobile (less bioavailable) forms. The broad purpose of the research presented in this dissertation was to acquire a deep understanding of selenium and iron microbial reduction and immobilization in the subsurface and to characterize in detail the nature of the bioreduction products. To this end, biofilms formed during a biostimulation experiment in a metal-contaminated aquifer adjacent to the Colorado River in Colorado, USA were studied. Biofilms develop in a wide variety of natural settings and the aqueous chemical conditions within biofilms are strongly affected by the presence of extracellular polymers that potentially confer biofilm cells with a greater tolerance to heavy metals than planktonic cells. This thesis integrates field and laboratory experimental methods to provide 2D and 3D ultrastructural information, 2D chemical speciation and community membership via metagenomics methods. In addition, physiological information was obtained via characterization of an isolated bacterium and insights related to the product structure and stability were achieved by chemical synthesis-based studies. In this dissertation, an apparatus permitting correlative cryogenic spectro-microscopy was developed (Appendix I) and applied to determine in detail the cell-mineral relationships and the speciation of selenium in the biofilms (Chapter 1). The research involved integration of both cryogenic electron microscopy and X-ray absorption spectroscopy datasets on the same sample region to document the size, structure and distribution of bioreduction products. Because many of the microbial species in the mine tailings-contaminated aquifer are novel and difficult to cultivate in the laboratory, part of the research involved phylogenic analyses of the biofilm organisms via analysis of 16S rRNA genes. A novel betaproteobacterium of the genus Dechloromonas (Dechloromonas selenatis strain RGW, Chapter 2) was isolated from the Rifle site and shown to be capable of reducing selenate to red amorphous elemental Se0. This isolate was also capable of reducing toxic arsenate. Chapter 3 investigates further the stability of elemental selenium colloids at ambient pressure as a function of temperature and particle size. The last chapter (Chapter 4) focuses on the distribution and speciation of iron in the Rifle aquifer 1 during a biostimulation experiment. The combined results demonstrate the importance of both clays and cell-associated ferric iron oxyhydroxide aggregates for growth of planktonic iron- reducing bacteria. These insights provide fundamental information about organisms that mediate selenium, iron and arsenic biogeochemical transformations in the subsurface and the nature of the product phases. The data may help to identify substrate amendment regimes for sustained Se remediation. Following short-term acetate addition to the aquifer, selenium remained immobile for at least one year, suggesting the acetate amendment approach has significant potential for bioremediation of selenium, in addition to uranium and vanadium as previously studied. Although focused on selenium and iron bio-reduction, the instrumentation and approaches developed here are generally applicable for accurate determination of cell-mineral interactions and metal speciation and can be further extended to constrain aquifer-scale reactive transport models in a wide range of environments. 2 To my brother i TABLE OF CONTENTS ACKNOWLEDGEMENTS INTRODUCTION CHAPTER 1. Correlative cryogenic spectro-microscopy to investigate selenium bioreduction products. CHAPTER 2. Dechloromonas selenatis, a Betaproteobacterium from a contaminated aquifer that reduces selenate to amorphous selenium. CHAPTER 3. Size and temperature-dependent crystallization of elemental selenium. CHAPTER 4. Iron speciation analysis indicates the use of clays and iron oxyhydroxides by planktonic- and biofilm-associated Fe-reducing bacteria. APPENDIX I. Microprobe cryogenic apparatus for correlative spectro- microscopy. APPENDIX II. Supplemental materials for Chapter 1. ii ACKNOWLEDGEMENTS As a part-time employee and graduate student, there are many people who have helped me these past years and without whom this PhD would simply not have been possible. First, to my graduate advisor Jillian Banfield who believed in me more than I did. She has been an incredible mentor. Her stimulating ideas and her vision are truly inspiring. To Howard Padmore who has made this whole journey possible, I am deeply and forever grateful. Both Jillian and Howard have supported me in more ways than I can count. I would like to thank my committee members, Jim Bishop and Céline Pallud, for taking the time to learn about my research and provide insightful feedback. I am indebted to the Advanced Light Source’s director Roger Falcone and the Berkeley Lab Learning Institute for financing me and for supporting a program where full time employees can earn a doctorate degree. I am very grateful to members of the Banfield’s group in particular Birgit Luef for teaching me the art of cryo-plunging samples and cryogenic electron microscopy, and who helped me a great deal with cryo-TEM data. I want to thank Sean Mullin, Cindy Castelle and Laura Hug who taught me the basics of microbiology and have greatly helped me with phylogenetic trees, Ken Williams for introducing me to the Rifle site and answering my tons of questions patiently. I would like to acknowledge Denise Schines for providing me with confocal data. Thanks to Roseann Csencsits, Kelly Wrighton, Luis Comolli, Kim Handley and Tyler Arbour for stimulating discussions over the years, as well as Margie Winn for administrative support. A big thanks to my Berkeley Lab colleagues, Matthew A. Marcus and Tony Warwick who always encouraged me and have been great mentors over the years; Tolek Tyliszczak, Mary K. Gilles and David K. Shuh who have always supported me; Jeff Kortright, Tony Young, Andrew Westphal and Anna Butterworth who lent me some important pieces of equipment at crucial times. A large thank you to Paul Baker and his team at Instec Inc. for help with the microprobe cryo-stage. Last, to my parents, who have always encouraged and supported me the best way they could. To my beautiful and smart brother, you are always on my mind, this one is for you. Finally to my husband, I love you so very much. I would not have made it without your unconditional love and support. iii Introduction 1.1 Introduction and motivation One of the most active current research in environmental science focuses on the bioremediation of contaminated environments. Centuries of anthropogenic activities have led to the accumulation of metal and metalloid contaminants into the environment, posing a direct threat to ecosystems and human health. By contrast to organic contaminants, heavy metals are not biodegradable and remain in the environment1. Their toxicity mostly depend on their forms, with the general rule that the more soluble they are, the more toxic2. Selenium, present in trace amounts in rock-forming minerals is a major environmental contaminant, present in the porphyry copper deposits of the western United States and around the world3. Globally, the largest fluxes in the Se cycle are from land into the marine system along aquatic pathways. Natural trace Se contamination occurs mostly through geochemical processes, such as erosion of soils and weathering of rocks (e.g. black shales)4, 5. However, the anthropogenic release is by far the major contributor to the Se cycle, releasing up to 88,000 tons of Se per year5. Oil refining, combustion of fossil fuels, drainage from mines, and agriculture represent the primary sources of contamination6. The biogeochemical cycling of selenium7, is still not well defined but is predominantly governed by microorganisms which play a crucial role in oxidation, reduction, methylation, and volatilization. Se oxyanions (selenate and selenite) which iv dominate in aqueous systems can be reduced by microbes (enzymatically, or indirectly) to comparatively insoluble, immobile and non-toxic forms (e.g. Se0). The research described in this dissertation stems from the Rifle Field Study and explores the potential for the stimulation of microorganisms at reducing and controlling the mobility of Se (and Fe) in the subsurface. 1.2 Contribution of this thesis and outline of the dissertation Determining accurately the distribution and forms of associated metals, as well as understanding the functioning of the microbial community present in contaminated systems are key
Load more

Recommended publications
  • 1 Microbial Transformations of Organic Chemicals in Produced Fluid From
    Microbial transformations of organic chemicals in produced fluid from hydraulically fractured natural-gas wells Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Morgan V. Evans Graduate Program in Environmental Science The Ohio State University 2019 Dissertation Committee Professor Paula Mouser, Advisor Professor Gil Bohrer, Co-Advisor Professor Matthew Sullivan, Member Professor Ilham El-Monier, Member Professor Natalie Hull, Member 1 Copyrighted by Morgan Volker Evans 2019 2 Abstract Hydraulic fracturing and horizontal drilling technologies have greatly improved the production of oil and natural-gas from previously inaccessible non-permeable rock formations. Fluids comprised of water, chemicals, and proppant (e.g., sand) are injected at high pressures during hydraulic fracturing, and these fluids mix with formation porewaters and return to the surface with the hydrocarbon resource. Despite the addition of biocides during operations and the brine-level salinities of the formation porewaters, microorganisms have been identified in input, flowback (days to weeks after hydraulic fracturing occurs), and produced fluids (months to years after hydraulic fracturing occurs). Microorganisms in the hydraulically fractured system may have deleterious effects on well infrastructure and hydrocarbon recovery efficiency. The reduction of oxidized sulfur compounds (e.g., sulfate, thiosulfate) to sulfide has been associated with both well corrosion and souring of natural-gas, and proliferation of microorganisms during operations may lead to biomass clogging of the newly created fractures in the shale formation culminating in reduced hydrocarbon recovery. Consequently, it is important to elucidate microbial metabolisms in the hydraulically fractured ecosystem.
    [Show full text]
  • Wastewater Treatment Plant Effluent Introduces Recoverable Shifts In
    Science of the Total Environment 613–614 (2018) 1104–1116 Contents lists available at ScienceDirect Science of the Total Environment journal homepage: www.elsevier.com/locate/scitotenv Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in receiving streams Jacob R. Price a, Sarah H. Ledford b, Michael O. Ryan a, Laura Toran b, Christopher M. Sales a,⁎ a Civil, Architectural, and Environmental Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, United States b Earth and Environmental Science, Temple University, 1901 N. 13th St, Philadelphia, PA 19122, United States HIGHLIGHTS GRAPHICAL ABSTRACT • Effluent affected diversity and structure of community downstream of WWTPs. • Effluent-impacts on community compo- sition changed with AMC. • WWTP-associated taxa significantly de- creased with distance from source. • Major nutrients (N and P) did not con- trol shifts in community structure. • Efficacy of using a microbial indicator subset was verified. article info abstract Article history: Through a combined approach using analytical chemistry, real-time quantitative polymerase chain reaction Received 28 June 2017 (qPCR), and targeted amplicon sequencing, we studied the impact of wastewater treatment plant effluent Received in revised form 30 August 2017 sources at six sites on two sampling dates on the chemical and microbial population regimes within the Accepted 16 September 2017 Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, Pennsylvania, USA. These water bodies Available online xxxx contribute flow to the Schuylkill River, one of the major drinking water sources for Philadelphia, Pennsylvania. fl fi fi Editor: D. Barcelo Ef uent was observed to be a signi cant source of nutrients, human and non-speci c fecal associated taxa.
    [Show full text]
  • Identical Bacterial Populations Colonize Premature Infant Gut, Skin, and Oral Microbiomes And
    Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates Matthew R. Olm1, Christopher T. Brown1, Brandon Brooks1, Brian Firek2, Robyn Baker3, David Burstein4, Karina Soenjoyo1, Brian C. Thomas4, Michael Morowitz2 and Jillian F. Banfield4,5,6* 1Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. 2Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. 3Division of Newborn Medicine, Children’s Hospital of Pittsburgh and Magee-Womens Hospital of UPMC, Pittsburgh, United States 4Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. 5Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA. 6Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. *Corresponding author Running title Metagenomics of infant skin, mouth, and gut Keywords Microbiome, metagenomics, growth rates, premature infants, strains Corresponding author contact info Jillian Banfield Department of Environmental Science, Policy, & Management UC Berkeley 130 Mulford Hall #3114 Berkeley, CA 94720 [email protected] (510) 643-2155 1 Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth and gut of two hospitalized premature infants during the first month of life.
    [Show full text]
  • Genome-Reconstruction for Eukaryotes from Complex Natural Microbial Communities
    Downloaded from genome.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press Genome-reconstruction for eukaryotes from complex natural microbial communities ,$ Patrick T. West1, Alexander J. Probst2 , Igor V. Grigoriev1,5, Brian C. Thomas2, Jillian F. Banfield2,3,4* 1Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. 2Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. 3Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA. 4Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. 5US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. * Corresponding Author $present address: Group for Aquatic Microbial Ecology, Biofilm Center, Department of Chemistry, University of Duisburg-Essen, Essen, Germany Running title Metagenomic Reconstruction of Eukaryotic Genomes Keywords metagenomics, eukaryotes, genome, gene prediction Corresponding author contact info Jillian Banfield Department of Environmental Science, Policy, & Management UC Berkeley 130 Mulford Hall #3114 Berkeley, CA 94720 [email protected] (510) 643-2155 1 Downloaded from genome.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Microbial eukaryotes are integral components of natural microbial communities and their inclusion is critical for many ecosystem studies yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer- based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation and prediction of metabolic potential.
    [Show full text]
  • Title: Investigation of the Active Biofilm Communities on Polypropylene
    1 Title: Investigation of the Active Biofilm Communities on Polypropylene 2 Filter Media in a Fixed Biofilm Reactor for Wastewater Treatment 3 4 Running Title: Wastewater Treating Biofilms in Polypropylene Media Reactors 5 Contributors: 6 Iffat Naz1, 2, 3, 4*, Douglas Hodgson4, Ann Smith5, Julian Marchesi5, 6, Shama Sehar7, Safia Ahmed3, Jim Lynch8, 7 Claudio Avignone-Rossa4, Devendra P. Saroj1* 8 9 Affiliations: 10 11 1Department of Civil and Environmental Engineering, Faculty of Engineering and Physical Sciences, University 12 of Surrey, Guildford GU2 7XH, United Kingdom 13 14 2Department of Biology, Scientific Unit, Deanship of Educational Services, Qassim University, Buraidah 51452, 15 KSA 16 3Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, Quaid- 17 i-Azam University, Islamabad, Pakistan 18 4 School of Biomedical and Molecular Sciences, Department of Microbial and Cellular Sciences, University of 19 Surrey, Guildford GU2 7XH, United Kingdom 20 5Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, United Kingdom 21 6Centre for Digestive and Gut Health, Imperial College London, London W2 1NY, United Kingdom 22 7Centre for Marine Bio-Innovation (CMB), School of Biological, Earth and Environmental Sciences (BEES), 23 University of New South Wales, Sydney, Australia 24 25 8Centre for Environment and Sustainability, Faculty of Engineering and Physical Sciences, University of Surrey, 26 Guildford GU2 7XH, United Kingdom 27 *Corresponding author 28 Devendra P. Saroj (PhD, CEnv, FHEA) 29 Department of Civil and Environmental Engineering 30 Faculty of Engineering and Physical Sciences 31 University of Surrey, Surrey GU2 7XH, United Kingdom 32 E: [email protected] 33 T : +44-0-1483 686634 34 35 1 36 Acknowledgements 37 The authors sincerely acknowledge the International Research Support Program (IRSIP) of the Higher 38 Education Commission of Pakistan (HEC, Pakistan) for supporting IN for research work at the University of 39 Surrey (UK).
    [Show full text]
  • And Allochthonous-Like Dissolved Organic Matter
    fmicb-10-02579 November 5, 2019 Time: 17:10 # 1 ORIGINAL RESEARCH published: 07 November 2019 doi: 10.3389/fmicb.2019.02579 Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter Elias Broman1,2*, Eero Asmala3, Jacob Carstensen4, Jarone Pinhassi1 and Mark Dopson1 1 Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden, 2 Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden, 3 Tvärminne Zoological Station, University of Helsinki, Hanko, Finland, 4 Department of Bioscience, Aarhus University, Roskilde, Denmark Coastal zones are important transitional areas between the land and sea, where both terrestrial and phytoplankton supplied dissolved organic matter (DOM) are respired or transformed. As climate change is expected to increase river discharge and water Edited by: temperatures, DOM from both allochthonous and autochthonous sources is projected Eva Ortega-Retuerta, to increase. As these transformations are largely regulated by bacteria, we analyzed Laboratoire d’Océanographie microbial community structure data in relation to a 6-month long time-series dataset of Microbienne (LOMIC), France DOM characteristics from Roskilde Fjord and adjacent streams, Denmark. The results Reviewed by: Craig E. Nelson, showed that the microbial community composition in the outer estuary (closer to the University of Hawai‘i at Manoa,¯ sea) was largely associated with salinity and nutrients, while the inner estuary formed United States Scott Michael Gifford, two clusters linked to either nutrients plus allochthonous DOM or autochthonous DOM University of North Carolina at Chapel characteristics. In contrast, the microbial community composition in the streams was Hill, United States found to be mainly associated with allochthonous DOM characteristics.
    [Show full text]
  • Michel Foucault Ronald C Kessler Graham Colditz Sigmund Freud
    ANK RESEARCHER ORGANIZATION H INDEX CITATIONS 1 Michel Foucault Collège de France 296 1026230 2 Ronald C Kessler Harvard University 289 392494 3 Graham Colditz Washington University in St Louis 288 316548 4 Sigmund Freud University of Vienna 284 552109 Brigham and Women's Hospital 5 284 332728 JoAnn E Manson Harvard Medical School 6 Shizuo Akira Osaka University 276 362588 Centre de Sociologie Européenne; 7 274 771039 Pierre Bourdieu Collège de France Massachusetts Institute of Technology 8 273 308874 Robert Langer MIT 9 Eric Lander Broad Institute Harvard MIT 272 454569 10 Bert Vogelstein Johns Hopkins University 270 410260 Brigham and Women's Hospital 11 267 363862 Eugene Braunwald Harvard Medical School Ecole Polytechnique Fédérale de 12 264 364838 Michael Graetzel Lausanne 13 Frank B Hu Harvard University 256 307111 14 Yi Hwa Liu Yale University 255 332019 15 M A Caligiuri City of Hope National Medical Center 253 345173 16 Gordon Guyatt McMaster University 252 284725 17 Salim Yusuf McMaster University 250 357419 18 Michael Karin University of California San Diego 250 273000 Yale University; Howard Hughes 19 244 221895 Richard A Flavell Medical Institute 20 T W Robbins University of Cambridge 239 180615 21 Zhong Lin Wang Georgia Institute of Technology 238 234085 22 Martín Heidegger Universität Freiburg 234 335652 23 Paul M Ridker Harvard Medical School 234 318801 24 Daniel Levy National Institutes of Health NIH 232 286694 25 Guido Kroemer INSERM 231 240372 26 Steven A Rosenberg National Institutes of Health NIH 231 224154 Max Planck
    [Show full text]
  • High-Rate Aerobic Treatment Combined with Anaerobic Digestion and Anammox
    High-Rate Aerobic Treatment Combined With Anaerobic Digestion and Anammox Project code: 2013/4006 Prepared by: Huoqing Ge, Damien Batstone, Jurg Keller Date Published: June 2015 Published by: Australian Meat Processor Corporation AMPC acknowledges the matching funds provided by the Australian Government to support the research and development detailed in this publication. Disclaimer: The information contained within this publication has been prepared by a third party commissioned by Australian Meat Processor Corporation Ltd (AMPC). It does not necessarily reflect the opinion or position of AMPC. Care is taken to ensure the accuracy of the information contained in this publication. However, AMPC cannot accept responsibility for the accuracy or completeness of the information or opinions contained in this publication, nor does it endorse or adopt the information contained in this report. No part of this work may be reproduced, copied, published, communicated or adapted in any form or by any means (electronic or otherwise) without the express written permission of Australian Meat Processor Corporation Ltd. All rights are expressly reserved. Requests for further authorisation should be directed to the Chief Executive Officer, AMPC, Suite 1, Level 5, 110 Walker Street Sydney NSW. Executive Summary Australian red meat processing facilities can produce significant volumes of wastewater during slaughtering and cleaning operations. This wastewater stream is typically characterised by highly variable levels of suspended solids, organic matter and nutrient compounds, sometimes at concentrations more than four times greater than domestic sewage. It is important to treat this wastewater before discharging it into the environment or sewers. Typical treatment methods involve pre-treatment (dissolved-air flotation), followed by treatment in anaerobic lagoons to remove organic matter, and removal of biological nutrients – often by adding chemicals to remove phosphorus (P) if required.
    [Show full text]
  • Genome-Resolved Metagenomics Reveals Site-Specific Diversity of Episymbiotic CPR Bacteria and DPANN Archaea in Groundwater Ecosystems
    ARTICLES https://doi.org/10.1038/s41564-020-00840-5 Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems Christine He 1, Ray Keren 2, Michael L. Whittaker3,4, Ibrahim F. Farag 1, Jennifer A. Doudna 1,5,6,7,8, Jamie H. D. Cate 1,5,6,7 and Jillian F. Banfield 1,4,9 ✉ Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host associa- tion of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproduc- ibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.
    [Show full text]
  • Biological Phosphorus Removal from Abattoir Wastewater at Very Short Sludge Ages Mediated by Novel PAO Clade Comamonadaceae
    Accepted Manuscript Biological phosphorus removal from abattoir wastewater at very short sludge ages mediated by novel PAO clade Comamonadaceae Huoqing Ge , Damien J. Batstone , Jürg Keller PII: S0043-1354(14)00796-9 DOI: 10.1016/j.watres.2014.11.026 Reference: WR 11009 To appear in: Water Research Received Date: 13 August 2014 Revised Date: 6 November 2014 Accepted Date: 16 November 2014 Please cite this article as: Ge, H., Batstone, D.J., Keller, J., Biological phosphorus removal from abattoir wastewater at very short sludge ages mediated by novel PAO clade Comamonadaceae, Water Research (2014), doi: 10.1016/j.watres.2014.11.026. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. ACCEPTED MANUSCRIPT MANUSCRIPT ACCEPTED ACCEPTED MANUSCRIPT 1 Biological phosphorus removal from abattoir wastewater at 2 very short sludge ages mediated by novel PAO clade 3 Comamonadaceae 4 Huoqing Ge, Damien J. Batstone, Jürg Keller* 5 AWMC, Advanced Water Management Centre, The University of Queensland, St Lucia, 6 4072, Queensland, Australia 7 8 *Corresponding author: 9 Jürg Keller 10 11 Advanced Water Management Centre (AWMC), 12 The University of Queensland, St Lucia, MANUSCRIPT 13 QLD 4072, Australia 14 Phone: +61 7 3365 4727 15 Fax: +61 7 3365 4726 16 Email: [email protected] 17 18 19 20 21 ACCEPTED 22 23 24 1 ACCEPTED MANUSCRIPT 25 Abstract: 26 Recent increases in global phosphorus costs, together with the need to remove phosphorus 27 from wastewater to comply with water discharge regulations, make phosphorus recovery 28 from wastewater economically and environmentally attractive.
    [Show full text]
  • Physiological and Genomic Features of Highly Alkaliphilic Hydrogen-Utilizing Betaproteobacteria from a Continental Serpentinizing Site
    ARTICLE Received 17 Dec 2013 | Accepted 16 Apr 2014 | Published 21 May 2014 DOI: 10.1038/ncomms4900 OPEN Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site Shino Suzuki1, J. Gijs Kuenen2,3, Kira Schipper1,3, Suzanne van der Velde2,3, Shun’ichi Ishii1, Angela Wu1, Dimitry Y. Sorokin3,4, Aaron Tenney1, XianYing Meng5, Penny L. Morrill6, Yoichi Kamagata5, Gerard Muyzer3,7 & Kenneth H. Nealson1,2 Serpentinization, or the aqueous alteration of ultramafic rocks, results in challenging environments for life in continental sites due to the combination of extremely high pH, low salinity and lack of obvious electron acceptors and carbon sources. Nevertheless, certain Betaproteobacteria have been frequently observed in such environments. Here we describe physiological and genomic features of three related Betaproteobacterial strains isolated from highly alkaline (pH 11.6) serpentinizing springs at The Cedars, California. All three strains are obligate alkaliphiles with an optimum for growth at pH 11 and are capable of autotrophic growth with hydrogen, calcium carbonate and oxygen. The three strains exhibit differences, however, regarding the utilization of organic carbon and electron acceptors. Their global distribution and physiological, genomic and transcriptomic characteristics indicate that the strains are adapted to the alkaline and calcium-rich environments represented by the terrestrial serpentinizing ecosystems. We propose placing these strains in a new genus ‘Serpentinomonas’. 1 J. Craig Venter Institute, 4120 Torrey Pines Road, La Jolla, California 92037, USA. 2 University of Southern California, 835 W. 37th St. SHS 560, Los Angeles, California 90089, USA. 3 Delft University of Technology, Julianalaan 67, Delft, 2628BC, The Netherlands.
    [Show full text]
  • Laboratory Directed Research and Development Program FY 2002
    LBNL/PUB -54 8 5 Laboratory Directed Research and Development Program FY 2002 March 2003 Disclaimer This document wlls prepared as an account or work sponsored by the United Stales Government. While this document is believed ta contain correct inrormution, neither the United Stntes Government nor any agcncy thereof, nor The Regents orthe University of California, nor any of their employees, makes any wmnty, express or implied. or assumes any legal linbility or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product or process disclased, or represents that its use would not infringc privately awned rights. Reference herein to any specific commcrcial product, process, or service by its tradc name, trademark, manufacturer, or otherwise, does not necessnrily constitute or imply its endoaemcnt, recommendation, or favoring by the United States Government or any ogency thereof, ar The Regcnls of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of ihe United Siates Gwernment or any agency thercol or The Regents of the University of Caliktmia nnd shall not be used lor advertising or product endorsement purposes. Ernest Orlnndo hwrence Berkeley National Laboratory is an equal opportunity employer. Report on Ernest Orlando Lawrence Berkeley National Laboratory Laboratory Directed Research and Development Program FY 2002 Ernest Orlando Lawrence Berkeley National Laboratory Berkeley, California 94720 Off ice of Science USDepartment
    [Show full text]