Integrative taxonomy of a new species of Rhyacodrilus (Annelida: Clitellata: Rhyacodrilinae) from Tibet Plateau rivers, with a preliminary assessment of its phylogenetic position.

A new Qinghai-Tibet Plateau species, Rhyacodrilus tanggulaensis Jiang & Cui sp. nov. (Annelida, Clitellata, Naididae, Rhyacodrilinae), is described, and its phylogenetic relationships within the genus is assessed on the basis of both mitochondrial (16S rDNA, COⅠ gene) and nuclear (ITS2) markers. Data from 32 species of Naididae, representing 7 subfamilies and 25 genera are used. Ten species were chosen as outgroup taxa. The molecular data were analyzed by Bayesian inference. The new species is distinguished from other species of Rhyacodrilus by the following combination of characters: dorsal and ventral chaetae with distal tooth 2-3 times longer than proximal, spermathecal and penial chaetae present, atria long and tubular, atrial duct conspicuous. The analyses of the combined molecular data corroborate the close relationship between Naidinae and the rhyacodriline genera Rhyacodrilus, Monopylephorus, and Ainudrilus, and show that the new species is more closely related to R. falciformis, R pigueti, R. okamikae and R. subterraneus, than to R. sinicus, another Chinese species, R. hiemalis and R. coccineus.

Organic wastes as soil amendments - Effects assessment towards soil invertebrates.

Using organic wastes, as soil amendments, is an important alternative to landfilling with benefits to soil structure, water retention, soil nutrient and organic matter concentrations. However, this practice should be monitored for its environmental risk due to the frequent presence, of noxious substances to soil organisms. To evaluate the potential of eight organic wastes with different origins, as soil amendments, reproduction tests with four soil invertebrate species (Folsomia candida, Enchytraeus crypticus, Hypoaspis aculeifer, Eisenia fetida) were performed using gradients of soil-waste mixtures. Results obtained demonstrated that contaminant concentrations required by current legislation might not be a protective measure for the soil ecosystem, as they do not properly translate the potential toxicity of wastes to soil invertebrates. Some wastes with contaminant loadings below thresholds showed higher toxicity than wastes with contaminants concentrations above legal limits. Also, test organism reproduction was differently sensitive to the selected wastes, which highlights the need to account for different organism sensitivities and routes of exposure when evaluating the toxicity of such complex mixtures. Finally this study shows that when combining chemical and ecotoxicological data, it is possible to postulate on potential sources of toxicity, contributing to better waste management practices and safer soil organic amendment products.

Exposure assessment to glyphosate of two species of annelids.

Adult mortality, biomass, fecundity and viability of cocoons were studied in Eisenia fetida and Octolasion tyrtaeum, in response to glyphosate exposure in soil. Exposure tests were carried out following USEPA procedure, with five concentrations of glyphosate in soil and a control. O. tyrtaeum was more sensitive to the highest concentration of glyphosate (50,000 mg kg(-1)), with 100 % mortality by day 7 of exposure, compared with 71 % for E. fetida. Although biomass of O. tyrtaeum was significantly different between the control and 5,000 mg kg(-1) dose at day 14, E. fetida was not affected at that concentration, and only showed a significant weight loss after 7 days of exposure to 50,000 mg kg(-1). Adverse effects upon adult fecundity and cocoon viability were observed at glyphosate concentrations of 5,000 mg kg(-1) and above. Adverse effects were observed at concentrations that greatly exceeded the recommended field application rates of glyphosate.

The impact and control of biofouling in marine aquaculture: a review.

Biofouling in marine aquaculture is a specific problem where both the target culture species and/or infrastructure are exposed to a diverse array of fouling organisms, with significant production impacts. In shellfish aquaculture the key impact is the direct fouling of stock causing physical damage, mechanical interference, biological competition and environmental modification, while infrastructure is also impacted. In contrast, the key impact in finfish aquaculture is the fouling of infrastructure which restricts water exchange, increases disease risk and causes deformation of cages and structures. Consequently, the economic costs associated with biofouling control are substantial. Conservative estimates are consistently between 5-10% of production costs (equivalent to US$ 1.5 to 3 billion yr(-1)), illustrating the need for effective mitigation methods and technologies. The control of biofouling in aquaculture is achieved through the avoidance of natural recruitment, physical removal and the use of antifoulants. However, the continued rise and expansion of the aquaculture industry and the increasingly stringent legislation for biocides in food production necessitates the development of innovative antifouling strategies. These must meet environmental, societal, and economic benchmarks while effectively preventing the settlement and growth of resilient multi-species consortia of biofouling organisms.

Evaluation of sampling sizes on the intertidal macroinfauna assessment in a subtropical mudflat of Hong Kong.

In this study, two types of sediment cores with different diameters were used to collect sediment samples from an intertidal mudflat in Hong Kong to investigate the influence of sampling unit on the quantitative assessment of benthic macroinfaunal communities. Both univariate and multivariate analyses were employed to detect differences in sampling efficiencies by the two samplers through total abundance and biomass, species richness and diversity, community structure, relative abundance of major taxa of the infaunal community. The species-area curves were further compared to find out the influence of the sampling units. Results showed that the two sampling devices provided similar information on the estimates of species diversity, density and species composition of the benthos in main part of the mudflat where the sediment was fine and homogenous; but at the station which contained coarse sand and gravels, the significant differences were detected between the quantitative assessments of macrobenthic infauna by the two samplers. Most importantly, the species-area curves indicated that more and smaller samples were better in capturing more species than less large ones when comparing an equal sampling area. Therefore, the efficiency of the sampler largely depended on the sediment properties, and sampling devices must be chosen based on the physical conditions and desired levels of precision on the organisms of the sampling program.

IQSeq: integrated isoform quantification analysis based on next-generation sequencing.

With the recent advances in high-throughput RNA sequencing (RNA-Seq), biologists are able to measure transcription with unprecedented precision. One problem that can now be tackled is that of isoform quantification: here one tries to reconstruct the abundances of isoforms of a gene. We have developed a statistical solution for this problem, based on analyzing a set of RNA-Seq reads, and a practical implementation, available from archive.gersteinlab.org/proj/rnaseq/IQSeq, in a tool we call IQSeq (Isoform Quantification in next-generation Sequencing). Here, we present theoretical results which IQSeq is based on, and then use both simulated and real datasets to illustrate various applications of the tool. In order to measure the accuracy of an isoform-quantification result, one would try to estimate the average variance of the estimated isoform abundances for each gene (based on resampling the RNA-seq reads), and IQSeq has a particularly fast algorithm (based on the Fisher Information Matrix) for calculating this, achieving a speedup of ~ 500 times compared to brute-force resampling. IQSeq also calculates an information theoretic measure of overall transcriptome complexity to describe isoform abundance for a whole experiment. IQSeq has many features that are particularly useful in RNA-Seq experimental design, allowing one to optimally model the integration of different sequencing technologies in a cost-effective way. In particular, the IQSeq formalism integrates the analysis of different sample (i.e. read) sets generated from different technologies within the same statistical framework. It also supports a generalized statistical partial-sample-generation function to model the sequencing process. This allows one to have a modular, "plugin-able" read-generation function to support the particularities of the many evolving sequencing technologies.

Toxicity of the pesticide alpha-cypermethrin to four soil nontarget invertebrates and implications for risk assessment.

Alpha-cypermethrin, a synthetic pyrethroid, is used as an insecticide in agricultural settings and is increasingly replacing organophosphates and carbamates because of lower application rates and lower toxicity to mammals. Because very little is known about the acute and chronic toxicity of this compound for soil-living organisms, the present study investigated acute and sublethal toxicity of alpha-cypermethrin for four terrestrial invertebrate species in an agricultural soil from Norway. Bioassays with the earthworm Eisenia fetida, the potworm Enchytraeus crypticus, the springtail Folsomia candida, and the land snail Helix aspersa were performed according to slightly modified versions of Organization for Economic Cooperation and Development (Paris, France) or International Organization for Standardization (Geneva, Switzerland) guidelines and resulted in median lethal concentrations of greater than >1,000 to 31.4 mg/kg and sublethal no-observed-effect concentrations of 2.51 to 82 mg/kg. A high acute to chronic ratio was found, especially in the earthworms. Interspecies differences in sensitivity may be explained by differences in exposure and differences in metabolization rate. When based on measured pore-water concentrations, terrestrial species overall appear to be approximately one order of magnitude less sensitive than aquatic species. Effect assessments conducted according to European guideline for risk assessment of pesticides reveal that assessments based on acute toxicity tests are not always conservative enough to determine environmentally safe concentrations in soil. Mandatory incorporation of sublethal toxicity data will ensure that in regions with temperate climate, the effects of pesticides on populations of soil-living organisms are unlikely.

Terrestrial ecotoxicity and effect factors of metals in life cycle assessment (LCA).

Life cycle impact assessment aims to translate the amounts of substance emitted during the life cycle of a product into a potential impact on the environment, which includes terrestrial ecosystems. This work suggests some possible improvements in assessing the toxicity of metals on soil ecosystems in life cycle assessment (LCA). The current available data on soil ecotoxicity allow one to calculate the chronic terrestrial HC50(EC50) (hazardous concentration affecting 50% of the species at their EC50 level, i.e. the level where 50% of the individuals of the species are affected) of nine metals and metalloids (As(III) or (V), Be(II), Cr(III) or (VI), Sb(III) or (V), Pb(II), Cu(II), Zn(II) and Ni(II)). Contrarily to what is generally advised in LCIA, the terrestrial HC50 of metals shall not be extrapolated from the aquatic HC50, using the Equilibrium Partitioning method since the partition coefficient (K(d)) of metals is highly variable. The experimental ecotoxicology generally uses metallic salts to contaminate artificial soils but the comparison of the EC50 or NOEC obtained for the same metal with different salts reveals that the kind of salt used insignificantly influences these values. In contrast, depending on the metallic fraction of concern, the EC50 may vary, as for cadmium: the EC50 of Folsomia candida, expressed as free Cd in pore water is almost 2.5 orders of magnitude lower than that expressed as total metal. A similar result is obtained with Eisenia fetida, confirming the importance of metals speciation in assessing their impact on soils. By ranking the metals according to the difference between their terrestrial and aquatic HC50 values, two groups are distinguished, which match the hard soft acids and bases (HSAB) concept. This allows to estimate their affinity for soil components and potential toxicity according to their chemical characteristics.

The risk assessment of heavy metals in the ecosystem of urban creeks.

This paper is focused on risk assessment of heavy metals in freshwater ecosystems of urban creeks. The paper reports changes in an aquatic ecosystem leading to remobilization of heavy metals and consequently to changes of bioavailability. Concentrations of metals in water, bed sediment and benthic organisms from several small urban streams are monitored and evaluated. In the small urban streams studied copper, zinc and lead were determined as the most significant hazard metals. Although concentrations of these metals in water are very low (often below the detection limit of analytical equipment), concentrations in sediment were found in risky levels mainly in sampling sites affected by CSOs and SSOs from industrial and heavy traffic areas. The benthic organisms showed different ability to accumulate heavy metals (HM). The feeding type collector gatherer had in most cases the highest body concentration of HM and the predator species cumulate, to a high level, only zinc which has a high tendency to release from sediment, hence it is the most bio-available. The collector-filterer had mostly low values. The differences among species are due to the different feeding habits of each trophic level.

Effects and risk assessment of linear alkylbenzene sulfonates in agricultural soil. 3. Sublethal effects on soil invertebrates.

Sewage sludge applied to agricultural soils often contains considerable amounts of linear alkylbenzene sulfonates (LAS). Toxic effects of LAS on soil organisms should, therefore. be evaluated to ensure safe use of sewage sludge as a fertilizer. In this study, dose-response relationships for the toxicity of Na-LAS to six species of soil invertebrates (survival, reproduction, and growth) were established using a sandy, agricultural soil as test substrate. In general, toxic effects on reproduction and growth appeared when the concentration in soil exceeded 40 to 60 mg/kg. Reproduction was approximately fourfold more sensitive in earthworms and enchytracids than in springtails and mites. It is argued that this difference in sensitivity is related to the dependency of soil pore water, which is high in the annelids but comparatively low in the arthropods.

An assessment of the toxicity of phthalate esters to freshwater benthos. 1. Aqueous exposures.

Tests were performed with the freshwater invertebrates Hyalella azteca, Chironomus tentans, and Lumbriculus variegatus to determine the acute toxicity of six phthalate esters, including dimethyl phthalate (DMP), diethyl phthalate (DEP), di-n-butyl phthalate (DBP), butylbenzyl phthalate (BBP), di-n-hexyl phthalate (DHP), and di-2-ethylhexyl phthalate (DEHP). It was possible to derive 10-d LC50 (lethal concentration for 50% of the population) values only for the four lower molecular weight esters (DMP, DEP, DBP, and BBP), for which toxicity increased with increasing octanol-water partition coefficient (Kow) and decreasing water solubility. The LC50 values for DMP, DEP, DBP, and BBP were 28.1, 4.21, 0.63, and 0.46 mg/L for H. azteca; 68.2, 31.0, 2.64, and > 1.76 mg/L for C. tentans; and 246, 102, 2.48, and 1.23 mg/L for L. variegatus, respectively. No significant survival reductions were observed when the three species were exposed to either DHP or DEHP at concentrations approximating their water solubilities.