Download or read book Effects of Redox cycling on Iron mineral Transformations and Metatranscriptome of Iron III reducing Bacteria in a Humid Tropical Forest Soil written by Jared Lee Wilmoth and published by . This book was released on 2016 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt: The reactivity of iron(III)-(oxyhydr)oxides toward microbial iron(III)-reduction is dependent on mineral reactive surface area and solubility, properties that can be altered by redox cycling. Because carbon (C) stability and nutrient availability can be influenced by redox dynamics, there is a need to evaluate the mechanisms that govern iron(III)-(oxyhydr)oxide transformations and strategies of microbial iron(III)-reducers to access these phases under fluctuating redox conditions in soils. To do this, we characterized the native iron phases in soils from the Bisley Watershed, Luquillo Critical Zone Observatory (LCZO), PR using selective chemical extractions, X-ray diffraction and 57Fe-Mössbauer spectroscopy. We then conducted laboratory experiments where we exposed the soils to redox cycles with variable iron(II)-oxidation rates and measured changes in the solution and solid phase iron speciation as well as sequenced mRNA extracted from native iron(III)-reducing bacteria. The native iron composition in the LCZO soil comprised goethite and lepidocrocite, with higher solid phase iron(II) correlated with higher lepidocrocite abundance and citrate-ascorbate extractable (low crystallinity) iron. 57Iron-Mössbauer spectra at 140 Kelvin (K) show that iron-(oxyhydr)oxides underwent either an increase or a decrease in crystal order due to rate of iron(II)-oxidation over multiple redox cycles in laboratory incubations. Soil RNA isolated following multiple redox cycles was subsequently depleted of rRNA and enriched for mRNA by linear amplification. De novo assembly of millions of paired-end Illumina reads was used to further examine the importance of several putative c-type cytochrome, pilin, exopolysaccharide, chemotaxis, TCA cycle and carbon degradation transcripts that were collectively binned to iron(III)-reducer genomes of Anaeromyxobacter, Geobacter and Desulfovibrio. We also enriched 57iron in soil incubations to track iron(III)-(oxyhydr)oxide formation. We found that rapid oxidation of enriched iron(II) generates short-range-ordered (i.e. low crystallinity) iron phases that are more readily solubilized by iron(III)-reducing microorganisms than the bulk native soil iron phases at the onset of iron(III)-reduction. Some 57iron-enriched solid iron(III) that is not reduced becomes incorporated into longer-range-order phases (i.e. higher crystallinity) during iron(III)-reduction. A portion of iron(II) formed in the solid phase during iron(III)-reduction displays weak magnetic order in the Mössbauer spectra collected at 4.5 K, perhaps arising from the formation of nano-magnetite or, more generally, iron(II) adsorbed/incorporated at the surface of short-range-ordered iron(III)-(oxyhydr)oxides. These processes regarding mineral-microbial interactions are expected to be linked to ecosystem-level nutrient cycling, carbon stability and global greenhouse gas emissions in highly-active, humid, tropical forest soils.

Download or read book Dynamics of Redox Reactions Structure Decomposition and Greenhouse Gas Fluxes in Humid Tropical Forest Soils written by Steven James Hall and published by . This book was released on 2013 with total page 110 pages. Available in PDF, EPUB and Kindle. Book excerpt: Upland humid tropical forest soils experience fluctuations in oxygen (O2) availability and redox potential as a consequence of high rainfall, clay content, and respiration rates. Research in wetland ecosystems suggests that spatial and temporal variation in redox reactions strongly affect the biogeochemical cycling of carbon (C) and nitrogen (N). Here, I explored the impact of soil redox dynamics on decomposition and soil-atmosphere greenhouse gas fluxes in humid tropical ecosystems of the Luquillo Experimental Forest (LEF), Puerto Rico. Traditional theory and ecosystem models predict that elevated soil moisture leads to O2 limitation, constraining the enzymatic processes that mediate organic matter decomposition, and promoting the accumulation of soil C. Testing these hypotheses in upland humid tropical soils revealed the need for a more nuanced conceptual framework. In short: variation in moisture alone did not determine redox dynamics, hydrolytic enzymes activities persisted under reducing conditions, and redox fluctuations promoted decomposition on short (days) and long-term (decades) timescales. In Chapter One, I showed a relative decoupling between the temporal dynamics of soil moisture, soil redox reactions, and greenhouse gas fluxes over scales of days to weeks, using a field moisture manipulation experiment. Anaerobic biogeochemical processes such as iron (Fe) reduction and methanogenesis co-occurred in proximity to a well-aerated soil atmosphere and were little affected by fluctuations in soil moisture. Instead, redox reactions and gas fluxes appeared to vary constitutively according to differences in microtopography. In Chapter Two, I further explored relationships between reducing conditions and organic matter decomposition, by analyzing extracellular hydrolytic enzyme activities within and among sites differing in topography and rainfall. The enzymatic latch hypothesis proposes that reducing conditions inhibit hydrolytic enzymes via an accumulation of phenolic substances. I found little evidence for an enzymatic latch, and instead documented a strong positive relationship between reducing conditions, using reduced Fe (Fe(II)) as a proxy, and hydrolytic enzyme activities in a subset of sites. Furthermore, enzyme activities generally did not decline in an anaerobic incubation relative to aerobic controls. The assumption that reducing conditions constrain the decomposition activities of hydrolytic enzymes does not appear generally applicable in humid tropical forests. Next, in Chapter Three I examined the influence of temporal redox fluctuations on decomposition. Anaerobic conditions by definition limit the activity of oxidative enzymes, which require O2. The redox cycling of Fe, however, can potentially generate reactive oxygen species that mimic the function of oxidative enzymes. We demonstrated that concentrations of Fe(II) explained most of the variation in phenol oxidative activity within and among several sites in the LEF. Furthermore, Fe(II) oxidation stimulated short-term respiration, likely via a pH-mediated increase in dissolved organic C. Thus, stimulatory effects of redox fluctuations on oxidative decomposition processes might partially counteract short-term effects of O2 limitation. Finally, in Chapter Four I examined the overall impact of reducing conditions in comparison with other variables as they related to spatial patterns in soil C concentrations and turnover across the LEF. Soil C increased with Fe(II), an index of reducing conditions, but C tended to decline with increasing concentrations of reducible Fe oxides. Furthermore, the residence time of mineral-associated C (modeled using measurements of bomb radiocarbon) declined with Fe(II) concentrations. Together, the findings from these studies suggest a complex relationship between moisture, redox dynamics, and decomposition. First, short-term fluctuations in rainfall may have little overall impact on redox dynamics and the overall decomposition process, but longer-term differences in moisture among sites are associated with characteristic differences in redox reactions and greenhouse gas fluxes. Second, portions of the decomposition process mediated by hydrolytic enzymes appear resistant to periodic O2 deprivation and chronic reducing conditions, as well as the accumulation of phenolic substances. Third, redox cycling may give rise to important emergent mechanisms not evident under static aerobic conditions, mediated by coupled biotic and abiotic reactions with Fe oxides. Fourth, reducing conditions are associated with elevated soil C concentrations at the landscape scale, although the presence of reducible Fe oxides constrains C accumulation, and redox cycling might accelerate the turnover of mineral C over decadal scales. Together, these findings have implications for understanding the biogeochemical function of humid tropical soils, and their response to altered precipitation regimes and feedbacks to climate change. Two mechanisms thought to underlie the persistence of C in soils--reducing conditions induced by high soil moisture and the presence of reactive Fe minerals--may actually play unexpected roles in the decomposition of soil organic matter, a finding with potentially broad application across terrestrial and aquatic ecosystems.

Download or read book Tropical Forest Soil Microbial Communities Couple Iron and Carbon Biogeochemistry written by and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: We report that iron-reducing bacteria are primary mediators of anaerobic carbon oxidation in upland tropical soils spanning a rainfall gradient (3500 - 5000 mm yr-1) in northeast Puerto Rico. The abundant rainfall and high net primary productivity of these tropical forests provide optimal soil habitat for iron-reducing and iron-oxidizing bacteria. Spatially and temporally dynamic redox conditions make iron-transforming microbial communities central to the belowground carbon cycle in these wet tropical forests. The exceedingly high abundance of iron-reducing bacteria (up to 1.2 x 109 cells per gram soil) indicated that they possess extensive metabolic capacity to catalyze the reduction of iron minerals. In soils from the higher rainfall sites, measured rates of ferric iron reduction could account for up to 44 % of organic carbon oxidation. Iron reducers appeared to compete with methanogens when labile carbon availability was limited. We found large numbers of bacteria that oxidize reduced iron at sites with high rates of iron reduction and large numbers of iron-reducers. the coexistence of large populations of ironreducing and iron-oxidizing bacteria is evidence for rapid iron cycling between its reduced and oxidized states, and suggests that mutualistic interactions among these bacteria ultimately fuel organic carbon oxidation and inhibit CH4 production in these upland tropical forests.

Download or read book Biogeochemical Cycling of Iron and Carbon in Humid sub tropical Forest Soils Under Fluctuating Redox Conditions written by Diego Barcellos and published by . This book was released on 2018 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: Iron (Fe) is essential to plants, microbes, and animals, is an important element in weathered soils from tropical and subtropical regions due to its reactivity toward carbon (C) and nutrients and its ability to serve as an electron acceptor for anaerobic respiration. Humid (sub)tropical and iron-rich soils naturally experience fluctuations in soil moisture, oxygen content, and hence, redox potential due to elevated but intermittent rainfall and high inputs of labile carbon from decomposed litter. Soils from the Luquillo Critical Zone Observatory (LCZO), Puerto Rico, are well-suited for studying the impact of redox fluctuations on Fe and C biogeochemistry. I conducted two laboratory experiments, exploring coupled Fe-C mechanisms, and one field experiment, using LCZO soils. Both lab experiments were conducted using soil in a slurry, which minimizes spatial variability and involved shifting between anoxic and oxic conditions. In the first lab study, I found that iron reduction rates increased when redox oscillations occurred more frequently. In the second lab experiment, I varied the time under oxic conditions (Ï4oxic) in both long and short oscillation periods. For the long treatments (Ï4anoxic at 6 d), I observed that as Ï4oxic decreased from 72 to 24 to 8 hours, Fe reduction rates increased, CO2 emissions remained unchanged, and CH4 emissions decreased; and for the short treatments (Ï4anoxic at 2 d), FeII and trace gases emissions decreased throughout the experiment. For the field experiment, I monitored several biogeochemical variables involved in Fe-C redox processes in triplicate catenas at ridge, slope, and valley positions. I found that soil moisture was a predictor for changes in FeII, rapidly-reducible Fe oxides (FeIIIRR), pH, Eh, and DOC. Valleys were more responsive to environmental changes than the other landscape positions. I also conducted three other lab studies (using LCZO soils) and one field experiment at the Calhoun CZO, in South Carolina (each are reported briefly in the Appendices). In conclusion, under natural and laboratory redox fluctuating systems, iron exerts a strong biogeochemical influence on the carbon dynamics of soils from humid (sub)tropical regions with important climate change and environmental implications.

Download or read book The microbial ferrous wheel iron cycling in terrestrial freshwater and marine environments written by David Emerson and published by Frontiers E-books. This book was released on with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the past 15 years, there has been steady growth in work relating to the microbial iron cycle. It is now well established that in anaerobic environments coupling of organic matter utilization to Fe reduction is a major pathway for anaerobic respiration. In iron-rich circumneutral environments that exist at oxic-anoxic boundaries, significant progress has been made in demonstrating that unique groups of microbes can grow either aerobically or anaerobically using Fe as a primary energy source. Likewise, in high iron acidic environments, progress has been made in the study of communities of microbes that oxidize iron, and in understanding the details of how certain of these organisms gain energy from Fe-oxidation. On the iron scarcity side, it is now appreciated that in large areas of the open ocean Fe is a key limiting nutrient; thus, a great deal of research is going into understanding the strategies microbial cells, principally phytoplankton, use to acquire iron, and how the iron cycle may impact other nutrient cycles. Finally, due to its abundance, iron has played an important role in the evolution of Earth’s primary biogeochemical cycles through time. The aim of this Research Topic is to gather contributions from scientists working in diverse disciplines who have common interests in iron cycling at the process level, and at the organismal level, both from the perspective of Fe as an energy source, or as a limiting nutrient for primary productivity in the ocean. The range of disciplines may include: geomicrobiologists, microbial ecologists, microbial physiologists, biological oceanographers, and biogeochemists. Articles can be original research, techniques, reviews, or synthesis papers. An overarching goal is to demonstrate the environmental breadth of the iron cycle, and foster understanding between different scientific communities who may not always be aware of one another’s work.

Download or read book Iron Nutrition in Plants and Rhizospheric Microorganisms written by Larry L. Barton and published by Springer Science & Business Media. This book was released on 2007-08-20 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive review on the status of iron nutrition in plants. It contains updated reviews of most relevant issues involving Fe in plants and combines research on molecular biology with physiological studies of plant-iron nutrition. It also covers molecular aspects of iron uptake and storage in Arabidopsis and transmembrane movement and translocation of iron in plants. This book should serve to stimulate continued exploration in the field.

Download or read book Effect of Redox on the Solubility and Mineral Transformations of Fe Zn Pb and Cd in Soils written by Edward William Brennan and published by . This book was released on 1994 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Rapidly Fluctuating Redox Regimes Frame the Ecology of Microbial Communities and Their Biogeochemical Function in a Humid Tropical Soil written by Jennifer Pett-Ridge and published by . This book was released on 2005 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Iron carbon Associations in Tropical Soils of the Luquillo Critical Zone written by Elizabeth K. Coward and published by . This book was released on 2017 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: Much of the uncertainty in the biogeochemical behavior of soil carbon (C) in humid tropical ecosystems derives from an incomplete understanding of soil C stabilization processes. Long-term soil C stability is traditionally attributed to organomineral interactions, however, the 2:1 phyllosilicate clays often associated with temperate organomineral complexation are largely absent in humid tropical soils due to extensive weathering. In contrast, these soils contain a spectrum of iron- and aluminum-bearing minerals, exhibiting a broad range of crystallinity, surface area and surface charge, and susceptible to frequent reduction-oxidation (redox) oscillations. This dissertation investigates the composition, distribution, and function of iron-mediated organomineral associations across a range of spatial scales within the Luquillo Critical Zone Observatory (LCZO). Underlain by contrasting lithologies, the LCZO is characterized by highly-weathered, volcaniclastic Oxisols or quartz diorite-derived Inceptisols, producing an experimental gradient of iron content and speciation. To characterize the interactions between inherently heterogeneous soil C and often amorphous mineralogy, this dissertation paired high-resolution analytical techniques and inorganic selective dissolution experiments. We found low-crystallinity, short-range-order (SRO) iron and crystalline iron phases exert control on distinct reservoirs of soil C across both soil types. Notably, organomineral associations were responsible for accumulation of a subset of soil C, rather than driving trends in total soil C. Examination of solid-phase speciation across soil types revealed evidence for unique mineral matrix architecture in each soil. SRO FeIII-oxhydroxide phases in Oxisol soils were also found to be resistant to laboratory reduction events, suggesting that these phases are immune to redox-induced dissolution and may provide a long-term C stabilization mechanism. Investigation of iron-associated C at the molecular scale revealed preferential complexation of distinct C compounds has occurred at mineral interfaces of varying crystallinity and reactivity, suggesting that the array of association mechanisms described may be fractionating soil C. This work demonstrates that iron-mediated organomineral association serves as a reactive filter for soil C across spatial and temporal scales, which may impact both the quantity and identity of C cycling through the critical zone.

Download or read book The Role of Organic Matter in Modern Agriculture written by Y. Chen and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: The use of organic residues as a means of maintaining and increasing soil fertility is of long-standing. This tradition has been somewhat neglected since the introduc tion of mineral fertilizers at low cost. More and more farmers and scientists are now showing renewed interest in the proper and effective use of org~tnic residues, composts and other recycled organic additives. The role and function of organic amendments in modern agricultural systems have become topics of major interest in the scientific and agricultural communities. Research work on residue disposal has provided new concepts on the interaction between organic components and soils as well as new handling technologies (e. g. pelletizing of organic residues). The trend to conserve energy has led scientists to study the minimal tillage system, to find ways of replacing conventional inorganic fertilizers with natural organic prod ucts or microbial preparations, and to develop new composting methods. The drive to achieve higher yields in commercial greenhouse farming has led to a search for optimum substrates as growth media and for improved management techniques. This has led to the introduction of organic substitutes for peat, nota bly those originating from agricultural wastes. Another important aspect is the current interest in organic farming, where use of synthetic chemicals is avoided or prohibited. An increasing percentage of the population in highly developed countries is willing to pay premium prices for food produced on soils where inorganic fertilizers and other agricultural chemicals have not been used.

Download or read book Microbial Metatranscriptomics Belowground written by Manoj Nath and published by Springer Nature. This book was released on 2021-06-02 with total page 677 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book emphasizes role of functional microbes in soil to improve fertility and plant health in agro-ecosystem. In this compendium main emphasis is on occurrence and distribution of microbial communities, In situ active microbial quorum in rhizosphere, metratranscriptomics for microflora- and fauna, and fnctional diversity in rhizosphere. The book also highlights the importance of PGPRs in rhizosphere, root endotrophic microbes, functional niche under biotic stress, functional niche under abiotic stress, functional root derived signals, as well as functional microbe derived signals. Approaches deployed in metatranscriptomics, and molecular Tools used in rhizosphere are also discussed in detail. The book presents content is useful for students, academicians, researchers working on soil rhizosphere and as a policy document on sustenance of agriculture.

Download or read book Diversity and Benefits of Microorganisms from the Tropics written by João Lucio de Azevedo and published by Springer. This book was released on 2017-06-10 with total page 441 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book addresses the diversity of tropical microorganisms and its applications in agriculture, renewable energy production and environmental protection. It covers several tropical habitats such as rain forests, mangroves, sea and river waters and describes how microorganisms isolated from these regions can be used to control insects and plant diseases, to improve sugar cane and biofuels production among other applications. The book also aims to bring researchers’ attention to the potential of tropical microorganisms for biotechnological purposes, an area that is still far from being well explored.

Download or read book Microbial Products for Health Environment and Agriculture written by Pankaj Kumar Arora and published by Springer Nature. This book was released on 2021-09-21 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: This edited volume discusses the role of various microbial products in healthcare, environment and agriculture. Several microbial products are directly involved in solving major health problems, agricultural and environmental issues. In healthcare sector, microbes are used as anti-tumor compounds, antibiotics, anti-parasitic agents, enzyme inhibitors and immunosuppressive agents. Microbial products are also used to degrade xenobiotic compounds and bio-surfactants, for biodegradation process. In agriculture, microbial products are used to enhance nutrient uptake, to promote plant growth, or to control plant diseases. The book presents several such applications of microbes in the ecosystems. The chapters are contributed from across the globe and contain up-to-date information. This book is of interest to teachers, researchers, microbiologists and ecologists. Also the book serves as additional reading material for undergraduate and graduate students of agriculture, forestry, ecology, soil science, and environmental sciences.

Download or read book Microbiome in Plant Health and Disease written by Vivek Kumar and published by Springer. This book was released on 2019-08-10 with total page 534 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book discusses the complex interactions between plants and their associated microbial communities. It also elucidates the ways in which these microbiomes are connected with the plant system, and how they affect plant health. The different chapters describe how microbiomes affect plants with regard to immunity, disease conditions, stress management and productivity. In addition, the book describes how an ‘additional plant genome’ functions as a whole organ system of the host, and how it presents both challenges and opportunities for the plant system. Moreover, the book includes a dedicated section on using omics tools to understand these interactions, and on exploiting them to their full potential.

Download or read book Microbial Genomics in Sustainable Agroecosystems written by Vijay Tripathi and published by Springer Nature. This book was released on 2019-11-23 with total page 377 pages. Available in PDF, EPUB and Kindle. Book excerpt: Today, microbiology is a rapidly growing discipline in the life sciences, and the technologies are evolving on a virtually daily basis. Next-generation sequencing technologies have revolutionized microbial analysis, and can help us understand the biology and genomic diversity of various bacterial species with significant impacts on agro-ecosystems. In addition, advances in molecular biology and microbiology techniques hold the potential to improve the productivity and sustainability of agriculture and forestry. This new volume addresses the role of microbial genomics in understanding the living systems that exist in the soil and their interactions with plants, an aspect that is also important for crop improvement. The topics covered focus on a deeper and clearer understanding of how microbes cause diseases, the genome-based development of novel antibacterial agents and vaccines, and the role of microbial genomics in crop improvement and agroforestry. Given its scope, the book offers a valuable resource for researchers and students of agriculture and infectious biology.

Download or read book Microbial Interventions in Agriculture and Environment written by Dhananjaya Pratap Singh and published by Springer Nature. This book was released on 2019-11-27 with total page 608 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbial communities and their functions play a crucial role in the management of ecological, environmental and agricultural health on the Earth. Microorganisms are the key identified players for plant growth promotion, plant immunization, disease suppression, induced resistance and tolerance against stresses as the indicative parameters of improved crop productivity and sustainable soil health. Beneficial belowground microbial interactions with the rhizosphere help plants mitigate drought and salinity stresses and alleviate water stresses under the unfavorable environmental conditions in the native soils. Microorganisms that are inhabitants of such environmental conditions have potential solutions for them. There are potential microbial communities that can degrade xenobiotic compounds, pesticides and toxic industrial chemicals and help remediate even heavy metals, and thus they find enormous applications in environmental remediation. Microbes have developed intrinsic metabolic capabilities with specific metabolic networks while inhabiting under specific conditions for many generations and, so play a crucial role. The book Microbial Interventions in Agriculture and Environment is an effort to compile and present a great volume of authentic, high-quality, socially-viable, practical and implementable research and technological work on microbial implications. The whole content of the volume covers protocols, methodologies, applications, interactions, role and impact of research and development aspects on microbial interventions and technological outcomes in prospects of agricultural and environmental domain including crop production, plan-soil health management, food & nutrition, nutrient recycling, land reclamation, clean water systems and agro-waste management, biodegradation & bioremediation, biomass to bioenergy, sanitation and rural livelihood security. The covered topics and sub-topics of the microbial domain have high implications for the targeted and wide readership of researchers, students, faculty and scientists working on these areas along with the agri-activists, policymakers, environmentalists, advisors etc. in the Government, industries and non-government level for reference and knowledge generation.

Download or read book Genomics of Soil and Plant Associated Fungi written by Benjamin A. Horwitz and published by Springer Science & Business Media. This book was released on 2013-08-30 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume addresses the similarities and also the differences in the genomes of soil saprophytes, symbionts, and plant pathogens by using examples of fungal species to illustrate particular principles. It analyzes how the specific interactions with the hosts and the influence of the environment may have shaped genome evolution. The relevance of fungal genetic research and biotechnological applications is shown for areas such as plant pathogenesis, biomass degradation, litter decomposition, nitrogen assimilation, antibiotic production, mycoparasitism, energy, ecology, and also for soil fungi turning to human pathogens. In addition to the model organisms Neurospora and Aspergillus, the following species are covered providing a view of pathogens and mutualists: Trichoderma, Fusarium oxysporum, Cochliobolus heterostrophus, Penicillium chrysogenum, Rhizopus oryzae, Podospora anserina, and species belonging to Agaricomycetes, Archaeorhizomycetes and Magnaporthaceae. Ecology and potential applications have guided the choice of fungal genes to be studied and it will be fascinating to follow the trends of future sequencing projects.