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Fungi are an heterogeneous assemblage of eukaryotic organisms united by an absorptive mode of nutrition in which they grow through the substrate, secreting degradative enzymes and absorbing nutrients. Because of this absorptive mode of nutrition, the fungi are ubiquitous, intimately associated with their substrates, and able to degrade a diverse range of organic and inorganic materials. The breakdown of substrates, primarily organic materials, by fungi results in the cycling of nutrients that is crucial for long term ecosystem maintenance. The relationships of fungi with their nutrient sources ranges from that of: obligate parasites, often causing serious diseases of plants, animals, and humans; obligate mutualists, as in the arbuscular mycorrhizal associations of the Glomales with roots of crops plants and in the anaerobic chytrids in the rumen of ruminant animals; obligate commensals, as in the Trichomycetes, a specialized group of fungi that exist in the hind guts of insects without causing any apparent harm to the host; to facultative relationships, primarily as saprobes degrading all kinds of plant material from simple sugars to the complex carbohydrates, lignin and chitin, often in specialized habitats, for example, yeasts fermenting flower nectar, as well as serving as hosts for viruses. Fungi often form complex communities interacting with other organisms inhabiting the same substrates. Thus, fungal diversity is reflected in the diversity of substrates available for fungal exploitation throughout evolutionary history and into the present and future. [ABSTRACT FROM AUTHOR]

"A bacterial species is what a taxonomist believes it is, in the broad sense." In the last century, microbiologists followed the system of botanists because early microbiologists were botanists and, of course, adopted the same concepts. During the next 70-80 years, shortcomings of this approach were noted, i.e., descriptions of species based solely on phenotype is of limited value; bacterial species usually do not provide enough information to detect differences; and biological species may not exist among bacteria. At the end of 1970, there were about 45,000 described species of bacteria. The majority of these species were misclassified. [ABSTRACT FROM AUTHOR]

Nitrogen (N) is a critical element in crop production for both paddy and upland soil ecosystems. In this chapter, we describe the role of microbial biomass and its activity in Nitrogen(N) cycling supporting rice growth in the paddy soil ecosystem. We also focus on the genetic diversity of N2-fixing bacteria in rice roots. Finally, we discuss the genetic diversity of both soil bacteria, in general, and rhizobia, specifically. [ABSTRACT FROM AUTHOR]

Bacteria as they occur in nature are very small, compared with bacteria cultured under enriched conditions of the laboratory, i.e., in vitro. In general, planktonic bacterial cells in the natural environment are less than 1 µm in length and, therefore, biovolumes of planktonic bacteria are usually less than 0.2 - 0.3 µm3. Planktonic bacteria are very small organisms, even among planktonic constituents of aquatic ecosystems. They constitute less than 1/100 of the biovolume of small phytoplankton and less than 1/10 of that of microflagellates (Fig. 1). Compared with large phytoplankton, cell size differences reach more than thousands-fold. However, as planktonic bacteria are plentiful in water, in the order of 105 to 107 per ml (xcVanEs and Meyer-Reil, 1982), their overall biovolume in aquatic ecosystems can be significant. In marine systems, small bacteria, with a diameter of ca. 0.2 - 0.6 µm usually predominate, but, even among these bacteria, significant variation in size exists. Therefore, the bacterial biomass of a given population cannot be estimated accurately from a roughly estimated mean value, even if the diameters range from 0.2 to 0.6 µm, since such differences can lead to a ten-fold increase in biovolume. When bacteria are observed under an epifluorescence microscope, very large cells are often found, even in samples of pelagic marine waters. Thus, it is necessary to determine the cell size of bacteria precisely. The development of a personal computer-assisted image analyzer, connected to an epifluorescent microscope via a charge-coupled device (CCD) camera, has enabled the size of small bacterial cells to be measured automatically (xcSieracki et al., 1985; xcBjørnsen, 1986). [ABSTRACT FROM AUTHOR]

The computer and networking have promoted the development of microbial ecology significantly. In detecting bacteria at the single cell level, an important theme in this field, computers are essential for designing of gene probes, preparing primers for PCR, carrying out homology searches, estimating ORF, etc. A brief introduction to the use of Internet in microbial ecology is provided. [ABSTRACT FROM AUTHOR]

Understanding the patterns of naturally occurring microbial diversity, how these patterns vary in space and time, and how they relate to ecosystem structure and function, remains a significant challenge for microbiologists. A variety of levels of microbial diversity are important and relevant from the perspective of microbial ecology, including trophic, physiological or functional diversity, intraspecific genetic diversity, or phylogenetic diversity of species and higher taxa. For the purpose of this chapter, "diversity" will be used to refer to phylogenetic variety at the level of species and higher taxa. One of the very first tasks necessary for assessing naturally occurring prokaryote diversity is to identify accurately those prokaryotic species predominant in a given habitat. This fundamental goal, representing the basis of understanding of the ecology or natural history of microbes, has rarely, if ever, been achieved for any naturally occurring microbial assemblage. We have a long way to go to catch up with the rest of biology! [ABSTRACT FROM AUTHOR]

DNA is the genetic material found in all living cells and is a molecule fundamental for life on this planet. Interest in the measurement of DNA in the oceans has evolved from a desire to quantitate biomass to a need to understand microbial diversity in the marine environment (see chapter by DeLong in this book). [ABSTRACT FROM AUTHOR]

The vast Brazilian tropical edaphic savannah, referred to as Cerrado, is considered to be one of the last frontiers of agricultural utilization (xcBorloug and Dowswell, 1994). Soils are deep but leached of nutrients and, in general, strongly acidic (pH averages 5.0 and aluminum is present at toxic levels, xcVerdade, 1971). Agricultural utilization of the Cerrado was stimulated in the sixties when soil amendments, appropriated technologies, and improved/adapted varieties became available. To bring the land to crop production requires a ritual that includes land clearance (dragging or slash and burning of the native vegetation), ploughing, liming, and fertiliser application. In a little over two decades, the Cerrado became a major grain producing area, reducing social pressures threatening the very fragile soils of the Amazon region. [ABSTRACT FROM AUTHOR]

Within the microbial world, soil bacteria demonstrate a unique metabolic versatility for degradation of a variety of aromatic compounds. The major aromatic pathways discovered in bacteria revealed that essentially all compounds are degraded through a variety of enzymatic steps to limited numbers of common intermediates, such as catechols, which are key compounds for further metabolism. The relationships among the different aromatic pathways and gene clusters often reveal evolutionary changes involved in the development of metabolic routes (xcvan der Meer et al., 1992). Such evolution derived from various genetic events. Biphenyl-utilizing bacteria, widely distributed in the natural environment, include both Gram negative and Gram positive strains (xcFurukawa, 1982). The substrate specificities of biphenyl catabolic enzymes are usually very relaxed. Some bph genes (coding for biphenyl catabolism) are very similar in different strains, suggesting that certain bph genes may transfer among soil bacteria (xcFurukawa et al., 1989). On the other hand, other bph genes are highly diversified and greatly rearranged. Toluene-utilizing bacteria are also widely distributed. Toluene can be metabolized by bacteria by different mechanisms, where substituted groups are modified before or after ring-cleavage, depending on the microorganism. In this communication, evolutionary relationships of catabolic function is discussed, focusing on biphenyl-utilizing and toluene-utilizing bacteria. [ABSTRACT FROM AUTHOR]

Many eukaryotic cells constitute the sole habitat for a vast and varied array of prokaryotic lineages (xcBuchner, 1965). These intracellular associations have evolved repeatedly and have had major consequences for the diversification of both bacteria and host. The magnitude of these consequences is immediately evident if one considers the examples of mitochondria and chloroplasts, now widely acknowledged to be descended from prokaryotes that invaded intracellular habitats (xcMargulis, 1970; xcGray and Doolittle, 1982). [ABSTRACT FROM AUTHOR]

A gnotobiotic aquatic microcosm, consisting of three species, including: bacteria, Escherichia coli; protozoa, Tetrahymena thermophila; and a primary producer, Euglena gracilis, was prepared, in which all species co-existed for over 130 days. Interactions among the species were analysed to clarify mechanisms involved in co-existence. The growth of T. thermophila depended on the number of E. coli, that is, T. thermophila grew when more than 106E. coli cells per ml were present. No T. thermophila survived in a medium without other organisms. It, however, did grow in the presence of Eu. gracilis. As T. thermophila does not feed on Eu. gracilis, it is hypothesized that a metabolite of Eu. gracilis had a positive effect on growth of T. thermophila. Competition between E. coli and Eu. gracilis for proteose peptone in the medium was not observed. These interactions appeared to depend on successful co-existence of the three species. These results were confirmed by mathematical analysis, using parameter sensitivity of a dynamic model. [ABSTRACT FROM AUTHOR]

Ecosystems comprise populations of individuals at different trophic levels that are connected through many interactions. In studies of insect-plant interactions, macroorganisms have been almost exclusively the focus. Yet, for many of the interactions in multitrophic systems, examples are available showing that microorganisms mediate interactions that were originally thought to occur between macroorganisms. This relates to a variety of aspects, including production of toxins, detoxification of toxins, provisioning of essential nutrients, induction of plant defense mechanism, production of information-conveying chemicals ("infochemicals"), etc. Microorganisms may function as external or internal symbionts, as pathogens, or as mutualists of plants, herbivorous arthropods, or carnivorous arthropods. This review shows that it is essential to investigate interactions between macroorganisms in more detail in order to identify precisely those organisms that interact. In doing so, we obtain a better understanding of the selective forces that operate in ecosystems, because selection in microorganisms results in much faster changes than selection in arthropods and plants, because of the significantly shorter generation time of microorganisms. [ABSTRACT FROM AUTHOR]

Termites are divided into two types, the lower termite, which possesses symbiotic protozoa and several species of bacteria in the intestine and the higher termite, which has no protozoa but several species of symbiotic bacteria in the intestine. The digestive system for cellulose differs in each. In the higher termites, the digestive system is complex, since several problems remain unresolved. In the lower termites, cellulose digestion depends on the intestinal protozoa and symbiotic relationships between the termite and its intestinal protozoa, first published by Cleveland in 1924 (xcCleveland, 1924A). Recent reports, however, show that the symbiotic relationship in the digestive system involving cellulose is more complex. xcYamaoka and Nagatani (1975) reported that the termites themselves produce a cellulase which differs from the cellulase produced by the intestinal protozoa. Since the concept of the cellulose digestion system has changed significantly, the role of intestinal bacteria and their diversity in termites are presented here. [ABSTRACT FROM AUTHOR]

The earth was born 4.6 billion years ago, as a planet of the solar system. Then, after the chemical evolution of organic compounds ca. 4.0 to 3.5 billion years ago, life was created by accident. Ancient living cells are presumed to have had RNA as their hereditary element (xcGilbert, 1986). RNA was substituted by DNA and the present form of living cells (possessing protein-synthesizing ability) is the DNA-based organism. DNA organisms evolved to the presently existing various descendents. Driving forces for the explosive evolution that occurred were environmental changes in the biosphere. The decrease in temperature of the biosphere was one of the most important environmental changes associated with early evolution (xcWoese, 1981; xcWoese, 1987). Ancient organisms, living before 3.0 billion years ago, are presumed to have been thermophiles, which required temperatures higher than 70°C. The temperature of the surface of the earth decreased gradually to below 70°C, after 3.0 billion years ago (xcTrakes, 1979), and thermophilic organisms were, thereafter, found in hot springs or in the hydrothermal vents of deep sea volcanos. The second important environmental change in the biosphere was generation of oxygen (xcCloud, 1983). Oxygen was produced by cyanobacteria in the sea, and after oxygen saturation of the sea, oxygen was released into the atmosphere. The generation of oxygen selected against the primitive anaerobic bacteria, leading to selection of aerobic bacteria. The primitive forms of anaerobic bacteria are presumed to be archaebacteria (xcWoese, 1981; xcWoese, 1987). As the concentration of atmospheric oxygen increased, aerobic eubacteria diversified explosively about 2.0 billion years ago. The eucaryotes were created by endosymbiosis about 2.0 billion years ago, and various multicellular organisms were created up to 0.7 billion years ago (xcCloud, 1983). [ABSTRACT FROM AUTHOR]

"The number of known species of fungi is about 69,000", but species of the fungal world are conservatively estimated to be 1.5 million (xcHawksworth, 1991). The fungi are of great consequence agronomically, bioindustrially, medically, and biologically. In spite of their importance, their taxonomic inventory is poor, particularly for the tropical regions. In addition, very little is known about the phylogeny and evolution of fungi and between these and other organisms. As pointed out by xcBruns et al. (1991), "their simple and frequently convergent morphology, their lack of a useful fossil record, and their diversity have been major impediments to progress in this field". [ABSTRACT FROM AUTHOR]

Viruses, like other living organisms, receive their genetic information from the past, maintain and transmit the information in the present, and replicate and send the information faithfully to time and space of the future. [ABSTRACT FROM AUTHOR]

It is well known, even by the general public, that there are many levels of biodiversity, such as the gene, species, higher taxa, and the ecosystem or landscape. All are important and significant components of biodiversity: i.e., the diversity of living materials or of ‘creatures' themselves. [ABSTRACT FROM AUTHOR]

Two molecular methods have proven successful in determining the whole range of relationships between prokaryotic organisms, i.e. from the level of strains to the level of domains. DNA:DNA hybridization is suitable for the elucidation of relationships among closely related strains, while all other levels, from remote to distant relationships, can be unravelled by the analysis of conserved macromolecules, preferably the RNA of the small subunit of ribosomes or the genes coding for it (16S rRNA/DNA) (xcStackebrandt and Goebel, 1994). It is obvious that DNA reassociation methods require pure cultures, in order to determine the degree of relatedness between individual organisms, while 16S rDNA sequences can be obtained from mixed bacterial populations by analysis of cloned DNA restriction fragments or PCR products (xcGiovannoni et al., 1990; xcWard et al., 1990). The presence of rDNA in every organism, and the availability of a broad range of molecular methods, including amplification techniques and detection methods, e.g., the use of taxon- specific PCR primers and oligonucleotide probes, makes sequence analysis and/or detection of 16S rDNA the superior approach for the assessment of phylogenetic diversity (xcPace et al., 1985). The analysis of this molecule does not allow determination of morphological and physiological activities, hence information about the ecological role played by an organism in its environment; but it reveals information about approximate relationships between naturally occurring organisms and cultured strains, and it allows us to determine the presence of novel types of prokaryotes. [ABSTRACT FROM AUTHOR]

The enormous diversity available at the microbial level is beginning to be recognized, but this richness of diversity amongst bacterial and virus species has yet to be cataloged. The number of species of bacteria that have been described is approximately 2,000- 4,000, whereas the estimated total number of bacterial species is approximately 3,000,000, most probably, a significant underestimation. The number of virus species may be in the same range. The role of microorganisms in ecological cycles is just beginning to be more fully understood. For example, viruses have been found to regulate/modulate algal abundance and distribution. Global cycles, including carbon, nitrogen, sulfur, and heavy metal cycles, are known to be mediated or influenced by microorganisms. A unique aspect of the diversity of microorganisms is their morphologyl, ranging from the ultramicroscopic to a recently described bacterial species visible to the naked eye. The shapes of bacteria may be rod, spherical, spiral, triangular, pyramidal, and rectangular, in brief, nearly every possible morphology. Morphology and function of bacteria are influenced by the environment, a demonstration of the inter-relationship of diversity and ecological processes. Inventorying and cataloging microbial diversity is a daunting task, requiring ingenuity and creativity, but offering substantial economic and social reward. [ABSTRACT FROM AUTHOR]

Prokaryotes are the oldest and most diverse group of organisms, encompassing a wide array of adaptations to extreme environmental conditions. The prokaryotes, including both Archaea and Eubacteria, comprise a large and versatile gene pool which can be translated to include highly versatile physiological responses to the environment, resulting in ability to grow within an extraordinarily-wide spectrum of environmental conditions. The communal metabolism of microorganisms is largely responsible for global cycling of elements, resulting in evolution of the Earth's biosphere throughout the living history of the Earth and in maintaining dynamic stability of the present biosphere. Microbial activities are also closely associated with present global climatic changes, both accelerating and slowing these processes. [ABSTRACT FROM AUTHOR]