Generalized site occupancy models allowing for false positive and false negative errors

Site occupancy models have been developed that allow for imperfect species detection or "false negative" observations. Such models have become widely adopted in surveys of many taxa. The most fundamental assumption underlying these models is that "false positive" errors are not possible. That is, one cannot detect a species where it does not occur. However, such errors are possible in many sampling situations for a number of reasons, and even low false positive error rates can induce extreme bias in estimates of site occupancy when they are not accounted for. In this paper, we develop a model for site occupancy that allows for both false negative and false positive error rates. This model can be represented as a two-component finite mixture model and can be easily fitted using freely available software. We provide an analysis of avian survey data using the proposed model and present results of a brief simulation study evaluating the performance of the maximum-likelihood estimator and the naive estimator in the presence of false positive errors.     

Species identity dominates the relationship between predator biodiversity and herbivore suppression

Agricultural pest suppression is an important ecosystem service that may be threatened by the loss of predator diversity. This has stimulated interest in the relationship between predator biodiversity and biological control. Multiple-predator studies have shown that predators may complement or interfere with one another, but few experiments have determined if the resulting effects on prey are caused by changes in predator abundance, identity, species richness, or some combination of these factors. We experimentally isolated the effect of predator species richness on the biological control of an important agricultural pest, the green peach aphid. We found no evidence that increasing predator species richness affects aphid biological control; overall there was no strong complementarity or interference among predator species that altered the strength of aphid suppression. Instead, our experiments revealed strong effects of predator species identity, because predators varied dramatically in their per capita consumption rates. Our results are consistent with other multiple-predator studies finding strong species-identity effects and suggest that, for the biological control of aphids, conservation strategies that directly target key species will be more effective than those targeting predator biodiversity more broadly.     

Antimicrobial activities of extracts from tropical Atlantic marine plants against marine pathogens and saprophytes

Studies investigating disease resistance in marine plants have indicated that secondary metabolites may have important defensive functions against harmful marine microorganisms. The goal of this study was to systematically screen extracts from marine plants for antimicrobial effects against marine pathogens and saprophytes. Lipophilic and hydrophilic extracts from species of 49 marine algae and 3 seagrasses collected in the tropical Atlantic were screened for antimicrobial activity against five ecologically relevant marine microorganisms from three separate kingdoms. These assay microbes consisted of the pathogenic fungus Lindra thalassiae, the saprophytic fungus Dendryphiella salina, the saprophytic stramenopiles, Halophytophthora spinosa and Schizochytrium aggregatum, and the pathogenic bacterium Pseudoaltermonas bacteriolytica. Overall, 90% of all species surveyed yielded extracts that were active against one or more, and 77% yielded extracts that were active against two or more assay microorganisms. Broad-spectrum activity against three or four assay microorganisms was observed in the extracts from 48 and 27% of all species, respectively. The green algae Halimeda copiosa and Penicillus capitatus (Chlorophyta) were the only species to yield extracts active against all assay microorganisms. Among all assay microorganisms, both fungi were the most resistant to the extracts tested, with less than 21% of all extracts inhibiting the growth of either L. thalassiae or D. salina. In contrast, over half of all lipophylic extracts were active against the stramenopiles H. spinosa and S. aggregatum, and the bacterium P. bacteriolytica. Growth sensitivity to hydrophilic extracts varied considerably between individual assay microorganisms. While 48% of all hydrophilic extracts were active against H. spinosa, 27% were active against P. bacteriolytica, and only 14% were active against S. aggregatum. Overall, more lipophilic extracts inhibited microbial growth than hydrophilic extracts. The variability observed in the antimicrobial effects of individual extracts against each assay microorganism reflects the importance of choosing appropriate test microbes in assays from which ecologically relevant information is sought. Results from this survey demonstrate that antimicrobial activities are prevalent among extracts from marine algae and seagrasses, suggesting that antimicrobial chemical defenses are widespread among marine plants.     

A new condensed toluene mechanism for Carbon Bond: CB05-TU

Toluene is ubiquitous in urban atmospheres and is a precursor to tropospheric ozone and aerosol (smog). An important characteristic of toluene chemistry is the tendency of some degradation products (e.g., cresols and methyl-catechols) to form organic nitro and nitrate compounds that sequester NOx (NO and NO₂) from active participation in smog formation. Explaining the NOx sinks in toluene degradation has made mechanism development more difficult for toluene than for many other organic compounds. Another challenge for toluene is explaining sources of radicals early in the degradation process. This paper describes the development of a new condensed toluene mechanism consisting of 26 reactions, and evaluates the performance of CB05 with this new toluene scheme (Toluene Update, TU) against 38 chamber experiments at 7 different environmental chambers, and provides recommendations for future developments. CB05 with the current toluene mechanism (CB05-Base) under-predicted the maximum O₃ and O₃ production rate for many of these toluene–NOx chamber experiments, especially under low-NOx conditions ([NOx]_t=0 < 100 ppb). CB05 with the new toluene mechanism (CB05-TU) includes changes to the yields and reactions of cresols and ring-opening products, and showed better performance than CB05-Base in predicting the maximum O₃, O₃ formation rate, NOx removal rate and cresol concentration. Additional environmental chamber simulations with xylene–NOx experiments showed that the TU mechanism updates tended to improve mechanism performance for xylene.     

Transport and retention of Cryptosporidium parvum oocysts in sandy soils

A series of miscible-displacement experiments was conducted to examine the retention and transport behavior of oocysts in natural porous media. Three soils and a model sand were used that differed in physical and geochemical properties. Transport behavior was examined under various treatment conditions to help evaluate retention mechanisms. Significant retention of oocysts was observed for all media despite the fact that conditions were unfavorable for physicochemical interactions with respect to DLVO theory. The magnitude of retention was not influenced significantly by alterations in solution chemistry (reduction in ionic strength) or soil surface properties (removal of soil organic matter and metal oxides). On the basis of the observed results, it appears that retention by secondary energy minima or geochemical microdomains was minimal for these systems. The porous media used for the experiments exhibited large magnitudes of surface roughness, and it is suggested that this surface roughness contributed significantly to oocyst retention.     

Laboratory-scale investigation of UV treatment of ammonia for livestock and poultry barn exhaust applications

The feasibility of using deep ultraviolet (UV) treatment for abatement of ammonia (NH(3)) in livestock and poultry barn exhaust air was examined in a series of laboratory-scale experiments. These experiments simulated moving exhaust air through an irradiation chamber with variables of UV wavelength and dose, NH(3) concentrations, humidity, and presence of hydrogen sulfide (H(2)S). Ammonia, initially at relevant barn exhaust concentrations in air, was substantially or completely reduced by irradiation with 185 nm light. Reactions were monitored using chemiluminescence detection, gas chromatography with mass spectrometry detection, and Fourier transform infrared spectrometry, of which the latter was found to be the most informative and flexible. Detected nitrogen-containing products included N(2)O, NH(4)NO(3), and HNO(3). It was presumed that atomic oxygen is the primary photochemical product that begins the oxidative cascade. The data show that removal of NH(3) is plausible, but they highlight concerns over pollution swapping due to formation of ozone and N(2)O.     

Phosphorus retention and remobilization in vegetated buffer strips: a review

Diffuse pollution remains a major threat to surface waters due to eutrophication caused by phosphorus (P) transfer from agricultural land. Vegetated buffer strips (VBSs) are increasingly used to mitigate diffuse P losses from agricultural land, having been shown to reduce particulate P transfer. However, retention of dissolved P (DP) has been lower, and in some cases VBSs have increased delivery to surface waters. The aims of this review were (i) to develop a conceptual model to enhance the understanding of VBS functioning in terms of DP, (ii) to identify key processes within the model that affect DP retention and delivery, and (iii) to explore evidence for the controls on these processes. A greater understanding in these areas will allow the development of management strategies that enhance DP retention. We found evidence of a surface layer in buffer strip soils that is enriched in soluble P compared with adjacent agricultural land and may be responsible for the reported increased DP delivery. Through increased biological activity in VBSs, plants and microorganisms may assimilate P from particulates retained in the VBSs or native soil P and remobilize this P in a more soluble form. These conclusions are based on a limited amount of research, and a better understanding of biogeochemical cycling of P in buffer strip soils is required.     

Exposure Times to the Spring Atrazine Flush Along a Stream-Reservoir System1

Stoeckel, James A., Jade Morris, Elizabeth Ames, David C. Glover, Michael J. Vanni, William Renwick, and María J. González, 2012. Exposure Times to the Spring Atrazine Flush Along a Stream-Reservoir System. Journal of the American Water Resources Association (JAWRA) 48(3): 616-634. DOI: 10.1111/j.1752-1688.2011.00633.x Abstract: We used enzyme-linked immunosorbent assay to examine reservoir-mediated shifts in spring to fall exposure of aquatic organisms to the spring atrazine pulse over four years in a Midwestern stream-reservoir system. Peak atrazine concentrations in the major inflowing stream exceeded 10 μg/l in all four years. The reservoir had a beneficial effect in two of four years by diluting atrazine below the 10 μg/l threshold. However, during the other two years, exposure times above 10 μg/l were approximately doubled in the reservoir compared to the major inflowing stream. Thresholds of 3 and 5 μg/l were exceeded during all four years in the reservoir. The uplake and downlake reservoir sites were four to five times more likely to exceed these thresholds and aquatic organisms were subjected to longer exposure times above these thresholds compared to the inflowing stream. Release of elevated atrazine concentrations from the reservoir extended exposure times in the outflowing stream. This effect was most pronounced just below the dam. Aquatic organisms upstream of the reservoir were most likely to experience acute exposures whereas organisms within and immediately downstream of the reservoir were more likely to experience chronic exposures. The ubiquity of reservoirs and the annual spring herbicide flush highlight the importance of considering the presence and relative location of reservoirs when assessing risk to aquatic communities as well as locations of drinking water intakes.     

Electrodisinfection of real swine wastewater for water reuse

Environmental Chemistry Letters - Swine production generates large volumes of wastewater, rich in organic matter, nutrients and pathogens. Electrodisinfection is used to remove organic matter and...