Download or read book Characterization of Soil Denitrifier Diversity written by Constance A. Roco and published by . This book was released on 2015 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: Denitrification is a part of the global nitrogen cycle in which reactive nitrogen in the biosphere is returned to the atmosphere, and is mediated by diverse communities of microorganisms. The work in this thesis was undertaken to gain a greater understanding of the ecology of denitrifying microorganisms. A combination of bioinformatic analysis of denitrification genes in pure cultures and environmental samples, as well as experimental work with denitrifying bacterial cultures and soil microcosms was performed to understand the relationship between genes and ecosystems in denitrification. First, we examined the diversity of denitrifiers in soil through genome sequencing of microbial isolates coupled to denitrification gas kinetic measurements. The results suggest that partial denitrifiers are common among soil bacteria and it was demonstrated that nitrogen oxide production could not always be predicted by the genetic potential of the isolates. This reveals there are different regulatory effects on each step of the denitrification pathway, which dictate the accumulation of denitrification products. Secondly, the prevalence of dissimilatory reduction of nitrate under aerobic conditions in soil was assessed. Bacteria capable of aerobic nitrate reduction were easily isolated and found to reduce nitrate at oxygen concentrations greater than levels associated with the onset of nitrite reduction and the genomic analysis of the nitrate reductase genes revealed a wide diversity of physiological controls. Finally, a soil microcosm study was performed to determine the influence of oxygen on denitrification gas kinetics and denitrifier community structure. Comparison of soils exposed to oxic, short anoxic and long anoxic conditions revealed the oxic soils had fastest denitrification rates, indicating denitrifiers were not hindered by oxic conditions. The genetic community structure, characterized through metagenomic and metatranscriptomic analysis, was shown to be an important factor in determining denitrification rates and end product ratios. In conclusion, denitrification is a complex pathway of ecological importance that is controlled by the interaction between genes and environmental factors. In order to develop useful tools to mitigate reactive nitrogen and other climate-forcing nitrogen species, a comprehensive understanding of the regulatory network of denitrification with respect to microbial physiology and environmental interactions is needed.

Download or read book Biology of the Nitrogen Cycle written by Hermann Bothe and published by Elsevier. This book was released on 2007 with total page 451 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Molecular Approaches to Soil Rhizosphere and Plant Microorganism Analysis written by John Eric Cooper and published by CABI. This book was released on 2006 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plants have evolved both general and highly specialized defence mechanisms that function to prevent diseases caused by the majority of microbial pathogens they encounter. Highly specialized defence is governed by specific interactions between pathogen avr (avirulence) genes' loci and alleles of the corresponding plant disease resistance (R) loci. These defences can be very dynamic as microbes from the same species can act differently in their co-evolution with the specific host plant, which in turn has similarly evolved its response to external threats. There have been major developments in the field of plant-microbe interactions in recent years, due to newly developed techniques and the availability of genomic information. Molecular Plant-Microbe Interactions explores these new discoveries, focusing primarily on the mechanisms controlling plant disease resistance, the cross-talk among the pathways involved and the strategies used by the pathogens to suppress these defences. By exploring developments in plant defences, pathogen's counter-defences and mutually beneficial plant-microbe interactions, this book will be useful for researchers and students in plant pathology and plant biology-related areas.

Download or read book Bacterial Diversity and Denitrifier Communities in Arable Soils written by Sara Victoria Coyotzi Alcaraz and published by . This book was released on 2014 with total page 99 pages. Available in PDF, EPUB and Kindle. Book excerpt: Agricultural management is essential for achieving optimum crop production and maintaining soil quality. Soil microorganisms are responsible for nutrient cycling and are an important consideration for effective soil management. The overall goal of the present research was to better understand microbial communities in agricultural soils as they relate to soil management practices. For this, we evaluated the differential impact of two contrasting drainage practices on microbial community composition and characterized active denitrifiers from selected agricultural sites. Field drainage is important for crop growth in arable soils. Controlled and uncontrolled tile drainage practices maintain water in the field or fully drain it, respectively. Because soil water content influences nutrient concentration, moisture, and oxygen availability, the effects of these two disparate practices on microbial community composition was compared in paired fields that had diverse land management histories. Libraries of the 16S rRNA gene were generated from DNA from 168 soil samples collected from eight fields during the 2012 growing season. Paired-end sequencing using next-generation sequencing was followed by read assembly and multivariate statistical analyses. Results showed that drainage practice exerted no measureable effect on the bacterial communities. However, bacterial communities were impacted by plant cultivar and applied fertilizer, in addition to sampled soil depth. Indicator species were only recovered for depth; plant cultivar or applied fertilizer type had no strong and specific indicator species. Among indicator species for soil depth (30-90 cm) were Chloroflexi (Anaerolineae), Betaproteobacteria (Janthinobacterium, Herminiimonas, Rhodoferax, Polaromonas), Deltaproteobacteria (Anaeromyxobacter, Geobacter), Alphaproteobacteria (Novosphingobium, Rhodobacter), and Actinobacteria (Promicromonospora). Denitrification in agricultural fields transforms nitrogen applied as fertilizer, reduces crop production, and emits N2O, which is a potent greenhouse gas. Agriculture is the highest anthropogenic source of N2O, which underlines the importance of understanding the microbiology of denitrification for reducing greenhouse gas emissions by altered management practices. Existing denitrifier probes and primers are biased due to their development based mostly on sequence information from cultured denitrifiers. To circumvent this limitation, this study investigated active and uncultivated denitrifiers from two agricultural sites in Ottawa, Ontario. Using DNA stable-isotope probing, we enriched nucleic acids from active soil denitrifiers by exposing intact replicate soil cores to NO3- and 13C6-glucose under anoxic conditions using flow-through reactors, with parallel native substrate controls. Spectrophotometric chemistry assays and gas chromatography confirmed active NO3- depletion and N2O production, respectively. Duplicate flow-through reactors were sacrificed after one and four week incubation periods to assess temporal changes due to food web dynamics. Soil DNA was extracted and processed by density gradient ultracentrifugation, followed by fractionation to separate DNA contributed by active denitrifiers (i.e., “heavy” DNA) from that of the background community (i.e., “light” DNA). Light and heavy DNA samples were analyzed by paired-end sequencing of 16S rRNA genes using next-generation sequencing. Multivariate statistics of assembled 16S rRNA genes confirmed unique taxonomic representation in heavy fractions from flow-through reactors fed 13C6-glucose, which exceeded any site-specific or temporal shifts in putative denitrifiers. Based on high relative abundance in heavy DNA, labelled taxa affiliated with the Betaproteobacteria (71%; Janthinobacterium, Acidovorax, Azoarcus, Dechloromonas), Alphaproteobacteria (8%; Rhizobium), Gammaproteobacteria (4%; Pseudomonas), and Actinobacteria (4%; Streptomycetaceae). Metagenomic DNA from the original soil and recovered heavy fractions were subjected to next-generation sequencing and the results demonstrated enrichment of denitrification genes with taxonomic affiliations to Brucella, Ralstonia, and Chromobacterium in heavy fractions of flow-through reactors fed 13C6-glucose. The vast majority of heavy-DNA-associated nitrite-reductase reads annotated to the copper-containing form (nirK), rather than the heme-containing enzyme (nirS). Analysis of recovered nirK genes demonstrated low sequence identity across common primer-binding sites used for the detection and quantification of soil denitrifiers, indicating that these active denitrifiers would not have been detected in molecular surveys of these same soils.

Download or read book Soil Nitrogen Uses and Environmental Impacts written by Rattan Lal and published by CRC Press. This book was released on 2018-03-15 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nitrogen (N) is potentially one of the most complex elements on the Earth. It is necessary for all biological activity, but creates negative impacts on water and air quality. There is a balancing act between deficiency and surplus and the forms of N available further complicate our understanding of the dynamics. Biological fixation provides some plants with N supply while others are totally dependent upon N being available in the soil profile for the roots to extract. Nevertheless, the demand for N will increase because the human population with its increasing growth requires more protein and thus more N. Understanding the global N cycle is imperative to meeting current and future nitrogen demands while decreasing environmental impacts. This book discusses availability, production, and recycling of N in air, water, plants, and soils. It features information on N impacts to soil and water quality, management of N in agroecosystems, and techniques to maximize the use efficiency while minimizing the risks of leakage of reactive N into the environment. This volume in the Advances in Soil Science series is specifically devoted to availability, production, and recycling of N with impact on climate change and water quality, and management of N in agroecosystems in the context of maximizing the use efficiency and minimizing the risks of leakage of reactive N (NO-3, N¬2O) into the environment.

Download or read book Metalloenzymes in Denitrification written by Isabel Moura and published by Royal Society of Chemistry. This book was released on 2016-11-15 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: The reduction of nitrate to nitrogen by metalloenzymes is a vital step in the nitrogen cycle. The importance of this pathway has inspired efforts to understand in greater depth the mechanisms involved. This book presents and discusses the latest information on multiple aspects of denitrification. Written by recognized specialists in the field, this book describes the bioinorganic aspects and the key enzymes involved in denitrification, including their structure, function and mechanisms. Active site modelling, novel methodologies for monitoring denitrification in vivo and biotechnological methods for water treatment are discussed. The book also focusses on the environmental implications of denitrification, such nitrate accumulation and the release of nitrous oxide into the atmosphere from excessive fertiliser use. An important topic in many biological, environmental and agricultural contexts, this book will aid teaching and help bioinorganic chemists and biotechnologists gain an up-to-date picture of the science behind the denitrification process.

Download or read book Soil Water Solute Process Characterization written by Javier Alvarez-Benedi and published by CRC Press. This book was released on 2004-12-28 with total page 816 pages. Available in PDF, EPUB and Kindle. Book excerpt: The practitioner or researcher often faces complex alternatives when selecting a method to characterize properties governing a soil process. After years of research and development, environmental and agricultural professionals now have an array of methods for characterizing soil processes. Well-established methods, however, may not be suitable for

Download or read book Nitrogen in the Marine Environment written by Edward J. Carpenter and published by Elsevier. This book was released on 2013-10-22 with total page 919 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nitrogen in the Marine Environment provides information pertinent to the many aspects of the nitrogen cycle. This book presents the advances in ocean productivity research, with emphasis on the role of microbes in nitrogen transformations with excursions to higher trophic levels. Organized into 24 chapters, this book begins with an overview of the abundance and distribution of the various forms of nitrogen in a number of estuaries. This text then provides a comparison of the nitrogen cycling of various ecosystems within the marine environment. Other chapters consider chemical distributions and methodology as an aid to those entering the field. This book discusses as well the enzymology of the initial steps of inorganic nitrogen assimilation. The final chapter deals with the philosophy and application of modeling as an investigative method in basic research on nitrogen dynamics in coastal and open-ocean marine environments. This book is a valuable resource for plant biochemists, microbiologists, aquatic ecologists, and bacteriologists.

Download or read book Environmental Heterogeneity Effects on Diversity and Nitrous Oxide Emissions from Soil in Restored Prairie written by Drew A. Scott and published by . This book was released on 2019 with total page 230 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ecological theory predicts that high environmental heterogeneity causes high biodiversity. Theory further predicts that more biodiversity results in greater ecosystem functioning. These theoretical predictions were evaluated in three studies using grassland restorations from agriculture. The 'environmental heterogeneity hypothesis' has been proposed as a mechanism that enables species coexistence through resource partitioning. In accordance with this hypothesis, plant diversity is predicted to increase with variability in resources, but there has been weak support for this hypothesis from experimental studies. The objective of this research was to characterize how resource availability and heterogeneity (coefficient of variation) change as plant communities develop using a chronosequence of restored prairies. More specifically, we quantified means and coefficients of variation in soil nitrate and light availability (proportion of photosynthetically active radiation [PAR] reaching soil surface) in prairies established on former agricultural lands for different times (ages) and their relationship to plant diversity and community structure using a geostatistically informed design. Nitrate availability decreased exponentially with restoration age, but there was no directional change in nitrate heterogeneity across the chronosequence. Light availability also decreased exponentially across the chronosequence, but PAR heterogeneity increased with restoration age. Heterogeneity in resources did not affect plant community structure, but heterogeneity in nitrate and light were positively related to plant Shannon's Diversity (H). The heterogeneity effects on H were less when considering nitrate and PAR availability. Similarly, richness responded positively to heterogeneity in nitrate and PAR, but only nitrate heterogeneity effects were weakened by resource availability. No significant heterogeneity effects were found for Pielou's evenness, suggesting diversity responses to heterogeneity were mostly driven by changes in richness. Overall, these results suggest that environmental heterogeneity corresponds with plant diversity as predicted by the 'environmental heterogeneity hypothesis', but high resource availability can weaken this relationship. Plant species identity, soil depth, soil nutrient availability, and their interactions have the potential to structure soil microbial communities. If distinct communities were present within combinations of different combinations of levels of these ecosystem properties, this would indicate heterogeneity promotes soil microbial diversity. I used a 20 year restored prairie with soil depth (shallow and deep) and nutrient manipulation (reduced N availability, ambient N availability, and elevated N availability) and used three plant treatments (Andropogon gerardii, Salvia azurea, and bare soil) to evaluate the relative effects of these treatments and their interactions on the soil microbial community as measured by phospholipid fatty acid (PLFA) profiles. Permutational multivariate analysis of variance of PLFA biomass was conducted as was mixed model analysis of Shannon diversity index (H), richness (S), and Pielou's evenness (J). Treatments had no effect on microbial community structure. The main effect of plant species treatment influenced PLFA H. This was due to differences between bare soil and the two rhizosphere soils, where rhizosphere soils had greater proportional arbuscular mycorrhizal fungi and Gram-negative bacteria. This indicates that increasing plant cover promotes microbial diversity. While we did not detect distinct microbial communities in treatment combinations, molecular methods may be more sensitive and indicate if environmental heterogeneity is likely to promote soil microbial diversity. Plant diversity has been shown to increase several ecosystem functions including primary productivity, nutrient retention, and carbon sequestration. We tested if plant diversity could mitigate nitrous oxide emissions. We used an initial survey to determine study design from quadrat and semivariogram analyses and to determine cutoffs for high- and low-plant diversity. We sampled high- and low-diversity plant communities from five 10 to 12 y restorations co-located at Nachusa grasslands (Franklin Grove, IL, USA). We demonstrated that the diversity treatments were associated with high- and low-levels of species richness, species evenness, and functional group richness. We found the nitrous oxide emissions from high-diversity plant communities were approximately half the emissions from low-diversity plant communities. Differences in emissions did not coincide with differences in water availability, nitrogen availability, carbon availability, or microbial activity. Soils exhibited more N2O emission hotspots from denitrification in the low plant diversity treatment. This suggests that plant diversity is affecting the physiology or the community structure of soil denitrifiers. This work indicates that nitrous oxide emissions can be managed by creating high-diversity plant communities.

Download or read book Coastal environmental and ecological data analysis written by Meilin Wu and published by Frontiers Media SA. This book was released on 2023-04-17 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Handbook of Soil Sciences Two Volume Set written by Pan Ming Huang and published by CRC Press. This book was released on 2018-10-03 with total page 2249 pages. Available in PDF, EPUB and Kindle. Book excerpt: An evolving, living organic/inorganic covering, soil is in dynamic equilibrium with the atmosphere above, the biosphere within, and the geology below. It acts as an anchor for roots, a purveyor of water and nutrients, a residence for a vast community of microorganisms and animals, a sanitizer of the environment, and a source of raw materials for co

Download or read book Emerging Frontiers of Microbial Functions in Sustainable Agriculture written by Manoj Kumar Solanki and published by Frontiers Media SA. This book was released on 2023-02-15 with total page 198 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Nucleic Acids and Proteins in Soil written by Paolo Nannipieri and published by Springer Science & Business Media. This book was released on 2006-09-22 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: With millions of different bacterial species living in soil, the microbial community is extremely complex, varying at very small scales. Microbe-driven functions are essential for most processes in soil. Thus, a better understanding of this microbial diversity will be invaluable for the management of the various soil functions. Nucleic Acids and Proteins in Soil combines traditional approaches in soil microbiology and biochemistry with the latest techniques in molecular microbial ecology. Included are methods to analyse the presence and importance of nucleic acids and proteins both inside and outside microbial cells, the horizontal gene transfer which drives bacterial diversity, as well as soil proteomes. Further chapters describe techniques such as PCR, fingerprinting, the challenging use of gene arrays for structural and functional analysis, stable isotope probing to identify in situ metabolic functions, and the use of marker and reporter genes in soil microbial ecology.

Download or read book The Ecology of Agricultural Landscapes written by Stephen K. Hamilton and published by Long-Term Ecological Research. This book was released on 2015 with total page 449 pages. Available in PDF, EPUB and Kindle. Book excerpt: Evidence has been mounting for some time that intensive row-crop agriculture as practiced in developed countries may not be environmentally sustainable, with concerns increasingly being raised about climate change, implications for water quantity and quality, and soil degradation. This volume synthesizes two decades of research on the sustainability of temperate, row-crop ecosystems of the Midwestern United States. The overarching hypothesis guiding this work has been that more biologically based management practices could greatly reduce negative impacts while maintaining sufficient productivity to meet demands for food, fiber and fuel, but that roadblocks to their adoption persist because we lack a comprehensive understanding of their benefits and drawbacks. The research behind this book, based at the Kellogg Biological Station (Michigan State University) and conducted under the aegis of the Long-term Ecological Research network, is structured on a foundation of large-scale field experiments that explore alternatives to conventional, chemical-intensive agriculture. Studies have explored the biophysical underpinnings of crop productivity, the interactions of crop ecosystems with the hydrology and biodiversity of the broader landscapes in which they lie, farmers' views about alternative practices, economic valuation of ecosystem services, and global impacts such as greenhouse gas exchanges with the atmosphere. In contrast to most research projects, the long-term design of this research enables identification of slow or delayed processes of change in response to management regimes, and allows examination of responses across a broader range of climatic variability. This volume synthesizes this comprehensive inquiry into the ecology of alternative cropping systems, identifying future steps needed on the path to sustainability.

Download or read book Advances in Agronomy written by and published by Elsevier. This book was released on 2007-10-31 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Agronomy continues to be recognized as a leading reference and a first-rate source for the latest research in agronomy. As always, the subjects covered are varied and exemplary of the myriad of subject matter dealt with by this long-running serial. Volume 96 contains seven superior reviews with 25 tables.* Maintains the highest impact factor among serial publications in Agriculture * Presents timely reviews on important agronomy issues * Enjoys a long-standing reputation for excellence in the field

Download or read book The Impact of Microorganisms on Consumption of Atmospheric Trace Gases written by Steffen Kolb and published by Frontiers Media SA. This book was released on 2017-11-29 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gases with a mixing ratio of less than one percent in the lower atmosphere (i.e. the troposphere) are considered as trace gases. Numerous of these trace gases originate from biological processes in marine and terrestrial ecosystems. These gases are of relevance for the climate as they contribute to global warming or to the troposphere’s chemical reactive system that builds the ozone layer or they impact on the stability of aerosols, greenhouse, and pollutant gases. These reactive trace gases include methane, a multitude of volatile organic compounds of biogenic origin (bVOCs) and inorganic gases such as nitrogen oxides or ozone. The regulatory function of microorganisms for trace gas cycling has been intensively studied for the greenhouse gases nitrous oxide and methane, but is less well understood for microorganisms that metabolize molecular hydrogen, carbon monoxide, or bVOCs. The studies compiled this Research Topic reflect this very well. While a number of articles focus on nitrous oxide and methane or carbon monoxide oxidation, only a few articles address conversion processes of further bVOCs. The Research Topic is complemented by three review articles about the consumption of methane and monoterpenes, as well as the role of the phyllosphere as a particular habitat for trace gas-consuming microorganisms, and point out future research directions in the field. The presented scientific work illustrates that the field of microbial regulation of trace glas fluxes is still in its infancy when one broadens the view on gases beyond methane and nitrous oxide. However, there is a societal need to better predict global dynamics of trace gases that impact on the functionality and warming of the troposphere. Upcoming modelling approaches will need further information on process rates, features and distribution of the driving microorganisms to fullfill this demanding task.

Download or read book Impact of Plant Identity Diversity and Composition on Diversity Composition and Function of NirK type Denitrifying Microorganisms in Temperate Grassland Soil written by and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The impact of plant species, the number of plant species (diversity) and the composition of plant species on nirK-type denitrifying microorganisms in soil was studied. NirK encodes the enzyme nitrite reductase which is the key enzyme for dissimilatory nitrate reduction. As a measure for denitrifier function, net and gross dinitrogenoxide (N2O) production rates and denitrifier enzyme activity were determined. Plant identity, diversity and composition influenced the composition of denitrifiers in soil and partially their function. The plant species were Arrhenatherum elatius, Anthoxanthum odoratum, Alopecurus pratensis, Holcus lanatus, Geranium pratense, Plantago lanceolata, Ranunculus acris and Taraxacum officinale. For this study, the following techniques were applied: T-RFLP (terminal restriction fragment length polymorphism), analysis of variance, analysis of covariance, correspondence analysis, canonical correspondence analysis, determination of diversity indices, maximum likelihood.