Microbial activities are key to our planet's habitability and sustainability since they play essential roles in shaping and controlling virtually every natural system including our atmosphere, oceans, soils, and every plant and animal. Microbes exist in different metabolic states in these systems: growing, active, dormant, and recently deceased. These metabolic states correspond to different degrees of influence that a microbe can have on its environment. Therefore, to understand the relationships between microbial community patterns and ecosystem functions, it is important to accurately associate microbial identity with concurrent metabolic state. Through my research I strive to improve our understanding of microbial population, community, and process dynamics in soils and how to apply this information to better predict changes in ecosystem function. I applied a combination of community molecular analyses, chemical and physical characterizations, and process measurements to explore microbial mechanisms, interactions, and responses to changes in their environment. Nucleic acid analysis has proven to be an effective avenue for characterizing the phylogenetic, taxonomic, and functional structure of microbial assemblages, but this approach has limitations when attempting to assess current metabolic state. Ribosomal RNA genes (rRNA genes) have frequently been used to identify microorganisms present in environmental samples regardless of metabolic state, while ribosomal RNA (rRNA) has been widely applied to identify the active fraction of microbes. Chapter 1 re-evaluates utilizing rRNA as an indicator of microbial activity in environmental samples. A growing body of evidence indicates that the general use of rRNA as an indicator of metabolic state in microbial assemblages has serious limitations. This chapter highlights the complex and often contradictory relationships between rRNA, growth, and activity. Potential mechanisms for confounding rRNA patterns are discussed, including differences in life histories, life strategies, and non-growth activities. Ways in which rRNA data can be used for meaningful characterization of microbial assemblages are presented. Chapter 2 presents direct measurements of growth, mortality, and survival for bacteria and fungi following the rewetting of dry soil. The rapid stimulation of microbial activity that occurs when a dry soil is rewetted has been well documented and is of great interest due to implications of changing precipitation patterns on soil C dynamics. Many studies have characterized net changes in microbial populations, but gross population dynamics for bacteria and fungi following wet-up are not well understood. Here, DNA stable isotope probing with H218O was coupled with quantitative PCR to characterize new growth, survival, and mortality for bacteria and fungi following the rewetting of a seasonally dried California annual grassland soil. This study documents both net and gross changes that bacterial and fungal populations underwent over the course of 7 days after wet-up. A pulse of non-growth activity appears to immediately follow wet-up followed by linear growth for both bacteria and fungi. Mortality dynamics indicate that dead microbial bodies provide a large pool of available C and nutrients, thus offering insight into possible C sources fueling the CO2 pulse following wet-up. Results reveal that a vibrant assemblage of growing and dying organisms may comprise a seemingly static microbial community following a change in the environment. The bacterial growth stimulated by the rewetting of dry soil was further characterized using high throughput sequencing of 16S rRNA genes, and results are presented in Chapter 3. Of the 25 different phyla present in the pre-wet community, members of the Firmicutes Bacillales order were the only detectable early responders with close to a 5% increase in relative abundance from growth in the first 3 h after wet up. The second group of growers detected at 24 h included only Betaproteobacteria and Bacteroidetes. Members of the Burkholderiales order in the Betaproteobacteria phylum were by far the dominant growers during this period with a 21% increase in relative abundance. The highest richness of growing bacteria was detected during the third time-period (between 24-72 h), with significant changes in relative abundance due to growth found in 11 phyla. Nonmetric multidimensional ordination of community composition data through time shows a somewhat cyclical pattern for phylogenetic composition of growing bacteria with composition at 3 hours differing slightly from the pre-wet community, differing greatly at 24 h, and then becoming progressively more similar to the pre-wet community at 72 and 168 h. This suggests a degree of community resilience in response to this abrupt environmental change. However, some net compositional changes were observed following wet-up. Actinobacteria were the most dominant pre-wet phylum, but Proteobacteria became the most dominant phylum by 168 h. This change in composition was likely driven by new growth since Proteobacteria were found to grow in abundance for most of the incubation while Actinobacteria only grew during two later time periods and with smaller increases in relative abundance. Sequential growth patterns found at the phylum and order level suggest that ecologically coherent response was observable at a high taxonomic level. Chapter 4 shifts emphasis to anaerobic oxidation of methane (AOM) in Tropical and Boreal soils. AOM is a considerable sink for the greenhouse gas methane (CH4) in marine systems, but the importance of this process in terrestrial systems is less clear. Lowland boreal soils and wet tropical soils are two hotspots for CH4 cycling, yet AOM has been essentially uncharacterized in these systems. We investigated AOM in soils from sites in Alaska and Puerto Rico. Isotope tracers were utilized in vitro to enable the simultaneous quantification of CH4 production and consumption without use of biological inhibitors. Boreal peat soil and tropical mineral soil oxidized small but significant quantities of CH4 to CO2 under anoxic conditions. Potential AOM rates were 21 ± 2 nmol gdw-1 d-1 and 2.9 ± 0.5 nmol gdw-1 d-1 for the boreal and tropical soils, respectively. The addition of terminal electron acceptors (NO3-, Fe(III), and SO42- ) inhibited AOM and methanogenesis in both soils. In all incubations, CH4 production occurred simultaneously with AOM, and CH4 production rates were always greater than AOM rates. There was a strong correlation between the quantity of CH4 produced and the amount of CH4 oxidized under anoxic conditions. CH4 oxidation under anoxic conditions was biological and likely mediated by methanogenic archaea. While only a small percentage of the total CH4 produced in these soils was oxidized under anoxic conditions (0.3% and 0.8% for Alaskan and Puerto Rican soils), this process is important to understand since it could play a measurable role in controlling net CH4 flux.

This innovative book integrates practical information from restoration projects around the world with the latest developments in successional theory. It recognizes the critical roles of disturbance ecology, landscape ecology, ecological assembly, invasion biology, ecosystem health, and historical ecology in habitat restoration. It argues that restoration within a successional context will best utilize the lessons from each of these disciplines.

With contributions that review research on this topic throughout the world, Oxidative Damage to Plants covers key areas of discovery, from the generation of reactive oxygen species (ROSs), their mechanisms, quenching of these ROSs through enzymatic and non-enzymatic antioxidants, and detailed aspects of such antioxidants as SOD and CAT. Environmental stress is responsible for the generation of oxidative stress, which causes oxidative damage to biomolecules and hence reduces crop yield. To cope up with these problems, scientists have to fully understand the generation of reactive oxygen species, its impact on plants and how plants will be able to withstand these stresses. - Provides invaluable information about the role of antioxidants in alleviating oxidative stress - Examines both the negative effects (senescence, impaired photosynthesis and necrosis) and positive effects (crucial role that superoxide plays against invading microbes) of ROS on plants - Features contributors from a variety of regions globally

The ideal starting point for investigating, developing, and implementing stable isotope technologies. • Guides researchers through basic, tested, and proven protocols including DNA, RNA, protein, and phospholipid fatty acid (PLFA) SIP, from concept and history through detailed methodology, troubleshooting, and interpretation to optimal and future uses. • Explores important and emerging applications of SIP in environmental microbiology, ranging from bioremediation and gene mining to carbon tracking and gut microflora function. • Examines explorations of further elegant isotope labeling technologies such as Raman-FISH, NanoSIMS, and isotope arrays. • Serves as a valuable resource for environmental microbiology students and researchers and genomics, biotechnology, and medical microbiology professionals.

Omics Technologies and Bio-Engineering: Towards Improving Quality of Life, Volume 1 is a unique reference that brings together multiple perspectives on omics research, providing in-depth analysis and insights from an international team of authors. The book delivers pivotal information that will inform and improve medical and biological research by helping readers gain more direct access to analytic data, an increased understanding on data evaluation, and a comprehensive picture on how to use omics data in molecular biology, biotechnology and human health care. - Covers various aspects of biotechnology and bio-engineering using omics technologies - Focuses on the latest developments in the field, including biofuel technologies - Provides key insights into omics approaches in personalized and precision medicine - Provides a complete picture on how one can utilize omics data in molecular biology, biotechnology and human health care

Principles of Nutrigenetics and Nutrigenomics: Fundamentals for Individualized Nutrition is the most comprehensive foundational text on the complex topics of nutrigenetics and nutrigenomics. Edited by three leaders in the field with contributions from the most well-cited researchers conducting groundbreaking research in the field, the book covers how the genetic makeup influences the response to foods and nutrients and how nutrients affect gene expression. Principles of Nutrigenetics and Nutrigenomics: Fundamentals for Individualized Nutrition is broken into four parts providing a valuable overview of genetics, nutrigenetics, and nutrigenomics, and a conclusion that helps to translate research into practice. With an overview of the background, evidence, challenges, and opportunities in the field, readers will come away with a strong understanding of how this new science is the frontier of medical nutrition. Principles of Nutrigenetics and Nutrigenomics: Fundamentals for Individualized Nutrition is a valuable reference for students and researchers studying nutrition, genetics, medicine, and related fields. - Uniquely foundational, comprehensive, and systematic approach with full evidence-based coverage of established and emerging topics in nutrigenetics and nutrigenomics - Includes a valuable guide to ethics for genetic testing for nutritional advice - Chapters include definitions, methods, summaries, figures, and tables to help students, researchers, and faculty grasp key concepts - Companion website includes slide decks, images, questions, and other teaching and learning aids designed to facilitate communication and comprehension of the content presented in the book