Soil microbiology

Fungi in certain forms can be readily seen without a microscope; thus, they received early study. The first book solely about fungi ("Theatrum Fungorium") published in 1675 by J. F. van Starbeck drew heavily on the drawings of Charles de'Egeluse prepared as early as 1601 (see Atlas, 1984). In 1665, Hooke published a work on the fruiting bodies of fungi, and by 1724, spores were known as fungal reproductive agents. Fungus-root associations were noted by earlier authors, but in 1877, Pfeffer recognized their symbiotic nature, and in 1885, Franck coined the word "mycorrhiza." Franck later distinguished between ecto and endo associations; a classification that is still applicable in present, extensive literature on this subject. In 1886, Adametz isolated fungi from soil and gave them names. The first detailed classification of soil fungi was conducted by Oedemans and Koning in 1902 (see Waksman, 1932). In the 1920s, Charles Thom made a detailed study of soil fungi, especially Penicillium and Aspergillus, the dominant soil fungi on most agar plates. Waksman also published extensively on soil fungi and actinomycetes.

Leeuwenhoek (1632-1723) is recognized as being the first to see bacteria in his self-designed microscopes. He observed the small animalcules in natural water and in water amended with a substrate (pepper or meat broth). The comprehensive classification system produced by Linnaeus in 1743 perhaps foretold the modern difficulties in bacterial classification when he placed all the organisms seen by Leeuwenhoek in infusions of vegetable matter and meat broth into the genus Chaos. In 1776, Nagelli (see Atlas, 1984) suggested that bacteria be placed into their own class entitled Schizomycetes. The work of Warington, Lawes, and Gilbert established the biological nature of many of the processes involved in N transformations, especially those involved with the growth of leguminous crops. Pasteur (1830-1890), in discrediting the theory of spontaneous generation, laid the foundation for microbiology. Although trained as a chemist, he developed vaccines for rabies and investigated many food microbiology problems. Pasteur and Liebig had both postulated that the process of nitrification was bacterial in nature. While studying sewage purification by land filters, Schloesing and Müntz found that the ammonia content of sewage passed through a sand filter did not alter for 20 days. After this period, ammonia was changed to nitrate, but the process could be stopped by a small amount of chloroform. The process could be restarted by soil extract, thus proving that this process was due to microorganisms or, as they said, "organized ferments."

S. Winogradsky (1856-1953) is recognized as the founder of soil microbiology for his contributions to nitrification, anaerobic N2 fixation, sulfur oxidation, and microbial autotrophy (Winogradsky, 1949). He succeeded in isolating two bacterial types involved in nitrification with the keen insight that they obtained their C from CO2. He thus also established autotrophy in microorganisms. In the period 18721876, Cohn published the first comprehensive study of the bacterial content of soil. Hellriegel and Wilfarth, in 1888, grew peas in the absence of a fixed N supply, showing that legumes obtained their N from the atmosphere, whereas oats did not have this capability. They knew that the peas had nodules, but could not isolate the bacteria within. Beijerinck, in 1888, isolated the bacteria that he called "Bacillus radicicola" (now usually called "Rhizobium"). This showed the dependence of the N cycle on bacteria. The N cycle was completed when Goppelsröder observed that nitrates were reduced to nitrites in the presence of soil organic matter. In 1868, Schoenbein ascribed the reaction to bacteria and Gayon and Dupetit further developed the knowledge that led to denitrification studies.

The latter half of the 19th century saw more details on microbial processes including symbiotic and asymbiotic N2 fixation, denitrification, and sulfate reduction and oxidation. The research on fermentation led to the delineation of anaerobic metabolism. Waksman, in his 1952 textbook "Soil Microbiology," gives a detailed account of the early contributions and also published photographs of many of our academic forefathers in soil microbiology. His 1932 book gives detailed historical references in each of the chapters, as well as a listing of the textbooks on the various topics to that date. He gives credit (together with Winogradsky) for the foundation of soil microbiology as a discipline to Martinis Beijerinck (1851-1931), who not only extracted the first viruses from plants, but also isolated many N2-fixing organisms and developed enrichment techniques. Basic and applied sciences were as intertwined in the beginning of our science as they are now. Winogradsky and Beijerinck are also recognized as founding members of microbial physiology and microbial ecology.

The first textbook to include soil microbiology was that of Löhnis, "Vorlesunen über Landwirtschaftliche Bäkteriologi," published in 1910 and 1913. English readers can gain an insight into its contents in the English version he published together with E. B. Fred in 1923, entitled "Textbook of Agricultural Bacteriology." That text contains very readable accounts of bacteria, fungi, and protozoa and a good discussion of relationships of microorganisms to their environment. J. G. Lipman (1874-1939), who established the Department of Soil Chemistry and Bacteriology at Rutgers University in 1901, was especially interested in the effects of soil organisms on soil fertility and plant growth. His 1911 book entitled "Bacteria in Relation to Country Life" was the first American treatise in this field. Waksman (1952) named the period from 1890 to 1910 as the Golden Age of soil microbiology when representatives of the soil biota carrying out the major soil and biogeochemical processes were identified. The identification of at least representative members of the microorganisms mediating soil fertility and nutrient transformations led to the belief that this knowledge could do for agriculture what the identification of major disease organisms did for medical treatment.

Successes in legume inoculation led to several premature attempts to alter soil C and N transformations by inoculation and to relate microbial numbers to soil fertility. This discussion continues to this day in the many questions concerning biodiversity and ecosystem functioning addressed later in this volume. The attempts to inoculate bacteria, other than symbionts, and control microbial pathogens of plants were seldom successful because of the lack of knowledge of microbial ecology and the other controls involved. These studies did, however, help transfer attention from pure cultures and laboratory investigations to field experiments and the need for replication to account for soil heterogeneity. This period also contained the interesting conclusion that if an organism did not grow on a gelatin or agar plate, it could not be important and thus was not worth studying.

The years from 1910 to the Second World War witnessed the employment of soil microbiologists in numerous new institutions in many parts of the world. This led to a better knowledge of the global distribution of, and management effects on, organisms capable of growth in the laboratory medium. The development and use of direct microscopy led to the realization that approximately only 1% of the soil population could be grown on laboratory media. The failure of inoculants, except in the case of symbiotic N2 fixation, to create meaningful management effects was a worry at that time. It is only now that we realize the huge number of unidentified organisms and that the unknown interactions between them and their environment (ecology) explain the often observed lack of impact of introduced organisms.

It was at first assumed that bacteria were the major players in soil fertility and decomposition as typified by the books of Löhnis in 1910 and Löhnis and Fred in

1923. In 1886, Adametz showed that fungi are abundant in soil. Additionally, Hiltner and Stormer had studied actinomycetes, which at that time were thought to be different from the bacteria. Cutler had studied the protozoa, and Russell and Hutchinson developed the theory that by consuming bacteria, protozoa could control the soil population and, thus, soil fertility. The early textbooks took as much license with their titles as modern ones. The Lohnis and Fred publication on agricultural bacteriology included extensive sections on the protozoa and fungi discussed under sections such as "Bacteria and related microorganisms." Waksman's "Soil Microbiology" included sections we would today call biochemistry. The effects of environmental factors on the rate of soil organic matter decomposition were described by Waksman in his 1932 book entitled "Principles of Soil Microbiology" and the Waksman and Starkey 1931 book entitled "The Soil and the Microbe."

The period between the two world wars saw work on microbial interactions and nutrient transformations. Fred, Baldwin, and McCoy's 1932 comprehensive volume on "Root Nodule Bacteria and Leguminous Plants" set the stage for the continued success in symbiotic N2 fixation. The C:N ratio required for plant-residue decomposition without N immobilization was determined as approximately 25:1, a number that is still appropriate unless large amounts of poorly degradable residues are involved, as in forest litter. Attempts to measure many of the microbial processes in soil were frustrated by the inaccuracy of the measurement techniques relative to the large stock of nutrients in soil. Waksman (1932) commented that it was difficult to measure N2 fixation by free-living organisms at levels less than 40 lb per acre, which was (and still is) the inherent error in the Kjeldahl or other methods of measuring total N. The Finnish scientist A. I. Virtanen received the 1945 Nobel Prize in Chemistry for his major contributions to legume nutrition, especially the role of rhizobia in symbiotic N2 fixation. Lie and Mulder (1971), in "Biological Nitrogen Fixation in Natural and Agricultural Habitats," provide a record of the many advances made in that field.

The Second World War led to a concentration on the war effort. This was, however, not without its success as witnessed by the use of the fungal antibiotic, penicillin, and the development of streptomycin, for which Waksman received the Nobel Prize in Medicine in 1952. The war also resulted in studies to overcome food spoilage and rotting of clothes, as well as the beginnings of biological warfare in both preventive and causative formats. Alexander's 1961 and 1977 "Introduction to Soil Microbiology" continued the general organization utilized by Waksman in his earlier volumes. He organized the section on the soil environment and bacteria, actinomycetes, fungi, algae, protozoa, and viruses into a section entitled "Microbial Ecology" and recognized the multitude of microbial and microbial-plant interactions. The 1960s saw an influx of new scientists that worked on symbiotic and asymbiotic N2 fixation, S cycling, the rhizosphere, mycorrhizas, and the effects of herbicides, pesticides, and pollutants on the microbial population. The mycorrhizal history to 1969 can be found in Harley (1969). The use of 15N and alternate substrates and inhibitors for specific enzyme interactions made possible for the first time the quantification of the processes in the N cycle at the levels that they occur in soil. However, method availability still hindered testing of concepts regarding microbial populations and diversity, and it was not until the advent of nucleic acid methodology, automated biochemical measurements, such as phospholipid fatty analysis (PLFA), computers, and modeling that the great thrust of knowledge covered in the subsequent chapters of this volume could come to fruition.

Volumes on soil microbiology include Subba Rao (1999), "Soil Organisms and Plant Growth," 4th ed.; Killham (1994), "Soil Ecology;" Lynch (1983), "Soil Biotechnology;" Metting et al. (1992), "Soil Microbial Ecology;" Alef and Nannipieri (1995), "Methods in Applied Soil Microbiology and Biochemistry;" Van Elsas et al. (1997), "Modern Soil Microbiology;" and Sylvia et al. (2005), "Principles and Applications of Soil Microbiology." Other volumes include Tate in 1994, "Soil Microbiology;" Harley and Smith in 1983, "Mycorrhizal Symbiosis;" Read et al. in 1992, "Mycorrhizas in Ecosystems;" and Makerji, Chamola, and Singh in 2000, "Mycorrhizal Biology." A community and ecosystem approach to the biology of soil is presented by Bardgett (2005) and the role of microbial diversity as a supplier of ecosystem services is presented in two edited volumes (Bardgett et al., 2005; Wall, 2004).

The advances in molecular techniques utilizing culture-independent direct retrieval of 16S rRNA genes have allowed an examination of the occurrence and biodiversity of microorganisms. A survey conducted by Morris et al. (2002) examined the primary scientific literature from 1975 to 1999 in 525 journals. Figure 1.1 shows data for six soil-associated habitats.


FIGURE 1.1 Publications per year from 1975 to 1999 in microbial diversity: (S) fungal-plant pathosystems, (▲) rhizosphere and mycorrhiza, (O) microbial habitats in soil, (♦) aquatic systems, (—) bacterium plant systems, and (■) food microbiology (Morris et al., 2002).


FIGURE 1.1 Publications per year from 1975 to 1999 in microbial diversity: (S) fungal-plant pathosystems, (▲) rhizosphere and mycorrhiza, (O) microbial habitats in soil, (♦) aquatic systems, (—) bacterium plant systems, and (■) food microbiology (Morris et al., 2002).

Fungus-plant pathosystems outnumbered the other five habitats and showed a 10-fold increase in papers; however, that number peaked in 1996. The rhizos-phere, including mycorrhizas, was still rapidly increasing in popularity in 1999. Microbial habitats in soil showed a similar trend, as did aquatic systems. Molecular techniques hold great promise for increasing our understanding of the links between organisms, processes, and the environment; thus soil microbiology, biochemistry, and ecology are best treated in one volume. The recent finding of ammonia-oxidizer genes in previously immeasurable Archaea is one example of new functional groups and maybe even new functions and processes that will be discovered by the readers of this book.

soil ecology

Soil ecology is the second leg of the scientific tripod supporting this textbook. Ecology has numerous definitions. The one that applies to this text is the interaction of organisms and their environment. Smith and Smith (2001) stated that Haeckel developed the term "ecology" in 1869 from the Greek term "oikos," meaning home or place to live. The first ecological publications are credited to the Greek scholar Theophrastus (371-288 BCE), who wrote nine books on "The History of Plants" and six on "The Causes of Plants." Continued work by naturalists during the 15th century, especially in the Middle East, was followed by the plant geographers, such as Wildenow (1765-1812) and Von Humboldt (1769-1859). These described vegetation by physical type and environmental conditions and coined the word "association" (see Smith and Smith, 2001). More plant geography, such as that of Schouw, who studied the effects of temperature on plant distribution, and Paczoski, who studied microenvironments created by plants, led to the study of plant communities. Scientists such as Coulter, Bessey, and Clements developed concepts of succession and gave ecology its hierarchical framework (see Major, 1969).

Aquatic research contributed much to ecological theory. In 1887, Forbes, who interestingly had no college degree (see Hagen, 1992), wrote the classic "The Lake as a Microcosm," which was a predecessor to ecosystem ecology and introduced the concepts of interrelationships through food chains. In 1931, European biologists Thieneman and Forel used the concept of organic nutrient cycling and developed the terms "producers" and "consumers." In 1926, agronomist Transeau was interested in improving agricultural production through a better understanding of photosynthetic efficiency and initiated our understanding of primary production. The early ecologists tended to concentrate on native plant and animal associations, whereas at that time soil microbiologists were associated with either agronomy or microbiology departments. Agronomists were primarily concerned with cultivated fields and the processes therein. To the soil zoologists, these fields seemed depauperate of interesting organisms, while the ecologist's obsession with native sites, and to some extent the environmental movement, was thought by the agronomists to greatly limit their interpretive capability.

Ecosystem science, a term coined by Tansley in 1935 (see Hagen, 1992), led to a more experimental approach and interdisciplinary work. The textbook organized around the ecosystem concept, "Fundamentals of Ecology" by E. P. Odum (1971), went through three editions and was translated into more than 20 languages. The International Biological Programme of the 1960s and 1970s demonstrated the need to investigate all the interacting components of the ecosystem and to model them using mathematically defined transformation processes. This required the active interaction of soil microbiologists and biochemists with plant and animal ecologists and agronomists. During this program, G. M. Van Dyne, a strong advocate of the ecosystem concept, described the editor of this volume as standing on a four-stranded barbed wire fence between ecology and agronomy, with the warning that some day I would slip, with the obvious drastic consequences. The title and chapters in this book indicate to me that this fence has finally been ripped out. Future great advances lie in the study of our exciting field by scientists with a variety of backgrounds and employment in institutions often as heterogeneous as the soils and organisms they study. At the same time, the more classically trained ecologists recognize that the soil, with its multitude of interacting organisms and complexity of interactions, is the last great frontier of ecology.

Today's researchers are finding that replicated, managed fields are excellent for studying and developing ecological and biogeochemical concepts in that they often have greater, more easily measured, nutrient fluxes than those in perennial vegetation. Uncultivated systems, whether prairie or forest, are essential as reference points, often with greater diversity. Other work, such as that in the Amazon Basin, is recognizing that many of the forests that were once thought to be pristine have had major past human interventions.

Russell's 11th edition of "Soil Conditions and Plant Growth," edited by Wild (1988), noted that Gilbert White, in 1777, observed that earthworms were promoters of vegetation by perforating and loosening the soil and drawing leaves underground. Feller et al. (2003a) note that Darwin first reported on the effect of earthworms in 1837, followed 34 years later by the publication "The Formation of Vegetable Mould through the Action of Earthworms." At that time, the term "vegetable mould" was used to designate surface horizons in a manner not that different from the earlier use of the term humus. Darwin showed that earthworms were important in soil formation by affecting rock weathering, humus formation, and profile differentiation. This led Feller et al. (2003a) to credit Darwin for the first scientific publication in Europe on the biological functioning of soils. In 1839, Ehrenberg had shown the presence of soil protozoa (see Feller et al., 2003a). Russell's work on partial sterilization and its benefits to fertility had involved the protozoa. Cutler and Crump, in 1920, observed the often reciprocal increase and decrease of amoebae and bacteria and attributed the concept of soil sickness resulting in lowered fertility to this phenomenon (see Waksman, 1932). This is in direct contrast to Russell's, and more recent, concepts in which faunal-derived microbial turnover is considered an advantage in nutrient release (Coleman et al., 2004). Stout et al. (1982) gave a detailed resume of the soil protozoa that included the slime molds.

The "Manual of Agricultural Helminthology" (Filipjev and Shuurmans-Stekhoven, 1941, published in The Netherlands), summarized nematode anatomy, systematics, methodology, and plant-parasite interactions to that date. G. Steiner states in the edited volume on nematology (Sasser and Jenkins, 1960) that the Incas of Peru had a regulation by which the replanting of potatoes on the same land needed to be deferred by a few years to control what must have been golden nema-tode infestation. He also stated that the "bush culture" that involved burning of tropical forests followed by planting of crops was not done on adjacent plots to stop invasion of nematodes from the old agricultural plots to the new ones. Kevan's 1965 description and count of soil fauna per square meter of a European grassland were quoted in the first edition of this textbook. A good introduction to the various members of the soil fauna is given by Burges and Raw (1967) and is updated by Lavelle and Spain (2001) and Coleman et al. (2004).

Wilde (1946) stated that the principals of soil science and ecology were introduced to silviculture by the German forester Grebe in his doctor's thesis in 1840. Grebe forecast Dokuchaiev's studies by stating,

"As silviculture horizons widen, the importance of environmental conditions becomes more sharply pronounced. It appears clearly to foresters that the form of forest management is determined by a number of physical influences related to topography, geology, type of soil, and climate."

In not mentioning organisms, maybe the quote does not belong in this book, but 80% correct isn't all bad.

Russian scientists have long credited Dokuchaiev and his associate Kostytchev with being the founders of soil science and for having a great influence on ecology. Wilde (1946) quotes Dokuchaiev as saying,

"The eternal genetical relationships that exist between the forces of the environment and physical matter, living and nonliving domains, plants and animals and man, his habits, and even his psychology—these relationships comprise the very nucleus of natural science."

Dokuchaiev recognized the effects of animals in soil formation in using the word "crotovina" for the filled-in remnants of mammal burrows. Russian soil science, ecology, geography, and plant ecology have always been closely associated (Major, 1969). Their word "biogeocoenoses" emphasizes the biology-landscape interactions, as well as exchanges of matter and energy, discussed so often in this text. Hilgard translated Dokuchaiev's work to English and mapped American soils relative to landscape, climate, and vegetation. Wilde credits Hilgard's 1906 publication "The Relation of Soils to Climate" for perhaps unintentionally laying the foundation of soil ecology in America. The interactions of Dokuchaiev's five factors of soil formation, climate, parent material, organisms, topography, and time were reiterated and placed in an equation form by Jenny (1941). Liebig has been credited as one of the first physiological ecologists for his work on mineral nutrition of plants.

The influence of Muller's 1878 monograph in characterizing forest soils in relation to the type of organic matter (Mull, Moder, and Mor) has been extensive. Wilde lists an extensive number of European authors who emphasized the role of soils in forest management. Other reviews on forest-microbiology-nutrient cycling include Jordan (1985), Pregitzer (2003), and Morris and Paul (2003). Rangeland science is equally dependent on soil processes, some of which are detailed in "Grasslands, Systems Analysis and Man," edited by Breymeyer and Van Dyne (1980), and in "Grassland Ecophysiology and Grazing Ecology" (Lemaire et al., 2000).

I did not know whether to place microbial ecology under soil microbiology or soil ecology. In concepts, methods, and application, microbial ecology has been closer to soil microbiology than to classical ecology. Numerous authors have bemoaned the fact that there is not an extensive idea and concept exchange between microbial ecology and ecology in general. However, this is rapidly changing with the recognition that the diverse and extensive soil and aquatic and sediment biota can now be studied with molecular methods. The great diversity and close interactions of organisms with mineral particles makes soil an ideal place to develop and test ecological concepts. According to Marshal (1993), microbial ecology has the goals of defining population dynamics in microbial communities and the phys-iochemical characteristics of microenvironments and understanding the metabolic processes carried out by microorganisms in nature. It recognizes as its founders the same scientists (Leeuwenhoek, Winogradsky, and Beijerinck) that developed soil microbiological thought. Microbial ecology has the ability to transcend different habitats, asking questions about soils, plants, animals, fresh waters, oceans, and sediments, as well as geological strata. It also has received great impetus from the recent advances in nucleic acid techniques and, thus, one of its more modern pioneering works has to be that of Watson and Crick, which eventually led to the nuclear-based techniques.

The first textbook published with the title "Microbial Ecology" was that of Brock (1966). Brock (1975), in "Milestones in Microbiology," published the key papers of Pasteur, Koch, and others in a translated, annotated format. The publication of the triennial meetings of the International Society of Microbial Ecology provides a useful chronology of advances in this field. Some include Ellwood et al. (1980), "Contemporary Microbial Ecology;" Klug and Reddy (1984), "Current Perspectives in Microbial Ecology;" and Guerrero and Pedros-Alio (1993), "Trends in Microbial Ecology." Other reviews include Lynch and Poole (1979) and the series "Advances in Microbial Ecology" published by Plenum Press. The training and background of microbial ecologists are often very different from those of classical ecologists, and until recently, there has not been enough cross-fertilization of ideas between the fields.

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