Soil dwelling microorganisms are essential components of numerous ecosystem processes and biogeochemical cycles. In particular, they are important actors in terrestrial carbon cycling, producing and turning over soil organic matter. Microbially mediated soil carbon cycling can be influenced by environmental conditions, with soil organic matter dynamics and carbon fate varying across biomes. Drastic alterations to soil habitat conditions brought about through anthropogenic changes to land-use (e.g. agriculture) can greatly influence these processes. However, we are limited in our understanding of how land-use regimes and other environmental conditions control microbially mediated soil carbon cycling. I took three approaches to explore this relationship. First, I examined how bacterial community assembly and composition differed across cropland, old-field, and forest soils. I found that homogeneous selection, whereby selection pressure causes bacterial communities to be more phylogenetically similar to each other than expected by random assembly from a metacommunity, was the dominant bacterial community assembly process across all three land-use types. However, I also found that land-use interacted with soil pH to drive the balance between stochastic and deterministic assembly processes. This result indicates a mechanism by which microbial communities may develop differently across land-use regimes. Second, I examined the overall organic matter turnover across land-use regimes and the identity of the bacterial taxa actively involved in this carbon processing. I found that the dynamics of organic matter turnover and the active bacterial populations involved were distinct across land-use regimes. From these patterns I developed a conceptual model explaining how initial microbial biomass, which is impacted by land-use, may control bacterial activities in organic matter turnover. Finally, I examined the genomic basis of bacterial life history strategies, specifically the copiotroph-oligotroph continuum. Life history strategy can explain both bacterial activity in soil carbon cycling and bacterial response to environmental change. I found that the abundance of transcription factor genes and genes encoding a secretion signal peptide were both genomic signatures of the copiotroph-oligotroph continuum. These signatures can be used to classify diverse microbes based on their life history strategy and may further explain the biological drivers of these strategies. I also developed a toolkit, MetaSIPSim, that simulates metagenomic DNA-stable isotope probing datasets. Such datasets can be used to improve metagenomic DNA-stable isotope probing methodologies and analyses, which in turn can be used to link microbial genes and genomes to in situ carbon cycling activity. Overall, this work advances our knowledge of, and ability to study the ecological and biological controls of bacterially mediated soil carbon cycling.

Microbiome Under Changing Climate: Implications and Solutions presents the latest biotechnological interventions for the judicious use of microbes to ensure optimal agricultural yield. Summarizing aspects of vulnerability, adaptation and amelioration of climate impact, this book provides an important resource for understanding microbes, plants and soil in pursuit of sustainable agriculture and improved food security. It emphasizes the interaction between climate and soil microbes and their potential role in promoting advanced sustainable agricultural solutions, focusing on current research designed to use beneficial microbes such as plant growth promoting microorganisms, fungi, endophytic microbes, and more. Changes in climatic conditions influence all factors of the agricultural ecosystem, including adversely impacting yield both in terms of quantity and nutritional quality. In order to develop resilience against climatic changes, it is increasingly important to understand the effect on the native micro-flora, including the distribution of methanogens and methanotrophs, nutrient content and microbial biomass, among others. Demonstrates the impact of climate change on secondary metabolites of plants and potential responses Incorporates insights on microflora of inhabitant soil Explores mitigation processes and their modulation by sustainable methods Highlights the role of microbial technologies in agricultural sustainability

The 21st century has witnessed a complete revolution in the understanding and description of bacteria in eco- systems and microbial assemblages, and how they are regulated by complex interactions among microbes, hosts, and environments. The human organism is no longer considered a monolithic assembly of tissues, but is instead a true ecosystem composed of human cells, bacteria, fungi, algae, and viruses. As such, humans are not unlike other complex ecosystems containing microbial assemblages observed in the marine and earth environments. They all share a basic functional principle: Chemical communication is the universal language that allows such groups to properly function together. These chemical networks regulate interactions like metabolic exchange, antibiosis and symbiosis, and communication. The National Academies of Sciences, Engineering, and Medicine's Chemical Sciences Roundtable organized a series of four seminars in the autumn of 2016 to explore the current advances, opportunities, and challenges toward unveiling this "chemical dark matter" and its role in the regulation and function of different ecosystems. The first three focused on specific ecosystemsâ€"earth, marine, and humanâ€"and the last on all microbiome systems. This publication summarizes the presentations and discussions from the seminars.

Carbon use efficiency (CUE) is the proportion of carbon consumed by a microbe that is converted to biomass, versus the proportion that is respired as CO2. CUE is an important measurement of the activity of soil microbial communities and a determinant of soil carbon storage. CUE varies significantly across ecosystems, environmental parameters, and taxonomic groups. Though the variation is well documented, the causation is less understood. In order to accurately model ecosystem C fluxes, CUE needs to be more precisely estimated. Using a soil chronosequence and fertility gradient (the "Ecological Staircase" at Jug Handle State Natural Reserve in Mendocino County, California) this dissertation aims to understand the edaphic and biologic controls on CUE. Chapter 1 uses data collected over two years from the Ecological Staircase to identify which edaphic factors are the best estimators of soil microbial CUE. The Ecological Staircase exhibits a wide range of values for many important soil characteristics including pH, nutrient availability and quality, water content, texture, and organic matter content. However, because the chronosequence spans a short distance (~2.5 miles) other confounding factors are kept constant such as vegetation type, climate, parent material, and topography. CUE varies significantly across the chronosequence, peaking at the mid-age site where the environment is limiting but not too stressful. Soil pH, organic matter content, and substrate quality are found to be the most important factors in estimating CUE. Together these factors account for 76% of the variation in CUE across the chronosequence. Chapter 2 focuses on the effects of microbial community composition and functional characteristics on CUE. This chapter utilizes metagenomic sequencing data on samples collected across the chronosequence over the same two-year period as the first chapter. The microbial community composition shifts significantly across the sites and slow-growing taxa like Acidobacteria and fungi are more associated with a higher CUE. Fast-growing taxa like Proteobacteria and Firmicutes are more associated with low CUE. Other important genetic factors include genome size, rRNA operon copy number, genetic diversity, and abundances of genes related to carbon cycling, maintenance metabolism, motility, and membrane transporters. Combined with the results from chapter 1, a conceptual model of ecological strategies across the chronosequence was developed to explain how edaphic, taxonomic, and functional characteristics influence microbial community C cycling. Chapter 3 investigates the mechanism of how soil pH affects CUE. Results from Chapter 1 show that the relationship between CUE and soil pH is non-linear, switching from being positively correlated when pH is below 4.7 to a negative correlation above that threshold. There are multiple reasons that this relationship could exist including changes in microbial community composition, direct stress on microbes when soil becomes too acidic, or other indirect effects on microbial community functions. In order to better understand this mechanism, soil pH was altered in samples from three of the five sites at the Ecological Staircase so that there were samples at low, medium, and high ends of the range of pH at these sites. After a month-long incubation at the new pH values, CUE was measured for each and DNA was extracted from the soils for 16S amplicon sequencing to determine if there were changes in the microbial community composition based on pH changes. Overall the relationship between CUE and pH was quadratic as seen from the observational data in Chapter 1. I determined that pH affects microbial community activity both directly through effects on cellular function as well as indirectly through the role of pH on microbial community composition. Which mechanism was dominant depended upon the initial community; those in the young, fertile sites were more resistant to the effects of pH whereas the infertile sites had much larger shifts in community composition. Together these three chapters provide a comprehensive overview of how edaphic factors, as well as microbial community composition and function, affect microbial carbon use efficiency. These findings are valuable for accurately estimating CUE in C cycling models. This thesis also provides information for determining which types of soils promote soil C accumulation. In addition to improving the understanding of how to incorporate CUE into ecosystem models, it demonstrates how ecological strategies of microbial communities vary across a range of soil fertility.

The fourth edition of Soil Microbiology, Ecology and Biochemistry updates this widely used reference as the study and understanding of soil biota, their function, and the dynamics of soil organic matter has been revolutionized by molecular and instrumental techniques, and information technology. Knowledge of soil microbiology, ecology and biochemistry is central to our understanding of organisms and their processes and interactions with their environment. In a time of great global change and increased emphasis on biodiversity and food security, soil microbiology and ecology has become an increasingly important topic. Revised by a group of world-renowned authors in many institutions and disciplines, this work relates the breakthroughs in knowledge in this important field to its history as well as future applications. The new edition provides readable, practical, impactful information for its many applied and fundamental disciplines. Professionals turn to this text as a reference for fundamental knowledge in their field or to inform management practices. New section on "Methods in Studying Soil Organic Matter Formation and Nutrient Dynamics" to balance the two successful chapters on microbial and physiological methodology Includes expanded information on soil interactions with organisms involved in human and plant disease Improved readability and integration for an ever-widening audience in his field Integrated concepts related to soil biota, diversity, and function allow readers in multiple disciplines to understand the complex soil biota and their function

Soil Carbon Storage: Modulators, Mechanisms and Modeling takes a novel approach to the issue of soil carbon storage by considering soil C sequestration as a function of the interaction between biotic (e.g. microbes and plants) and abiotic (climate, soil types, management practices) modulators as a key driver of soil C. These modulators are central to C balance through their processing of C from both plant inputs and native soil organic matter. This book considers this concept in the light of state-of-the-art methodologies that elucidate these interactions and increase our understanding of a vitally important, but poorly characterized component of the global C cycle. The book provides soil scientists with a comprehensive, mechanistic, quantitative and predictive understanding of soil carbon storage. It presents a new framework that can be included in predictive models and management practices for better prediction and enhanced C storage in soils. Identifies management practices to enhance storage of soil C under different agro-ecosystems, soil types and climatic conditions Provides novel conceptual frameworks of biotic (especially microbial) and abiotic data to improve prediction of simulation model at plot to global scale Advances the conceptual framework needed to support robust predictive models and sustainable land management practices