THE DISTRIBUTION AND FUNCTION OF DENITRIFICATION GENES: EXPLORING AGRICULTURAL MANAGEMENT AND SOIL CHEMICAL IMPLICATIONS

Denitrification is a microbially-mediated process that converts nitrate (NO3-) to dinitrogen (N2) gas and has implications for soil fertility, climate change, and water quality. Using PCR, qPCR, and T-RFLP, the effects of environmental drivers and land management on the abundance and composition of functional genes were investigated. Environmental variables affecting gene abundance were soil type, soil depth, nitrogen concentrations, soil moisture, and pH, although each gene was unique in its spatial distribution and controlling factors. The inclusion of microbial variables, specifically genotype and gene abundance, improved denitrification models and highlights the benefit of including microbial data in modeling denitrification. Along with some evidence of niche selection, I show that nirS is a good predictor of denitrification enzyme activity (DEA) and N2O:N2 ratio, especially in alkaline and wetland soils. nirK was correlated to N2O production and became a stronger predictor of DEA in acidic soils, indicating that nirK and nirS are not ecologically redundant.

Study the methods of connecting jacket to the seabed and choosing the best method for Persian Gulf according to soil characteristics

Offshore structures with numerous applications in different environments throughout the world and used at different depths. Due to the expansion of marine industries, including offshore oil industry in Iran , particularly in the Persian Gulf region, in order to more accurately model these structures and to prevent incidents such as the Overturning of the platform serious damage to the South Pars Phase ١٣ was platforms, the use New Technic is essential technologies. One of the methods that are used in the construction of offshore wind turbines, using a pre-pile. In this method, a template is constructed with the dimensions specified in the workshop. After making templates using special vessels for placement in the desired location on the sea bed is carried, then the template is placed on the sea bed, Then, using a hammer for Pile Driving Operation Started Vibration hammer and fit the template of 3 or 4 piles of crushed within this template on the seabed . The next step piling, templates have been removed from the site And Jacket placed on piles. The system was installed on the deck on piles and Consequently Deck Load pile inserted on .It should be noted that the design of these types of platforms, base diameter of the pile diameter independent of the choice as one of the major advantages of this system is. This thesis examines a Template Fixed Platform in the oil Soroush Using the Pre-Piling and the Common Piling systems in the Persian Gulf were studied and the effect of different design compared to the Pre-Piling Platforms Persian Gulf were evaluated. The results suggest that Pre-Piling system compared with conventional systems piling in the Persian Gulf, as a more appropriate model structure and behavior Top Model economic efficiency is selected. It should be noted that all calculations and analyzes were performed using Software Abaqus.

Bacterial communities of the specialty crop phyllosphere: response to biological soil amendment use, rainfall, and insect visitation

Microorganisms in the plant rhizosphere, the zone under the influence of roots, and phyllosphere, the aboveground plant habitat, exert a strong influence on plant growth, health, and protection. Tomatoes and cucumbers are important players in produce safety, and the microbial life on their surfaces may contribute to their fitness as hosts for foodborne pathogens such as Salmonella enterica and Listeria monocytogenes. External factors such as agricultural inputs and environmental conditions likely also play a major role. However, the relative contributions of the various factors at play concerning the plant surface microbiome remain obscure, although this knowledge could be applied to crop protection from plant and human pathogens. Recent advances in genomic technology have made investigations into the diversity and structure of microbial communities possible in many systems and at multiple scales. Using Illumina sequencing to profile particular regions of the 16S rRNA gene, this study investigates the influences of climate and crop management practices on the field-grown tomato and cucumber microbiome. The first research chapter (Chapter 3) involved application of 4 different soil amendments to a tomato field and profiling of harvest-time phyllosphere and rhizosphere microbial communities. Factors such as water activity, soil texture, and field location influenced microbial community structure more than soil amendment use, indicating that field conditions may exert more influence on the tomato microbiome than certain agricultural inputs. In Chapter 4, the impact of rain on tomato and cucumber-associated microbial community structures was evaluated. Shifts in bacterial community composition and structure were recorded immediately following rain events, an effect which was partially reversed after 4 days and was strongest on cucumber fruit surfaces. Chapter 5 focused on the contribution of insect visitors to the tomato microbiota, finding that insects introduced diverse bacterial taxa to the blossom and green tomato fruit microbiome. This study advances our understanding of the factors that influence the microbiomes of tomato and cucumber. Farms are complex environments, and untangling the interactions between farming practices, the environment, and microbial diversity will help us develop a comprehensive understanding of how microbial life, including foodborne pathogens, may be influenced by agricultural conditions.

The Ecology of Urbanization: A Study of Soil Microbial Community Rosponse

Urbanization is associated with global biodiversity loss of macrophauna and flora through direct and indirect mechanisms, but to date few studies have examined urban soil microbes. Although there are numerous studies on the influence of agricultural management on soil microbial community composition, there has been no global-scale study of human control over urban soil microbial communities. This thesis extends the literature of urban ecology to include soil microbial communities by analyzing soils that are part of the Global Urban Soil Ecology and Education Network (GLUSEEN). Chapter 1 sets the context for urban ecology; Chapters 2 addresses patterns of community assembly, biodiversity loss, and the phylogenetic relationships among community members; Chapter 3 addresses the metabolic pathways that characterize microbial communities existing under different land-uses across varying geographic scales; and Chapter 4 relates Chapter 2 and 3 to one another and to evolutionary theory, tackling assumptions that are particular to microbial ecology.

Soil characteristics in Doon Valley (north west Himalaya, India) by inversion of H/V spectral ratios from ambient noise measurements

Past and recent observations have shown that the local site conditions significantly affect the behavior of seismic waves and its potential to cause destructive earthquakes. Thus, seismic microzonation studies have become crucial for seismic hazard assessment, providing local soil characteristics that can help to evaluate the possible seismic effects. Among the different methods used for estimating the soil characteristics, the ones based on ambient noise measurements, such as the H/V technique, become a cheap, non-invasive and successful way for evaluating the soil properties along a studied area. In this work, ambient noise measurements were taken at 240 sites around the Doon Valley, India, in order to characterize the sediment deposits. First, the H/V analysis has been carried out to estimate the resonant frequencies along the valley. Subsequently, some of this H/V results have been inverted, using the neighborhood algorithm and the available geotechnical information, in order to provide an estimation of the S-wave velocity profiles at the studied sites. Using all these information, we have characterized the sedimentary deposits in different areas of the Doon Valley, providing the resonant frequency, the soil thickness, the mean S-wave velocity of the sediments, and the mean S-wave velocity in the uppermost 30 m.

Buckwheat as a Cover Crop in Florida: Mycorrhizal Status, Soil Analysis, and Economic Assessment

This thesis analyses buckwheat as a cover crop in Florida. The study was designed to demonstrate: soil enrichment with nutrients, mycorrhizal arbuscular fungi interactions, growth in different soil types, temperature limitations in Florida, and economic benefits for farmers. Buckwheat was planted at the FIU organic garden (Miami, FL) in early November and harvested in middle December. After incorporation of buckwheat residues, soil analyses indicated the ability of buckwheat to enrich soil with major nutrients, in particular, phosphorus. Symbiosis with arbuscular mycorrhizal fungi increased inorganic phosphorus uptake and plant growth. Regression analysis on aboveground buckwheat biomass weight and soil characteristics showed that high soil pH was the major limiting factor that affected buckwheat growth. Spatial analysis illustrated that buckwheat could be planted in South Florida throughout the year but might not be planted in North and Central Florida in winter. An economic assessment proved buckwheat to be a profitable cover crop.

Physical soil attributes of Conilon coffee (Coffea canephora) under organic and conventional management systems.

Coffea sp. is cultivated in large areas, using both conventional and organic management. However, information about the sustainability of these two management systems is still deficient. The objective of the present study was to evaluate the physical properties of soil cultivated with Conilon coffee (C. canephora) under organic and conventional management. Two areas cultivated with Conilon coffee (under organic and conventional management) and a fragment of Atlantic forest, used as a reference, were selected for the experiment. Soil granulometry, hydraulic conductivity, water retention curve, resistance to penetration, porosity, optimal hydric interval, and other physical characteristics were measured at depths of 0 to 10 and 10 to 20 cm. The data was submitted to multivariate and descriptive statistical analyses. Higher similarity was observed between the soil cultivated with Conilon coffee under organic management and the Atlantic forest soil. Soil resistance to penetration at 10, 30, 100, 500 and 1500 kPa, macro porosity, density and total porosity were the main physical properties that differentiated both management systems studied. The non-use of agricultural machinery and the addition of organic matter may be the main reasons for higher soil sustainability observed under organic management when compared with the conventional system.

Soil management, seed treatment and soil compaction on the sowing furrows affect grain yields of upland rice genotypes.

The water availability for flood irrigated rice (Oryza sativa L.) is decreasing worldwide. Therefore, developing technologies to allow growing rice in aerobic condition, such as a no-tillage system (NTS) can contribute to produce upland rice grains without yield losses and also in saving more water. The objective of this study was to determine the effect of soil management, seed treatment and compaction on the sowing furrow on grain yield of upland rice genotypes. We made two trials, one in an NTS and another using conventional tillage, CT (one plowing and two diskings). The field experiments were performed in the Central Region of Brazil in Cerrado soils. For each trial, the experimental design was a randomized block design in a factorial scheme, with three replications. The treatments consisted of a combination of 10 genotypes with 2 compaction pressures on the sowing furrow (25 kPa and 126kPa) and 2 types of seed treatment (with and without pesticide). Under CT, the seed treatment did not contribute to increase upland rice grain yields. However, under NTS the grain yield of some genotypes [BRS Esmeralda (from 723 to 1,766 kg ha-1), BRS Pepita (from 930 to 1,874 kg ha-1), AB072044 (from 523 to 1,579 kg ha-1), and AB072085 (from 632 to 1,636 kg ha-1) at 25 kPA soil compaction pressure, and Sertaneja (from 994 to 2,167 kg ha-1), BRS Pepita (from 1,161 to 2,100 kg ha-1), and AB072085 (from 958 to 2,213 kg ha-1), at 126 kPA soil compaction pressure] increased with the use of this practice. At CT the higher soil compaction pressure on the sowing furrow (from 25 kPa to 126 kPa) increased rice grain yield only when it was used seed treatment and the genotypes Serra Dourada (from 1,239 to 2,178 kg ha-1), Sertaneja (from 1,510 to 2,379 kg ha-1), and Cambará (from 1,877 to 2,831 kg ha-1). On the other hand, under NTS, increasing soil compaction pressure on the sowing furrow allowed for an increased rice grain yield of Serra Dourada (from 1,553 to 2,347 kg ha-1), Esmeralda (from 723 to 1,643 kg ha-1), AB072044 (from 523 to 2,040 kg ha-1), and Cambará (from 1,243 to 2,032 kg ha-1) without seed treatment and Sertaneja (from 1,385 to 2,167 kg ha-1) and AB072044 (from 1,579 to 2,356 kg ha-1) with seed treatment. In CT the most productive genotypes were AB062008 (2,714 kg ha-1) and BRSMG Caravera (2,479 kg ha-1), while at NTS were the genotypes: BRSGO Serra Dourada (2,118 kg ha-1), AB072047 (1,888 kg ha-1), AB062008 (1,823 kg ha-1), BRSMG Caravera (1,737 kg ha-1), Cambará (1,716 kg ha-1), AB072044 (1,625 kg ha-1), BRS Esmeralda (1,604 kg ha-1), and BRS Pepita (1,516 kg ha-1).

Changes In The Bacterial Community Of Soil From A Neutral Mine Drainage Channel.

Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments.

Evaluation Of Fe Uptake And Translocation In Transgenic And Non-transgenic Soybean Plants Using Enriched Stable (57)fe As A Tracer.

A tracer experiment is carried out with transgenic T (variety M 7211 RR) and non-transgenic NT (variety MSOY 8200) soybean plants to evaluate if genetic modification can influence the uptake and translocation of Fe. A chelate of EDTA with enriched stable (57)Fe is applied to the plants cultivated in vermiculite plus substrate and the (57)Fe acts as a tracer. The exposure of plants to enriched (57)Fe causes the dilution of the natural previously existing Fe in the plant compartments and then the changed Fe isotopic ratio ((57)Fe/(56)Fe) is measured using a quadrupole-based inductively coupled plasma mass spectrometer equipped with a dynamic reaction cell (DRC). Mathematical calculations based on the isotope dilution methodology allow distinguishing the natural abundance Fe from the enriched Fe (incorporated during the experiment). The NT soybean plants acquire higher amounts of Fe from natural abundance (originally present in the soil) and from enriched Fe (coming from the (57)Fe-EDTA during the experiment) than T soybean ones, demonstrating that the NT soybean plants probably absorb higher amounts of Fe, independently of the source. The percentage of newly incorporated Fe (coming from the treatment) was approximately 2.0 and 1.1% for NT and T soybean plants, respectively. A higher fraction (90.1%) of enriched Fe is translocated to upper parts, and a slightly lower fraction (3.8%) is accumulated in the stems by NT plants than by T ones (85.1%; 5.1%). Moreover, in both plants, the Fe-EDTA facilitates the transport and translocation of Fe to the leaves. The genetic modification is probably responsible for differences observed between T and NT soybean plants.

Bacterial Diversity Assessment In Soil Of An Active Brazilian Copper Mine Using High-throughput Sequencing Of 16s Rdna Amplicons.

Mining activities pose severe environmental risks worldwide, generating extreme pH conditions and high concentrations of heavy metals, which can have major impacts on the survival of organisms. In this work, pyrosequencing of the V3 region of the 16S rDNA was used to analyze the bacterial communities in soil samples from a Brazilian copper mine. For the analysis, soil samples were collected from the slopes (geotechnical structures) and the surrounding drainage of the Sossego mine (comprising the Sossego and Sequeirinho deposits). The results revealed complex bacterial diversity, and there was no influence of deposit geographic location on the composition of the communities. However, the environment type played an important role in bacterial community divergence; the composition and frequency of OTUs in the slope samples were different from those of the surrounding drainage samples, and Acidobacteria, Chloroflexi, Firmicutes, and Gammaproteobacteria were responsible for the observed difference. Chemical analysis indicated that both types of sample presented a high metal content, while the amounts of organic matter and water were higher in the surrounding drainage samples. Non-metric multidimensional scaling (N-MDS) analysis identified organic matter and water as important distinguishing factors between the bacterial communities from the two types of mine environment. Although habitat-specific OTUs were found in both environments, they were more abundant in the surrounding drainage samples (around 50 %), and contributed to the higher bacterial diversity found in this habitat. The slope samples were dominated by a smaller number of phyla, especially Firmicutes. The bacterial communities from the slope and surrounding drainage samples were different in structure and composition, and the organic matter and water present in these environments contributed to the observed differences.

Toxicity Of Fungal-generated Silver Nanoparticles To Soil-inhabiting Pseudomonas Putida Kt2440, A Rhizospheric Bacterium Responsible For Plant Protection And Bioremediation.

Silver nanoparticles have attracted considerable attention due to their beneficial properties. But toxicity issues associated with them are also rising. The reports in the past suggested health hazards of silver nanoparticles at the cellular, molecular, or whole organismal level in eukaryotes. Whereas, there is also need to examine the exposure effects of silver nanoparticle to the microbes, which are beneficial to humans as well as environment. The available literature suggests the harmful effects of physically and chemically synthesised silver nanoparticles. The toxicity of biogenically synthesized nanoparticles has been less studied than physically and chemically synthesised nanoparticles. Hence, there is a greater need to study the toxic effects of biologically synthesised silver nanoparticles in general and mycosynthesized nanoparticles in particular. In the present study, attempts have been made to assess the risk associated with the exposure of mycosynthesized silver nanoparticles on a beneficial soil microbe Pseudomonas putida. KT2440. The study demonstrates mycosynthesis of silver nanoparticles and their characterisation by UV-vis spectrophotometry, FTIR, X-ray diffraction, nanosight LM20 - a particle size distribution analyzer and TEM. Silver nanoparticles obtained herein were found to exert the hazardous effect at the concentration of 0.4μg/ml, which warrants further detailed investigations concerning toxicity.

Motivating Medical Students To Learn Basic Science Concepts Using Chronic Myeloid Leukemia As An Integration Theme.

To report on the use of chronic myeloid leukemia as a theme of basic clinical integration for first year medical students to motivate and enable in-depth understanding of the basic sciences of the future physician. During the past thirteen years we have reviewed and updated the curriculum of the medical school of the Universidade Estadual de Campinas. The main objective of the new curriculum is to teach the students how to learn to learn. Since then, a case of chronic myeloid leukemia has been introduced to first year medical students and discussed in horizontal integration with all themes taught during a molecular and cell biology course. Cell structure and components, protein, chromosomes, gene organization, proliferation, cell cycle, apoptosis, signaling and so on are all themes approached during this course. At the end of every topic approached, the students prepare in advance the corresponding topic of clinical cases chosen randomly during the class, which are then presented by them. During the final class, a paper regarding mutations in the abl gene that cause resistance to tyrosine kinase inhibitors is discussed. After each class, three tests are solved in an interactive evaluation. The course has been successful since its beginning, 13 years ago. Great motivation of those who participated in the course was observed. There were less than 20% absences in the classes. At least three (and as many as nine) students every year were interested in starting research training in the field of hematology. At the end of each class, an interactive evaluation was performed and more than 70% of the answers were correct in each evaluation. Moreover, for the final evaluation, the students summarized, in a written report, the molecular and therapeutic basis of chronic myeloid leukemia, with scores ranging from 0 to 10. Considering all 13 years, a median of 78% of the class scored above 5 (min 74%-max 85%), and a median of 67% scored above 7. Chronic myeloid leukemia is an excellent example of a disease that can be used for clinical basic integration as this disorder involves well known protein, cytogenetic and cell function abnormalities, has well-defined diagnostic strategies and a target oriented therapy.