There is increasing interest in the use of prescribed fire to reduce fuel loadings and other management objectives in ecosystems of the Madrean Province. Fuel loadings were measured on the same pine-oak ecosystem occurring on five different sites with a range of different fire frequencies. To determine the effects of fire frequencies on fuel loading. Study sites located in Mexico were characterized by a high fire frequency. Study sites in the United States were characterized by low and intermediate fire frequencies. Heavy fuel loadings on sites with high fire frequencies were below the recommended amounts for coarse woody debris. Sites with intermediate fire frequencies were within recommended amounts of coarse woody debris while sites with low fire frequencies were above recommended amounts for coarse woody debris. There was no difference in fine fuel loading among sites with 2, 5, 9, and 13 fires since 1900. Total fuel loading was inversely related to fire frequency. The effects of intermediate fire frequencies can be used to assess ecosystem function and meet multiple use management objectives.

<p> The Riverlands Migratory Bird Sanctuary (1500 ha) was established in 1988 on US Army Corps of Engineers (USACE) land along the Mississippi river in West Alton, Missouri (38.87&deg; N, -90.17&deg; W). It is now cooperatively operated by USACE and the National Audubon Society. About 485 ha consist of actively managed restored bottomland prairie and marshland. The Great Flood of 1993 caused prolonged inundation and destroyed vegetation beds and moist soil plants in the Sanctuary&mdash;an impact still visible today. The goal of this study was to improve plant species diversity and cover, as well as generate more natural vegetation. We employed differing degrees of soil disturbance (tilling and disking) as a means stimulate seed germination from the seed bank. We predicted that the more extreme soil disturbance, tilling, would achieve our goals best. Six replicate marshes within the Sanctuary were chosen for this study. Each marsh was divided into three similarly sized areas and which were randomly assigned one of three treatments: disking, tilling, and control. Vegetative cover and species presence were recorded in 0.25 m² sampling plots at random intervals along each transect in each treatment area. A pre-treatment sample was obtained for comparison. ANOVA of a randomized complete block design revealed strong interactions between marsh (block) and treatment for nearly every community measure. However, marsh effects for cover, species richness, and Shannon diversity were significant beyond this effect. Treatment effects were not significant. Community ordinations by NMDS revealed a strong tendency for plots to aggregate by marsh, not treatment. Preliminary management recommendations can be given based on this study. Restoration activities should focus on site specific characteristics such as the species pool and local hydrology and lean away from immediate additional disturbances. </p>

<p> Disturbances such as fire and mowing temporarily increase available resources for plants, opening a window of opportunity for establishment. During the recovery of vegetation after disturbance in remnant prairies, seedling establishment is often negligible compared to vegetative regrowth. It is unclear if this is the case in reconstructions. I tested the contribution of seedlings to diversity after disturbance in two, 25-year-old, low diversity reconstructed prairies by removing seedlings, allowing seedlings, and adding seed in 1 m² plots. Disturbance frequency effects were tested by clipping each treatment zero, one, or multiple times. After two growing seasons, in the wetter field site, seedlings removed plots had the lowest species richness and highest evenness, plots with seedlings from the seed bank were intermediate, and plots with added seed had the highest richness and lowest evenness. In the drier site, only adding seed impacted richness (higher) and evenness (lower). In both sites, the seeds present in the seed bank were over 80% from non-native species. Seedling establishment was quantified along with light, water, and nitrate availability within each seeded plot. In the wetter site, resource levels did not predict seedling numbers, but seedlings were more numerous in more frequently clipped, lighter plots. In the drier site, seedlings were more numerous in less frequently clipped plots which received less light and may have remained moister. Seedling establishment from any source never affected community diversity suggesting that while some seeds establish, reconstructions are primarily maintained by vegetative reproduction. The inconsistent effect of clipping highlights the need for management to adapt to varying precipitation, however, given the non-native dominated seed banks, any management intended to increase seedling establishment could result in increased non-native cover. </p>

<p> Effective conservation strategies for imperiled species require an understanding of processes that influence fitness throughout the organism's life cycle and across the range of habitats needed to complete that cycle. I evaluated factors that affect population viability of bull trout <i>Salvelinus confluentus, </i> a threatened freshwater char species, throughout individual life stages and over the entire life cycle. </p><p> I assessed the relationship between bull trout egg incubation success and environmental variables. Egg survival was negatively related to the percent of fine sediment in redds and positively related to hydraulic conductivity and the strength of downwelling. Next, I quantified juvenile bull trout survival rates and described movement patterns for this life stage. Juvenile bull trout emigrated from natal headwaters into larger rivers throughout the entire year and across a range of sizes. Estimates of juvenile survival rates improved dramatically when emigration was incorporated into the analysis. </p><p> I integrated my observations of bull trout survival, growth, and movement to create a life-cycle model, which I used to better understand how populations respond to changes in specific demographic rates. Bull trout populations were particularly sensitive to changes in juvenile growth and survival. The relative effect of changes to fertility rates and adult survival varied depending upon whether a population was composed primarily of large, migratory, or smaller, resident individuals. Dispersal helped to lower the probability of extinction for small or declining populations when neighboring populations were stable. </p><p> My research demonstrates that bull trout require access to habitats throughout entire watersheds to maintain population viability. My results suggest that limiting anthropogenic sources of fine sediment and maintaining areas of channel complexity that promote downwelling can be important for bull trout embryo survival. Management decisions should also consider the diverse behavior of juvenile bull trout and the wide range of habitat they use. Additionally, connectivity between populations is likely to be important for declining populations to persist. The diversity of life-history strategies expressed by bull trout helps maintain demographic stability within and among populations. As such, preservation of habitat integrity and full life-history diversity is imperative for conservation and recovery of bull trout populations range-wide.</p>

<p> To evaluate the success of reestablishing tidal connection to salt marshes as a method of creating new fish habitat, both newly-restored and previously-restored (hereafter termed "reference") habitats within the Huntington Beach Wetlands Complex were monitored over a two year period. Although fish abundance and diversity metrics were generally equivalent between marshes within one year, community composition remained different. Newly-restored habitat generally had higher abundances of planktivores (e.g., <i>Atherinops affinis</i>), and lower abundances of benthic carnivores (e.g., <i>Fundulus parvipinnis </i>) relative to reference habitat. To determine the possible mechanisms driving fish habitat use patterns, trophic support was assessed for juvenile California halibut, <i>Paralichthys californicus,</i> using gut content and stable isotope analyses of wild-caught and caged individuals. Observed differences in the diet of halibut across size classes indicated ontogenetic shifts in feeding behaviors, while similarity in diet among marshes suggested the potential for rapid development of trophic support within restored habitats for this species. </p>

<p> In this study, the Weather Research and Forecasting Model (WRF) is coupled with the Advanced Canopy-Atmosphere-Soil Algorithm (ACASA), a high complexity land surface model (LSM). Although WRF is a state-of-the-art regional atmospheric model with high spatial and temporal resolutions, the land surface schemes available in WRF are simple and lack the capability to simulate carbon dioxide, for example, the popular NOAH LSM. ACASA is a complex multilayer land surface model with interactive canopy physiology and full surface hydrological processes. It allows microenvironmental variables such as air and surface temperatures, wind speed, humidity, and carbon dioxide concentration to vary vertically. </p><p> Simulations of surface conditions as well as reference and actual evapotranspiration from WRF-ACASA and WRF-NOAH are compared with surface observations for year 2005 and 2006. Results show that the increase in complexity in the WRF-ACASA model not only maintains model accuracy, it also properly accounts for the dominant biological and physical processes describing ecosystem-atmosphere interactions that are scientifically valuable. The different complexities of physical and physiological processes in the WRF-ACASA and WRF-NOAH models also highlight the impacts of different land surface and model components on atmospheric and surface conditions. </p><p> Lastly, unlike the simple big-leaf WRF-NOAH model with no carbon dioxide simulation, the high complexity WRF-ACASA model is used to quantify the carbon dioxide exchange between the biosphere and atmosphere and to examine the importance of atmospheric carbon dioxide concentration on surface processes on a regional scale. A new carbon dioxide (COCO₂) tracer is introduced into the WRF-ACASA coupled model to allow atmospheric CO₂ concentration to vary spatially and temporally according to surface plant physiological processes. The comparison between the two model simulations with and without a COCO₂ tracer shows that the impact of atmospheric COCO₂ concentration and transportation are important, and therefore these should not be neglected when simulating COCO₂ flux at regional scales. Overall, this study shows that the high complexity WRF-ACASA model is robust and able to simulate the surface conditions and COCO₂ fluxes well across the region, particularly when given accurate surface representations. </p>

<p> Uncertainty of predicted change in precipitation frequency and intensity motivates the scientific community to better understand, quantify, and model the possible outcome of dryland ecosystems. In pulse dependent ecosystems (i.e. monsoon driven) soil moisture is tightly linked to atmospheric processes. Here, I analyze three overarching questions; Q1) <i>How does soil moisture presence or absence in a shallow or deep layer influence the surface energy budget and planetary boundary layer characteristics?,</i> Q2) <i> What is the role of vegetation on ecosystem albedo in the presence or absence of deep soil moisture?,</i> Q3) <i>Can we develop empirical relationships between soil moisture and the planetary boundary layer height to help evaluate the role of future precipitation changes in land surface atmosphere interactions? </i>. To address these questions I use a conceptual framework based on the presence or absence of soil moisture in a shallow or deep layer. I define these layers by using root profiles and establish soil moisture thresholds for each layer using four years of observations from the Santa Rita Creosote Ameriflux site. Soil moisture drydown curves were used to establish the shallow layer threshold in the shallow layer, while <i>NEE</i> (Net Ecosystem Exchange of carbon dioxide) was used to define the deep soil moisture threshold. Four cases were generated using these thresholds: Case 1, dry shallow layer and dry deep layer; Case 2, wet shallow layer and dry deep layer; Case 3, wet shallow layer and wet deep layer, and Case 4 dry shallow and wet deep layer. Using this framework, I related data from the Ameriflux site SRC (Santa Rita Creosote) from 2008 to 2012 and from atmospheric soundings from the nearby Tucson Airport; conducted field campaigns during 2011 and 2012 to measure albedo from individual bare and canopy patches that were then evaluated in a grid to estimate the influence of deep moisture on albedo via vegetation cover change; and evaluated the potential of using a two-layer bucket model and empirical relationships to evaluate the link between deep soil moisture and the planetary boundary layer height under changing precipitation regime. My results indicate that (1) the presence or absence of water in two layers plays a role in surface energy dynamics, (2) soil moisture presence in the deep layer is linked with decreased ecosystem albedo and planetary boundary layer height, (3) deep moisture sustains vegetation greenness and decreases albedo, and (4) empirical relationships are useful in modeling planetary boundary layer height from dryland ecosystems. Based on these results we argue that deep soil moisture plays an important role in land surface-atmosphere interactions. </p>

I used sapling population data collected since 1980 to investigate how canopy disturbance interacts with chronic understory disturbance to determine regeneration patterns. I reconstructed flooding history using a combination of river gauging, a local water-level recorder, and contour maps. 1979 was an extreme flood year for this site, as was 1989. Reduction in flooding frequency since dam construction in 1965 was significant for all elevations, while reduction in flooding duration was significant only for the upper half of the site. Using constrained ordination, I showed that sapling occurrence varies primarily along a flooding/soil moisture gradient, and secondarily along a canopy-openness gradient. This confirms that both flooding and light influence local variation in species composition. Small sapling density increased by more than five times during the decade, while large sapling density increased over 70%. I suggest that this increase is related to the decline in frequency and duration of flooding, and specifically, to the pattern of flooding from 1979-1989, characterized by severe flooding in 1979 and 1989. Sapling survivorship also responded to temporal variation in flooding over the decade. A damage survey revealed a size component to flooding damage, with small individuals making up a disproportionate share of those in the highest damage classes. In addition, there is a relationship between river flow and the elevation of saplings that died, suggesting that the effects of elevation are not simply related to flooding, but perhaps to soil moisture as well. Analyses of sapling growth suggest that there is a trade-off between tolerating flooding in wet years and being subject to moisture stress in dry years. I presented evidence that canopy gaps play an important role in determining sapling growth. Gaps appear to be crucial to the continued success of large saplings, and the fastest-growing individuals are found in them. This may also confer a measure of flood-tolerance related to sapling size.

Texas coastal wetlands will be increasingly endangered over the coming century as sea level rises due to global warming. Since estimates of sea-level rise may be similar to trends interpreted from Holocene sediments, a paleoecologic analysis of wetland peats may provide a predictive model for wetland succession. Three areas of focus are necessary to achieve predictive power, however: ecologic, sedimentalogic, and taphonomic. No single microtaxonomic group is well preserved in all depositional environments. Foraminiferal assemblages delineate salt to brackish marsh environments, but are absent in fresh marsh sediments. Ostracodes and diatoms occur in all marsh types, but ostracodes are sporadically preserved and diatom thanatocoenoses from different environments become too similar to significantly indicate different biocoenoses. A combined thanatocoenosis composed of microtaxa with similar ecological requirements but different taphonomic signatures provides an effective method of identifying sea-level history from wetland sediment cores, however, since taphonomic effects on selected groups overlap. Calcium carbonate and silicate dissolve according to pH, while proteinaceous cements of many agglutinated foraminifera withstand dissolution and are removed only through oxidation-reduction reactions. An analysis of these trends in the Galveston Bay system supports the following taphonomic model: During accretionary still stands, in-situ preservation is high for each thanatocoenosis. This is due to the effects of time averaging over an otherwise harsh and patchy chemical environment. During rapid sea-level rise, fresh marsh sediments become inundated with brackish to salt water. This tends to raise the pH and Eh, enhancing preservation. The thanatocoenoses grade sharply from mixed to distinct. During flooding, or progradation, fresh water inundates brackish to salt water sediments. This tends to lower pH and Eh, decreasing preservation. In situ thanatocoenoses are reduced to only a few species or eliminated completely. This taphonomic model suggests that the traditional approach of using a single microfossil group to interpret sea-level trends may be inadequate. The combined thanatocoenosis approach can produce better controls on paleoecologic and paleoclimatic interpretations, and will allow for better predictions of future trends.

Redox measurements were used to study whether different mitigation options affect methane emission and production by altering the electrochemical environment in rice paddy soil. These mitigation options include field drainage, use of different cultivars, and changing soil texture. Results indicate that the redox potential (Eh) is an accurate indicator of whether or not methane is produced. Also, the timing of methane production and emission was found to be dependent upon the reduction of iron and subsequent increase of the ferrous ion concentration. Field drainage is a mitigation option that successfully lowers methane emission rates by increasing the Eh. By studying the other mitigation options, it was found that once sufficiently negative Eh values are reached, different non-redox parameters control the actual amount of methane emitted.