TM Marcel Dekker, Inc. New York • Basel edited by Richard G. Burns University of Kent Canterbury, Kent England Richard P. Dick Oregon State University Corvallis, Oregon Copyright © 2002 by Marcel Dekker, Inc. All Rights Reserved. Copyright © 2002 Marcel Dekker, Inc. ISBN: 0-8247-0614-5 This book is printed on acid-free paper. Headquarters Marcel Dekker, Inc. 270 Madison Avenue, New York, NY 10016 tel: 212-696-9000; fax: 212-685-4540 Eastern Hemisphere Distribution Marcel Dekker AG Hutgasse 4, Postfach 812, CH-4001 Basel, Switzerland tel: 41-61-261-8482; fax: 41-61-261-8896 World Wide Web http:/ /www.dekker.com The publisher offers discounts on this book when ordered in bulk quantities. For more information, write to Special Sales/Professional Marketing at the headquarters address above. Copyright  2002 by Marcel Dekker, Inc. All Rights Reserved. Neither this book nor any part may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, microfilming, and recording, or by any informa- tion storage and retrieval system, without permission in writing from the publisher. Current printing (last digit): 10987654321 PRINTED IN THE UNITED STATES OF AMERICA Copyright © 2002 Marcel Dekker, Inc. Dedicated to the memory of A. Douglas McLaren Copyright © 2002 Marcel Dekker, Inc. Preface Enzymes that function within plants, animals, and microorganisms are fundamental to life, and their contributions to metabolic pathways and processes have been studied exten- sively. For over 100 years there has been interest in what today is called ecological or environmental enzymology. This aspect of enzymology originates from the work of Woods, who, in 1899, wrote about the survival and function in soil of plant peroxidases following their release from decaying plant roots. Environmental enzymologists recognize that the measured activity may be a composite of reactions taking place in different loca- tions and at different rates. Thus, in addition to being intracellular, enzymes can be extra- cellular and attached to the external surfaces of cells, associated with microbial and plant debris, diffused or actively excreted into the solution phase, and complexed with minerals and organic compounds. Although most extracellular enzymes released from cells are rapidly denatured or degraded, some will survive in solution, if only for short periods. This allows them to complex with adjacent and appropriate substrates and hydrolyze molecules that are too large or insoluble to pass through the cell wall or for which there are no uptake mecha- nisms. These soluble, low molecular mass products can then be utilized as carbon and/ or energy sources by the cell. What this means is that the catalysis of a substrate does not necessarily represent a homogeneous enzymatic reaction but may be the result of isoenzymes derived from plants, microorganisms, or animals, and found in various loca- tions within the soil or sediment matrix. Much ecological enzymology research is driven by the need to understand the bio- logical processes that are important for essential aquatic and terrestrial ecosystem func- tions. These include: organic matter decomposition in relation to both local and global biogeochemistry; mineralization and the release of inorganic nutrients for use by microbes, plants, and animals; complex combinations of reactions that determine and maintain soil Copyright © 2002 Marcel Dekker, Inc. fertility and soil productivity; and the response to and recovery of soil and aquatic systems from various natural and anthropogenic perturbations. Until very recently there have been two large but rather separate camps in the study of ecological enzymology: those involved with aquatic environments and those who have concentrated on soil. In aquatic systems the early work included that by Fermi in 1906, who showed proteolysis activity in stagnant pools, and Harvey in 1925, who suggested that seawater had catalase and oxidase activity. Subsequent researchers, such as Kreps, Elster, and Einsele in the 1930s, showed that aquatic bacteria could excrete enzymes into solution and that these retained a portion of their catalytic activity. Pioneering soil science work by Rotini and Waksman, among others, was focused on catalase, although the 1940s saw a surge in influential papers on urease by Conrad and phosphatases by Rogers. Until the 1950s ecological enzyme research made incremental progress. However, since then there has been an ever-increasing research output on ecological enzymology, and in the past 20 years well over 1000 papers have been published. On the aquatic side, this rapid growth of research was initiated by Overbeck and Reichardt, who demonstrated the role of extracellular phosphatases from bacteria in the mineralization of organic P compounds. They showed that the released phosphate was then used by algae that lacked the ability to directly utilize organic P, thereby showing an important microbial ecological mechanism for extracellular enzyme activity in aquatic systems. They also carried out pioneering research on the temporal and spatial distribution of enzyme activities in lake water. On the soil science front, pioneering work in the 1960s by, among others, McLaren, Kiss, Ross, Galstyan, Voets, and their coworkers gave an impetus that still drives much of today’s research. Soil enzymology up to the late 1970s was summarized in the book Soil Enzymes (Academic Press, 1978). Ecological enzymology can be divided into two broad and overlapping divisions that are both well represented in this book. The first can be categorized as microbial ecology and biochemistry: the study of enzymatic activities in order to better comprehend the processes or mechanisms that are operating in a given system (Chapters 1, 2, and 3). This research may have fundamental objectives targeted toward a greater understanding of highly complex environments such as the rhizosphere (Chapter 4), plant leaves and shoots (Chapter 6), soil surfaces (Chapter 11), or biofilms (Chapter 12). On the other hand, it may have explicit applied goals related to manipulating or preserving the environment in question. These applications include: microbe–plant symbioses (Chapter 5), controlling plant pathogens (Chapter 7), understanding organic matter decomposition and its impact on local and global carbon and nitrogen cycles (Chapters 8, 9, and 10), and environmental remediation of contaminated soils and sediments (Chapters 18, 19, and 20). The second category of ecological enzymology research includes the use of enzymes (or microbial cells) as sensors to detect microbial activity and stresses due to pollution, management, or climatic changes in aquatic and terrestrial ecosystems (Chapters 15, 16, and 17). In this mode, enzymes can be used to assess nutrient turnover, soil health and the presence of plant pathogens, and the progress of remediation of polluted soils and waters. Conventional enzyme assays are attractive as sensors because their integrative nature, specificity of reactions, and relatively simple methodology make them feasible for adoption by commercial environmental laboratories. Alternatively, molecular methods using reporter systems linked to enzymatic processes are being developed for assessing microbial diversity and function (Chapter 14). This book, in part, was the result of the historic conference ‘‘Enzymes in the Envi- ronment: Ecology, Activity and Applications,’’ held in Granada, Spain, in July 1999. This Copyright © 2002 Marcel Dekker, Inc. meeting of over 200 scientists from 34 countries was unique because it brought together scientists from diverse backgrounds around the world who do not normally interact or attend the same professional meetings. Those enjoying the busy sessions included bio- chemists and microbial ecologists who study terrestrial or aquatic systems, and environ- mental and agronomic scientists. Some of the research presented at this meeting was pub- lished in a special issue of Soil Biology & Biochemistry (Vol. 32, Issue 13, 2000). There will be a follow-up conference in Prague in July 2003. An interesting observation arising from the Granada conference was that research into such diverse microbial ecosystems as plant surfaces, soil aggregates, and biofilms of aquatic systems or populations at 1000 meters below the surface of the ocean presented strikingly similar methodological challenges and difficulties in the interpretation of the information derived (Chapter 21). How do you get a representative environmental sample? What are the appropriate assay conditions? What do the measured activities tell us about processes in the environment? What is the microbial and macroecological significance of extracellular enzymes? Are there commercial applications of extracellular enzymes in remediation and nutrient provision? And are there lots of microbes and enzymes out there waiting to be discovered and exploited (Chapter 13)? All these questions and more were heard frequently. The multidisciplinary group also discussed the ‘‘big’’ issues and respon- sibilities of current and future developments in environmental enzymology. Two of the most pressing of these are adequate and sustainable food production in terrestrial and aquatic ecosystems and counteracting global warming through carbon sequestration and other processes in soils and aquatic systems. This book presents 21 reviews by interna- tional experts who attempt to address all these questions and issues. Research progress in ecological enzymology in terrestrial and aquatic ecosystems is brought into the twenty- first century. Richard Burns wishes to thank his wife, Wendy, for her support through this and other writing adventures and Hugo Z., who continues to give a sense of perspective to this confusing life. Richard Dick acknowledges Joan Sandeno for her editing assistance. Richard G. Burns Richard P. Dick Copyright © 2002 Marcel Dekker, Inc. Contents Preface Contributors 1. Enzyme Activities and Microbiological and Biochemical Processes inSoil Paolo Nannipieri, Ellen Kandeler, and Pacifico Ruggiero 2.EcologyofMicrobialEnzymesinLakeEcosystems Ryszard Jan Chro ´ st and Waldemar Siuda 3.EcologicalSignificanceofBacterialEnzymesintheMarineEnvironment Hans-Georg Hoppe, Carol Arnosti, and Gerhard F. Herndl 4.EnzymesandMicroorganismsintheRhizosphere David C. Naseby and James M. Lynch 5.EnzymesintheArbuscularMycorrhizalSymbiosis Jose ´ Manuel Garcı ´ a-Garrido, Juan Antonio Ocampo, and Inmaculada Garcı ´ a-Romera 6.MicrobesandEnzymesAssociatedwithPlantSurfaces Ian P. Thompson and Mark J. Bailey Copyright © 2002 Marcel Dekker, Inc. 7. Microbial Enzymes in the Biocontrol of Plant Pathogens andPests Leonid Chernin and Ilan Chet 8.MicrobiologyandEnzymologyofCarbonandNitrogenCycling Robert L. Tate III 9.EnzymeandMicrobialDynamicsofLitterDecomposition Robert L. Sinsabaugh, Margaret M. Carreiro, and Sergio Alvarez 10.FungalCommunities,Succession,Enzymes,andDecomposition Annelise H. Kjøller and Sten Struwe 11. Enzyme Adsorption on Soil Mineral Surfaces and Consequences for the CatalyticActivity Herve ´ Quiquampoix, Sylvie Servagent-Noinville, and Marie-He ´ le ` ne Baron 12.MicrobesandEnzymesinBiofilms Jana Jass, Sara K. Roberts, and Hilary M. Lappin-Scott 13. Search for and Discovery of Microbial Enzymes from Thermally ExtremeEnvironmentsintheOcean Jody W. Deming and John A. Baross 14. Molecular Methods for Assessing and Manipulating the Diversity of MicrobialPopulationsandProcesses Søren J. Sørensen, Julia R. de Lipthay, Anne Kirstine Mu ¨ ller, Tamar Barkay, Lars H. Hansen, and Lasse Dam Rasmussen 15. Bioindicators and Sensors of Soil Health and the Application of Geostatistics Ken Killham and William J. Staddon 16.HydrolyticEnzymeActivitiestoAssessSoilDegradationandRecovery Tom W. Speir and Des J. Ross 17.EnzymaticResponsestoPollutioninSedimentsandAquaticSystems Sabine Kuhbier, Hans-Joachim Lorch, and Johannes C. G. Ottow 18.MicrobialDehalogenationReactionsinMicroorganisms Lee A. Beaudette, William J. Staddon, Michael B. Cassidy, Marc Habash, Hung Lee, and Jack T. Trevors 19. Isolated Enzymes for the Transformation and Detoxification of Organic Pollutants Liliana Gianfreda and Jean-Marc Bollag Copyright © 2002 Marcel Dekker, Inc. 20. Enzyme-Mediated Transformations of Heavy Metals/Metalloids: ApplicationsinBioremediation Robert S. Dungan and William T. Frankenberger, Jr. 21.EnzymesinSoil:ResearchandDevelopmentsinMeasuringActivities M. Ali Tabatabai and Warren A. Dick Copyright © 2002 Marcel Dekker, Inc. Contributors Sergio Alvarez Department of Ecology, Universidad Auto ´ noma de Madrid, Madrid, Spain Carol Arnosti Department of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina Mark J. Bailey Molecular Microbial Ecology Group, Centre for Ecology and Hydrol- ogy, Oxford, England Tamar Barkay Department of Biochemistry and Microbiology, Cook College, Rutgers University, New Brunswick, New Jersey Marie-He ´ le ` ne Baron Laboratoire de Dynamique, Interactions et Re ´ activite ´ , Centre Na- tional de la Recherche Scientifique, Universite ´ Paris VI, Thiais, France John A. Baross School of Oceanography, University of Washington, Seattle, Wash- ington Lee A. Beaudette Department of Environmental Biology, University of Guelph, Guelph, Ontario, Canada Jean-Marc Bollag Laboratory of Soil Biochemistry, Center for Bioremediation and De- toxification, The Pennsylvania State University, University Park, Pennsylvania Margaret M. Carreiro Department of Biology, University of Louisville, Louisville, Kentucky Copyright © 2002 Marcel Dekker, Inc. [...]... Amidase l-Glutaminase Urease Nitrate reductase Range Reference 1. 33– 312 5.00 µmol glucose g 1 24 h 1 0.4–80.0 µmol glucose g 1 24 h 1 0. 61 13 0 µmol glucose g 1 h 1 0.09–405.00 µmol p-nitrophenol g 1 h 1 0.06–50.36 µmol p-nitrophenol g 1 h 1 (14 , 49, 50, 51, 52, 53, 54, 55) (14 , 56, 57) 0.5–2.7 µmol p-tyrosine g 1 h 1 0.08 1. 73 µmol leucine g 1 h 1 0.07–0.86 µmol N-NH 3 g 1 h 1 0. 31 4.07... 1 h 1 Phospholipase C Other enzyme activities Dehydrogenase 5.02–8 .15 µg p-nitrophenol g 1 h 1 (14 , 42, 43, 51, 86, 92, 93, 94, 95) (96, 97) (42, 43, 69, 86, 94, 95, 98, 99, 10 0, 10 1) (14 ) Fluorescein diacetate hydrolysis Catalase a 0.002 1. 073 µmol TPF g 1 24 h Ϫ1a 0.003–0.0 51 µmol INF g 1 24 h Ϫ1a 0 .12 –0.52 µmol fluorescein g 1 h 1 (14 , 42, 50, 61, 69, 92, 93, 10 2, 10 3, 10 4, 10 5) (10 2, 10 5)... hydroquinone (13 1 ,13 2) Similar results were obtained when pyrogallol was used as the precursor (13 3) In systems containing phenolic compounds and amino acids, Ca-illite catalyzed the formation of N-containing humic acids (13 4) The yields and nitrogen contents depended on the kind of amino acids used In 19 97 Bosetto and colleagues (13 5) studied the formation of humiclike polymers from l-tyrosine and homoionic... variable effects, depending on soil and enzyme assay conditions (46 ,12 0 ,16 2 ,16 3) The kinetic analysis of the decline in the activity of l-histidine NH 3-lyase during a 96-h incubation period with a biostatic agent (toluene or Na azide) was described as a two-component model in which each component declined according to the first-order kinetics (16 4 ,16 5) The decline of the labile and the stable components... µmol N-NH 3 g 1 h 1 0.24 12 .28 µmol N-NH 3 g 1 h 1 1.36–2.64 µmol N-NH 3 g 1 h 1 0 .14 14 .29 µmol N-NH 3 g 1 h 1 1.86–3.36 µg N g 1 h 1 (14 , 50, 51, 67, 68, 69, 70) (52, 53, 58, 59) (42, 56, 57, 60, 61, 62, 63, 64, 65, 66) (56, 57, 61) (60) (14 , 42, 69, 71, 72, 73, 74) (60, 65, 75, 76) (60, 65, 75) (75, 77) (42, 69, 78, 79, 80, 81, 82, 83, 84) (14 ) Many enzyme activities have been detected in. .. reliable assay either has not been developed or has been developed, but long after the initial report For example, hydrolysis of laminarin and inulin occurs in soil (11 0 11 2), but there is no specific assay protocol l-glutaminase, which catalyzes the hydrolysis of l-glutamine, yielding l-glutamic acid and NH 3 , was first detected in soil by Galstyan and Saakyan (11 3), but a simple and rapid method was... Dekker, Inc CO 2 and NH 3 occurred and were followed by polycondensation of semiquinone radicals, aliphatic fragments, and amino acids to form humic polymers Similar mechanisms have been proposed in systems involving phenoloxidase enzymes The deamination of amino acids, such as serine, phenylalanine, proline, methionine, and cysteine by birnessite, and the role of pyrogallol in influencing their mineralization... both L- and D- glutamic acid The PLP-Cu 2ϩ-smectite has acted as a ‘‘pseudoenzyme’’ wherein the PLP was active and independent of the protein matrix of the enzyme and the silicate structure substituted for the apoenzyme (15 7) The deamination of glutamic acid also occurred in the presence of montmorillonite saturated with various cations and in the absence of any cofactor The reaction products were α-hydroxyglutaric... determine the different locations of the enzyme activities C Soil Minerals as Catalysts (Pseudoenzymes) in Biochemical Reactions Soil minerals can affect the fate of biochemical compounds in soil in at least three main ways: (1) incorporation of N-, P-, and S-bearing organics into the structural network of mineral colloids and adsorption of these organics to their surface: consequently the dynam- Copyright... soil for the 0-, 5 0-, and 10 0-t sewage sludge ha 1 soil treatments, respectively In the case of dry soils, significant correlations between the phosphatase activity and the ATP content were observed at 0- ( p Ͻ 0.05) and 10 0- ( p Ͻ 0. 01) t sewage sludge ha 1 treatments (96) Negative intercepts were observed at 0- and 50-t sewage sludge ha 1 treatments, and they were postulated to be due to the absence . g 1 (60) h 1 Arginine deaminase 0.07–0.86 µmol N-NH 3 g 1 h 1 (14 , 42, 69, 71, 72, 73, 74) l-Asparaginase 0. 31 4.07 µmol N-NH 3 g 1 h 1 (60, 65, 75, 76) Amidase 0.24 12 .28 µmol N-NH 3 g 1 (60,. 61) g 1 h 1 Enzymes involved in N trans- formations Protease (casein-hydrolyzing 0.5–2.7 µmol. p-tyrosine g 1 (14 , 50, 51, 67, 68, 69, 70) proteases) h 1 Dipeptidase 0.08 1. 73 µmol leucine. 4, Postfach 812 , CH-40 01 Basel, Switzerland tel: 4 1- 6 1- 2 6 1- 8 482; fax: 4 1- 6 1- 2 6 1- 8 896 World Wide Web http:/ /www.dekker.com The publisher offers discounts on this book when ordered in bulk quantities.