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Douglas McLaren Preface Enzymes that function within plants, animals, and microorganisms are fundamental to life,andtheircontributionstometabolicpathwaysandprocesseshavebeenstudiedexten- 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 followingtheirreleasefromdecayingplantroots.Environmentalenzymologistsrecognize thatthemeasuredactivitymaybeacompositeofreactionstakingplaceindifferentloca- tionsandatdifferentrates.Thus,inadditiontobeingintracellular,enzymescanbeextra- cellularandattachedtotheexternalsurfacesofcells,associatedwithmicrobialandplant debris,diffusedoractivelyexcretedintothesolutionphase,andcomplexedwithminerals 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 derivedfrom plants, microorganisms, oranimals, and foundin various loca- tions within the soil or sediment matrix. Muchecologicalenzymologyresearchisdrivenbytheneedto understandthebio- 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;mineralizationandthereleaseofinorganicnutrientsforusebymicrobes, plants, andanimals; complexcombinations ofreactions thatdetermine and maintainsoil v vi Preface fertilityandsoilproductivity;andtheresponsetoandrecoveryofsoilandaquaticsystems from various natural and anthropogenic perturbations. Untilveryrecentlytherehavebeentwolargebutratherseparatecampsinthestudy ofecologicalenzymology:thoseinvolvedwithaquaticenvironmentsandthosewhohave 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,andEinseleinthe1930s,showedthataquaticbacteriacouldexcreteenzymesinto solutionandthattheseretainedaportionoftheircatalyticactivity.Pioneeringsoilscience workbyRotiniandWaksman,amongothers,wasfocusedoncatalase,althoughthe1940s 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, andinthepast20yearswellover1000papershavebeenpublished.Ontheaquaticside, thisrapidgrowthofresearchwasinitiatedbyOverbeckandReichardt,whodemonstrated the role of extracellular phosphatases from bacteria in the mineralization of organic P compounds.Theyshowedthatthereleasedphosphatewasthenusedbyalgaethatlacked theabilitytodirectlyutilizeorganicP,therebyshowinganimportantmicrobialecological 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.Onthesoilsciencefront,pioneeringworkinthe1960sby,amongothers,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 ecologyandbiochemistry:thestudyofenzymaticactivitiesinordertobettercomprehend theprocesses ormechanismsthatare operatinginagiven system(Chapters1,2, and3). 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(Chapter6),soilsurfaces(Chapter11),orbiofilms(Chapter12).Ontheotherhand, it mayhave explicit appliedgoals related to manipulating or preservingthe environment inquestion.Theseapplicationsinclude:microbe–plantsymbioses(Chapter5),controlling plant pathogens (Chapter 7), understanding organic matter decomposition and its impact onlocalandglobalcarbonandnitrogencycles(Chapters8,9,and10),andenvironmental remediation of contaminated soils and sediments (Chapters 18, 19, and 20). Thesecondcategoryofecologicalenzymologyresearchincludestheuseofenzymes (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 foradoptionbycommercialenvironmentallaboratories.Alternatively,molecularmethods using reporter systems linked to enzymatic processes are being developed for assessing microbial diversity and function (Chapter 14). Thisbook,inpart,wastheresultofthehistoricconference‘‘EnzymesintheEnvi- ronment:Ecology,ActivityandApplications,’’heldinGranada,Spain,inJuly1999.This Preface vii meeting of over 200scientists from 34 countries was uniquebecause 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- mentalandagronomicscientists.Someoftheresearchpresentedatthismeetingwaspub- lishedinaspecialissueof SoilBiology &Biochemistry(Vol. 32,Issue13,2000).There will be a follow-up conference in Prague in July 2003. An interesting observation arising from the Granada conference was that research intosuchdiversemicrobialecosystemsasplantsurfaces,soilaggregates,andbiofilmsof 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 informationderived(Chapter21).Howdoyougetarepresentativeenvironmentalsample? Whataretheappropriateassayconditions?Whatdothemeasuredactivitiestellusabout processes in the environment? What is the microbial and macroecological significance of extracellularenzymes? Arethere commercial applicationsof extracellular enzymesin remediationandnutrientprovision?Andaretherelotsofmicrobesandenzymesoutthere waitingto bediscovered andexploited (Chapter13)? Allthese questionsandmore were heardfrequently.Themultidisciplinarygroupalsodiscussedthe‘‘big’’issuesandrespon- 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 inecologicalenzymologyinterrestrialandaquaticecosystemsisbroughtintothetwenty- 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 Contents Preface iii Contributors xiii 1. Enzyme Activities and Microbiological and Biochemical Processes in Soil 1 Paolo Nannipieri, Ellen Kandeler, and Pacifico Ruggiero 2. Ecology of Microbial Enzymes in Lake Ecosystems 35 Ryszard Jan Chro´st and Waldemar Siuda 3. Ecological Significance of Bacterial Enzymes in the Marine Environment 73 Hans-Georg Hoppe, Carol Arnosti, and Gerhard F. Herndl 4. Enzymes and Microorganisms in the Rhizosphere 109 David C. Naseby and James M. Lynch 5. Enzymes in the Arbuscular Mycorrhizal Symbiosis 125 Jose´ Manuel Garc´ıa-Garrido, Juan Antonio Ocampo, and Inmaculada Garc´ıa-Romera 6. Microbes and Enzymes Associated with Plant Surfaces 153 Ian P. Thompson and Mark J. 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