Multinomial mixture model with heterogeneous classification probabilities

Royle and Link (Ecology 86(9):2505?C2512, 2005) proposed an analytical method that allowed estimation of multinomial distribution parameters and classification probabilities from categorical data measured with error. While useful, we demonstrate algebraically and by simulations that this method yields biased multinomial parameter estimates when the probabilities of correct category classifications vary among sampling units. We address this shortcoming by treating these probabilities as logit-normal random variables within a Bayesian framework. We use Markov chain Monte Carlo to compute Bayes estimates from a simulated sample from the posterior distribution. Based on simulations, this elaborated Royle-Link model yields nearly unbiased estimates of multinomial and correct classification probability estimates when classification probabilities are allowed to vary according to the normal distribution on the logit scale or according to the Beta distribution. The method is illustrated using categorical submersed aquatic vegetation data.     

A synthesis of current knowledge on forests and carbon storage in the United States

Using forests to mitigate climate change has gained much interest in science and policy discussions. We examine the evidence for carbon benefits, environmental and monetary costs, risks and trade-offs for a variety of activities in three general strategies: (1) land use change to increase forest area (afforestation) and avoid deforestation; (2) carbon management in existing forests; and (3) the use of wood as biomass energy, in place of other building materials, or in wood products for carbon storage. We found that many strategies can increase forest sector carbon mitigation above the current 162-256 Tg C/yr, and that many strategies have co-benefits such as biodiversity, water, and economic opportunities. Each strategy also has trade-offs, risks, and uncertainties including possible leakage, permanence, disturbances, and climate change effects. Because approximately 60% of the carbon lost through deforestation and harvesting from 1700 to 1935 has not yet been recovered and because some strategies store carbon in forest products or use biomass energy, the biological potential for forest sector carbon mitigation is large. Several studies suggest that using these strategies could offset as much as 10-20% of current U.S. fossil fuel emissions. To obtain such large offsets in the United States would require a combination of afforesting up to one-third of cropland or pastureland, using the equivalent of about one-half of the gross annual forest growth for biomass energy, or implementing more intensive management to increase forest growth on one-third of forestland. Such large offsets would require substantial trade-offs, such as lower agricultural production and non-carbon ecosystem services from forests. The effectiveness of activities could be diluted by negative leakage effects and increasing disturbance regimes. Because forest carbon loss contributes to increasing climate risk and because climate change may impede regeneration following disturbance, avoiding deforestation and promoting regeneration after disturbance should receive high priority as policy considerations. Policies to encourage programs or projects that influence forest carbon sequestration and offset fossil fuel emissions should also consider major items such as leakage, the cyclical nature of forest growth and regrowth, and the extensive demand for and movement of forest products globally, and other greenhouse gas effects, such as methane and nitrous oxide emissions, and recognize other environmental benefits of forests, such as biodiversity, nutrient management, and watershed protection. Activities that contribute to helping forests adapt to the effects of climate change, and which also complement forest carbon storage strategies, would be prudent.     

Effects of ferric hydroxide on methanogenesis from lipids and long-chain fatty acids in anaerobic digestion.

The addition of ferric hydroxide to sludge from a municipal anaerobic digester stimulated the rate of methanogenesis from canola oil when the initial oil concentration was high (4600 mg/L; P < 0.002), but not when it was low (920 mg/L; P > 0.05). Similar trends were observed when oleic acid, a fatty acid that is a major component of canola oil triglycerides, was provided, but the effects were statistically significant only when the initial concentration of ferric hydroxide was also high (18 g/L; P = 0.015). Iron reduction occurred when ferric hydroxide was added to microcosms containing anaerobic digester sludge, but the extent of ferrous iron production was much less in acetate-amended microcosms than in those that were provided with canola oil or oleic acid. Methanogenesis and acetate consumption were completely inhibited when the initial acetate concentration was approximately 5000 mg/L, regardless of the initial ferric hydroxide concentration. The main effect of ferric hydroxide in this system appears to have been a result of stimulation of the rate of fatty acid oxidation.     

GIS‐Based Stream Classification in a Mountain Watershed for Jurisdictional Evaluation

This study analyzed stream characteristics in a mountain watershed in southwestern Colorado and developed a three‐level hierarchical classification scheme using national datasets to demonstrate jurisdictional evaluation as “waters of the United States (U.S.)” under U.S. Clean Water Act Section 404 at the watershed scale. The National Hydrography Dataset and USGS StreamStats were used with field observations to classify streams in the 53 km² Cement Creek Watershed based on flow duration (Level 1), stream order (Level 2), and other biophysical metrics (Level 3). Kruskal‐Wallis tests and discriminant analysis showed significant differences among Level 2 classes. Level 3 classification used cluster analysis for stream length, distance to the downstream traditional navigable water (TNW), and the ratio of mean annual flow from the source stream to the TNW. Results showed all perennial and intermittent streams are jurisdictional relatively permanent waters (RPWs), which include over a third of all streams, 64% are intermittent or ephemeral, and almost half are ephemeral first order. All ephemeral reaches are non‐RPWs requiring significant nexus evaluation to determine jurisdiction. These ephemeral first‐order streams can contribute 5% of the annual flow to the TNW at the confluence, while the Cement Creek main stem contributes 21% of the TNW flow. The study demonstrated that the classification provides key biophysical and regulatory information to aid jurisdictional evaluations in mountain watersheds.     

An evaluation of procedures for the digestion of soils and vegetation from areas with metalliferous pollution

Various digestion or extraction processes are available for the determination of trace metals in environmental samples using diverse analytical techniques. Our research examines the most efficient and reproducible methods of digestion utilising readily available laboratory equipment, reagents and instrumentation. Extraction procedures reported in over 80 recent research works were considered and the most common methods were critically evaluated. Thus nitric acid, nitric acid/perchloric acid, aqua regia, nitric acid/hydrogen peroxide and microwave-assisted methods were investigated using soil and leaf samples collected adjacent to three old metalliferous workings. Analysis was carried out using Flame Atomic Absorption Spectrometry and the results were evaluated. Differences in efficiency of extraction relative to specific metals and different substrates are highlighted and recommendations made for a digestion procedure suitable for environmental samples. Aqua regia produced the most accurate, efficient and reproducible results; we consider methods of improving both of these factors and sample preparation. Our recommended methodology has applications in environmental surveys, environmental geology, environmental toxicology, geochemistry and provides a means of obtaining meaningful and reliable results for the determination of metals present in soils, minerals and vegetation.     

Untangling positive and negative biotic interactions: views from above and below ground in a forest ecosystem

In ecological communities, the outcome of plant-plant interactions represents the net effect of positive and negative interactions occurring above and below ground. Untangling these complex relationships can provide a better understanding of mechanisms that underlie plant-plant interactions and enhance our ability to predict population, community, and ecosystem effects of biotic interactions. In forested ecosystems, tree seedlings interact with established vegetation, but the mechanisms and outcomes of these interactions are not well understood. To explore such mechanisms, we manipulated above- and belowground interactions among tree seedlings, shrubs, and trees and monitored seedling survival and growth of six species (Pinus banksiana, Betula papyrifera, P. resinosa, Quercus rubra, P. strobus, and Acer rubrum) in mature pine-dominated forest in northern Minnesota, USA. The forest had a moderately open canopy and sandy soils. Understory manipulations were implemented in the forest interior and in large gaps and included removal of shrubs (no interactions), tieback of shrubs (belowground), removal of shrubs with addition of shade (aboveground), and unmanipulated shrubs (both below- and aboveground). We found that shrubs either suppressed or facilitated seedling survival and growth depending on the seedling species, source of interaction (e.g., above- or belowground), and ecological context (e.g., gap or forest interior). In general, shrubs strongly influenced survival and growth in gaps, with more modest effects in the forest interior. In gaps, the presence of shrub roots markedly decreased seedling growth and survival, supporting the idea that belowground competition may be more important in dry, nutrient-poor sites. Shrub shade effects were neutral for three species and facilitative for the other three. Facilitation was more likely for shade-tolerant species. In the forest interior, shrub shade negatively affected seedling survival for the most shade-intolerant species. For several species the net effect of shrubs masked the existence of both positive and negative interactions above and below ground. Our results highlight the complexity of plant-plant interactions, demonstrate that outcomes of these interactions vary with the nature of resource limitation and the ecophysiology of the species involved, and suggest that ecological theory that rests on particular notions of plant-plant interactions (e.g., competition) should consider simultaneous positive and negative interactions occurring above and below ground.     

Gypsum addition to soils contaminated by red mud: implications for aluminium, arsenic, molybdenum and vanadium solubility

Red mud is highly alkaline (pH 13), saline and can contain elevated concentrations of several potentially toxic elements (e.g. Al, As, Mo and V). Release of up to 1 million m³ of bauxite residue (red mud) suspension from the Ajka repository, western Hungary, caused large-scale contamination of downstream rivers and floodplains. There is now concern about the potential leaching of toxic metal(loid)s from the red mud as some have enhanced solubility at high pH. This study investigated the impact of red mud addition to three different Hungarian soils with respect to trace element solubility and soil geochemistry. The effectiveness of gypsum amendment for the rehabilitation of red mud-contaminated soils was also examined. Red mud addition to soils caused a pH increase, proportional to red mud addition, of up to 4 pH units (e.g. pH 7 → 11). Increasing red mud addition also led to significant increases in salinity, dissolved organic carbon and aqueous trace element concentrations. However, the response was highly soil specific and one of the soils tested buffered pH to around pH 8.5 even with the highest red mud loading tested (33 % w/w); experiments using this soil also had much lower aqueous Al, As and V concentrations. Gypsum addition to soil/red mud mixtures, even at relatively low concentrations (1 % w/w), was sufficient to buffer experimental pH to 7.5–8.5. This effect was attributed to the reaction of Ca²⁺ supplied by the gypsum with OH^? and carbonate from the red mud to precipitate calcite. The lowered pH enhanced trace element sorption and largely inhibited the release of Al, As and V. Mo concentrations, however, were largely unaffected by gypsum induced pH buffering due to the greater solubility of Mo (as molybdate) at circumneutral pH. Gypsum addition also leads to significantly higher porewater salinities, and column experiments demonstrated that this increase in total dissolved solids persisted even after 25 pore volume replacements. Gypsum addition could therefore provide a cheaper alternative to recovery (dig and dump) for the treatment of red mud-affected soils. The observed inhibition of trace metal release within red mud-affected soils was relatively insensitive to either the percentage of red mud or gypsum present, making the treatment easy to apply. However, there is risk that over-application of gypsum could lead to detrimental long-term increases in soil salinity.