Soil Microbiology and Biochemistry

277 Pages·1989·5.327 MB·English

by  Eldor A. Paul (Auth.)

Ε. Α. Paul
Department of Crop and Soil Sciences
Michigan State University
East Lansing, Michigan
F. E. Clark
Agricultural Research Service
United States Department of Agriculture
and
Colorado State University
Fort Collins, Colorado
Soil Microbiology
and Biochemistry
Academic Press, Inc.
Harcourt Brace Jovanovich, Publishers
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United Kingdom Edition published by
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Library of Congress Cataloging-in-Pubiication Data
Paul, Eldor Alvin.
Soil microbiology and biochemistry.
Includes bibliographies and index.
1. Soil microbiology. 2. Soil biochemistry.
I. Clark, Ε Ε. (Francis Eugene), Date.
II. Title.
QR111.P335 1988 651.4'6 88-7681
ISBN 0-12-546805-9 (alk. paper)
PRINTED IN THE UNITED STATES OF AMERICA
88 89 90 91 9 8 7 6 5 4 3 21
Preface
The driving force in the formation of the alHed fields of soil microbiology
and soil biochemistry was the need to know about the organisms and re­
actions occurring in soil. Among the natural processes initially of concern
and that now have been given roughly a full century of investigation are
those of carbon mineralization, nitrogen fixation, sulfur oxidation, my­
corrhizal formation, nitrification, and denitrification. As knowledge has
accumulated about these and other soil processes, so too has the need
intensified for an integrated level of approach to applied problems in
agronomy, forestry, and environmental science. That has been our ob­
jective in the current text. In the writing of the several chapters, a process-
oriented approach is used to provide the student with a unified perspective
on nutrient cycling and the fundamental soil processes that are driven by
microorganisms.
The text is aimed at the advanced undergraduate already holding some
background in biology and chemistry and with some knowledge of the
environment, especially of soils. In a book such as this, it is impossible
to present all the necessary background information. Chapter 2, on the
soil habitat, and Chapter 4, on soil biology, are offered as summarizing
orientations. Chapters 1, 3, and 5 also present background material. Sup­
plemental reading lists and a brief glossary are also offered as a conven­
ience to the student.
Problems posed by current stresses on global ecosystems emphasize
the need for good management of agricultural and forestry resources. Ad­
vances being made in the genetic control of microbial capabilities offer
great potential for altering interactions between host plants and micro­
organisms. Our hope for this text is that it will give the student an adequate
introduction to soil microbiology and soil biochemistry, and especially an
understanding of the basic microbial processes in soil. Given that, the
student should be able to envision possibilities for field applications of
forthcoming advances in our area of science.
xii Preface
Acknowledgments
The production of a volume such as this can only be accomplished with
much assistance. We thank Scott Smith, William Horwath, Ken Horton,
and David Harris for assistance in editing. The original artwork is credited
to the craftsmanship of Phyllis Paul and Marlene Cameron. Linda Salemka
is thanked for the manuscript preparation and placement onto the computer
disk. Francis Clark, formerly an employee of the Agricultural Research
Service, and currently a collaborator, thanks his co-workers for their many
helpful suggestions.
ELDOR A. PAUL
FRANCIS E. CLARK
Chapter 1
Soil Microbiology and
Biochemistry in
Perspective
Definition and Scope
Soil microbiology is the study of organisms that live in the soil. The main
thrust is on their metabolic activities and their roles in the energy flow
and cycling of nutrients associated with primary productivity. Additionally,
the discipline is concerned with the environmental impacts, both favorable
and unfavorable, of soil organisms and the processes they mediate. To a
large extent soil microbiology, if viewed from a mechanistic viewpoint,
is soil biochemistry. The codisciplines were initially concerned with the
microscopic life in the soil but became extended to include organisms of
macroscopic size that reside in soil and participate in soil dynamics. Cur
rently included in the soil biota together with the unicellular organisms
are the soil-dwelling small invertebrates called the soil mesofauna. These
may be either microscopic or macroscopic. Some protozoa are macro
scopic, and many algae and fungi form communal or ñlamentous structures
that are measurable in centimeters or decimeters.
The micro- and mesofauna play ancillary roles in organic matter trans
formations, but they lack the wide range of enzyme capabilities of the soil
microflora. Inclusion of the small invertebrates within the scope of soil
microbiology was only slowly accomplished; a similar delay occurred with
respect to mycorrhizas. For many years only relatively few mycologists
engaged in the study of the fungus-root association known as a mycorrhiza.
As soil microbiologists became more concerned with nutrient transfers,
they realized that the study of mycorrhizas was a central rather than a
peripheral part of their discipline.
1. Soil Microbiology and Biochemistry in Perspective
Pioneering Contributions
Although such phenomena as the spontaneous fermentation of fruit juices
to yield wine and the souring of drawn milk have been observed by humans
since the beginning of historical time, soil microbiology as a science can
be assigned the same year of origin commonly given to bacteriology and
protozoology. In 1676, the Dutch lens grinder Antonius van Leeuwenhoek
reported that he had seen small animalcules in natural waters and in water
in which pepper had lain. Inasmuch as his observations were on micro­
organisms in the presence of decaying plant material, he could possibly
be designated the father of soil microbiology. This designation, however,
is commonly and justifiably given to Sergei Winogradsky (1856-1953) in
recognition of his many contributions to the newly emerging science. Es­
pecially noteworthy was his discovery of the nitrifying bacteria and their
role in the phenomenon of nitrification. This resulted in the concept of
microbial autotrophy, wherein inorganic substrates are used as a source
of growth energy by microorganisms.
Contemporaries of Winogradsky must be credited with another landmark
discovery, namely, the formation of mycorrhizas by fungi and plant roots.
Although eariier workers had noted the occurrence of fungus-plant root
associations, it remained for Pfeffer (1877) to recognize the symbiotic na­
ture of the association. A. B. Frank (1885) coined the term mycorrhiza;
he later distinguished between ectotrophic and endotrophic mycorrhizas.
The last half of the nineteenth century saw other important discoveries
concerning microbial processes. These included symbiotic nitrogen fix­
ation, denitrification, sulfate reduction, and asymbiotic nitrogen fixation.
The researches of Louis Pasteur (1830-19(X)) on microbial fermentations
were of special significance; they led to the delineation of anaerobic me­
tabolism. All multicellular forms of life, plant and animal, are dependent
on an aerobic metabolism. Some soil bacteria are capable only of aerobic
metabolism; others, only of anaerobic metabolism; while still others can
switch from one form to the other. Several of Pasteur's predecessors had
recognized that yeasts are involved in fermentations, but it remained for
Pasteur to demonstrate that the production of alcohols and organic acids
by microorganisms is linked to a basic metabolism that permits life without
air. Büchner (1897) showed that yeast cells could be disrupted to yield a
cell-free liquid capable of causing alcoholic fermentation; thus he must
be credited for pioneer work in microbial enzymology.
In the years between the observations of Leeuwenhoek and those of
Winogradsky, Pasteur, and contemporaries, there were general or back­
ground contributions, such as the disproving of spontaneous generation,
the linking of microorganisms to plant and animal diseases, and great
Early Twentieth Century
progress in the descriptive taxonomy of soil organisms. Linnaeus (1707-
1778), the founder of binomial taxonomy, recognized the existence of mi­
croscopic forms of life but skirted a taxonomic quagmire by simply placing
all microbes in a group designated ''Chaos." Currently, microbial tax­
onomy remains controversial, but at least it has progressed from chaotic
to utilitarian.
Soil Microbiology in the Early Twentieth Century
By the opening of the current century, the young science of soil micro­
biology was firmly established. Major research emphasis was on symbiotic
nitrogen fixation, organic matter decomposition, and mineral nitrogen
transformations. Successes in legume inoculations led to several premature
attempts of other practical applications. Kluyver (1956) observed that
''since Pasteur's startling discoveries of the important role played by mi­
crobes in human affairs, microbiology as a science has always suffered
from its eminent practical implications." Around the turn of the century,
considerable effort was expended in making census counts of soil organ­
isms and attempting to use such counts as indices of soil fertility. This
concept failed to take into account that, at best, the number of propagules
capable of forming viable colonies on agar plates represents only a small
percentage of the total microbial population, and also, that there are many
other determinants of soil fertility, any one of which, under Liebig's law
of the minimum, may restrict plant productivity. Attempts were also made
to increase asymbiotic nitrogen fixation by inoculating nitrogenase-pro-
ducing organisms into soil. These attempts failed because of the lack of
knowledge concerning microbial competition. They, however, were at least
partly responsible for transferring attention from the test tube to what
microbes do or do not accomplish in the field.
The establishment of the general relationship between microbial growth
and the transfers and transformations of organic nitrogen was among the
early achievements. The carbon:nitrogen ratio required for plant residue
degradation without a net tie-up (immobilization) of nitrogen was deter­
mined as approximately 25:1, and the effects of environmental factors on
differential rates of plant decomposition were defined. The possibility of
soil biota turnover with a subsequent release of nitrogen during decom­
position was recognized. In summarizing the early work, Harmsen and
van Schreven (1955) wrote, "The study of the general course of miner­
alization of organic nitrogen in soil was practically completed before 1935.
It is suφrising that many of the modern publications still consider it
worthwhile to consider parenthetically observations dealing with those
1. Soil Microbiology and Biochemistry in Perspective
entirely solved problems." These authors, however, then pointed out that
the relationships between carbon and nitrogen and the effects of envi­
ronmental factors had to be determined for each soil type. This indicated
that the underlying principles were not understood.
Progress and Diversification in Recent Years
With time, the scope of soil microbiology was gradually expanded from
primary concern with nitrogen and organic matter to such areas as soil
enzymes, the rhizosphere microflora, microbial participation in soil struc­
ture formation, degradation of manmade pesticides and other recalcitrants,
microbial ecology, transformations of metals, and microbial impacts on
the environment. Microbiologists participated in the empirical approach
to agricultural productivity and range and forest management that coin­
cided with the advent of cheap and available energy for tillage and fertilizer
production during the period 1950-1980. This period also saw the devel­
opment of tracer techniques. Norman (1946) wrote, "The availability of
the stable nitrogen isotope '^N and the carbon isotope '^C will make it
possible to verify quantitatively the various nitrogen transformations in
relation to the carbon cycle and should aid greatly in establishing the forms
of nitrogen present in the soil."
Jansson (1958) noted the preferential utilization of NH4^ rather than
NO3' by microorganisms and the feasibility of using mathematical equa­
tions to describe mineralization-immobilization interactions. The literature
in the 1960s documented the introductory work on the characterization
of soil organic matter (SOM) into biologically meaningful fractions in ad­
dition to the classical fractionation techniques that provided humic and
fulvic acids. The concept of a small, nutritionally active fraction with a
significantly faster turnover than that of the large recalcitrant fraction
greatly improved the inteφretation of SOM dynamics and led to realistic
mathematical models of SOM turnover. It also assisted in the development
of soil tests for the potential bioavailability of nitrogen. The recognition
of large and significant organic phosphorus and sulfur cycles coincided
with the incoφoration of soil biology and enzymology into ecosystems
research.
Significant contributions to genetics, including bacterial genetics, oc­
curred during the first half of this century. Griffith (1928), presented the
first evidence of bacterial transformation by showing that avirulent, non­
capsulated cells of Streptococcus pneumoniae could be transformed to
virulent, capsulated cells by injecting host animals with heat-killed virulent
cells together with live, avirulent cells. In 1941, N. A. Krassilnikov pub-
Progress and Diversification
lished results showing the transformation of a noninfective Rhizobium to
an infective one. There was, however, some question about the purity of
his inoculum. The work of Avery et al. (1944) on the chemical nature of
the substance inducing transformation was followed by the Nobel Prize-
winning description of the structure of deoxyribonucleic acid (DNA) by
Crick and Watson in 1953. The mechanism of heredity control was shown
to be a sequence of four nucleotides arranged as a two-stranded molecule
in a double helix. The work in the mid-1970s on plasmid biology, DNA
sequencing (the determination of the specific sequence of nucleotide bas­
es), and the discovery of transcription enzymes set the stage for genetic
engineering techniques. These have great potential for use in agricultural
and environmental microbiology. Some of the possibilities are discussed
in later paragraphs.
Areas of interest in soil microbiology and shifts therein within soil sci­
ence are reflected in the Division III publications in the Soil Science Society
of America Journal during the years 1946-1985 (Fig. 1.1). The histograms
show only six categories, but "miscellaneous" covers a dozen or so topics
(e.g., fauna, rhizosphere, enzymes, census counts, antibiotics, mycor­
rhizas), any of which, if classed separately, would include only about 1%
of the total number of publications in each decade. Over the time span
covered, studies on nitrogen fixation were at a low ebb for the middle
decades, during which time studies on soil structure and on pesticide deg­
radations peaked and then subsided. Emphasis on soil structure studies
occurred during years in which much attention was being given to the use
of soil additives for promoting soil structure formation. Emphasis on pes­
ticide studies occurred during years characterized by environmental con­
cerns and, in the United States, the establishment of the Environmental
Figure 1.1. Soil microbiology publications in the So/7 Science Society of America Journal for
the years 1946-1985.
100 h
'Miscelloneous
g 80 ^Soil Structure
Pesticide
Microbiology
Organic Matter
e(f)
and Residues
40 •Nitrogen
c - _-Ί Transformations
o 20 -
•Dinitrogen
Fixotion
1946-55 1956-65 1966-75 1976-85