Unveiling Microbial Carbon Cycling Processes In Key Us Soils Using Omics PDF Download

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Unveiling Microbial Carbon Cycling Processes in Key U.S. Soils Using "Omics."

Unveiling Microbial Carbon Cycling Processes in Key U.S. Soils Using
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Release: 2014
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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.

Controls of Microbially Mediated Soil Carbon Cycling

Controls of Microbially Mediated Soil Carbon Cycling
Author: Samuel Evan Barnett
Publisher:
Total Pages: 0
Release: 2021
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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.

Carbon and Nitrogen Cycling in Soil

Carbon and Nitrogen Cycling in Soil
Author: Rahul Datta
Publisher: Springer Nature
Total Pages: 498
Release: 2019-08-24
Genre: Nature
ISBN: 9811372640
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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.

Changes in Soil Microbial Communities After Long-term Warming Exposure

Changes in Soil Microbial Communities After Long-term Warming Exposure
Author: William G. Rodríguez-Reillo
Publisher:
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Release: 2019
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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.

Microbes in Land Use Change Management

Microbes in Land Use Change Management
Author: Jay Shankar Singh
Publisher: Elsevier
Total Pages: 611
Release: 2021-08-20
Genre: Science
ISBN: 0323858945
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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

Soil Carbon Dynamics

Soil Carbon Dynamics
Author: Werner L. Kutsch
Publisher: Cambridge University Press
Total Pages: 301
Release: 2010-01-07
Genre: Technology & Engineering
ISBN: 1139483161
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Carbon stored in soils represents the largest terrestrial carbon pool and factors affecting this will be vital in the understanding of future atmospheric CO2 concentrations. This book provides an integrated view on measuring and modeling soil carbon dynamics. Based on a broad range of in-depth contributions by leading scientists it gives an overview of current research concepts, developments and outlooks and introduces cutting-edge methodologies, ranging from questions of appropriate measurement design to the potential application of stable isotopes and molecular tools. It includes a standardised soil CO2 efflux protocol, aimed at data consistency and inter-site comparability and thus underpins a regional and global understanding of soil carbon dynamics. This book provides an important reference work for students and scientists interested in many aspects of soil ecology and biogeochemical cycles, policy makers, carbon traders and others concerned with the global carbon cycle.

Soil Carbon Stabilization to Mitigate Climate Change

Soil Carbon Stabilization to Mitigate Climate Change
Author: Rahul Datta
Publisher: Springer Nature
Total Pages: 336
Release: 2021-08-25
Genre: Technology & Engineering
ISBN: 9813367652
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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

Revealing the Unforeseen Role and Sensitivity of Anoxic Protection in Soil Carbon Cycling

Revealing the Unforeseen Role and Sensitivity of Anoxic Protection in Soil Carbon Cycling
Author: Emily Morgan Lacroix
Publisher:
Total Pages: 0
Release: 2022
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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.

Microbial Food Web Mapping

Microbial Food Web Mapping
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Total Pages: 5
Release: 2015
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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.

The Effect of Compost on Carbon Cycling and the Active Soil Microbiota

The Effect of Compost on Carbon Cycling and the Active Soil Microbiota
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Release: 2014
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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.