Importance of individual and environmental variation for invasive species spread: a spatial integral projection model

Plant survival, growth, and flowering are size dependent in many plant populations but also vary among individuals of the same size. This individual variation, along with variation in dispersal caused by differences in, e.g., seed release height, seed characteristics, and wind speed, is a key determinant of the spread rate of species through homogeneous landscapes. Here we develop spatial integral projection models (SIPMs) that include both demography and dispersal with continuous state variables. The advantage of this novel approach over discrete-stage spread models is that the effect of variation in plant size and size-dependent vital rates can be studied at much higher resolution. Comparing Neubert-Caswell matrix models to SIPMs allowed us to assess the importance of including individual variation in the models. As a test case we parameterized a SIPM with previously published data on the invasive monocarpic thistle Carduus nutans in New Zealand. Spread rate (c*) estimates were 34% lower than for standard spatial matrix models and stabilized with as few as seven evenly distributed size classes. The SIPM allowed us to calculate spread rate elasticities over the range of plant sizes, showing the size range of seedlings that contributed most to c* through their survival, growth and reproduction. The annual transitions of these seedlings were also the most important ones for local population growth (lambda). However, seedlings that reproduced within a year contributed relatively more to c* than to lambda. In contrast, plants that grow over several years to reach a large size and produce many more seeds, contributed relatively more to lambda than to c*. We show that matrix models pick up some of these details, while other details disappear within wide size classes. Our results show that SIPMs integrate various sources of variation much better than discrete-stage matrix models. Simpler, heuristic models, however, remain very valuable in studies where the main goal is to investigate the general impact of a life history stage on population dynamics. We conclude with a discussion of future extensions of SIPMs, including incorporation of continuous time and environmental drivers.     

Utilizing pyrosequencing and quantitative PCR to characterize fungal populations among house dust samples

Molecular techniques are an alternative to culturing and counting methods in quantifying indoor fungal contamination. Pyrosequencing offers the possibility of identifying unexpected indoor fungi. In this study, 50 house dust samples were collected from homes in the Yakima Valley, WA. Each sample was analyzed by quantitative PCR (QPCR) for 36 common fungi and by fungal tag-encoded flexible (FLX) amplicon pyrosequencing (fTEFAP) for these and additional fungi. Only 24 of the samples yielded amplified results using fTEFAP but QPCR successfully amplified all 50 samples. Over 450 fungal species were detected by fTEFAP but most were rare. Twenty-two fungi were found by fTEFAP to occur with at least an average of ≥0.5% relative occurrence. Many of these fungi seem to be associated with plants, soil or human skin. Combining fTEFAP and QPCR can enhance studies of fungal contamination in homes.     

Paleolimnological assessment of Grove and Plow Shop Ponds, Ayer, Massachusetts, USA--a superfund site

Three sediment cores from each of severely polluted Grove and Plow Shop Ponds, Ayer, Massachusetts, USA, were dated using (210)Pb, characterized for plant macrofossil assemblages, and analyzed for H(2)O, loss-on-ignition, stable Pb isotopes, and concentrations of As, Ca, Cd, Cr, Cu, Fe, Hg, methyl-Hg, Ni, Pb, and Zn. A core from nearby kettle Spectacle Pond, Littleton, Massachusetts, was similarly characterized (except for plant macrofossil assemblages) to assess the regional air pollution signal in sediment for comparison with the six cores. Accumulation rates for metals (mass per area per year), the anthropogenic component (mass per area per year), and total accumulation of the anthropogenic component (mass per area) indicate that As, Cd, Cr, Cu, Hg, methyl-Hg, Ni, Pb, and Zn have accumulated in sediment as a consequence of point source pollution from within the drainage basins of Grove and Plow Shop Ponds. Three distinct sources of pollution are inferred. As is entering Plow Shop Pond via groundwater in the southwest. Cd, Ni, Pb, and Zn are entering the system predominantly at the eastern end of, or upstream from, Grove Pond. Pb also comes from the northwest corner of Grove Pond, the principal source of Cr, Cu, and Hg. These results are consistent with chemistry of modern surface sediments. The history of pollution extends back more than 100 years. Intra- and inter-core variability of concentrations and accumulation rates indicate that much of the pollution was likely in particulate form with little physical redistribution. Recently, concentrations and accumulation rates have generally decreased substantially for those elements present in excessive concentrations in the past. This is a consequence of accumulation of recent, less polluted sediment. In Spectacle Pond, the nearby reference lake, accumulation rates for As, Cd, Hg, and Pb, adjusted for background values and changes in sedimentation rate, increased above background starting in the late 19th century, peaked about 1980, and declined substantially to 2000. These decreases suggest that the anthropogenic (pollution) component of atmospheric deposition of these elements declined after 1980 by at least 50%(As), 80%(Cd), 80%(Hg), and 80%(Pb).     

Quantitative PCR analysis of house dust can reveal abnormal mold conditions

Indoor mold concentrations were measured in the dust of moldy homes (MH) and reference homes (RH) by quantitative PCR (QPCR) assays for 82 species or related groups of species (assay groups). About 70% of the species and groups were never or only rarely detected. The ratios (MH geometric mean : RH geometric mean) for 6 commonly detected species (Aspergillus ochraceus, A. penicillioides, A. unguis, A. versicolor, Eurotium group, and Cladosporium sphaerospermum) were >1 (Group I). Logistic regression analysis of the sum of the logs of the concentrations of Group I species resulted in a 95% probability for separating MH from RH. These results suggest that it may be possible to evaluate whether a home has an abnormal mold condition by quantifying a limited number of mold species in a dust sample. Also, four common species of Aspergillus were quantified by standard culturing procedures and their concentrations compared to QPCR results. Culturing underestimated the concentrations of these four species by 2 to 3 orders of magnitude compared to QPCR.     

Inorganic nitrogen transformations in the treatment of landfill leachate with a high ammonium load: A case study

The inorganic nitrogen transformations occurring at a municipal waste leachate treatment facility were investigated. The treatment facility consisted of a collection well and an artificial wetland between two aeration ponds. The first aeration pond showed a decrease in ammonium (from 3480 (± 120) to 630(± 90) mg ⋅ L⁻¹), a reduction in inorganic nitrogen load (3480 to 1680 mg N ⋅ L⁻¹), and an accumulation of nitrite (< 1.3 mg-N ⋅ L⁻¹ in the collection well, to 1030 mg-N ⋅ L⁻¹). Incomplete ammonium oxidation was presumably the result of the low concentration of carbonate alkalinity (∼2 mg ⋅ L⁻¹), which may cause a limitation in the ammonium oxidation rate of nitrifiers. Low carbonate alkalinity levels may have been the result of stripping of CO₂ from the first aeration pond at the high aeration rates and low pH. Various chemodenitrification mechanisms are discussed as the reason for the reduction in the inorganic nitrogen load, including; the reduction of nitrite by iron (II) (producing various forms of gaseous nitrogen); and reactions involving nitrous acid. It is suggested that the accumulation of nitrite may be the result of inhibition of nitrite oxidizers by nitrous acid and low temperatures. Relative to the first aeration pond, the speciation and concentration of inorganic nitrogen was stable in the wetlands and 2nd aeration pond. The limited denitrification in the wetlands most probably occurred due to low concentrations of organic carbon, and short retention times.     

Using variance components to estimate power in a hierarchically nested sampling design

We used variance components to assess allocation of sampling effort in a hierarchically nested sampling design for ongoing monitoring of early life history stages of the federally endangered Devils Hole pupfish (DHP) (Cyprinodon diabolis). Sampling design for larval DHP included surveys (5 days each spring 2007–2009), events, and plots. Each survey was comprised of three counting events, where DHP larvae on nine plots were counted plot by plot. Statistical analysis of larval abundance included three components: (1) evaluation of power from various sample size combinations, (2) comparison of power in fixed and random plot designs, and (3) assessment of yearly differences in the power of the survey. Results indicated that increasing the sample size at the lowest level of sampling represented the most realistic option to increase the survey’s power, fixed plot designs had greater power than random plot designs, and the power of the larval survey varied by year. This study provides an example of how monitoring efforts may benefit from coupling variance components estimation with power analysis to assess sampling design.     

Using Ion-Exchange Resins to Study Soil Response to Experimental Watershed Acidification

Ion-exchange resins (IER) offer alternative approaches to measuring ionic movement in soils that may have advantages over traditional approaches in some settings, but more information is needed to understand how IER compare with traditional methods of measurement in forested ecosystems. At the Bear Brook Watershed in Maine (BBWM), one of two paired, forested watersheds is treated bi-monthly with S and N (28.8 and 25.2kgha⁻¹yr⁻¹ of S and N, respectively). Both IER and ceramic cup tension lysimeters were used to study soil solution responses after ∼11 years of treatment. Results from both methods showed treatments resulted in the mobilization of base cations and Al, and higher SO₄—S and inorganic N in the treated watershed. Both methods indicated similar differences in results associated with forest type (hardwoods versus softwoods), a result of differences in litter quality and atmospheric aerosol interception capacity. The correlation between lysimeter and IER data for individual analytes varied greatly. Significant correlations were evident for Na (r=0.75), Al (r=0.65), Mn (r=0.61), Fe (r=0.57), Ca (r=0.49), K (r=0.41) and NO₃—N (r=0.59). No correlation was evident between IER and soil solution data for NH₄—N and Pb. Both IER and soil solution techniques suggested similar interpretations of biogeochemical behavior in the watershed.     

Selecting Species for Marine Assessment of Radionuclides Around Amchitka: Planning for Diverse Goals and Interests

Considerable attention has been devoted to selecting bioindicator species as part of monitoring programs for exposure and effects from contaminants in the environment. Yet the rationale for selection of bioindicators is often literature-based, rather than developed with a firm site-specific base of data on contaminant levels in a diverse range of organisms at different trophic levels in the same ecosystem. We suggest that this latter step is an important phase in the environmental assessment process that is often missing. In this paper we address the problem of how to select a wide range of species representing different trophic levels that serve as a basis for selecting a few species suitable as bioindicators. We illustrate this with our assessment of radionuclides on Amchitka Island, Alaska. We propose a multi-stage process for arriving at the list of available species that includes review of literature, review by experts experienced in the area, review by interested and affected parties, selection of trophic levels or groups for analysis, arraying of possible species, and selection of species within each trophic level group for sample collection. We first had to identify all likely species, then narrow our focus to those we could collect and analyze. In all cases, review includes suggestions for possible target species with justifications. While this method increases the up-front costs of developing bioindicators for an ecosystem, it has the advantage of providing information for selection of species that will be most informative in the long run, including those that are the best bioaccumulators, thus providing the earliest warning of any potential environmental consequences. Further, the recognition that a range of stakeholder's needs and interests should be included increases the utility for public-policy makers, and the potential for continued usage to establish long-term trends.     

Reproductive status of Octopus pallidus, and its relationship to age and size

Age-specific information on individual octopus reproductive development and investment from wild populations has until recently been unobtainable. Using daily-formed increments within stylets (internal shells) the individual ages of 503 wild Octopus pallidus were determined. In addition, detailed reproductive information was collected for each of the aged octopus, along with reproductive data for an additional 925 octopus. All of the octopus were collected from Bass Strait waters in south-eastern Australia from November 2004 to November 2006. This information was used to investigate seasonal trends in reproductive scheduling and investment, fecundity and egg size. Maturation in O. pallidus primarily depends on size with little relationship to age and is highly variable between genders, with females >350 days still maturing in comparison to all males >142 days being mature. Size at 50% maturity for females was approximately 473 g, which is considerably larger than male 100% maturity at <250 g. This indicates that for females at least, maturity does not necessarily come with age. Seasonal scheduling in reproductive investment between genders revealed an optimal spawning period between late summer and early autumn. These results reinforce the view that individual growth and maturity is highly variable in cephalopods.     

Multiple sources of predictive uncertainty in modeled estimates of net ecosystem CO2 exchange

Net ecosystem CO₂ exchange (NEE) is typically measured directly by eddy covariance towers or is estimated by ecosystem process models, yet comparisons between the data obtained by these two methods can show poor correspondence. There are three potential explanations for this discrepancy. First, estimates of NEE as measured by the eddy-covariance technique are laden with uncertainty and can potentially provide a poor baseline for models to be tested against. Second, there could be fundamental problems in model structure that prevent an accurate simulation of NEE. Third, ecosystem process models are dependent on ecophysiological parameter sets derived from field measurements in which a single parameter for a given species can vary considerably. The latter problem suggests that with such broad variation among multiple inputs, any ecosystem modeling scheme must account for the possibility that many combinations of apparently feasible parameter values might not allow the model to emulate the observed NEE dynamics of a terrestrial ecosystem, as well as the possibility that there may be many parameter sets within a particular model structure that can successfully reproduce the observed data. We examined the extent to which these three issues influence estimates of NEE in a widely used ecosystem process model, Biome-BGC, by adapting the generalized likelihood uncertainty estimation (GLUE) methodology. This procedure involved 400,000 model runs, each with randomly generated parameter values from a uniform distribution based on published parameter ranges, resulting in estimates of NEE that were compared to daily NEE data from young and mature Ponderosa pine stands at Metolius, Oregon. Of the 400,000 simulations run with different parameter sets for each age class (800,000 total), over 99% of the simulations underestimated the magnitude of net ecosystem CO₂ exchange, with only 4.07% and 0.045% of all simulations providing satisfactory simulations of the field data for the young and mature stands, even when uncertainties in eddy-covariance measurements are accounted for. Results indicate fundamental shortcomings in the ability of this model to produce realistic carbon flux data over the course of forest development, and we suspect that much of the mismatch derives from an inability to realistically model ecosystem respiration. However, difficulties in estimating historic climate data are also a cause for model-data mismatch, particularly in a highly ecotonal region such as central Oregon. This latter difficulty may be less prevalent in other ecosystems, but it nonetheless highlights a challenge in trying to develop a dynamic representation of the terrestrial biosphere.