Ralph mitchell, ji dong gu environmental Microbi(BookZZ org)

ENVIRONMENTAL MICROBIOLOGY SECOND EDITION Edited by Ralph Mitchell and Ji-Dong Gu A JOHN WILEY & SONS, INC., PUBLICATION ENVIRONMENTAL MICROBIOLOGY ENVIRONMENTAL MICROBIOLOGY SECOND EDITION Edited by Ralph Mitchell and Ji-Dong Gu A JOHN WILEY & SONS, INC., PUBLICATION Copyright © 2010 by Wiley-Blackwell All rights reserved Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley’s global Scientific, Technical, and Medical business with Blackwell Publishing No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the 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for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages For general information on our other products and services or for technical support, please contact our Customer Care Department within the United States at 877-762-2974, outside the United States at 317-572-3993 or fax 317-572-4002 Wiley also publishes its books in a variety of electronic formats Some content that appears in print may not be available in electronic formats For more information about Wiley products, visit our web site at www.wiley.com Library of Congress Cataloging-in-Publication Data: Environmental microbiology : second edition / edited by Ralph Mitchell, Ji-Dong Gu p cm Includes bibliographical references and index ISBN 978-0-470-17790-7 (cloth) Printed in the United States of America 10 CONTENTS Contributors vii Preface ix Bacteria in the Greenhouse: Marine Microbes and Climate Change Hugh W Ducklow, Xos´e Anxelu G Mor´an, and Alison E Murray Control of Waterborne Pathogens in Developing Countries 33 Tim Ford and Steve Hamner New Molecular Methods for Detection of Waterborne Pathogens 57 Alison M Cupples, Joan B Rose, and Irene Xagoraraki Microbial Transformations of Radionuclides in the Subsurface 95 Matthew J Marshall, Alexander S Beliaev, and James K Fredrickson Eutrophication of Estuarine and Coastal Ecosystems 115 Nancy N Rabalais Microbial Deterioration of Cultural Heritage Materials 137 Christopher J McNamara, Nick Konkol, and Ralph Mitchell Sorption and Transformation of Toxic Metals by Microorganisms 153 Xu Han and Ji-Dong Gu Bioremediation of Hazardous Organics 177 Jennifer G Becker and Eric A Seagren Biosensors as Environmental Monitors 213 Steven Ripp, Melanie L DiClaudio, and Gary S Sayler 10 Effects of Genetically Modified Plants on Soil Microorganisms 235 Nicole Weinert, Remo Meincke, Michael Schloter, Gabriele Berg, and Kornelia Smalla 11 Anaerobic Digestion of Agricultural Residues 259 Vincent O’Flaherty, Gavin Collins, and Th´er´ese Mahony v vi 12 CONTENTS Anaerobic Biodegradation of Solid Waste 281 Morton A Barlaz, Bryan F Staley, and Francis L de los Reyes III 13 Low-Energy Wastewater Treatment: Strategies and Technologies 301 Thomas P Curtis 14 Bioremediated Geomechanical Processes 319 Eric A Seagren and Ahmet H Aydilek Index 349 CONTRIBUTORS Ahmet H Aydilek, Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland Morton A Barlaz, Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, North Carolina Jennifer G Becker, Department of Environmental Science and Technology, University of Maryland, College Park, Maryland Alexander S Beliaev, Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington Gabriele Berg, Environmental Biotechnology, Graz University of Technology, Graz, Austria Gavin Collins, Microbial Ecology Laboratory, Department of Microbiology and Environmental Change Institute, National University of Ireland, Galway, Ireland Alison M Cupples, Michigan State University, Department of Civil and Environmental Engineering, East Lansing, Michigan Thomas P Curtis, School of Engineering and Geosciences, Newcastle University, Newcastle, United Kingdom Francis L de los Reyes III, Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, North Carolina Melanie L DiClaudio, Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee Hugh W Ducklow, Marine Biological Laboratory, The Ecosystems Center, Woods Hole, Massachusetts Tim Ford, University of New England, Biddeford, Maine James K Fredrickson, Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington Ji-Dong Gu, Division of Microbiology, School of Biological Sciences, The University of Hong Kong, Hong Kong, China Steve Hamner, Montana State University, Department of Microbiology, Bozeman, Montana Xu Han, Division of Microbiology, School of Biological Sciences, The University of Hong Kong, Hong Kong, China vii 362 INDEX Stoichiometry (Continued) solid waste decomposition, 289–291 Stone, cultural materials deterioration, 144–146 Substrate utilization anaerobic digestion, 266 biotransformation kinetics, 196–198 Subsurface contamination, radionuclides biochemistry, 96–97 mechanistic studies complexation, 106–107 c-type cytrochomes, 99–103 extracellular electron shuttles, 104–106 hydrogenases, 103–104 indirect mechanisms, 107 microbiological transformation electron microscopies and spectroscopies, 107–108 future research issues, 109 mechanistic studies, 99–107 microorganisms for reduction, 97–99 nuclear weapons legacy wastes, 95–96 Sulfate-reducing bacteria (SRB) anaerobic digestion, 262–263 chromium biotransformation, 158 Sulfur-oxidizing bacteria, cultural materials deterioration, 146–147 Surveillance, waterborne pathogen control, 50–52 Syntrophic acetate oxidation, solid waste anaerobic decomposition, 286–291 T4-lysozyme, genetically modified potatoes, 246–248 Technetium ions, radionuclide bioreduction c-type cytochrome mechanisms, 102–103 hydrogenase reduction, 103–104 indirect mechanisms, 107 Temperature anaerobic digestion, 264–265 bacterial activity and, 9–14 bioremediation and, 199 low-energy wastewater treatment, methanogenic systems, 305–306 Terminal electron-accepting processes (TEAPs), benzene, toluene, ethylbenzene, xylene (BTEX) isomers, 188 Terminal restriction fragment length polymorphism (T-RFLP), landfill microbial isolation and nucleic acid extraction, 292–293 Tert-butyl alcohol (TBA), biodegradation and formation of, 189 Tetrachloroethene (PCE), biodegradation mechanisms chlorinated aliphatic hydrocarbons, 190 energy conservation and growth, 181 genetic capability, 193–194 Thermodynamics, bioremediation treatment systems, 195–196 Thermophilic anaerobic digestion agricultural residues, 264 organic fraction of municipal solid waste, 296–297 Three-pot treatment system, water borne pathogen control, 46–50 Toxic algae, genetic characterization, 67–68 Toxin-coregulated pilus (TCP), virulence factor, 36 Transmission electron microscopy (TEM) dissimilatory metal-reducing bacteria, radionuclide bioreduction, 98–99 radionuclide biotransformation, 107–108 Treatability assays, contaminant biodegradation, genetic capability, 192–194 Trichloroethylene (TCE) biodegradation mechanisms, 178–179 chlorinated aliphatic hydrocarbons, 190 cometabolism transformation, 183 energy conservation and growth, 179–180 genetic capability, 193–194 initiation, 184–185 stoichiometry, 196 whole-cell biosensors, 219–223 Tropical regions, climate change and plankton ecology, 19–20 Ultrafiltration, waterborne pathogen detection, 76 Ultramicrobacteria, geomechanical processes, soil ecosystems, 330–331 Ultraviolet (UV) water treatment technologies molecular parasite detection, 72–73 waterborne disease control, 46–50 Uranium, biotransformation, 165–167 Uranium oxides, metal-microbial sorption and transformation, 154–155 Uranyl ions, radionuclide bioreduction, 96–97 complexation, 106–107 c-type cytochrome mechanisms, 100–103 hydrogenase mechanisms, 104 Uranyl reductase isolation, radionuclide bioreduction, c-type cytochrome mechanisms, 99–103 Vaccination programs, waterborne pathogens, 35–36 van der Waals forces, metal-microbial sorption and transformation, 154 van’t Hoff–Arrhenius equation, temperature and ocean bacterial production, 11–14 Vertical density stratification, climate change and plankton ecology, 15–17 Viable but nonculturable cells (VBNCs), E coli detection, 67 Vibrio cholerae See also Cholera outbreaks discovery and characterization, 57 flooding and outbreaks of, 45–46 persistence in aquatic environments, 36–41 VIRADEL viral concentration technique, waterborne pathogen detection, 76 INDEX Virulence factors, Vibrio cholerae, 36 Virus concentration, waterborne pathogen detection, 76 Volatile fatty acids (VFAs), anaerobic digestion microbiology, 260–261 pH levels, 265 Wastewater treatment, low-energy strategies and technologies basic principles, 302 carbon capture, 313–314 conventional and nutrient removal systems, 314–315 extensive systems, 312–313 future research issues, 316–317 known options, 304 methanogenic systems, 305–307 microbial fuel cells, 307–312 applications, 311 biology, 309–310 economics, 310–311 electrochemistry, 310 materials, 309 nutrient removal, 310 research issues, 312 oxidation and disinfection, 315–316 research background, 301–302 technical philosophy, 302–303 Waterborne pathogens Asian Tsunami of December 2004 case study, 46 detection techniques, 60–67 antibiotic-resistant gene detection, 68–69 conventional methods, 58 E coli in water, 63–67 microarrays, 63 microbial source tracking, 69 molecular parasite detection, 72–74 mRNA viability targeting, 62–63 multiplex polymerase chain reaction, 62 new methods, 59–60 parasites, 69–72 polymerase chain reaction, 74–75 recent developments in, 77–83 sample collection and virus concentration, 76–77 toxic algae genetic characterization, 67–68 developing countries’ control of classification and dose definitions, 36–45 363 disease control, 35–36 disease history, 33–34 discovery, characterization and monitoring, 57–60 flooding and, 45–46 infectious dose, 36 new world diseases, 44–45 old and re-emerging pathogens, 36–41 parasites collection, concentration, and purification, 72 detection, 69–72 rotaviruses, 41–42 surveillance, prediction, and modeling, 50–52 transmission cycles, 33–34 treatment options, 46–50 Water circulation systems, in situ bioremediation, 203–204 Water clarity, eutrophication, estuarine/coastal ecosystems, 122 Water storage, waterborne disease treatments and, 46–50 Wet digestion, organic fraction of municipal solid waste, 296–297 Wet reactors, anaerobic digestion plants, 272 Whole-cell biosensors, environmental monitoring, 217–223 Wood cultural materials, microbial deterioration, 143–144 WWE1 bacterial phylum, anaerobic digestion, 263–264 Xanthan, geomechanical processes, soil ecosystems, 330–331 X-ray absorption spectroscopy (XAS) metal-microbial sorption and transformation, 154–155 radionuclide biotransformation, 108 X-ray diffraction (XRD) analysis, metal-microbial sorption and transformation, 155 X-ray fluorescence (XRF), radionuclide biotransformation, 108 X-ray photoelectron spectroscopy (XPS), metal-microbial sorption and transformation, 155 Yeast spores, paper cultural materials deterioration, 139–140 YieF enzyme, chromium biotransformation, 156–158 ATMOSPHERE 780 + 3/yr decomposition 58 R 59 55 GPP 120 rivers VEGETATION 550 + 0.5 92 90.5 SURFACE OCEAN 1.6 dissolved organic 25 dissolved CO2 700 + 0.3 NPP 48 0.4 LITTER & SOIL 1500 42 BIOTA land-use change LAND R 37 11 DEEP OCEAN dissolved organic 1000 dissolved CO2 36,000 + 1.4 0.05 SEDIMENT OCEAN FOSSIL HYDROCARBONS 5000–10,000 Figure 1.1 The global carbon cycle, including human perturbations in the 1990s The quantities in the boxes are the size of the carbon reservoir in petagrams (Pg; 1015 g), with the annual growth, if any, due to the perturbations Note that there is direct exchange between the atmosphere and terrestrial ecosystems, whereas exchange with the ocean is mediated by the physicochemical exchange across the air–sea interface The downward transport of organic carbon, both particulate and dissolved, constitutes the biological pump There is a riverine input of about 0.5 Pg from the land to ocean, balanced by outgassing and burial in sediments Currently, the annual net land sink for atmospheric CO2 is Pg and the ocean sink is 2, leaving an annual net anthropogenic accumulation in the atmosphere of 3.2 Pg (Modified from Houghton, 2007.) Figure 1.2 Multimodel mean of annual mean surface warming (surface air temperature change,◦ C) for scenarios B1, A1B, and A2, and three time periods, 2011 to 2030 (left), 2046 to 2065 (middle), and 2080 to 2099 (right) Stippling is omitted for clarity (see the text) Anomalies are relative to the average of the period 1980–1999 (From IPCC, 2007b, with permission of the IPCC, http://www.ipcc.ch/graphics/graphics.htm.) °C A SST (Future-Control) 90°N 10.0 7.5 5.0 4.0 3.0 2.0 1.5 1.0 0.5 0.0 −0.5 45°N 0° 45°S 90°S 0° 90° 180° 270° −1.0 360° meters shallower B Mixed Layer Depth (Future-Control) 1000 500 300 100 50 30 10 −3 −5 −10 −30 −50 −100 −300 −500 −1000 90°N 45°N 0° 45°S 90°S 0° 90°N 90° 180° 270° 360° deeper (kg m−4) more strat 0.0300 C dρ/d at 50m (Future-Control) 0.0100 0.0030 45°N 0.0010 0.0003 0.0000 0° −0.0003 −0.0010 45°S −0.0030 −0.0100 90°S 0° 90° 180° 270° 360° −0.0300 less strat Figure 1.3 Projected climate-mediated changes in ocean physical forcing (future-control, i.e., 2060–2070 minus the present) from the NCAR Community Climate System Model for (A) sea surface temperature, (B) mixed-layer depth, and (C) upper ocean (50 m) stratification (From Boyd and Doney, 2002, with permission of the American Geophysical Union.) Figure 1.4 Microbial food-web diagram, showing exchanges of carbon in the oceanic surface layer The flows are normalized to NPP = 1.0 The partitioning of flows among compartments is based on the physiological budget model given in Anderson and Ducklow (2001) Note that the carbon flows are dominated by zooplankton grazing (70% of NPP), DOC uptake by bacteria (50%), and heterotrophic respiration (80%) In this depiction the respiration is divided evenly among zooplankton and bacteria, but note that oceanic zooplankton may be dominated by protozoans smaller then 20 μm Here the bacterial production is 12% of the particulate NPP, the fraction approximated by traditional 14 C assays, and a typical value for the open sea (Ducklow, 1999) Solid lines, biomass flows and respiration; dotted lines, dissolved flows; dashed–dotted lines, detrital flows and mortality 43 42 Temperature (1/kT, eV−1) 41 40 39 38 Metabolism (log10 fgC cell−1d−1) = BGE BR BP ↓ BGE −1 −2 −3 Chlorophyll concentration < 0.5 mg m −3 0.5 > Chlorophyll concentration < mg m −3 Chlorophyll concentration > mg m −3 10 20 Temperature (°C) 30 Figure 1.6 Individual rates of bacterial production (BPi ) and respiration (BRi ) versus temperature at three levels of chlorophyll concentration The black line represents the relationship between ln BRi and 1/kT (y = 26.49 − 0.59x) and the colored lines represent the ln BPi –temperature relationships for each data subset (green, y = 18.14 − 0.42x; red, 20.54 − 0.50x; blue, 22.58 − 0.58x) An increase in temperature with no changes in resource availability would result in similar increases in BPi and BRi (i.e., the same BGE: case 1) Resource limitation would slow the rate of increase of BPi with temperature compared to BRi , thus lowering BGE (case 2) (Modified from L´opez-Urrutia and Mor´an, 2007.) mg m−2 A Chlorophyll (Future-Control) 90°N 45°N 0° 45°S 90°S 0° 90°N 90° 180° 270° 360° 270° mmol N m−2 y−1 500 200 100 90 80 70 60 50 40 30 20 10 360° 270° mmol N m−2 y−1 1000 500 100 50 10 −1 −5 −10 −50 −100 −500 360° B N2 Fixation (Control) 45°N 0° 45°S 90°S 90°N 0° 90° 180° C N2 Fixation (Future−Control) 45°N 0° 45°S 90°S 0° 90° 180° 2.00 1.00 0.80 0.60 0.40 0.20 0.10 0.01 0.00 −0.00 −0.10 −0.20 −0.40 −0.60 −0.80 −1.00 −2.00 Figure 1.8 Numerical model simulations of ocean ecosystems using the CSSM (see Figure 1.3) with an off-line, multispecies pelagic ecosystem model for (A) the difference between predicted chlorophyll with warming and a control run (future-control), (B) N2 fixation (control), and (C) N2 fixation (future-control) (From Boyd and Doney, 2002, with permission of the American Geophysical Union.) Figure 2.1 Transmission cycles of lymphatic filariasis, malaria, dracunculiasis, and schistosomiasis (From Fenwick, 2006.) Figure 2.2 Multiple uses of the Ganges River, Varanasi, India, in which E coli O157:H7 has been detected Clockwise, beginning from upper left: religious bathing, commercial laundry washing, washing and watering of cattle, milkmen washing pails in a “least polluted” section of the river, where the fecal coliform count exceeds 104 CPU/1000 mL (From Hamner et al., 2006, 2007.) A B U(VI) U(IV)O2 U(VI) Outer Membrane MtrC OmcA MtrB U (IV )O U (V I) MtrA c -type cytochrome e- eCymA CymA e- e- Menaquinone Menaquinone Cell Membrane Figure 4.2 Working model for cytochrome c –facilitated U(VI) reduction in Shewanella oneidensis MR-1: (A) reduction of U(VI) by periplasmic c-type cytochromes; (B) reduction of U(VI) by outer membrane c-type cytochromes A B Tc(IV)O2 Tc(VII) Tc(VII) Outer Membrane MtrC OmcA MtrB MtrA Tc (V - e- + H CymA H2 & 2e e II) - Tc (IV )O Hydrogenase eMenaquinone Cell Membrane Figure 4.3 Working model for Tc(VII) reduction in Shewanella oneidensis MR-1: (A) outer membrane cytochrome c –facilitated Tc(VII) reduction; (B) periplasmic hydrogenase-facilitated Tc(VII) reduction A B Fe(III)-oxide Fe(III)-oxide Fe(II)soluble Fe(II)soluble Humicred Humicox Flavinred Outer Membrane MtrC MtrC OmcA MtrB Flavinox OmcA MtrB MtrA MtrA e- eCymA e- Menaquinone Cell Membrane Figure 4.4 Working model for shuttle-facilitated Fe(III)-oxide reduction in Shewanella oneidensis MR-1: (A) reduction via an exogenous electron shuttle (humics); (B) reduction via an endogenous electron shuttle (flavins) Greater input of growth limiting nutrient Higher concentration of that nutrient in the water More filamentous algae Less light penetration Increased phytoplankton production and algal blooms Increased zooplankton Increased sedimentation of organic matter More fish above the oxycline Oxygen deficiency & hydrogen sulfide formation More benthic animals above the oxycline Reduced demersal & benthic abundance and diversity Less fish below, and potentially above, the oxycline Less macroalgae and seagrass Less suitable habitat for feeding, predator avoidance and reproduction Figure 5.1 Series of responses within a coastal ecosystem to the increased input of a limiting nutrient Green processes indicate eutrophication Blue processes or conditions indicate increased secondary production Red processes or conditions indicate the negative effects of eutrophication 7,000 120 6,000 Symptoms of Eutrophication 5,000 Developed Countries 4,000 3,000 100 80 Developing Countries 60 40 2,000 20 1,000 1800 1850 1900 Humans millions Legumes/Rice Tg N 1950 2000 2050 Fertilizer Tg N NOx emissions Tg N Figure 5.2 Period of the explosive increase in coastal eutrophication in relation to global additions of anthropogenically fixed nitrogen Most of the symptoms for developed nations were manifested in the 1960s to 1980s (aqua) but are becoming more evident in developing countries with increases in fossil-fuel consumption and use of artificial fertilizers (lavender) (Modified from Boesch, 2002; Galloway and Cowling, 2002.) PHOSPHORUS NITROGEN 4% 8% 12% 37% 16% 25% 52% 9% 5% 18% 14% Sources Corn and soybean crops Other Crops Pasture and range Urban and population-related sources Atmospheric deposition Natural land PHOSPHORUS NITROGEN 10% 9% 22% 69% Riverine Coastal Point Atmospheric N2 Fixation 22% 7% 61% Figure 5.3 Relative proportion of sources or transport mechanisms of nitrogen and phosphorus to the northern Gulf of Mexico from the Mississippi River watershed (upper panels) (from Alexander et al., 2008, http://water.usgs.gov/nawqa/sparrow/gulf findings/) and to the Baltic Proper (from Grimvall and St˚alnacke, 2001.) (B) (A) Figure 6.2 (A) Reddish-brown fox spots in the book Lives of the Brothers Humboldt, published in 1854 (B) Scanning electron micrograph of fungal growth occurring in a fox spot on paper (Adapted from Florian, 1996.) (A) (B) Figure 6.3 Painting of a bull on a wall in Lascaux before (A) and after (B) growth of grayish-black fungi (From Bahn, 2008.) A 107 B 106 107 C D Figure 9.5 S cerevisiae luxCDABE bioreporter assay in a high-throughput 96-well microtiter plate format imaged in real time with a Xenogen IVIS Lumina imaging system Bioluminescence emission (as photon counts per second) by the bioreporters BLYRa (A) and BLYES (B) in response to a range of 17β-estradiol concentrations, and bioreporters BLYRa (C) and BLYAS (D) after exposure to a range of dihydrotestosterone concentrations Each panel shows an 18-well exposure profile ranging from 1μM (top, left well) to 2.5 pM (bottom, right well) (1 : 10 dilutions were performed across each row and 1:2 dilutions down each column) Quantification of bioluminescence output from each well permits formulation of a standard curve and determination of estrogenic or androgenic equivalents present in the sample B antibodies incubation phase dye flow cell volume surface A analytes laser pigtail IO-chip C Figure 9.6 The AWACSS immunosensor (A) is capable of simultaneous multianalyte detection of up to 32 different target contaminants Its detection methodology uses a semiconductor laser flow cell (B) to excite fluorophore-tagged antibody/target analyte complexes bound to the surface of a multisensor optical waveguide chip (C) (From Tschmelak et al., 2005, with permission.) A B cm Figure 9.7 The screen-printed electrode (A) consists of three electrodes: a graphite working electrode in the center onto which the DNA is immobilized, and a silver reference electrode and graphite counter electrode on either side The handheld potentiostat (B) on the right monitors variations in the electrochemical properties of the DNA, such as those occurring upon mutagenic chemical exposure (From Lucarelli et al., 2003, with permission.) Fluorescent tag Substrate strand RNA link Hybridize with catalytic DNA Quencher Catalytic DNA strand Substrate strand cleaved Fluorescence suppressed Pb2+ Fluorescence signal unmasked Figure 9.8 Catalytic beacon fluorosensor for lead (Pb2+ ) In its uninduced state, fluorescence is suppressed due to close quencher proximity Upon exposure to lead, the substrate strand is cleaved, thereby disassociating the fluorescent tag from the quencher to yield a quantifiable fluorescent signal (From Borman et al., 2000, with permission.) .. .ENVIRONMENTAL MICROBIOLOGY SECOND EDITION Edited by Ralph Mitchell and Ji- Dong Gu A JOHN WILEY & SONS, INC., PUBLICATION ENVIRONMENTAL MICROBIOLOGY ENVIRONMENTAL MICROBIOLOGY... www.wiley.com Library of Congress Cataloging-in-Publication Data: Environmental microbiology : second edition / edited by Ralph Mitchell, Ji- Dong Gu p cm Includes bibliographical references and index ISBN... matter is cycled through particulate and dissolved forms and Environmental Microbiology, Second Edition Edited by Ralph Mitchell and Ji- Dong Gu Copyright © 2010 Wiley-Blackwell BACTERIA IN THE GREENHOUSE: