Multi-services cover crops (MSCC) grown during fallow period between two cash crops provide various ecosystem services. Among species used as MSCC, crucifers can efficiently prevent nitrate and sulphate leaching by catching residual soil mineral nitrogen (N) and sulphur (S) afterthe preceding cash crop (N and S catch crop services). Crucifers also have a unique capacity to suppress pathogens due to the biocidal hydrolysis products of endogenous secondary metabolites called glucosinolates (GSL). The aim of our study was to assess the provision of various ecosystem services linked to N, S cycles and biocontrol potential for a wide range of bispecific crucifer-legume mixtures in comparison to sole cover crops of legume and crucifer. We carried out experiments in 2 contrasted sites (Toulouse and Orléans regions, France) during 2 years in order to assess these services and the compatibility of various bi-specific crucifer-legume mixtures. We tested a great diversity of species, such as i) crucifers : rape, white mustard, Indian mustard, Ethiopian mustard, turnip, turnip rape, radish and rocket, and ii) legumes: Egyptian clover, crimson clover, common vetch, purple vetch, hairy vetch, pea, soya bean, faba bean, and white lupin. Our study demonstrated that crucifer-legume mixtures can provide and mutualize various ecosystem services by reaching from 2 thirds (GSL production, S and N green manure) to the same level ofservice (N and S catch crop) than the best sole family of species. GSL profile and concentration did not change in mixtures meaning that crucifer-pests interactions were identical. Through a literature review we also illustrated that biocontrol services of crucifers could be largely maintained in crucifer-legume mixtures for a wide range of pathogens and weeds while reducing potential disservices on beneficials and increasing N related service

The Upper Mississippi River (UMR) basin contributes over 50,000 metric tons of nitrogen (N) to the Gulf of Mexico each year, resulting in a “dead zone” inhospitable to aquatic life. Land-applied N (fertilizer) in the corn-belt is attributed with a majority of the N-load reaching the Gulf and is difficult to treat as run-off is considered a non-point source of pollution (i.e. not from a pipe). One solution to this “grand challenge” of intercepting N pollution is utilizing filter-feeding organisms native to the UMR. Freshwater mussel (order Unionidae) assemblages collectively filter over 14 billion gallons of water, remove tons of biomass from overlying water, and sequester tons of N each day. Our previous research showed mussel excretions increased the sediment porewater concentrations of ammonium by 160%, and indirectly increased nitrate and nitrite by 40%, presumably from microbial degradation of ammonium. In response, the goal of this research was to characterize how mussels influenced microbial communities (microbiome) to determine the fate of N in UMR sediment. First, we used qPCR and non-targeted amplicon sequencing within sediment layers to identify the N-cycling microbiome and characterized microbial community changes attributable to freshwater mussels. qPCR identified that anaerobic ammonium oxidizing (anammox) bacteria were increased by a factor of 2.2 at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced microbial species richness and diversity and indicated that sediment below mussels harbored distinct microbial communities. Furthermore, mussels increased the abundance of ammonia oxidizing bacteria (family Nitrosomonadaceae), nitrite oxidizing bacteria (genus Nitrospira), but decreased the abundance of ammonia oxidizing archaea (genus Candidatus Nitrososphaera), and microorganisms which couple denitrification with methane oxidation. These findings suggested that mussels may enhance microbial niches at the interface of oxic and anoxic conditions, presumably through excretion of N and burrowing activity. In response, we performed metagenomic shotgun sequencing to identify which genes of the microbiome were most impacted by mussels. We hypothesized that genes responsible for ammonia and nitrite oxidation would be greater in the sediment with mussel assemblages. We found the largest abundance of N-cycling genes were responsible for nitrate reduction and nitrite oxidation, which is corroborated by the high concentration of nitrates in UMR water. Linear discriminant analysis statistical analyses showed nitrification genes were most impacted by mussels, and this presented an opposing effect on genes responsible for producing nitrous oxide, a potent greenhouse gas. Further investigation showed an increased abundance of a novel organism capable of completely oxidizing ammonia to nitrate (Candidatus Nitrospira inopinata) and coexisted with metabolically flexible Nitrospira (sp. moscoviensis), likely enhancing both carbon and N-cycling. We demonstrated that native mussels harbor a unique niche for N-cycling microorganisms with large metabolic potentials to degrade mussel excretion products. Our findings suggest the ecosystem services of mussels extend beyond water filtration, and includes enhanced biogeochemical cycling of carbon, N, and reduces the potential for a potent microbially-produced greenhouse gas. Ultimately, this research could be used to advocate for mussel habitat restoration in the UMR to lessen the impacts of non-point pollution.

Since the late 1880's western juniper has expanded in range and increased in density in sagebrush-bunchgrass, riparian, and forested plant communities of the Pacific Northwest. Succession to western juniper woodland has been shown to reduce the productivity and diversity of the understory component, result in concentration of soil nutrients beneath juniper canopies, and reduces soil moisture storage. This study assessed understory plant succession, soil nitrogen (N) cycling, litter decomposition, and soil moisture availability following cutting of a western juniper woodland on Steens Mountain, Oregon. Cutting of western juniper reduced below-ground competition for water and N, increasing soil moisture storage and N availability for understory species. Leaf water potentials were less negative, and N concentration and biomass in understory plants were greater in the cut treatment. Understory species responded to improved growth conditions with increased cover, biomass, density, and diversity. In 1993, total understory biomass and canopy cover were 870% and 300% greater, respectively, in the cut treatment than the uncut woodland. Understory succession was dominated by plants present on the site prior to cutting. Results indicated initial that bunchgrass densities of 2 plants/m2 were sufficient for perennial grasses to dominate following juniper cutting. Juniper cutting is an effective method for restoring the understory component in sagebrush rangelands that are currently dominated by western juniper woodland. Nitrogen availability was greatest in cut-interspace locations the first year following treatment and in cut-duff locations in the second year. Nitrification was lowest in cut-slash and woodland-duff locations, areas receiving fresh litter inputs and experiencing lower temperatures than interspace (cut and woodland treatments) and cut-duff locations. Decomposition of juniper litter was two times faster in the cut treatment, however the release of litter N occurred earlier in the woodland. Large inputs of N poor litter from cut juniper slash were hypothesized to have increased microbial demand for N, resulting in immobilization of litter N. Immobilization of litter N may be important in conserving N on sites following cutting. / Graduation date: 1997

Nitrogen fixation is an ecologically important microbial process that can contribute bioavailable combined N to habitats low in N. Shipworms, or wood-boring bivalves, host N2-fixing and cellulolytic symbiotic bacteria in gill bacteriocytes, which have been implicated as a necessary adaptation to an N-poor C-rich (wooden) diet. Shipworm symbionts are known to fix N within the gill habitat and newly fixed N is subsequently incorporated into non-symbiont containing host tissue. The presence of N2-fixation in gill bacteriocytes presents a conundrum because N2-fixation is tightly regulated by oxygen in most other diazotrophic microbes. Also, the direct evidence of new N being incorporated into the host tissue indicates that there are potentially complex nutrient cycles in this symbiosis, which have not been investigated. We used the cultivated symbiont Teredinibacter turnerae, which has been isolated from many shipworm species, as a model organism to elucidate controls on N2-fixation and N release in the shipworm symbiosis. Our results indicate that headspace oxygen concentration does not control biomass specific N2-fixation and respiration activity in T. turnerae, but it does influence the magnitude of the growth rate and timing of culture growth. Also, we examined the controls of oxygen on inorganic nutrient uptake rates, and documented a small amount of dissolved inorganic nitrogen release. While the N budget is only partially balanced, we provide indirect evidence for the allocation of fixed N to the excretion of exopolymeric substances and dissolved organic nitrogen; future studies that measure these additional N sinks are necessary to close the N budget. Although there are limitations of using pure cultures to investigate a complex symbiotic system, this study provides direct experimental evidence that T. turnerae has adaptations that are conducive to N2-fixation in gill bacteriocytes.

Thesis (Ph. D.)--College of William and Mary. / Vita. Includes bibliographical references. Also available online.

Over-enrichment of nutrients in coastal waters has been a growing problem as population growth has enhanced agricultural and industrial processes. Enhanced nitrogen (N) fluxes from land to coast continue to be the result of over fertilization and pollution deposition. This over-enrichment of nutrients has led to eutrophication and hypoxic conditions in coastal environments. This study was conducted along the Gulf of Mexico, through the state of Texas, in order to quantify all agricultural and industrial sources of N in a region which contains a large precipitation gradient, three major metropolitan areas, and one of the top livestock industries in the United States. Nitrogen inputs from fertilizer, livestock, crop fixation, and oxidized deposition from both dry and wet atmospheric processes were quantified and compiled into a Texas Anthropogenic N Budget (TX-ANB). In addition, comparisons and regional enhancements were made to the Net Anthropogenic Nitrogen Input dataset (NANI toolbox), which is a national dataset developed at Cornell University by Hong et al. [2011]. These enhancements ultimately will help understand the full pathways of anthropogenic influences on coastal systems in a regional setting. All three datasets (NANI, NANI Regional, and TX-ANB) indicate agriculture to be the primary contributor to the N cycle in Texas, with TX-ANB showing 38% of inputs from fertilizer, 37% of inputs from livestock, and 2% of inputs from legumes. N input due to atmospheric deposition of oxidized N clearly highlights urban areas, indicating a strong influence of urbanization on the N cycle due to anthropogenic impacts; 23% of N input in Texas is the result of deposition of oxidized N. Quantification of inputs spatially indicates a strong enhancement of N from human influence in the coastal plain where nutrient export is heightened by major storm events. This enhancement of N along a coastal drainage area will likely have a negative impact on downstream environments. / text

published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

The current literature shows that global climate is changing with temperatures generally increasing, precipitation patterns becoming less predictable and extreme weather events becoming more frequent. However, the literature is often unclear not only about how changes in temperature will affect soil processes but even about how soil temperatures themselves are changing. This thesis has found that soil temperatures over recent decades have increased at rates comparable to air temperatures (average mean of 0.71 in soil and 0.93 °C in air over the total length of the data sets used). There were differences in seasonal trends between soil and air, for example, winter air temperatures increased twice as quickly as spring air temperatures whereas in soil winter and spring temperatures were increasing at similar rates. This highlights potential problems for predicting how soil functions such as biogeochemical cycling will respond to realistic temperature change. In order to assess the effects of changing soil temperatures on particular reactions involved in soil Nitrogen cycling incubation experiments, both short and longer term in the laboratory as well as soil warming in the field were carried out. Realistic warming was found to increase the rates of protease and urease activity during all tests; however, amidase activity was only measurable after the addition of labile carbon and even then showed no temperature sensitivity. This thesis also considered the effect of temperature change on the size and structure of the soil microbial community at these realistic soil temperatures. Both in the lab and the field changes in rates of soil processes (enzyme activity) as a result of temperature change are not accompanied by a change in either size or structure of the microbial community as measured by phospholipid fatty acid analysis, suggesting high levels of functional redundancy within the soil microbial community. The effects of organic matter input in the field were found to have only small effects on the rates of enzyme activity although this was more important during laboratory incubations. Organic matter quality was also important during lab incubations where lower quality organic matter provoked greater enzyme activity in accordance with q-theory; however, there was no evidence for greater temperature sensitivity of low quality organic matter. The size and structure of the microbial community, both in the field and in the lab, were not affected by either the rate of organic matter input (in the field) or they quality of organic matter (in the lab). The size of the microbial community, however, decreased over time in both situations, the ratio of bacteria to fungi in the soil seemed to increase over time also.

Increased N fertilizer efficiency in crop production is essential for agronomic, economic, and environmental improvement. In order to increase efficiency, a basic knowledge of fertilizer-soil-crop relationships and components is required. Nitrogen components in the soil-corn system were determined on two soils (Chicot sandy clay loam, Grey Brown Luvisol; Ste. Rosalie clay, Humic Gleysol). Fall soil NO$ sb3 sp-$-N levels increased linearly with increasing N rates above the 170 kg ha$ sp{-1}$ N rate. Changes in soil NO$ sb3 sp-$-N over winter were a function of both fall soil NO$ sb3 sp-$-N levels and winter precipitation. Denitrification rates during the non-growing season ranged from 7 to 24 kg N ha$ sp{-1}$, mainly dependent on N fertilizer rates the previous growing season on the Ste. Rosalie soil. Denitrification losses were a small portion of NO$ sb3 sp-$ disappearance over the non-growing season. Almost all fertilizer N at 170 kg N ha$ sp{-1}$ was recovered as crop N, clay fixed NH$ sb4 sp+$ and organic immobilized N at the end of the growing season, where at 400 kg ha$ sp{-1}$ N fall mineral N and unaccounted for N were a major component of the N fractions. High rates (400 kg N ha$ sp{-1}$) compared to normal rates (170 kg N ha$ sp{-1}$) resulted in some increase in yield, greater microbial activity and greater soil organic N, and a significant loss of fertilizer N by denitrification or leaching.

Research for a dissolved nitrogen budget was conducted at Mer Bleue bog near Ottawa, ON, from May 20, 2003 to May 21, 2004. Mer Bleue is located within an area experiencing the highest levels of atmospheric nitrogen deposition in North America, although these levels are only low to moderate compared to those in Europe. Continuous measurements of precipitation, evapotranspiration, bog water table level and outflow water depth were used in conjunction with discrete measurements of precipitation and outflow to determine the hydrologic budget. Water samples were taken from precipitation collectors, piezometers at various depths and locations throughout the bog, and an outflow point in order to gauge changes and patterns in chemical concentrations at various points throughout the bog. The nature of the bog morphology and landscape allowed for collection of water samples from a single outflow point. / Chemical analysis combined with the water budget revealed that the majority of the dissolved nitrogen is entering the bog as NO3-N and NH 4-N (inorganic nitrogen), and leaving the bog as dissolved organic nitrogen (DON). Export of nitrogen was generally low relative to the input, and was only a very small fraction of the huge amount of nitrogen stored in the bog. Bog porewater concentrations were dominated by DON and did not show spatial patterns in relation to the bog edge. When comparing the annual accretion of nitrogen at the bog to the long-term storage numbers, it was apparent that there is a missing source of nitrogen. From the literature and patterns in the bog, it appears that this missing input at Mer Bleue is likely due to a combination of previously unmeasured nitrogen fixation and more diverse usage of DON by bog vegetation.