Download or read book Unveiling Microbial Carbon Cycling Processes in Key U S Soils Using Omics written by and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Soils process and store large amounts of C; however, considerable uncertainty still exists about the details of that influence microbial partitioning of C into soil C pools, and what are the main influential forces that control the fraction of the C input that is stabilized. The soil microbial community is genotypically and phenotypically diverse. Despite our ability to predict the kinds of regional environmental changes that will accompany global climate change, it is not clear how the microbial community will respond to climate-induced modification of precipitation and inter-precipitation intervals, and if this response will affect the fate of C deposited into soil by the local plant community. Part of this uncertainty lies with our ignorance of how the microbial community adapts genotypically and physiologically to changes in soil moisture brought about by shifts in precipitation. Our overarching goal is to harness the power of multiple meta-omics tools to gain greater understanding of the functioning of whole-soil microbial communities and their role in C cycling. We will do this by meeting the following three objectives: 1. Further develop and optimize a combination of meta-omics approaches to study how environmental factors affect microbially-mediated C cycling processes. 2. Determine the impacts of long-term changes in precipitation timing on microbial C cycling using an existing long-term field manipulation of a tallgrass prairie soil. 3. Conduct laboratory experiments that vary moisture and C inputs to confirm field observations of the linkages between microbial communities and C cycling processes. We took advantage of our state-of-the-art expertise in community "omics" to better understand the functioning soil C cycling within the Great Prairie ecosystem, including our ongoing Konza Prairie soil metagenome flagship project at JGI and the unique rainfall manipulation plots (RaMPs) established at this site more than a decade ago. We employed a systems biology approach, considering the complex soil microbial community as a functioning system and using state-of-the-art metatranscriptomic, metaproteomic, and metabolomic approaches. These omics tools were refined, applied to field experiments, and confirmed with controlled laboratory studies. Our experiments were designed to specifically identify microbial community members and processes that are instrumental players in processing of C in the prairie soils and how these processes are impacted by wetting and drying events. This project addresses a key ecosystem in the United States that current climate models predict will be subjected to dramatic changes in rainfall patterns as a result of global warming. Currently Mollisols, such as those of the tallgrass prairie, are thought to sequester more C than is released into the atmosphere, but it is not known what changes in rainfall patterns will have on future C fluxes. Through an analysis of the molecular response of the soil microbial community to shifts in precipitation cycles that are accompanied by phenologically driven changes in quality of plant C rhizodeposits, we gained deeper insight into how the metabolism of microbes has adapted to different precipitation regimes and the impact of this adaption on the fate of C deposited into soil. In doing so, we addressed key questions about the microbial cycling of C in soils that have been identified by the DOE.
Download or read book Controls of Microbially Mediated Soil Carbon Cycling written by Samuel Evan Barnett and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Carbon and Nitrogen Cycling in Soil written by Rahul Datta and published by Springer Nature. This book was released on 2019-08-24 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: Several textbooks and edited volumes are currently available on general soil fertility but‚ to date‚ none have been dedicated to the study of “Sustainable Carbon and Nitrogen Cycling in Soil.” Yet this aspect is extremely important, considering the fact that the soil, as the ‘epidermis of the Earth’ (geodermis)‚ is a major component of the terrestrial biosphere. This book addresses virtually every aspect of C and N cycling, including: general concepts on the diversity of microorganisms and management practices for soil, the function of soil’s structure-function-ecosystem, the evolving role of C and N, cutting-edge methods used in soil microbial ecological studies, rhizosphere microflora, the role of organic matter (OM) in agricultural productivity, C and N transformation in soil, biological nitrogen fixation (BNF) and its genetics, plant-growth-promoting rhizobacteria (PGPRs), PGPRs and their role in sustainable agriculture, organic agriculture, etc. The book’s main objectives are: (1) to explain in detail the role of C and N cycling in sustaining agricultural productivity and its importance to sustainable soil management; (2) to show readers how to restore soil health with C and N; and (3) to help them understand the matching of C and N cycling rules from a climatic perspective. Given its scope, the book offers a valuable resource for educators, researchers, and policymakers, as well as undergraduate and graduate students of soil science, soil microbiology, agronomy, ecology, and the environmental sciences. Gathering cutting-edge contributions from internationally respected researchers, it offers authoritative content on a broad range of topics, which is supplemented by a wealth of data, tables, figures, and photographs. Moreover, it provides a roadmap for sustainable approaches to food and nutritional security, and to soil sustainability in agricultural systems, based on C and N cycling in soil systems.
Download or read book Changes in Soil Microbial Communities After Long term Warming Exposure written by William G. Rodríguez-Reillo and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbial metabolism is a key controller of ecosystem processes (e.g., carbon cycling). However, we are only starting to identify the molecular mechanisms and feedback in response to long-term warming. My dissertation integrates multi-omics techniques to capture changes in soil microbial communities after long-term warming exposure. The research projects leverage three warming sites (i.e., SWaN, Barre Woods, and Prospect Hill) located in Western Massachusetts at Harvard Forest. These sites provided a unique experimental setup to better understand microbes in response to long-term temperature change. For the three research projects, we delved into the (i) microbial biodiversity across all three warming sites, (ii) integration of soil carbon chemistry and metatranscriptomics at the Barre Woods site, (iii) and a time series of soil metatranscriptomes at the Prospect Hill site. Overall, these studies revealed a broader scope of changes occurring with long-term warming than anticipated. The warming treatment induced shifts in fungi groups and recalcitrant carbon decomposer bacteria. Changes in microbial functions involved metabolic pathways associated to biogeochemical and cellular stability as result of nutrient limitation. Further, our results provided new insights in microbial response to chronic temperature stress, suggested an ongoing change in community structure and function, and linked soil carbon decrease to cellular processes using high throughput molecular techniques. This information will help to better understand interactions between microbial communities and the Earth's climate.
Download or read book Soil Carbon Stabilization to Mitigate Climate Change written by Rahul Datta and published by Springer Nature. This book was released on 2021-08-25 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt: Carbon stabilization involves to capturing carbon from the atmosphere and fix it in the forms soil organic carbon stock for a long period of time, it will be present to escape as a greenhouse gas in the form of carbon dioxide. Soil carbon storage is an important ecosystem service, resulting from interactions of several ecological processes. This process is primarily mediated by plants through photosynthesis, with carbon stored in the form of soil organic carbon. Soil carbon levels have reduced over decades of conversion of pristine ecosystems into agriculture landscape, which now offers the opportunity to store carbon from air into the soil. Carbon stabilization into the agricultural soils is a novel approach of research and offers promising reduction in the atmospheric carbon dioxide levels. This book brings together all aspects of soil carbon sequestration and stabilization, with a special focus on diversity of microorganisms and management practices of soil in agricultural systems. It discusses the role of ecosystem functioning, recent and future prospects, soil microbial ecological studies, rhizosphere microflora, and organic matter in soil carbon stabilization. It also explores carbon transformation in soil, biological management and its genetics, microbial transformation of soil carbon, plant growth promoting rhizobacteria (PGPRs), and their role in sustainable agriculture. The book offers a spectrum of ideas of new technological inventions and fundamentals of soil sustainability. It will be suitable for teachers, researchers, and policymakers, undergraduate and graduate students of soil science, soil microbiology, agronomy, ecology, and environmental sciences
Download or read book Microbes in Land Use Change Management written by Jay Shankar Singh and published by Elsevier. This book was released on 2021-08-20 with total page 611 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbes in Land Use Change Management details the various roles of microbial resources in management of land uses and how the microbes can be used for the source of income due to their cultivation for the purpose of biomass and bioenergy production. Using various techniques, the disturbed and marginal lands may also be restored eco-friendly in present era to fulfil the feeding needs of mankind around the globe. Microbes in Land Use Change Management provides standard and up to date information towards the land use change management using various microbial technologies to enhance the productivity of agriculture. Needless to say that Microbes in Land Use Change Management also considers the areas including generation of alternative energy sources, restoration of degraded and marginal lands, mitigation of global warming gases and next generation -omics technique etc. Land use change affects environment conditions and soil microbial community. Microbial population and its species diversity have influence in maintaining ecosystem balance. The study of changes of microbial population provides an idea about the variation occurring in a specific area and possibilities of restoration. Meant for a multidisciplinary audience Microbes in Land Use Change Management shows the need of next-generation omics technologies to explore microbial diversity. Describes the role of microbes in generation of alternative source of energy Gives recent information related to various microbial technology and their diversified applications Provides thorough insight in the problems related to landscape dynamics, restoration of soil, reclamation of lands mitigation of global warming gases etc. eco-friendly way using versatility of microbes Includes microbial tools and technology in reclamation of degraded, disturbed and marginal lands, mitigation of global warming gases
Download or read book Revealing the Unforeseen Role and Sensitivity of Anoxic Protection in Soil Carbon Cycling written by Emily Morgan Lacroix and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Increasing soil carbon (C) content promises to mitigate climate change and enhance soil fertility. Soil C content is determined, in part, by microbial respiration, which converts soil C into carbon dioxide. Carbon protection mechanisms represent processes and conditions that limit microbial respiration of soil C. Anoxic microsites, zones of oxygen depletion in otherwise oxic soils, are a recently recognized and under-studied soil C protection mechanism. In this dissertation, I use field and laboratory methods to determine the extent and contribution of anoxic microsites to soil C protection within natural and agricultural systems. In Chapter 2, I measure the dissolved oxygen content of soil porewater from California agricultural soils. I show that physical disturbance destroys anoxic microsites through enhancing oxygen supply to the smallest soil pores. In Chapter 3, I show that oxygen limitations constrain OM turnover in a Hawaiian rainforest soil, an environment where mineral content is presumed to be the dominant soil C protection mechanism. In Chapter 4, I examine a soil textural gradient at the Stanford Dish and demonstrate that anoxic microsites are particularly important for protecting C in coarsely textured soils. Finally, in Chapter 5, I use droplet digital PCR to quantify anaerobe DNA (a proxy for anoxic microsites) in soils from four long-term agricultural experiments across the continental United States. I show that anoxic microsites vary with soil properties, respond to management, and uniquely contribute to soil C stabilization within cropland soils. In sum, this dissertation reveals that anoxic microsites represent a vulnerability in the soil C stock but also an opportunity to enhance soil C storage.
Download or read book Microbial Food Web Mapping written by and published by . This book was released on 2015 with total page 5 pages. Available in PDF, EPUB and Kindle. Book excerpt: Soil represents a massive reservoir of active carbon and climate models vary dramatically in predicting how this carbon will respond to climate change over the coming century. A major cause of uncertainty is that we still have a very limited understand the microorganisms that dominate the soil carbon cycle. The vast majority of soil microbes cannot be cultivated in the laboratory and the diversity of organisms and enzymes that participate in the carbon cycle is staggeringly complex. We have developed a new toolbox for exploring the carbon cycle and the metabolic and ecological characteristics of uncultivated microorganisms. The high-resolution nucleic acid stable isotope probing approach that we have developed makes it possible to characterize microbial carbon cycling dynamics in soil. The approach allows us to track multiple 13C-labeled substrates into thousands of microbial taxa over time. Using this approach we have discovered several major lineages of uncultivated microorganisms that participate in cellulose metabolism and are found widely in soils (including Verrucomicrobia and Chloroflexi, which have not previously been implicated as major players in the soil carbon cycle). Furthermore, isotopic labelling of nucleic acids enables community genomics and permits genome fragment binning for a majority of these cellulolytic microorganisms allowing us to explore the metabolic underpinnings of cellulose degradation. This approach has allowed us to describe unexpected dynamics of carbon metabolism with different microbial taxa exhibiting characteristic patterns of carbon substrate incorporation, indicative of distinct ecological strategies. The data we describe allows us to characterize the activity of novel microorganisms as they occur in the environment and these data provide a basis for understanding how the physiological traits of discrete microorganisms sum to govern the complex responses of the soil carbon cycle.
Download or read book Microbial Ecology written by Diana Marco and published by . This book was released on 2019-01-31 with total page 126 pages. Available in PDF, EPUB and Kindle. Book excerpt: Selected recent hot-topics in the application of advanced omics methods to the field of microbial ecology.
Download or read book The Effect of Compost on Carbon Cycling and the Active Soil Microbiota written by and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Rangelands cover an estimated 40-70percent of global landmass, approximately one-third of the landmass of the United States and half of California. The soils of this vast land area has high carbon (C) storage capacity, which makes it an important target ecosystem for the mitigation of greenhouse gas emission and effects on climate change, in particular under land management techniques that favor increased C sequestration rates. While microbial communities are key players in the processes responsible for C storage and loss in soils, we have barely shed light on these highly complex processes in part due to the tremendous and seemingly intractable diversity of microbes, largely uncultured, that inhabit soil ecosystems. In our study, we compare Mediterranean grassland soil plots that were amended with greenwaste compost in a single event 6 years ago. Subsampling of control and amended plots was performed in depth increments of 0-10 cm. We present data on greenhouse gas emissions and budgets of carbon, nitrogen, phosphorus, and micronutrients in dependence of compost amendment. Changes in the active members of the soil microbial community were assessed using a novel approach combining flow cytometry and 16S tag sequencing disclosing who is active. This is the first study revealing the nature of actively metabolizing microbial community members linked to the geochemical characteristics of compost-amended soil.
Download or read book Illuminating Microbial Contributions To Soil Carbon Cycling Dynamics Using High Resolution Stable Isotope Probing written by Ashley Nicole Campbell and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Soil Microbiome in Green Technology Sustainability written by Sesan Abiodun Aransiola and published by Springer Nature. This book was released on with total page 601 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Soil Microbial Responses to Different Precipitation Regimes Across a Southwestern United States Elevation Gradient written by Brittney Monus and published by . This book was released on 2019 with total page 49 pages. Available in PDF, EPUB and Kindle. Book excerpt: Soil organic carbon (SOC) is a critical component of the global carbon (C) cycle, accounting for more C than the biotic and atmospheric pools combined. Microbes play an important role in soil C cycling, with abiotic conditions such as soil moisture and temperature governing microbial activity and subsequent soil C processes. Predictions for future climate include warmer temperatures and altered precipitation regimes, suggesting impacts on future soil C cycling. However, it is uncertain how soil microbial communities and subsequent soil organic carbon pools will respond to these changes, particularly in dryland ecosystems. A knowledge gap exists in soil microbial community responses to short- versus long-term precipitation alteration in dryland systems. Assessing soil C cycle processes and microbial community responses under current and altered precipitation patterns will aid in understanding how C pools and cycling might be altered by climate change. This study investigates how soil microbial communities are influenced by established climate regimes and extreme changes in short-term precipitation patterns across a 1000 m elevation gradient in northern Arizona, where precipitation increases with elevation. Precipitation was manipulated (50% addition and 50% exclusion of ambient rainfall) for two summer rainy seasons at five sites across the elevation gradient. In situ and ex situ soil CO2 flux, microbial biomass C, extracellular enzyme activity, and SOC were measured in precipitation treatments in all sites. Soil CO2 flux, microbial biomass C, extracellular enzyme activity, and SOC were highest at the three highest elevation sites compared to the two lowest elevation sites. Within sites, precipitation treatments did not change microbial biomass C, extracellular enzyme activity, and SOC. Soil CO2 flux was greater under precipitation addition treatments than exclusion treatments at both the highest elevation site and second lowest elevation site. Ex situ respiration differed among the precipitation treatments only at the lowest elevation site, where respiration was enhanced in the precipitation addition plots. These results suggest soil C cycling will respond to long-term changes in precipitation, but pools and fluxes of carbon will likely show site-specific sensitivities to short-term precipitation patterns that are also expected with climate change.
Download or read book Soil Carbon Cycling Constrained by Oxygen dependent Enzyme Activity and Microbial Energetics written by Hannah Rose Naughton and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Soils contain up to three times as much dynamic carbon as the atmosphere, making them a critical carbon sink. Soil organic carbon (SOC) performs ecosystem services such as atmospheric carbon sequestration, retention of nutrients and water, promotion of good soil structure, and fueling microbial activity that leads to soil fertility. However, future climate and land use change endanger soil carbon stocks. An incomplete understanding of the mechanisms behind SOC degradation hinders our ability to model carbon cycling, particularly considering temporally and spatially heterogeneous soils. One key factor is the role oxygen availability plays in microbial energetics and enzyme activity, information critical to providing mechanistic predictions of SOC decay. My research explores how oxygen limitations and ensuing redox heterogeneity in soils control both the energetics of respiration, which ultimately controls greenhouse gas production of soils, and microbial access to organic substrates via oxidative enzyme depolymerization. I use both laboratory soil reactors and a floodplain field site as soil environments with spatially or temporally varying oxygen availability to test for enzymatic and thermodynamic limitations on SOC degradation and accompanying greenhouse gas production. Soil redox environment altered dissolved organic carbon (DOC) composition and chemistry over short times in the reactor setup and over short spatial scales in field soils. Oxygen-limited soils had more reduced organic C corresponding to lower thermodynamic favorability as a microbial substrate in anaerobic metabolisms. The reactors had a stark increase in relative abundance of lignin-like carbon going from aerobic to anaerobic environments, indicative of enzymatic limitations, but field soils indicated plant inputs counteract this often depth-related pattern. Aeration of soils resulted in equivalent respiration when normalized to SOC content, regardless of original microbial community or SOC composition, even in methanogenic soils lacking saprotrophic communities. This finding prompted exploration of the potential for abiotic, metal-catalyzed processes to depolymerize SOC in redox-heterogeneous floodplain soils. Ferrous iron better corresponded to phenol oxidation potential than any microbial or carbon-related predictors, highlighting the potential for rapid oxidative SOC depolymerization upon aeration of permanently or temporarily saturated soils containing reduced transition metals. Altogether, this work highlights the rapidity with which novel redox status of soils alters SOC composition, favorability as a microbial substrate, and potential for unexpected greenhouse gas release. Terrestrial carbon models are unlikely to accurately predict future stocks and fluxes of SOC if they do not account for the influence of heterogeneity of oxygen availability and ensuing effects on carbon lability.
Download or read book The New Science of Metagenomics written by National Research Council and published by National Academies Press. This book was released on 2007-06-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Marine OMICS written by Se-Kwon Kim and published by CRC Press. This book was released on 2016-11-18 with total page 922 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides comprehensive coverage on current trends in marine omics of various relevant topics such as genomics, lipidomics, proteomics, foodomics, transcriptomics, metabolomics, nutrigenomics, pharmacogenomics and toxicogenomics as related to and applied to marine biotechnology, molecular biology, marine biology, marine microbiology, environmental biotechnology, environmental science, aquaculture, pharmaceutical science and bioprocess engineering.
Download or read book Modern Soil Microbiology Second Edition written by Jan Dirk van Elsas and published by CRC Press. This book was released on 2006-12-21 with total page 704 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the ten years since the publication of Modern Soil Microbiology, the study of soil microbiology has significantly changed, both in the understanding of the diversity and function of soil microbial communities and in research methods. Ideal for students in a variety of disciplines, this second edition provides a cutting-edge examination of a fascinating discipline that encompasses ecology, physiology, genetics, molecular biology, and biotechnology, and makes use of biochemical and biophysical approaches. The chapters cover topics ranging from the fundamental to the applied and describe the use of advanced methods that have provided a great thrust to the discipline of soil microbiology. Using the latest molecular analyses, they integrate principles of soil microbiology with novel insights into the physiology of soil microorganisms. The authors discuss the soil and rhizosphere as habitats for microorganisms, then go on to describe the different microbial groups, their adaptive responses, and their respective processes in interactive and functional terms. The book highlights a range of applied aspects of soil microbiology, including the nature of disease-suppressive soils, the use of biological control agents, biopesticides and bioremediation agents, and the need for correct statistics and experimentation in the analyses of the data obtained from soil systems.
