Growing unculturable bacteria

The bacteria that can be grown in the laboratory are only a small fraction of the total diversity that exists in nature. At all levels of bacterial phylogeny, uncultured clades that do not grow on standard media are playing critical roles in cycling carbon, nitrogen, and other elements, synthesizing novel natural products, and impacting the surrounding organisms and environment. While molecular techniques, such as metagenomic sequencing, can provide some information independent of our ability to culture these organisms, it is essentially impossible to learn new gene and pathway functions from pure sequence data. A true understanding of the physiology of these bacteria and their roles in ecology, host health, and natural product production requires their cultivation in the laboratory. Recent advances in growing these species include coculture with other bacteria, recreating the environment in the laboratory, and combining these approaches with microcultivation technology to increase throughput and access rare species. These studies are unraveling the molecular mechanisms of unculturability and are identifying growth factors that promote the growth of previously unculturable organisms. This minireview summarizes the recent discoveries in this area and discusses the potential future of the field.     

Metagenomics: DNA sequencing of environmental samples

Although genomics has classically focused on pure, easy-to-obtain samples, such as microbes that grow readily in culture or large animals and plants, these organisms represent only a fraction of the living or once-living organisms of interest. Many species are difficult to study in isolation because they fail to grow in laboratory culture, depend on other organisms for critical processes, or have become extinct. Methods that are based on DNA sequencing circumvent these obstacles, as DNA can be isolated directly from living or dead cells in various contexts. Such methods have led to the emergence of a new field, which is referred to as metagenomics.     

The effects of temperature upon the toxicity of chemicals to aquatic organisms

Although rather extensive bibliographies give the impression that there is a vast amount of literature on the effects of temperature on aquatic organisms, when one tries to apply this information to specific interactions, such as the effects of temperature changes on chemical toxicity to aquatic organisms, often very little of the evidence is applicable. Although the most useful information on this relationship has been acquired in laboratory situations even this body of literature (which forms the bulk of this paper) is not adequate to make any scientifically justifiable generalizations. Field data on this relationship is almost non-existent and it is unlikely that much will become available unless specific studies are initiated which are directed toward this end. This is equally true of the laboratory information although it seems more likely that this will be generated as a spinoff from other research activities. In order to develop water quality management programs for steam-electric power plants one should understand the relationship between temperature and the response of aquatic organisms to toxic chemicals. Not only do some power plants discharge chlorine and other similar materials as well as heated waste water but those that discharge the latter only may be located near discharges of toxic chemicals. Since temperature and chemical stress to aquatic organisms are most commonly discussed independently we felt a paper covering this relationship would be useful.     

Microarray-based genetic identification of beneficial organisms as a new tool for quality control of laboratory cultures

The use of beneficial organisms to help control pests and pathogens in field and greenhouse crops is constantly increasing. Insects and mites are commonly used as beneficial organisms and, nowadays, rearing companies have to produce them in large quantities. Because of the peculiarities of laboratory culture conditions, the quality of lab-reared organisms generally degrades over time. To maintain high fitness levels, cultures are refreshed with field specimens at regular intervals. However, this bears the risk of contaminating laboratory cultures with species or strains other than the intended natural enemy. To ensure that the correct species is produced and also to facilitate surveys after field release, we have developed a diagnostic microarray for identification of beneficial species. Probes have been designed from the different haplotypes of a fragment of the mitochondrial cytochrome oxidase I (COI) gene of each species. Hybridization of labeled PCR amplicons of COI on the microarray chip allows precise identification of 28 economically relevant arthropod species.     

Predominant Catalase-negative Soil Bacteria. I. Streptococcal Population Indigenous to Soil

Streptococci related to Streptococcus sanguis were shown to represent a major segment of the bacterial flora of certain soils. Upon initial isolation, these streptococci were quite pleomorphic and displayed morphological characteristics common to several other genera of bacteria, but after prolonged cultivation on laboratory media the isolates demonstrated a typical streptococcal morphology. It was proposed that a requirement for correction of the control mechanisms affecting growth rate and cell wall synthesis in part might explain the difficulty encountered in isolation of these organisms from soil and their initial pleomorphism and cultural instability. The possible role of these soil organisms as etiological agents of disease and the occurrence of other groups of streptococci in soil were discussed.     

Gastric campylobacter-like organisms: their role in gastric disease of laboratory animals

Campylobacter pylori, first isolated in 1982, is now recognized as a primary cause of acute gastritis in man, and there is substantial data suggesting that this organism also plays an important role in the pathogenesis of duodenal ulcers. More recently, Campylobacter-like organisms and other morphologically distinct spiral bacteria have been isolated from gastric lesions in a variety of laboratory animal species. The zoonotic significance of C. pylori and other gastric spiral bacteria isolated from man as well as laboratory and domestic animals requires further study. An appreciation of the ecological and pathological role of gastric spiral bacteria in domestic and laboratory animals is an essential first step when considering the role and proper selection of animal models in the study of C. pylori gastroduodenal disease.     

MouseCyc: a curated biochemical pathways database for the laboratory mouse

Linking biochemical genetic data to the reference genome for the laboratory mouse is important for comparative physiology and for developing mouse models of human biology and disease. We describe here a new database of curated metabolic pathways for the laboratory mouse called MouseCyc . MouseCyc has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human.     

Identification of Zoogloea species and the relationship to zoogloeal matrix and floc formation

Three floc-forming, gram-negative, polarly flagellated rods were isolated and characterized. Our isolates were compared to four similar floc-forming organisms previously isolated in another laboratory and classified as two species of Zoogloea, one of Pseudomonas, and as one unidentified gram-negative rod. Possession of zoogloeal matrix or flocculent growth habit was examined in relation to growth and biochemical patterns of the bacteria. A possible relationship of Zoogloea to other gelatinous matrix-producing bacteria is also discussed.     

Molecular and physiological approaches to understanding the ecology of pollutant degradation

Pollutant biodegradation in the environment occurs in the context of various interactions among microorganisms. To understand this ecological process, identification of functionally important populations is considered to be the primary step, which can be followed by isolation and laboratory pure-culture studies of the important organisms. Laboratory studies can then proceed to the analysis of in situ activity and interactions with other organisms. Such studies will shape a deeper understanding of the ecology of pollutant degradation and facilitate the development of new bioremediation strategies.     

The concept of the organism in physiology

Summary The growth of physiology in the 19^th and 20^th centuries was accompanied by the development of disciplinary boundaries between physiology and other biological sciences. Physiology became the study of the mechanisms that underlie the functions of organisms and their component parts. Concern with the internal workings of organisms has led physiologists to focus on the maintenance of homeostasis in the internal environment rather than on the interactions of organisms with their external environments. Moreover, interest in the cellular or biochemical mechanisms that underlie organismal function has resulted in the use of inbred populations of laboratory animals in which these mechanisms can be most rigorously studied. Finally, emphasis on the function of fully developed or adult organisms has been accompanied by a relative neglect of developmental processes. Disregard for the environment, for variation, and for development has made possible major advances in our knowledge of physiological mechanisms but has led to an impoverished concept of organisms. Incorporation of evolutionary, ecological, and developmental perspectives into the study of organisms might help to unite physiology more closely with the other biological sciences and lead to a richer and fuller understanding of organisms.     

New model systems for studying the evolutionary biology of aging: Crustacea

Progress in any area of biology has generally required work on a variety of organisms. This is true because particular species often have characteristics that make them especially useful for addressing specific questions. Recent progress in studying the evolutionary biology of senescence has been made through the use of new species, such asCaenorhabditis elegans andDrosophila melanogaster, because of the ease of working with them in the laboratory and because investigators have used theories for the evolution of aging as a basis for discovering the underlying mechanisms.I describe ways of finding new model systems for studying the evolutionary mechanisms of aging by combining the predictions of theory with existing information about the natural history of organisms that are well-suited to laboratory studies. Properties that make organisms favorable for laboratory studies include having a short generation time, high fecundity, small body size, and being easily cultured in a laboratory environment. It is also desirable to begin with natural populations that differ in their rate of aging. I present three scenarios and four groups of organisms which fulfill these requirements. The first two scenarios apply to well-documented differences in age/size specific predation among populations of guppies and microcrustacea. The third is differences among populations of fairy shrimp (anostraca) in habitat permanence. In all cases, there is an environmentla factor that is likely to select for changes in the life history, including aging, plus a target organism which is well-suited for laboratory studies of aging.     

Conjugal transfer of R68.45 and FP5 between Pseudomonas aeruginosa strains in a freshwater environment

Recent concern over the release of genetically engineered organisms has resulted in a need for information about the potential for gene transfer in the environment. In this study, the conjugal transfer in Pseudomonas aeruginosa of the plasmids R68.45 and FP5 was demonstrated in the freshwater environment of Fort Loudoun Resevoir, Knoxville, Tenn. When genetically well defined plasmid donor and recipient strains were introduced into test chambers suspended in Fort Loudoun Lake, transfer of both plasmids was observed. Conjugation occurred in both the presence and absence of the natural microbial community. The number of transconjugants recovered was lower when the natural community was present. Transfer of the broad-host-range plasmid R68.45 to organisms other than the introduced recipient was not observed in these chambers but was observed in laboratory simulations when an organism isolated from lakewater was used as the recipient strain. Although the plasmids transferred in laboratory studies were genetically and physically stable, a significant number of transconjugants recovered from the field trials contained deletions and other genetic rearrangements, suggesting that factors which increase gene instability are operating in the environment. The potential for conjugal transfer of genetic material must be considered in evaluating the release of any genetically engineered microorganism into a freshwater environment.     

Model Organisms Retain an “Ecological Memory” of Complex Ecologically Relevant Environmental Variation

Although tractable model organisms are essential to characterize the molecular mechanisms of evolution and adaptation, the ecological relevance of their behavior is not always clear because certain traits are easily lost during long-term laboratory culturing. Here, we demonstrate that despite their long tenure in the laboratory, model organisms retain “ecological memory” of complex environmental changes. We have discovered that Halobacterium salinarum NRC-1, a halophilic archaeon that dominates microbial communities in a dynamically changing hypersaline environment, simultaneously optimizes fitness to total salinity, NaCl concentration, and the [K]/[Mg] ratio. Despite being maintained under controlled conditions over the last 50 years, peaks in the three-dimensional fitness landscape occur in salinity and ionic compositions that are not replicated in laboratory culturing but are routinely observed in the natural hypersaline environment of this organism. Intriguingly, adaptation to variations in ion composition was associated with differential regulation of anaerobic metabolism genes, suggesting an intertwined relationship between responses to oxygen and salinity. Our results suggest that the ecological memory of complex environmental variations is imprinted in the networks for coordinating multiple cellular processes. These coordination networks are also essential for dealing with changes in other physicochemically linked factors present during routine laboratory culturing and, hence, retained in model organisms.     

Conjugal transfer of R68.45 and FP5 between Pseudomonas aeruginosa strains in a freshwater environment.

Recent concern over the release of genetically engineered organisms has resulted in a need for information about the potential for gene transfer in the environment. In this study, the conjugal transfer in Pseudomonas aeruginosa of the plasmids R68.45 and FP5 was demonstrated in the freshwater environment of Fort Loudoun Resevoir, Knoxville, Tenn. When genetically well defined plasmid donor and recipient strains were introduced into test chambers suspended in Fort Loudoun Lake, transfer of both plasmids was observed. Conjugation occurred in both the presence and absence of the natural microbial community. The number of transconjugants recovered was lower when the natural community was present. Transfer of the broad-host-range plasmid R68.45 to organisms other than the introduced recipient was not observed in these chambers but was observed in laboratory simulations when an organism isolated from lakewater was used as the recipient strain. Although the plasmids transferred in laboratory studies were genetically and physically stable, a significant number of transconjugants recovered from the field trials contained deletions and other genetic rearrangements, suggesting that factors which increase gene instability are operating in the environment. The potential for conjugal transfer of genetic material must be considered in evaluating the release of any genetically engineered microorganism into a freshwater environment.     

Interaction of Agromyces ramosus with Other Bacteria in Soil

Agromyces ramosus occurs in very high numbers in most soils and, based on studies of laboratory isolates, does not require host cells for growth. Nevertheless, it attacked and destroyed most of the gram-positive and gram-negative bacterial species tested as possible host organisms. A. ramosus also attacked and destroyed Saccharomyces cerevisiae. The possibility of attack on fungi was unclear. Among the bacteria serving as hosts were the important soil species Azotobacter vinelandii, Rhizobium leguminosarum, Rhizobium meliloti, and Agrobacterium tumefaciens. Dead cells were not attacked. A. vinelandii cysts were attacked but left unharmed. To some extent, A. vinelandii seemed to survive this attack by encysting. Attack by A. ramosus occurred in natural soil and over a broad range of nutritional levels in laboratory media. The attack did not seem to be a means for obtaining an increased supply of commonly available nutrients. Instead, it seemed to be a means of obtaining something produced, perhaps in small amounts, by a variety of organisms, but not by all organisms. Several types of culture filtrates were tested for activity. The filtrates neither stimulated nor inhibited the growth of A. ramosus or the host organisms. The availability of catalase activity in host organisms did not seem to be involved. It is not known whether the attack by Agromyces ramosus in soil can be manipulated to cause a decrease in numbers of Agrobacterium tumefaciens or other pathogens without simultaneously depressing the numbers of beneficial organisms in this habitat.     

Idealization in evolutionary developmental investigation: a tension between phenotypic plasticity and normal stages

Idealization is a reasoning strategy that biologists use to describe, model and explain that purposefully departs from features known to be present in nature. Similar to other strategies of scientific reasoning, idealization combines distinctive strengths alongside of latent weaknesses. The study of ontogeny in model organisms is usually executed by establishing a set of normal stages for embryonic development, which enables researchers in different laboratory contexts to have standardized comparisons of experimental results. Normal stages are a form of idealization because they intentionally ignore known variation in development, including variation associated with phenotypic plasticity (e.g. via strict control of environmental variables). This is a tension between the phenomenon of plasticity and the practice of staging that has consequences for evolutionary developmental investigation because variation is conceptually removed as a part of rendering model organisms experimentally tractable. Two compensatory tactics for mitigating these consequences are discussed: employing a diversity of model organisms and adopting alternative periodizations.     

Molecular epidemiological investigation of enterohaemorrhagic Escherichia coli isolates in Japan

We have established several measures for control and prevention of EHEC infection including designation of the disease as notifiable since there was the sudden increase in the incidence of infection with EHEC O157:H7 in Japan in 1996, involving multiple outbreaks. Improvements in methodologies for isolation of these organisms and enhanced laboratory screening have revealed a variety of sources in food and animals. Although there seems to be a bovine reservoir for O157 EHEC in Japan as well as North America and UK, different foods have been linked to EHEC infection including salads, radish sprouts and salmon roe. There is clear evidence that divergent clones of EHEC O157:H7 are prevalent throughout Japan based on laboratory surveillance, however, we still need to better define the role of EHEC serogroups other than Escherichia coli O157 as important causes of human infection.     

Developing a statistical support system for environmental hazard evaluation

Estimating the hazard or risk to both human health and the environment has been based almost exclusively on single species toxicity tests low in environmental realism and without validation of their accuracy in more complex systems. While this may be quite appropriate for humans in a large variety of circumstances, there is no substantive body of direct experimental evidence indicating that precise predictions of harm from hazardous materials can be extrapolated from single species laboratory tests (or even multispecies laboratory tests) to the more complex highly variable natural systems. Now added to the hazardous chemical assessment problem is the accidental or deliberate release of genetically engineered microorganisms into the environment that have the additional capability of multiplying and expanding their numbers and also transferring genetic information to other organisms. This paper focuses entirely on hazard evaluation for organisms other than humans, namely predicting the potential risk or probability of harm to natural systems based on laboratory toxicity testing using single species. Not only will the basic risk assessment strategy itself be examined but also the question of determining the statistical reliability of various extrapolations from one level of biological organization to another. ‘For every complex problem, there is a simple, direct solution ... and it is invariably wrong!’ H. L. Mencken