1. Recent Advances in Understanding Microbial Systematics

Radhey S. Gupta and Beile Gao

The higher taxonomic groups within prokaryotes are presently distinguished mainly on the basis of their branching in phylogenetic trees. In most cases, no molecular, biochemical or physiological characteristics are known that are uniquely shared by species from these groups. Analyses of genome sequences are leading to discovery of novel molecular characteristics that are specific for different groups of bacteria and archaea and provide more precise means for identifying and circumscribing these groups of microbes in clear molecular terms and for understanding their evolution. These new approaches and their limited applications for clarifying microbial systematics are described here. Because of their taxa specificities, further studies on these newly discovered molecular characteristics should lead to discovery of novel biochemical and physiological characteristics that are unique to different groups of microbes.

2. Comparative Microbial Genomics: Analytical Tools, Population Genetic Patterns and Evolutionary Implications

Yingqin Luo, Kui Lin and Jianping Xu

Microbes are ubiquitous in the world in which we live. With the development of high throughput DNA sequencing technology, there has been an explosion of DNA sequence data on microbes. The major aim of future microbial genomics will be to identify the functional significances of individual gene and genomic fragments and to use the information to help improve human health and promote our society development. One current major undertaking to understand genomic information is the comparative analyses between genomes that are not only distantly related, but also closely related ones. Such comparative analyses between genomes that have diverged at different evolutionary time scales allow us to extract different types of information about biological functions and evolutionary processes. We review the tools and databases that have been established for comparative analyses of microbial genomes and discuss the implications of such analyses on our understandings of the common properties of life, the extent of genome plasticity and diversity within and between species, the processes and mechanisms underlie the observed genome diversity, and the origin and evolution of life.

3. Patterns of Horizontal Gene Transfer in Bacteria

Weilong Hao and G. Brian Golding

Horizontal gene transfer, as a major force in shaping bacterial gene content, has gained incredible attention over the last decade. Along with the fast growing bacterial genome sequence data, there have been an increasingly large number of studies focused on horizontal gene transfer. The studies have been gradually transformed from identifying individual genes that have been horizontally transferred to assessing the general patterns of horizontal gene transfer and evaluating the systematic consequences of massive gene transfers. The rates of gene transfers have been measured by various methods such as parsimony and maximum likelihood methods. Different phylogenetic methods were applied to a variety of data sets to assess whether there exists a congruent and meaningful bacterial tree. Even though some consensus has been reached, many contradictions have emerged and need to be solved in future studies. Our goal here is to review recent studies on this subject with an emphasis on the emerging patterns in horizontal gene transfer research.

4. Population Genetics of Human Pathogenic Bacteria: Implications for Source Tracking and Rapid Identification

Ruifu Yang, Yujun Cui, Yanjun Li and Yanfeng Yan

Population genetics examine variation in genes among a group of strains of a particular species. Its major theme is to look at how different environmental factors and selective pressures can affect the distribution of genes and alleles. In this chapter Yersinia pestis was employed as an example to illustrate how the techniques are used for population genetic studies and how the achievements of these kinds of studies can be used for rapid identification and tracing the origin of pathogenic bacteria. New emerging techniques, including high throughput sequencing technologies, will give us unprecedented opportunities to understand microevolution and pathogenesis of bacterial pathogens.

5. Population Genetics of the Symbiotic Nitrogen-fixing Bacteria Rhizobia

Bertrand D. Eardly and Jianping Xu

Symbiotic nitrogen-fixing Rhizobia are of global significance, both in terms of their ecological relationships and their importance as an environmentally benign source of nitrogen for crop plants. These bacteria are capable of forming mutualistic relationships with a variety of legume hosts, where they convert atmospheric nitrogen (N₂) to ammonia that is used to help meet the nitrogen needs of the host plant. In this chapter, we review our current understanding of the population genetics of this diverse group of bacteria. First we briefly describe the various types of genomic architectures that are found within rhizobial species. Next we outline the phylogenetic relationships among the recognized taxa. We then summarize the results of studies that have examined patterns of molecular genetic variation in rhizobial populations at local, regional, and global levels. The results of these studies have revealed several important insights, including the existence of extensive diversity within, as well as significant genetic differentiation between local and regional populations. The results also provide evidence for long-distance gene flow between continental populations. Several studies have also indicated the existence of low-to-intermediate levels of recombination within rhizobial populations. Fine-scale studies of specific genomic components (e.g., symbiotic plasmids) have also shown that certain genomic elements appear to be more prone to recombination than others. The results also showed that the different loci responsible for the development of the symbiosis appear to be under different forms of selection. Because most the population studies to date have focused on strains from root nodules, surprisingly little is known on the population genetics of the more numerous non-nodulating soil rhizobia. Future efforts to characterize these populations should significantly enhance our ability to manipulate rhizobial populations in agricultural ecosystems.

6. The Population Genetics of Cyanobacteria

Scott R. Miller

Cyanobacteria are a group of ecologically diverse photosynthetic bacteria. Because niche differentiation is ultimately the product of differences among individuals within populations, understanding the evolutionary origins of this diversity ultimately requires a population genetics perspective. This chapter considers the current state of our understanding of the mechanisms that generate variation in cyanobacteria, the distribution of this diversity and its potential functional importance, with an emphasis on recent work from our laboratory regarding diversity within and among populations of the cosmopolitan, multicellular cyanobacterium, Mastigocladus laminosus. It concludes with an appraisal of the potential to take a population genomics approach to address fundamental questions regarding the nature of adaptive variation and niche differentiation in these microorganisms.

7. Population Genetics of Microalgae

Jim Provan

Algae are a highly diverse group of protists, ranging from simple, unicellular organisms to complex, multicellular entities with a range of differentiated tissues and distinct organs. They are found among diverse aquatic ecosystems and play important roles by supplying carbon and energy as well as providing habitat to other members of the biological communities. Some algae cause significant environmental and health problems. However, despite their importance, relatively little is known about this group of organisms. The first section of this chapter briefly summarizes our current understanding of the diversity and evolution of the algae. The second section reviews the molecular markers used to address algal population genetic issues. The third section summarizes the population genetic analyses of three algal groups: the dinoflagellates, the diatoms and the haptophytes. With the application of genomics information and technology, the field of algal population genetics is approaching an exciting period of development and expansion.

8. Population Genetics of Fungal Mutualists of Plants

Teresa E. Pawlowska

Mutualisms are reciprocal exploitations that nonetheless increase the fitness of each interacting partner. Two groups of fungal mutualists of plants, epichloë endophytes of grasses and arbuscular mycorrhizal fungi, were selected as focal systems to discuss population-level processes that contribute to the establishment and maintenance of mutualistic interactions. These two classes of fungal cooperators of plants are subject to different and often conflicting selective pressures and represent distinct trajectories of mutualism evolution. Yet, in both cases population structure of symbionts is a source of information critical for understanding how these fungi interact with their hosts.

9. Population Genetics of Pathogenic Fungi in Humans and Other Animals

Thomas G. Mitchell

This article reviews the more common DNA-based markers that are used to genotype fungi, as well as other eukaryotes, and presents several examples of their application to elucidate the population genetics of mammalian pathogenic fungi. The most common fungal infections are briefly summarized to illustrate the issues that are routinely addressed by population genetics approaches. This exciting area of research is continually growing as the methods become more accessible and medical mycologists recognize the value of studying natural isolates of pathogenic fungi.

10. Population Genetics of Human Malaria Parasites

Deirdre A. Joy

Genetic diversity, population structure, and evolutionary history of malaria parasites are among the key factors that will influence our ability to identify genes contributing to drug resistance, parasite development, and disease pathogenesis. These factors also have an impact on vaccine and drug development, parasite source tracking, as well as the formulation of other disease prevention and control measures. For example, a highly polymorphic parasite population will contain ample genetic diversity capable of generating drug resistance genotypes at an accelerated rate; while the presence of homogeneous parasite populations should aid in the development of an effective malaria vaccine. Malaria research in the post-genomic era offers many new tools for use in population genetics analyses.

11. The Population Genetics and Epidemiology of Human Viral Pathogens

Fernando González Candelas and Rafael Sanjuán

Many viral pathogens, especially those with an RNA genome, are characterized by their high mutation rates and large population sizes. These features are responsible for the high levels of genetic variation usually found in viral populations and for their rapid response to different selective challenges encountered during their infection and transmission processes. They are quantitatively and qualitatively so different from most other organisms that special models and concepts, such as the quasispecies model, have been developed to better describe the evolutionary dynamics of viral populations. Here, we review these and other salient features of viral pathogens, with a species emphasis on RNA viruses. We describe how population genetics theory provides an adequate frame-work for analyzing and interpreting genetic variation in viral populations, for understanding their dynamics, and to study adaptive processes occurring therein. However, not all the evolutionary changes observed are due to the action of positive selection and this is not an all-mighty agent of evolutionary change. We finish this review by introducing a recently developed framework for integrating the evolutionary and epidemic behavior of infectious organisms, known as phylodynamics, which is especially well-suited for fast evolving organisms such as viruses.

12. Population Genetics in the Age of Metagenomics: Impact on Investigations of Viral, Bacterial, Archaeal and Eukaryotic Microbial Communities

Jianping Xu

Microbial population genetics examines the spatial and temporal patterns of genetic variation across diverse geographic scales and ecological niches. With the arrival of molecular biological techniques, the past 40 years have seen tremendous progresses in microbial population genetics. However, in recent years, the analyses of genetic materials directly from natural environments have revolutionized our approaches and understandings of the diversity, function, and inter-relationships among microorganisms in diverse natural ecological niches. The emergence and development of this expanding new field, that of metragenomics, has been primarily driven by technical and analytical methods developed from high throughput platforms for cloning, microfluidics, DNA sequencing, robotics, high-density microarrays, 2D-gel electrophoresis, and mass spectrometry as well as associated bioinformatics softwares. In this chapter, I present a general overview of this exciting development, including the general approaches and common tools used for identifying the diversity and function of microorganisms in natural biological communities. Of special notes are the potential impacts of recent developments in single cell isolation, whole-genome amplification, pyrosequencing, and database warehousing on our understanding of microbial population structures in nature. These exciting developments are bringing significant opportunities as well as new challenges to the field of microbial population genetics.