Compositional analysis of overdispersed counts using generalized estimating equations

Multivariate abundance data are commonly collected in ecology, and used to explore questions of “community composition”—how relative abundance of different taxa changes with environmental conditions. In this paper, we propose a log-linear marginal modeling approach for analyzing such compositional count data, via generalized estimating equations. This method exploits the multiplicative nature of log-linear models for counts, by reparameterizing models that describe marginal effects on mean abundance. This allows partitioning into “main effects” and compositional effects, which is appealing for interpretation. We apply the proposed approach to reanalyze compositional counts of benthic invertebrates from Delaware Bay, and data of invertebrate communities inhabiting Acacia plants in eastern Australia. In both cases we resort to a resampling approach to make inferences about regression parameters, because the number of clusters was not large compared to cluster size.     

Topsoil inversion as a restoration measure in sand dunes,early results from a UK field-trial

Over-stabilisation and eutrophication affect many dune systems in north-west Europe. This leads to lower diversity of typical dune species and an accumulation of soil nutrients. Existing management techniques to remove excess nutrients include mowing, with removal of cuttings, and turf stripping. A new restoration technique called topsoil inversion or deep ploughing may also be able to counter some of the negative effects of eutrophication. It simulates the burial of established soils with fresh mineral sand, by inverting the soil profile. A trial was carried out on two small blocks of eutrophic dune grassland in North Wales, UK. Nutrient-rich surface soils were buried beneath mineral sub-sand using a double-bladed plough, designed to plough to depths of up to 100 cm. Results show that the organic soil horizons were buried to a depth of 80 cm, and covered with 40–50 cm of mineral sand. The pH and organic matter of the surface layers became comparable to those of mobile dunes. Fifteen months after ploughing, bare sand cover was still 70–90%, but significant sand loss through wind erosion resulted in a thinning of the mineral sand over-burden, leaving the buried organic layer closer to the surface. Natural vegetation colonisation was slow, with the first surviving plants observed after 8 months. The majority of species present at 15 months were present before ploughing and had regenerated from rhizomes or root fragments. The effect of excluding disturbance caused by rabbits, people and dogs was assessed within fenced areas. After 11 months, vegetation cover was greater in the fenced areas than in plots exposed to disturbance, therefore disturbance replaced physical conditions as the dominant influence on plant growth and establishment. These early results suggest the trial has been partially successful, but that topsoil inversion could be combined with other methods such as turf stripping or by stabilisation of the ploughed surface by planting with pioneer species, depending on the ultimate restoration goal.     

Assessing the Effects of Non-Point Source Pollution on American Samoa’s Coral Reef Communities

Surveys were completed on Tutuila Island, American Samoa, to characterize reef development and assess the impacts of non-point source pollution on adjacent coral reefs at six sites. Multivariate analyses of benthic and coral community data found similar modern reef development at three locations; Aoa, Alofau, and Leone. These sites are situated in isolated bays with gentle sloping foundations. Aoa reefs had the highest estimates of crustose coralline algae cover and coral species richness, while Leone and Alofau showed high abundances of macroalgae and Porites corals. Aoa has the largest reef flat between watershed discharge and the reef slope, and the lowest human population density. Masefau and Fagaalu have a different geomorphology consisting of cemented staghorn coral fragments and steep slopes, however, benthic and coral communities were not similar. Benthic data suggest Fagaalu is heavily impacted compared with all other sites. Reef communities were assessed as bio-criteria indicators for waterbody health, using the EPA aquatic life use support designations of (1) fully supportive, (2) partially supportive, and (3) non-supportive for aquatic life. All sites resulted in a partially supportive ranking except Fagaalu, which was non-supportive. The results of this rapid assessment based upon relative benthic community measures are less desirable than long-term dataset analyses from monitoring programs, however it fills an important role for regulatory agencies required to report annual waterbody assessments. Future monitoring sites should be established to increase the number of replicates within each geological and physical setting to allow for meaningful comparisons along a gradient of hypothesized pollution levels.     

Toxicity of the mosquito control pesticide Scourge to adult and larval grass shrimp (Palaemonetes pugio)

This study investigated the toxicity of various concentrations of technical resmethrin and Scourge on adult and larval Palaemonetes pugio, a common grass shrimp species. Two types of tests were conducted for each of the resmethrin formulations using adult and larval grass shrimp life stages, a 96-h static renewal aqueous test without sediment, and a 24-h static nonrenewal aqueous test with sediment. For resmethrin, the 96-h aqueous LC50 value for adult shrimp was 0.53 microg/L (95% confidence interval (CI): 0.46-0.60 microg/L), and for larval shrimp was 0.35 microg/L (95% CI: 0.28-0.42 microg/L). In the presence of sediment, technical resmethrin produced a 24-h LC50 value for adult shrimp of 5.44 microg/L (95% CI: 4.52-6.55 microg/L), and for larval shrimp of 2.15 microg/L (95% CI: 1.35-3.43 microg/L). For Scourge, the 96-h aqueous LC50 for adult shrimp was 2.08 microg/L (95% CI: 1.70-2.54 microg/L), and for larval shrimp was 0.36 microg/L (95% CI: 0.24-0.55 microg/L). The 24-h sediment test yielded an LC50 value of 16.12 microg/L (95% CI: 14.79-17.57 microg/L) for adult shrimp, and 14.16 microg/L (95% CI: 12.21-16.43 microg/L) for larvae. Adjusted LC50 values to reflect the 18% resmethrin concentration in Scourge are 0.37 microg/L (adult), 0.07 microg/L (larvae) for the 96-h aqueous test, and 2.90 microg/L (adult), 2.6 microg/L (larvae) for the 24-h sediment test. Larval grass shrimp were more sensitive to technical resmethrin and Scourge than the adult life stage. The results also demonstrate that synergized resmethrin is more toxic to P. pugio than the nonsynergized form, and that the presence of sediment decreases the toxicity of both resmethrin and Scourge.     

Application of a pathogenicity marker found in Escherichia coli for the assessment of irrigation water quality.

A polymerase chain reaction (PCR)-based method was developed to differentiate between pathogenic and nonpathogenic Escherichia coli (E. coli). A pathogenicity marker, linked to the deletion of the ygfB gene, was identified in 80% of the clinical E. coli isolates tested. This marker, combined with the malic acid dehydrogenase gene, formed the duplex PCR that was subsequently used to screen E. coli isolates recovered from two secondary wastewater treatment plants (STPs) and a river site. All waters samples are used to irrigate dairy farm pasture in the West Gippsland region of Victoria, Australia. Results from three consecutive months of sampling (December 2001 and January and February 2002) indicated that Longwarry STP showed 8, 8, and 0% pathogenic E. coli; Pakenham STP showed 0, 12.5, and 33%; and the Bunyip river site showed 20, 12, and 25% respectively.     

Influence of MBBR carrier geometrical properties and biofilm thickness restraint on biofilm properties, effluent particle size distribution, settling velocity distribution, and settling behaviour

The relatively poor settling characteristics of particles produced in moving bed biofilm reactor (MBBR) outline the importance of developing a fundamental understanding of the characterization and settleability of MBBR-produced solids. The influence of carrier geometric properties and different levels of biofilm thickness on biofilm characteristics, solids production, particle size distribution (PSD), and particle settling velocity distribution (PSVD) is evaluated in this study. The analytical ViCAs method is applied to the MBBR effluent to assess the distribution of particle settling velocities. This method is combined with microscopy imaging to relate particle size distribution to settling velocity. Three conventionally loaded MBBR systems are studied at a similar loading rate of 6.0 g/(m² •day) and with different carrier types. The AnoxK™ K5 carrier, a commonly used carrier, is compared to so-called thickness-restraint carriers, AnoxK™ Z-carriers that are newly designed carriers to limit the biofilm thickness. Moreover, two levels of biofilm thickness, 200 μm and 400 μm, are studied using AnoxK™ Z-200 and Z-400 carriers. Statistical analysis confirms that K5 carriers demonstrated a significantly different biofilm mass, thickness, and density, in addition to distinct trends in PSD and PSVD in comparison with Z-carriers. However, in comparison of thickness-restraint carriers, Z-200 carrier results did not vary significantly compared to the Z-400 carrier. The K5 carriers showed the lowest production of suspended solids (0.7 ± 0.3 g-TSS/day), thickest biofilm (281.1 ± 8.7 µm) and lowest biofilm density (65.0 ± 1.5 kg/m³). The K5 effluent solids also showed enhanced settling behaviour, consisting of larger particles with faster settling velocities.     

CO2SINK—From site characterisation and risk assessment to monitoring and verification: One year of operational experience with the field laboratory for CO2 storage at Ketzin, Germany

The CO₂SINK pilot project at Ketzin is aimed at a better understanding of geological CO₂ storage operation in a saline aquifer. The reservoir consists of fluvial deposits with average permeability ranging between 50 and 100 mDarcy. The main focus of CO₂SINK is developing and testing of monitoring and verification technologies. All wells, one for injection and two for observation, are equipped with smart casings (sensors behind casing, facing the rocks) containing a Distributed Temperature Sensing (DTS) and electrodes for Electrical Resistivity Tomography (ERT). The in-hole Gas Membrane Sensors (GMS) observed the arrival of tracers and CO₂ with high temporal resolution. Geophysical monitoring includes Moving Source Profiling (MSP), Vertical Seismic Profiling (VSP), crosshole, star and 4-D seismic experiments. Numerical models are benchmarked via the monitoring results indicating a sufficient match between observation and prediction, at least for the arrival of CO₂ at the first observation well. Downhole samples of brine showed changes in the fluid composition and biocenosis. First monitoring results indicate anisotropic flow of CO₂ coinciding with the “on-time” arrival of CO₂ at observation well one (Ktzi 200) and the later arrival at observation well two (Ktzi 202). A risk assessment was performed prior to the start of injection. After one year of operations about 18,000 t of CO₂ were injected safely.     

Representing the Connectivity of Upland Areas to Floodplains and Streams in SWAT+

In recent years, watershed modelers have put increasing emphasis on capturing the interaction of landscape hydrologic processes instead of focusing on streamflow at the watershed outlet alone. Understanding the hydrologic connectivity between landscape elements is important to explain the hydrologic response of a watershed to rainfall events. The Soil and Water Assessment Tool+ (SWAT+) is a new version of SWAT with improved runoff routing capabilities. Subbasins may be divided into landscape units (LSUs), e.g., upland areas and floodplains, and flow can be routed between these LSUs. We ran three scenarios representing different extents of connectivity between uplands, floodplains, and streams. In the first and second scenarios, the ratio of channelized flow from the upland to the stream and sheet flow from the upland to the floodplain was 70/30 and 30/70, respectively, for all upland/floodplain pairs. In the third scenario, the ratio was calculated for each upland/floodplain pair based on the upland/floodplain area ratio. Results indicate differences in streamflow were small, but the relative importance of flow components and upland areas and floodplains as sources of surface runoff changed. Also, the soil moisture in the floodplains was impacted. The third scenario was found to provide more realistic results than the other two. A realistic representation of connectivity in watershed models has important implications for the identification of pollution sources and sinks.