The Ecological Genomics Of Fungi

Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. We provide an advanced-level book that covers this recent research and proposes future development for this field. A synthesis of the field of ecological genomics emerges from this volume. Ecological Genomics covers a wide array of organisms (microbes, plants and animals) in order to be able to identify central concepts that motivate and derive from recent investigations in different branches of the tree of life. Ecological Genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation.

Fungi are cryptic, understudied and hyperdiverse organisms. Fungi are poorly documented organisms and the phylogenetic relationships within the kingdom are not yet fully understood, but recent efforts have been shedding light on the evolutionary history of the Fungi. Fungi have been known and used by humans for centuries, but mycology traces beginnings to the 18th century, with the development of the microscope. While much has been discovered since then, fungi remain today a cryptic and understudied group of organisms. The tools of molecular biology and genomics can help us meet this challenge. Over the past decades, genomics, and genome sequencing in particular, have emerged as powerful tools for biological research. In the last few years, due to the introduction of the next-generation sequencing (NGS) technologies, these tools went through dramatic transformations. Ecological Genomics of Fungi brings together studies related to pathogenic fungi, fungal biology, and all other aspects of fungal research. It covers a broad diversity of fungal systems and provides unique insight into the functions of those fungi in various ecosystems - from soil, to plant, to human. It also discusses tools, applications, and the most recent developments available to explore the biology of soil fungi at the molecular level. This book addresses the wonders of fungal diversity, including recent advances on the understanding of the evolution of the kingdom Fungi, approaches to documenting and interpreting fungal diversity, and current efforts concerning fungal conservation. The book also includes investigations of fungi and their traditional allies that relate structure and function to growth, reproduction, morphogenesis, differentiation, its role as pathogen and parasites, its applications in various fields like industry and agriculture and medicinal uses.

This volume details protocols covering nearly all aspects of fungal genomics. New and updated chapters guide the reader through experimental genomics, biotechnologies, and the analysis and processing of data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Fungal Genomics : Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

This volume addresses the similarities and also the differences in the genomes of soil saprophytes, symbionts, and plant pathogens by using examples of fungal species to illustrate particular principles. It analyzes how the specific interactions with the hosts and the influence of the environment may have shaped genome evolution. The relevance of fungal genetic research and biotechnological applications is shown for areas such as plant pathogenesis, biomass degradation, litter decomposition, nitrogen assimilation, antibiotic production, mycoparasitism, energy, ecology, and also for soil fungi turning to human pathogens. In addition to the model organisms Neurospora and Aspergillus, the following species are covered providing a view of pathogens and mutualists: Trichoderma, Fusarium oxysporum, Cochliobolus heterostrophus, Penicillium chrysogenum, Rhizopus oryzae, Podospora anserina, and species belonging to Agaricomycetes, Archaeorhizomycetes and Magnaporthaceae. Ecology and potential applications have guided the choice of fungal genes to be studied and it will be fascinating to follow the trends of future sequencing projects.

The authors also provide a comparative survey of the properties of genomes (genome size, gene families, synteny, and polymorphism) for prokaryotes as well as the main eukaryotic models.

Entirely rewritten and updated throughout, this Second Edition maintains and enhances the features of the first edition. The Fungal Community, Second Edition continues to cover the entire spectrum of fungal ecology, from studies of individual fungal populations to the functional role of fungi at the ecosystem level, and to present mycological ecology as a rational, organized body of knowledge.;Acting as a bridge between mycological data and ecological theory, The Fungal Community, Second Edition offers such new features as an emphasis on the nonequilibrium perspective, including the impact of habitat disturbance and environmental stress; more information on the ecological genetics of fungal populations; a chapter on the fitness of genetically altered fungi when released into the environment; an examination of fungal morphological and physiological adaptations from the evolutionary ecologist's point-of-view; an explication of the effect of fungi and insect interactions on fungal community structure and decomposition processes; a section on the importance of fungi in determining patterns of plant community development; and a chapter on modeling fungal contributions to decomposition and nutrient cycling in ecosystems.;With over 3700 references, The Fungal Community, Second Edition is a resource for mycologists; microbial ecologists; microbiologists; geneticists; virologists; plant pathologists; cell and molecular biologists; biotechnologists; soil, forest, and environmental scientists; and graduate-level students in these disciplines.

Fungi research and knowledge grew rapidly following recent advances in genetics and genomics. This book synthesizes new knowledge with existing information to stimulate new scientific questions and propel fungal scientists on to the next stages of research. This book is a comprehensive guide on fungi, environmental sensing, genetics, genomics, interactions with microbes, plants, insects, and humans, technological applications, and natural product development.

This volume guides researchers on how to characterize, image rare, and hitherto unknown taxa and their interactions, to identify new functions and biomolecules and to understand how environmental changes condition the activity and the response of the organisms living with us and in our environment. Chapters cover different organism types (i.e., archaea, bacteria, fungi, protest, microfauna and microeukaryotes) and propose detailed protocols to produce high quality DNA, to analyse active microbial communities directly involved in complex interactions or processes through stable isotope probing, to identify and characterize of new functional genes, to image in situ interactions and to apply bioinformatics analysis tools to complex metagenomic or RNAseq sequence data. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbial Environmental Genomics (MEG): Methods and Protocols, Second Edition aims to serve as a primary research reference for researchers in microbiology working to in the expanding field of molecular ecology and environmental genomics.

The volume is divided into four sections, the first of which, Genome Sequences and Beyond, illustrates the impact of genome-based information and techniques on research ranging from model organisms like yeast to less-studied basal fungal lineages. Furthermore, it highlights novel types of analysis made possible by multi-genome comparisons as well as the impact of genomics on culture collections and vice versa. The second section, Cell and Developmental Biology, addresses questions that are important for fungal biology, e.g. the development of fungal fruiting bodies, and biology in general, e.g. chromatin organization and circadian rhythms. The third section, Genomics for Biotechnology, covers the search for plant biomass-converting enzymes in fungal genomes and work with industrially important fungi. The fourth section, focusing on Pathogenicity, offers chapters on the genomic analysis of plant and animal/human pathogens. It illustrates how genomics at all levels, from genome to metabolome, is used to study mechanisms of the interactions of fungi with other organisms.