The main objective of this thesis was to develop statistical and analytical methods for untargeted analyses of complex environmental matrices like soil and sediment. Untargeted analyses are notoriously difficult to perform in matrices like soil and sediment because of the complexity of organic matter composition within these matrices. This thesis aimed to (1) Develop and compare extraction methods for untargeted analyses of soil and sediment while also developing data handling and quality control protocols; (2) Investigate novel applications of untargeted analyses for environmental classification and monitoring; and (3) Investigate the experimental factors that can influence the organic matter composition of untargeted extractions. CHAPTER TWO is a literature review of metabolomics protocols, and these protocols were incorporated into a proposed workflow for performing untargeted analysis in oil, soil, and sediment. This thesis contains the first application of untargeted analysis to freshwater lake sediment organic matter (i.e. sedimentomics) in CHAPTER THREE, and this has implications for discovering new biomarkers for paleolimnology (APPENDIX ONE). I demonstrated successful extraction methods for both sedimentomics and soil metabolomics studies in CHAPTER THREE and CHAPTER FIVE, respectively, using the proposed workflow from CHAPTER TWO. I also applied sedimentomics to the classification of lake sediments using machine learning and geostatistics based on sediment organic matter compositions in CHAPTER FOUR; this was a novel application of sedimentomics that could have implications for ecosystem classifications and advance our knowledge of organic matter cycling in lake sediments. Lastly, in CHAPTER FIVE I determined microbial activity, extraction method, and soil type can all influence the composition of soil organic matter extracts in soil metabolomics experiments. I also developed novel quality controls and quantitative methods that can help control these influences in CHAPTER FIVE and APPENDIX THREE. APPENDIX TWO was written in collaboration with multiple researchers and is a review of all “omics” types of analyses that can be performed on soil or sediment, and how methods like the untargeted analysis of soil and sediment organic matter can be linked with metagenomics, metatranscriptomics, and metaproteomics for a comprehensive metaphenomics analysis of soil and sediment ecosystems. In CHAPTER SIX the conclusions and implications for each chapter and overall for this thesis are detailed and I describe future directions for the field. In the end the overall conclusions of this thesis were: 1) Quality controls are necessary for sedimentomics and soil metabolomics studies, 2) Sedimentomics is a valid technique to highlight changes in sediment organic matter, 3) Soil metabolomics and sedimentomics yield more information about carbon cycling than traditional measurements, and 4) Soil metabolomics organic matter extractions are more variable and require more quality controls.

Ensyeh Sarikhani Soil microbial communities in agroecosystems and natural habitats contributing to resistance and resilience of the soil environment. Summary The control of common scab of potatoes (CS) includes resistant varieties (cultivars), precise fertilization, increase of soil moisture, and chemical treatments. Yet, these management practices do not have common or reproducible results at differing sites. A monitoring study was done in 32 sites to evaluate the relation between CS and biological/chemical soil parameters. Correlations were observed between scab severity and content of nutrients such as Fe, N, and Ca in soil and periderm, and between disease severity and abundance of actinobacteria and total bacteria, together with the pathogenicity determinant, txtB gene (biosynthetic gene of thaxtomin) in both soil and periderm of potatoes. The findings led to novel conclusions, which can help to understand relationships applicable in scab control. Peat and DTPA chelated iron were supplemented to pots filled with soil conducive for CS in order to determine the effects of soil organic matter, iron and pH on CS development. The results were compared with data obtained for a suppressive soil from a nearby field with naturally low CS severity. Both peat and iron supplements decreased CS and the combination...

No-till management for agronomic crop production is recognized as an effective practice to regain a portion of soil organic matter lost following decades of cultivation. Increasing soil organic matter sequesters C, conserves organic N and concomitantly improves soil quality. Objectives of this research were to: i) quantify C sequestration rate and N conservation with duration of continuous no-till; ii) measure C stratification with continuous no-till as an indicator of soil quality; and iii) evaluate the Illinois soil N test (ISNT) for its value to predict fertilizer N needs of corn in Virginia. Objectives i and ii were achieved by collecting soil samples from 63 production fields in the Virginia Coastal Plain that were managed using continuous no-till from 0 to 14 yrs. No-till management resulted in sequestration of 0.308 ± 0.280 Mg C ha⁻¹ y⁻¹ and conservation of 22.2 ± 21.2 kg N ha⁻¹ yr⁻¹ (0-15 cm). The C stratification ratio (0-2.5 cm: 7.5-15 cm) increased with increasing duration of continuous no-till (0.133 ± 0.056 yr⁻¹) due to the accumulation of organic matter at the soil surface indicating improved soil quality with continuous no-till management. Objective iii was addressed by conducting 29 on-farm fertilizer N response trials in major corn producing areas of Virginia with the duration of continuous no-till management ranging from 0 to 25 yrs. The ISNT values were significantly related to yield without fertilizer N (r² = 0.57; p<0.001) and relative yield (r² = 0.64; p<0.0001). We also found that the ISNT extracted a relatively consistent percentage of total soil N (16.3 ± 0.73 %) suggesting it is a poor indicator of labile N. Total soil N values did almost as well as the ISNT in predicting yield without fertilizer N (r² = 0.53; p = 0.0002), and equally well predicting relative yield (r² = 0.64; p<0.0001). Results do not suggest the ISNT is useful for measuring mineralizalbe N or improving fertilizer N recommendations in Virginia cropping systems. / Ph. D.

Concern over rising atmospheric CO2 due to fossil fuel combustion has intensified research into carbon-neutral energy and fuel production. Therefore, bioenergy production has expanded during the last decade, increasing demand for forest-based bioenergy feedstocks. Millions of acres of privately and industrially owned pine plantations exist across the southeastern US, representing a vast area of land that could be utilized to produce bioenergy without significant land-use change or diversion of agricultural resources from food production. Furthermore, loblolly pine (Pinus taeda L.) plantations offer the unique opportunity to utilize space between rows of planted trees to grow an herbaceous bioenergy crop, such as switchgrass (Panicum virgatum L.). This novel forest management regime has the potential to provide positive environmental and economic services, but hinges in part on impacts to soil carbon (C) and nitrogen (N) cycling, availability of belowground resources, and potential negative impacts of competition between pine and switchgrass on plant productivity. Three specific objectives were addressed in this study: 1) compare different bioenergy management regimes in regards to temporal dynamics of N cycling and availability following forest establishment (see Chapter 2); 2) determine the impact of loblolly pine and switchgrass intercropping on microbial N cycling processes (see Chapter 3); and 3) evaluate chemical and physical mechanisms of soil organic matter (SOM) stabilization and test their sensitivity to pine-switchgrass intercropping (see Chapter 4). The study site was located in the Lower Coastal Plain physiographic province in Lenoir County, North Carolina, USA (35-12'59'' N; 077-26'13'' W). Soils were mapped as Pantego (fine‐loamy, siliceous, semiactive, thermic Umbric Paleaquults) or Rains (fine‐loamy, siliceous, semiactive, thermic Typic Paleaquults) soil series, both of which are very poorly drained. However, previous site management in the late 1960’s and early 1970’s included installation of ditches to lower the water table and reduce saturation at the soil surface. Additionally, bedding of soil in rows was used to raise root systems of planted loblolly pine seedlings above the water table, increase soil aeration, and reduce competition. Space between bedded rows of pine trees was referred to as the interbed. Results from Chapter 2 showed that switchgrass significantly reduced interbed soil NH4 + and NO3 - concentrations by 39% and 60%, respectively, over the course of the timeframe (30 months) of this study. Surprisingly, in beds of the pine-switchgrass treatment significant increases in NO3 - concentration were measured from July - December 2011. From Chapter 3, gross N mineralization rates ranged from 0.18 - 4.7 µg N g -1 soil d-1 , while gross nitrification rates ranged from 0.02 - 0.47 µg N g-1 soil d-1 . At the 0-5 cm depth in switchgrass interbeds, gross N mineralization was reduced from April to November potentially reflecting microbial C limitations due to reduced soil C concentrations. At the 0-5 cm depth in beds of the pine-switchgrass treatment, gross N mineralization rates were elevated by 1.29 µg N iii g -1 soil d-1 in November and 1.02 µg N g-1 soil d-1 in February on average corresponding to a 305% and 193% increase, respectively. From Chapter 4, total C content in beds and interbeds ranged from 15 to 88 Mg C ha-1 and was reduced by 27% in beds of the pine-switchgrass treatment. Average C concentration for aggregate fractions was significantly lower in beds of the pine-switchgrass treatment at 0-5, 15- 30, and 30-45 cm depths, amounting to ~23%, ~28%, and ~34% reduction, respectively. Values of δ 13C for the >2000 µm aggregate size fraction at the 0-5 cm depth were diluted, corresponding to estimates of 13 - 25% of the >2000 µm C pool comprised of new pine-derived C. For SOM fractionated by density, elevated C concentrations were found in the occluded light fractions in both beds and interbeds of the pine-switchgrass treatment. Enriched δ13C in occluded light fractions led to estimates of 2.5 - 12.5% of this C fraction comprised of new switchgrass-derived C. In the free light fraction, new pine-derived C accounted for 15% and 9% of C at the 5-15 and 15-30 cm depth, respectively. Three overarching conclusions were generated from my research: 1) switchgrass grown between loblolly pine trees effectively utilized excess soil NH4 + and NO3 - when N availability was high following harvesting of a mature plantation proceeded by establishment of a second rotation of loblolly pine (see Chapter 2); 2) gross N mineralization rates were reduced under switchgrass during the growing season when soil C availability was low, but were elevated under switchgrass and adjacent loblolly pines when switchgrass was dormant and C availability was likely higher (see Chapter 3); and 3) SOM stabilized by physical or chemical mechanisms responded differently to pine-switchgrass intercropping, with losses in aggregate-stabilized C and gains in occluded, mineral-stabilized C. Furthermore, losses of aggregate C was associated with a significant reduction in total soil C in beds of the pine-switchgrass treatment. Results from 13C mass balance suggested incorporation of switchgrass-derived C into occluded light fractions of beds and interbeds. Finally, incorporation of new pine-derived C into the >2000 µm aggregate size fraction and free light fraction indicate pine inputs of particulate organic matter into these SOM fractions in beds of the pine-switchgrass treatment (see Chapter 4). I hypothesize that loblolly pines have increased root growth in beds in response to competition with switchgrass for N in the interbed, thereby alleviating seasonal microbial C limitations and stimulating microbial N cycling processes and increasing plant-available N. Overall, this research suggests that soil C and N cycling in pine plantations is altered by intercropping of pine and switchgrass. Through a mechanistic understanding of how C and N are cycled in forests and the impact of various forest management regimes on soil C and N cycling, effective management strategies can be implemented to utilize forests for intensive biomass production while limiting loss of soil C and N, and in some cases even enhancing soil C and N retention. Future research initiatives should seek to unravel the complex belowground interactions between roots of different plant species and soil microbial communities competing for limiting resources. Understanding how these interactions drive soil C storage, N cycling and availability, and forest productivity will ultimately improve resource utilization in these managed ecosystems as well as our basic understanding of how natural and managed ecosystems function. / Ph. D.

Agricultural activities have significant impacts on global biogeochemical cycles, particularly carbon and nitrogen. Conventional row-crop agriculture accelerates the decomposition of soil organic matter, contributing to atmospheric carbon and declining soil fertility. Planting perennial warm season grasses is a useful management alternative to row crop agriculture because these species have been shown to be effective at increasing soil carbon storage and retaining nitrogen. The objectives of this research were to examine how converting row crops to a native perennial warm season grass (Panicum virgatum L., common name switchgrass) influences the recovery of soil organic matter fractions and nitrogen retention within an agricultural watershed in the Shenandoah Valley of Virginia. Soil samples were analyzed for total carbon and nitrogen, three particulate organic matter fractions, root biomass, mineralizable carbon and nitrogen pools, and microbial biomass. Surprisingly, I observed significant declines in bulk soil organic matter and surface particulate organic matter pools following switchgrass establishment. There were no differences in mineralizable carbon and microbial biomass pools between row crop and switchgrass soils, but labile carbon pools and nitrogen immobilization increased as switchgrass stands matured. These results are potentially due to switchgrass litter inputs stimulating microbial communities and accelerating the decomposition of recalcitrant soil organic matter, leading to declines in soil organic carbon stocks. The results from this study will be used to understand the environmental and economic benefits of implementing switchgrass plantings in agricultural watershed as a means to mitigate agriculturally-induced effects on carbon storage and nitrogen retention in soils. / Master of Science

No description available.

Soil respiration is an important source of atmospheric CO2, with the potential for large positive feedbacks with global warming. The size of these feedbacks will depend on the relative sensitivity to temperature of very large global pools of highly stable soil organic matter (SOM), with residence times of centuries or longer. Conflicting evidence exists as to the relationships between temperature sensitivity of respiration and stability of SOM, as well as the temperature sensitivity of individual stabilisation mechanisms. This PhD considers the relationship between different stabilisation mechanisms and the temperature sensitivity of SOM decomposition. I used physical fractionation to isolate SOM pools with a variety of turnover rates, from decadal to centennially cycling SOM, in a peaty gley topsoil from Harwood Forest. Mean residence times of SOM as determined by 14C dating was most strongly affected by depth, providing stability on a millienial scale, while OM-mineral associations and physical protection of aggregates provided stability to around 500 years. Chemical characteristics of organic material in these fractions and whole soils (13C CP-MAS NMR spectroscopy, mass spectrometry, FTIR spectroscopy, thermogravimetric analysis, ICP-OES) indicated the relative contribution of different stabilisation mechanisms to the longevity of each of these fractions. Two long-term incubations of isolated physical fractions and soil horizons at different temperatures provided information about the actual resistance to decomposition in each SOM pool, as well as the temperature sensitivity of respiration from different pools. Naturally 13C-labelled labile substrate additions to the mineral and organic horizons compared the resistance to priming by labile and recalcitrant substrates. Manipulation of soil pore water was investigated as a method for isolating the respiration of SOM from physically occluded positions within the soil architecture. Contadictory lines of evidence emerged on the relative stability of different SOM pools from 14C dating, incubation experiments and chemical characterisation of indicators of stability. This led to the interpretation that physical aggregate protection primarily controls SOM stability within topsoils, while mineral and Fe oxide stability provides more lasting stability in the mineral horizon. Less humified and younger SOM was found to have a higher sensitivity to temperature than respiration from well-humified pools, in contrast to predictions from thermodynamics.

This thesis presents results from several studies that have focused on the carbon and nutrient dynamics in soils at the forest – tundra ecotone in Fennoscandia. The main objectives of the study were: (i) to investigate the links between the physical environment, above-ground vegetation communities, soil carbon storage, nutrient status and the chemical composition of the soil organic matter (SOM), and (ii) to quantify trace gas fluxes (methane and carbon dioxide) between mesic soils and the atmosphere. Four main field areas spanning an 8 degree latitudinal gradient were established at the ecotone in 1998 and studied for four years. In addition to the natural gradients we also established a warming treatment. Decomposition rates (i.e. carbon dioxide efflux and litter decomposition) were higher at our forest sites. This was linked principally to the more favourable physical environment at the forest sites, rather than to SOM quality, despite some indications of higher SOM quality at forest sites based upon conventional chemical analysis and 13C NMR techniques. Tundra soils stored large amounts of potentially labile carbon that could readily be accessed by microorganisms when transferred to a forest environment. The interrelation between increased soil temperature and reduced soil moisture content is likely to moderate the response of decomposition rates to increased temperatures. Generally, these mesic soils showed net methane uptake from the atmosphere, which was enhanced by the warming treatment. No differences between forest or tundra soils could be detected. The major conclusions presented here are that (1) soil carbon storage is likely to be reduced if mountain birch forest replaces tundra heath and (2), methane uptake in mesic soils in the Fennoscandian mountains represents a negative feedback to further environmental change in a warmer climate.

Forest fires can have a great impact on the relationship between soil organic matter (SOM) and soilbulk density (SBD). SOM will reduce with increased fire intensity, which ultimately leads to more compaction of the soil. The compaction rate might increase to the limit of where root growth will be absent thus leading to actions to restore the soil. This study investigates changes in the relationship between SOM and SBD in spodosol and histosol in Seglingsberg, located in South-central Sweden, where a forest fire occurred summer 2014.  In addition, changes of pH values in the two types of soilwere examined in order to receive information about the chemical states of the different soil types.A total of 29 samples at depths of 0-17 cm were received from one day of fieldwork and these were later analysed concerning the pH, the SBD and the SOM content. The results showed an increase of pH-values in the fire-exposed area compared to pH values measured at the reference site (pH ~5). More importantly, the results from the SBD and SOM analyses indicated that there was in fact an inversely proportional relationship between the two soil parameters. In addition, high pH values were measured at the same subareas of which the highest SBD- and the lowest SOM values were obtained.Statistical analyses were applied on the results in order to conclude if the soil property changes caused by the fire were significantly different from normal conditions or not. The results from the statistical analyses revealed that 25% of the fire-exposed sites had changed significantly. However, more samples should have been taken while in field, since lack of data is thought to have had a great impact on the final results.Although there were no strong statistical evidence for the hypothesis, it is clear that the forest firein Västmanland year 2014 affected both the SOM, SBD and pH values in the soils. / Under sommaren år 2014 utbröt en omfattande skogsbrand i Västmanlands län, vilket medföljdedramatiska konsekvenser för framförallt ett flertal skogsbolag, men även för boende i området. Med skogsbränder följer negativa såväl som positiva konsekvenser, där de positiva framförallt gäller med avseende på arter som har evolverat i samband med bränder. Förutom ovannämnda konsekvenser så finns det risk för att markförhållandena ändras till följd av en skogsbrand. I denna studie undersöktes hur  markegenskaper  i  torv-  samt  podsoljordar  hade  förändrats  med  avseende  på  pH,  halten  avorganiskt material samt packningsgrad. Fältstudien genomfördes i ett drabbat brandområde strax norrom Seglingsberg, Surahammars kommun. Totalt togs 29 stycken jordprover inom fem stycken transekter i området. Av dessa kunde 25 stycken användas till alla tre analyserna. Resultaten från jordprovsanalyserna användes därefter till att genomföra statistiska undersökningar. Detta för att se hur stor spridningen var mellan och inom de fem transekterna samt för att kunna avgöra om jordproverna visade sig vara signifikant förändrade från ursprungsförhållanden.Resultaten från jordprovsanalyserna visade att det fanns mest organiskt material kvar i de östra delarna av området, medan det var kraftigt reducerat ju längre nordväst jordproverna hade hämtats. I samband med att markens organiska material hade reducerats kunde man även bevittna att jordtäcket hade blivit mer kompakterat. Resultaten från pH-analysen pekar också på att förändringarna varit som störst i de nordvästliga delarna. pH-analysen bevisade att markkemin ser annorlunda ut än innanbranden, då värdena ibland låg 2 enheter för högt än vad man vanligen brukar observera i podsol- ochtorvjordar. Då pH-skalan är logaritmisk innebär detta en minskad försurning med 100 gånger. Resultaten från alla jordprovsanalyser tyder att branden varit som mest intensiv i den nordvästra delen av undersökningsområdet, i området bestående av ungskog.Även om resultaten från jordprovsanalyserna pekade på att branden orsakat tydliga mark- förändringar, visade majoriteten av de statistiska undersökningarna inte på signifikanta förändringar. Det är därför inte möjligt att generalisera resultaten och således applicera dessa på hela brandområdet i Västmanland.Eftersom att naturligt förekommande skogsbränder är relativt få till antalet i Sverige, finns därmed få studier tillgängliga inom ämnesområdet. Det finns en upplaga av studier inom kontrollerade och anlagda brandfält, men i och med att dessa förhållanden är fixerade, så påverkas markegenskaperna sällan avsevärt. Forskningsrapporter indikerar på ett mer extremt klimat i framtiden, som förmodas leda till en ökad omfattning samt ett ökat antal naturligt förekommande skogsbränder. Om denna prognos stämmer är det viktigt att undersöka markförhållandena, då en skogsbrand kan ha direktavgörande effekt på återväxten.

Soils represent an important terrestrial carbon (C) sink, storing up to three times the amount of atmospheric C, however climate and land use changes may transform soils into C sources. River corridor (RC) soils and associated C are at risk to become mobilized by erosion such as bank failure and scour events. Once soil-derived organic C is transferred into the stream, microbial processes and photodegradation of the dissolved, labile (or bioavailable) fractions can lead to the production of CO2, which can evade and increase atmospheric CO2 levels. Because predicted increases in heavy precipitation will likely increase this type of riverine erosion, it is important to better understand the potential for the release of bioavailable C from RCs. One objective of this thesis was therefore to identify and characterize representative samples of soils from a typical Vermont RC for common land covers and simulate the production of dissolved organic matter (DOM) during riverine soil erosion. Field sites representative of typical agricultural and forested land uses were selected based on the analysis of 106 existing samples and resampled multiple times over the summer of 2015. Production of DOM from riverine erosion was simulated using aqueous soil extracts (ASE), where soil and water were shaken at fixed ratios followed by the separation of the extract. To study the characteristics of these extracts (which serve as analogue of stream water after erosion), water extractable C (WEOC) concentrations, water extractable nitrogen, fluorescence properties of DOM, and bioavailability were determined. Results indicated a common, dominantly terrestrial source material for all land covers, but C concentrations and fluorescence properties differed. High but variable amounts of soil organic C and WEOC were observed in agricultural riparian and agricultural stream bank samples, and lower concentrations in agricultural field, forest, forest riparian, and forest stream banks. WEOC bioavailability was high in all agricultural land covers and low in forested land covers. Because this study is the first in which ASE are used as analogues for stream water after riverine erosion, a second objective was to test laboratory methods used in this study for their effect on WEOC, fluorescence properties, and bioavailability. Specifically, the effects of soil drying, soil storage, and the effects of the extraction solution were tested. For this, ASE were prepared from soils that were field moist, dried, and after two years of storage. In addition, dried soils were extracted using different solutions including a salt solution, river water, and double deionized (DDI) water. Results indicated WEOC concentration and microbial humic-like fluorescence from extracts of dried soils were higher than those in extracts of field moist soils, while WEOC concentration and microbial humic-like fluorescence was highest in extracts of soils stored long term. In addition, the bioavailability of WEOC was higher in dried soils than field moist soils. The extraction solutions of DDI water and river water produced DOM with similar fluorescence properties, while the salt solution extracted a different, less humified pool of C. Overall, the ASE methods used in this study are effective in simulating stream bank erosion and subsequent C release into stream water, however the effects of drying the soils need to be considered when assessing DOM.