Enzymes in the Environment. Activity, Ecology and Applications

631 Pages·2016·7.45 MB·English

by  Burns R.G.

ISBN: 0-8247-0614-5
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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. Bailey
ix