INTRODUCTION

Evolutionary biology and microbiology, with the ushering in of the molecular revolution, developed a tenuous relationship (Woese, 1994). Further isolating these disciplines, once unified university biology departments split in two, with organismal versus molecular emphases. Because phage biologists were pioneers in molecular biology, they were placed on the molecular side of the divide along with the rest of microbiology, whereas evolutionary biologists, with their less reductionist approaches to biology, were grouped with researchers in zoology, botany, paleontology, and ecology (Rouch, 1997). Consequently, microbiologists were physically isolated from model organism researchers such as Drosophila evolutionary geneticists, and intellectually removed from discoveries such as rapid ecological radiations of wild populations and theories explaining biodiversity and speciation. Evolutionary biologists, in turn, were isolated from microbial experiments that bore on evolution, even though some historically significant discoveries in evolutionary biology used microbes, especially bacteriophages. Despite these past rifts, there exists a newfound appreciation for the power of using microbes to explore evolution and ecology: as molecular researchers had long realized, there are profound advantages to employing small, relatively simple, and rapidly replicating organisms as models for deciphering universal biological truths. Microbiologists, too, in this age of genomics, are increasingly aware of the crucial importance of ecology and evolution in their research.

INTRODUCTION

A virus depends intimately upon its host in order to reproduce, which makes the host organism a crucial part of the virus's environment. This basic facet of viral existence means that ecology, the scientific field focusing on how organisms interact with each other and their environment, is particularly relevant to the study of viruses. In this chapter we explore some of the ways in which the principles of ecology apply to viruses that infect bacteria — the bacteriophages (or “phages” for short). In turn, we also discuss how the study of phages and their bacterial hosts has contributed to different subfields of ecology.

Due to their ease of manipulation, large population sizes, short generation times, and wealth of physiological and genetic characterization, laboratory communities of microbial organisms have been popular experimental tools for testing ecological theory (Drake et al., 1996; Jessup et al., 2004). Building upon this foundation of knowledge, the ecological experimentalist can explore whether mechanistic understanding at the organismal level informs an understanding of patterns at the community level (Bohannan and Lenski, 2000a). Further, the initial composition of microbial consortia can be controlled, and thus researchers are able to probe the effects of different community structures on ecological phenomena, such as stability, diversity, and resilience to invasion.

INTRODUCTION

Found in Clostridium botulinum, Corynebacterium diphtheriae, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, Vibrio cholerae, etc., prophage-encoded bacterial virulence factors (øVFs) provide an additional level of interaction between phages, bacteria, and environments (Langley et al., 2003; Brüssow et al., 2004;øVF, which stands for phage-encoded virulence factor, we pronounce “phee-vee-eff.”). In some cases multiple prophages are present in the same cell and each may encode a separate virulence factor (VF). For example, some strains of enteropathogenic E. coli encode several variants of the VF, Shiga toxin, and in a number of Salmonella strains about 5% of the genome consists of prophages, most of which contain VF genes. Despite their unambiguous genomic association with prophages, a question still under debate is whether these VF genes should be considered phage genes or bacterial genes. Supporting the concept that they are simply unusually located bacterial genes, in some bacterial strains the prophage is clearly defective and no progeny phage will ever be produced. On the other hand, there are some VFs that cannot be released from the bacterial cell except following prophage induction, implying a great deal of phage involvement in VF expression. In this chapter we consider the evolutionary ecology and ecological impact — on phages, bacteria, and animals — of phage encoding of bacterial VF genes, especially prophage-encoded exotoxins.

INTRODUCTION

How do bacteriophages exist in the hostile environments that their bacterial hosts inhabit? In most environments, from the desert to the mammalian gut, bacteria live for most of their existence in a starved state (Koch, 1971; Morita, 1997) where energy, carbon, and other resources are in scarce supply. Under such conditions we know that the latency period for phage infection lengthens, that the burst size is greatly reduced (Kokjohn et al., 1991), and that the half-life of virion infectivity (rate of decay) is short (Miller, 2006); yet total counts of virus-like particles present in environmental samples are high. Clearly bacteriophages have evolved strategies for surviving under these unfavorable conditions. As survival-enhancement strategies, many biological entities, from bears to bacteria, have evolved dormant states. During phage infection we recognize analogous dormant states as lysogeny and as pseudolysogeny. In this chapter we explore several aspects of the ecological consequences of these “reductive” infections.

In addition to the material presented here, we direct the reader to additional reviews considering lysogeny, pseudolysogeny, and phage infection of starved bacteria: Barksdale and Arden (1974), Ackermann and DuBow (1987), Schrader et al. (1997a), Robb and Hill (2000), and Miller and Ripp (2002). Related issues, especially of phage contribution to bacterial genotype and phenotype, are also considered in Chapters 11 and 14.

The deciphering of the human genome at the dawn of our twenty-first century not only fueled expectation of an increase in speed of developing therapies for many diseases but also exploded some cherished myths. Among the myths exploded was the belief that there were about 100,000 genes in the human genome and that this would lead to thousands of new ‘targets’ (receptors, enzymes, transporters, ion channels, etc.) for the discovery of new drugs. Although still somewhat in question, the number of genes in the human genome is felt to be about 30,000, thus dampening considerably some of the initial euphoria over the anticipated results of this outstanding achievement: the deciphering of the human genome. Another disappointing projection is that the number of druggable targets will only increase some threefold, from about 550 to 1500. Nonetheless, this incredible achievement, enabled by many technologies associated with genome sequencing, has fueled additional technologies, such as proteomics and metabolomics, for the innovation of new drugs and diagnostics.

The dawn of this century has also seen an increase in awareness of the importance of unwanted side effects in marketed drugs and safety issues in device usage. This debate has not only captured the attention of the public, as some widely used drugs, such as Vioxx and Pergolide, have been removed from the market, but also that of the Congress.

This book will help readers draw a roadmap of the process of taking a biomedical invention and creating a product that can pass regulatory approval to be successfully commercialized. The regulated products included in this context are drugs (both small molecules and biologics), medical devices, diagnostics, and their combination products, as defined by the Food and Drug Administration (FDA) – the regulatory agency that is responsible for overseeing the world's single largest healthcare market, the United States. The term “biomedical technologies” refers to the collective technologies underlying these FDA-regulated products: biotechnology, various engineering technologies, chemistry and materials science, etc.

The book highlights key issues that might help improve chances of success through the complete commercialization process for biomedical technologies and products. This text started as an expansion of a series of lectures given to students at the Lally School of Management and Technology, Rensselaer Polytechnic Institute in Troy, NY as part of a class called “Commercializing biomedical technology.” However, going beyond the classroom in writing this book, information has been taken from many sources and experienced people from industry have contributed to add current and practical information to various segments of the book.

This book could be used to bring science and engineering students together with business and law students, and show them the benefits of approaching this complex process as a team. Many of these students have found the information useful in job interviews and in planning careers in the biotech industry and its service sectors.

Introduction

Bioremediation is a viable option for the cleanup of hydrocarbon-contaminated soils. Although this technology has proven effective for various temperate soils, extrapolation to cold soils is hindered by the lack of information about specific microbes, genes, and enzymes involved in hydrocarbon biodegradation in cold soils. These environments present multiple challenges to bioremediation besides low temperature and concomitantly lower enzymatic reaction rates: for example, cold soils are often poor in nutrients, low in available water, and may exhibit extremes of pH and salinity. Also in such environments the physical nature of the contaminant(s) is affected, with increased viscosity of liquid hydrocarbons and reduced volatilization of toxic, low molecular weight hydrocarbons. Despite these constraints, the biodegradation of many of the components of petroleum hydrocarbons by indigenous cold-adapted microbial populations has been observed at low temperatures in hydrocarbon-contaminated soils (e.g. Braddock et al. 1997; Aislabie et al. 1998; Margesin and Schinner 1998; Whyte et al. 1999a; Mohn and Stewart 2000). However, because hydrocarbons tend to persist in polar soils, there are obvious limitations to the activity of the indigenous microbes in situ.

In this chapter we review the literature describing hydrocarbon-degrading bacteria indigenous to cold soils, with a focus on polar soils. We discuss their adaptations to environmental parameters that challenge their activity in situ, including cold and fluctuating temperatures, limited nutrient availability, extremes in pH and salinity, and desiccation. We provide recommendations for methods to determine whether a soil contains the appropriate microbial community for applying bioremediation.