The global mandate for safer, cleaner and renewable energy has accelerated research on microbes that convert carbon sources to end-products serving as biofuels of the so-called first, second or third generation – e.g., bioethanol or biodiesel derived from starchy, sugar-rich or oily crops; bioethanol derived from composite lignocellulosic biomass; and biodiesels extracted from oil-producing algae and cyanobacteria, respectively. Recent advances in ‘omics’ applications are beginning to cast light on the biological mechanisms underlying biofuel production. They also unravel mechanisms important for organic solvent or high-added-value chemical production, which, along with those for fuel chemicals, are significant to the broader field of Bioenergy. The Frontiers in Microbial Physiology Research Topic that led to the current e-book publication, operated from 2013 to 2014 and welcomed articles aiming to better understand the genetic basis behind Bioenergy production. It invited genetic studies of microbes already used or carrying the potential to be used for bioethanol, biobutanol, biodiesel, and fuel gas production, as also of microbes posing as promising new catalysts for alternative bioproducts. Any research focusing on the systems biology of such microbes, gene function and regulation, genetic and/or genomic tool development, metabolic engineering, and synthetic biology leading to strain optimization, was considered highly relevant to the topic. Likewise, bioinformatic analyses and modeling pertaining to gene network prediction and function were also desirable and therefore invited in the thematic forum. Upon e-book development today, we, at the editorial, strongly believe that all articles presented herein – original research papers, reviews, perspectives and a technology report – significantly contribute to the emerging insights regarding microbial-derived energy production. Katherine M. Pappas, 2016

Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.

The U.S. Department of Energy (DOE) promotes scientific and technological innovation to advance the national, economic, and energy security of the United States. Recognizing the potential of microorganisms to offer new energy alternatives and remediate environmental contamination, DOE initiated the Genomes to Life program, now called Genomics: GTL, in 2000. The program aims to develop a predictive understanding of microbial systems that can be used to engineer systems for bioenergy production and environmental remediation, and to understand carbon cycling and sequestration. This report provides an evaluation of the program and its infrastructure plan. Overall, the report finds that GTL's research has resulted in and promises to deliver many more scientific advancements that contribute to the achievement of DOE's goals. However, the DOE's current plan for building four independent facilities for protein production, molecular imaging, proteome analysis, and systems biology sequentially may not be the most cost-effective, efficient, and scientifically optimal way to provide this infrastructure. As an alternative, the report suggests constructing up to four institute-like facilities, each of which integrates the capabilities of all four of the originally planned facility types and focuses on one or two of DOE's mission goals. The alternative infrastructure plan could have an especially high ratio of scientific benefit to cost because the need for technology will be directly tied to the biology goals of the program.

Recent major advances in the field of comparative genomics and cytogenomics of plants, particularly associated with the completion of ambitious genome projects, have uncovered astonishing facets of the architecture and evolutionary history of plant genomes. The aim of this book was to review these recent developments as well as their implications in our understanding of the mechanisms which drive plant diversity. New insights into the evolution of gene functions, gene families and genome size are presented, with particular emphasis on the evolutionary impact of polyploidization and transposable elements. Knowledge on the structure and evolution of plant sex chromosomes, centromeres and microRNAs is reviewed and updated. Taken together, the contributions by internationally recognized experts present a panoramic overview of the structural features and evolutionary dynamics of plant genomes.This volume of Genome Dynamics will provide researchers, teachers and students in the fields of biology and agronomy with a valuable source of current knowledge on plant genomes.