Evidence-based guidelines for automated conservation assessments of plant species

Assessing species’ extinction risk is vital to setting conservation priorities. However, assessment endeavors, such as those used to produce the IUCN Red List of Threatened Species, have significant gaps in taxonomic coverage. Automated assessment (AA) methods are gaining popularity to fill these gaps. Choices made in developing, using, and reporting results of AA methods could hinder their successful adoption or lead to poor allocation of conservation resources. We explored how choice of data cleaning type and level, taxonomic group, training sample, and automation method affect performance of threat status predictions for plant species. We used occurrences from the Global Biodiversity Information Facility (GBIF) to generate assessments for species in 3 taxonomic groups based on 6 different occurrence-based AA methods. We measured each method's performance and coverage following increasingly stringent occurrence cleaning. Automatically cleaned data from GBIF performed comparably to occurrence records cleaned manually by experts. However, all types of data cleaning limited the coverage of AAs. Overall, machine-learning-based methods performed well across taxa, even with minimal data cleaning. Results suggest a machine-learning-based method applied to minimally cleaned data offers the best compromise between performance and species coverage. However, optimal data cleaning, training sample, and automation methods depend on the study group, intended applications, and expertise.     

Wildfire effects on soil nutrients and leaching in a tahoe basin watershed

A wildfire burned through a previously sampled research site, allowing pre- and post-burn measurements of the forest floor, soils, and soil leaching near Lake Tahoe, Nevada. Fire and post-fire erosion caused large and statistically significant (P < or = 0.05) losses of C, N, P, S, Ca, and Mg from the forest floor. There were no statistically significant effects on mineral soils aside from a decrease in total N in the surface (A11) horizon, an increase in pH in the A11 horizon, and increases in water-extractable SO4(2-) in the A11 and A12 horizons. Burning caused consistent but nonsignificant increases in exchangeable Ca2+ in most horizons, but no consistent or statistically significant effects on exchangeable K+ or Mg2+, or on Bray-, bicarbonate-, or water-extractable P concentrations. Before the burn, there were no significant differences in leaching, but during the first winter after the fire, soil solution concentrations of NH4+, NO3-, ortho-P, and (especially) SO4(2-) were elevated in the burned area, and resin lysimeters showed significant increases in the leaching of NH4+ and mineral N. The leaching losses of mineral N were much smaller than the losses from the forest floor and A11 horizons, however. We conclude that the major short-term effects of wildfire were on leaching whereas the major long-term effect was the loss of N from the forest floor and soil during the fire.     

Development,Calibration and Use of a Plume Evaluation Training Unit

The Bay Area Air Pollution Control District adopted a regulation limiting plume visibility in terms of the Ringelmann Chart and also in terms of obscuration of the observer’s view. Since both limitations were adopted in terms requiring the judgment of an observer, preparation for enforcement required development and calibration of a training unit, so that inspectors could be qualified to testify as expert witnesses under this regulation.

This paper summarizes the design, calibration and use of the training unit developed for this purpose.     

Towards the selection of a produced water enrichment for biological gas hydrate inhibitors

Economic concerns associated with the recovery of non-conventional hydrocarbon reserves include unexpected ice as well as ice-like gas hydrate formation. Antifreeze proteins (AFPs) inhibit ice growth, and experiments with fish, plant, and insect AFPs have shown promise of effective gas hydrate inhibition in lab-scale experiments. If produced on an industrial scale, AFPs could provide a more environmentally friendly alternative to kinetic inhibitors, but a large-scale production of these AFPs is not currently feasible. We believe that these difficulties could be surmounted by the production of microbial AFPs, but to date, only a few such proteins have been identified and purified, and none of these are associated with hydrocarbon reserves. Here, we have used ice-affinity and freeze-thaw stress to select microbes derived from oil and gas formation water, or produced water, as a source of anaerobic microbial communities. Ice-affinity successfully incorporated anaerobic bacteria under aerobic conditions, and the mixed culture had ice-associating properties. Under these conditions, ice-affinity selection does not result in cultivatable isolates, but similar, cultivable microbes were obtained following freeze-thaw selection under anaerobic conditions. Since these mixed cultures inhibited the growth of ice crystals, they also have the potential to inhibit hydrate growth. Overall, freeze-thaw selection provides a promising first step towards the isolation of microbes capable of the inhibition of ice and gas hydrate growth, for possible application for energy exploration and recovery at high-latitudes and in-deep, cold waters.     

Monitoring water quality in Sydney Harbour using blue mussels during remediation of the Sydney Tar Ponds,Nova Scotia,Canada

Using mussels as monitoring tools we measured water quality in Sydney Harbour during a large scale, multi-year remediation project of the Sydney Tar Ponds (STPs); one of Canada's most contaminated sites. Chemical contaminants were measured in blue mussels (Mytilus edulis) in Sydney Harbour, which were used as monitoring tools to assess the spatio-temporal distribution of polycyclic aromatic hydrocarbons (PAHs); polychlorinated biphenyls (PCBs); metals (As, Cd, Cu, Hg, Pb, Zn) and lipid content during baseline and 3 years of remediation. The overall spatio-temporal distribution of chemicals in mussels was also compared to contaminants in other marine indicators (e.g., sediment, water and crab tissue). Measured metal concentrations in mussels showed some minor temporal variability (4 years), but these did not appear to be directly related to remediation activities, with the highest concentrations of As, Hg and Zn measured at reference stations. Most measured contaminants showed stable or potentially decreasing concentrations during the study, except Pb and Zn. Individual PAH compounds were mostly undetected during baseline and remediation, except for fluoranthene and pyrene. Concentrations of fluoranthene in mussels and deep water samples were moderately related. Generally, PCBs were undetected (<0.05 μg g^?1), except during year 2 remediation at some near-field stations. Contaminants measured during this study were at much lower concentrations than previously reported in other studies of mussels in Sydney Harbour and eastern Canada. This is likely due to the ongoing natural recovery of Sydney Harbour and to a lesser extent because of the environmental mitigation protection measures implemented during remediation activities at the STPs. The lack of detection of most individual PAHs and PCBs, plus relatively low bio-accumulation of metals observed during baseline and remediation attest to the effectiveness of using mussels as monitoring tools for environmental quality.     

Effects of residual antibiotics in groundwater on Salmonella typhimurium: changes in antibiotic resistance, in vivo and in vitro pathogenicity

An outbreak-causing strain of Salmonella enterica serovar Typhimurium was exposed to groundwater with residual antibiotics for up to four weeks. Representative concentrations (0.05, 1, and 100 μg L(-1)) of amoxicillin, tetracycline, and a mixture of several other antibiotics (1 μg L(-1) each) were spiked into artificially prepared groundwater (AGW). Antibiotic susceptibility analysis and the virulence response of stressed Salmonella were determined on a weekly basis by using human epithelial cells (HEp2) and soil nematodes (C. elegans). Results have shown that Salmonella typhimurium remains viable for long periods of exposure to antibiotic-supplemented groundwater; however, they failed to cultivate as an indication of a viable but nonculturable state. Prolonged antibiotics exposure did not induce any changes in the antibiotic susceptibility profile of the S. typhimurium strain used in this study. S. typhimurium exposed to 0.05 and 1 μg L(-1) amoxicillin, and 1 μg L(-1) tetracycline showed hyper-virulent profiles in both in vitro and in vivo virulence assays with the HEp2 cells and C. elegans respectively, most evident following 2nd and 3rd weeks of exposure.     

Monitoring effects of remediation on natural sediment recovery in Sydney Harbour, Nova Scotia

Chemical contaminants were assessed in Sydney Harbour, Nova Scotia during pre-remediation (baseline) and 3 years of remediation of a former coking and steel facility after nearly a century of operation and historical pollution into the Sydney Tar Ponds (STP). Concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls, metals, and inorganic parameters measured in sediments and total suspended solids in seawater indicate that the overall spatial distribution pattern of historical contaminants remains unchanged, although at much lower concentrations than previously reported due to natural sediment recovery, despite remediation activities. Measured sediment deposition rates in bottom-moored traps during baseline were low (0.4–0.8 cm?year^?1), but during dredging operations required for construction of new port facilities in the inner Sydney Harbour, sedimentation rates were equivalent to 26–128 cm year^?1. Measurements of sediment chemical contaminants confirmed that natural recovery rates of Sydney Harbour sediments were in broad agreement with predicted concentrations, or in some cases, lower than originally predicted despite remediation activities at the STP site. Overall, most measured contaminants in sediments showed little temporal variability (4 years), except for the detection of significant increases in total PAH concentrations during the onset of remediation monitoring compared to baseline. This slight increase represents only a short-term interruption in the overall natural recovery of sediments in Sydney Harbour, which were enhanced due to the positive impacts of large-scale dredging of less contaminated outer harbor sediments which were discharged into a confined disposal area located in the inner harbor.     

Comparison of total mercury and methylmercury cycling at five sites using the small watershed approach

The small watershed approach is well-suited but underutilized in mercury research. We applied the small watershed approach to investigate total mercury (THg) and methylmercury (MeHg) dynamics in streamwater at the five diverse forested headwater catchments of the US Geological Survey Water, Energy, and Biogeochemical Budgets (WEBB) program. At all sites, baseflow THg was generally less than 1ng L(-1) and MeHg was less than 0.2ng L(-1). THg and MeHg concentrations increased with streamflow, so export was primarily episodic. At three sites, THg and MeHg concentration and export were dominated by the particulate fraction in association with POC at high flows, with maximum THg (MeHg) concentrations of 94 (2.56)ng L(-1) at Sleepers River, Vermont; 112 (0.75)ng L(-1) at Rio Icacos, Puerto Rico; and 55 (0.80)ng L(-1) at Panola Mt., Georgia. Filtered (<0.7microm) THg increased more modestly with flow in association with the hydrophobic acid fraction (HPOA) of DOC, with maximum filtered THg concentrations near 5ng L(-1) at both Sleepers and Icacos. At Andrews Creek, Colorado, THg export was also episodic but was dominated by filtered THg, as POC concentrations were low. MeHg typically tracked THg so that each site had a fairly constant MeHg/THg ratio, which ranged from near zero at Andrews to 15% at the low-relief, groundwater-dominated Allequash Creek, Wisconsin. Allequash was the only site with filtered MeHg consistently above detection, and the filtered fraction dominated both THg and MeHg. Relative to inputs in wet deposition, watershed retention of THg (minus any subsequent volatilization) was 96.6% at Allequash, 60% at Sleepers, and 83% at Andrews. Icacos had a net export of THg, possibly due to historic gold mining or frequent disturbance from landslides. Quantification and interpretation of Hg dynamics was facilitated by the small watershed approach with emphasis on event sampling.