Development and environmental application of a genus-specific quantitative PCR approach for Pseudo-nitzschia species

Quantitative polymerase chain reaction (qPCR) for the identification and quantification of microbes has become a common tool for the study of harmful algal blooms (HABs). We developed a qPCR method for the diatom genus Pseudo-nitzschia. Several species of this genus form toxic blooms through the production of the neurotoxin domoic acid (DA). Outbreaks of toxicity attributed to DA along the US west coast have caused sickness and death of marine mammals and seabirds through food web contamination. The method developed here quantifies Pseudo-nitzschia spp. at low abundances in natural samples, thereby, providing a method to improve our understanding of the environmental conditions leading to blooms of these species. This has been accomplished previously by techniques for identification and quantification that are slow and laborious compared to qPCR. The approach was successfully tested and validated using eight species of Pseudo-nitzschia and 33 non-target organisms and employed to follow local bloom dynamics.     

Alimentary niche partitioning in the Galapagos sea lion, Zalophus wollebaeki

Sea lions are generally considered opportunistic feeders. However, studies from different areas suggest their diet consists mostly of four to five types of prey. Previous studies in Galapagos sea lions have identified at least three feeding strategies for this species, suggesting diversification of their diet. Diet diversification is favored in organisms with relatively high trophic position and subject to high intra-specific and low inter-specific competition. Zalophus wollebaeki meet these criteria as the only pinniped on San Cristobal Island, where three sea lion rookeries are located within 11 km: a distance considerably shorter than their 41 km foraging range. To measure the degree of diet diversification, we used scats and stable isotope analyses. A total of 270 scat samples from lactating females and 142 fur samples from sea lion pups were collected during the breeding season 2006. The scat analysis identified distinct diets among rookeries, with minimal trophic overlap (Cλ = 0.19), a trophic level TL = 4.5 (secondary–tertiary carnivore), and trophic breadth of a specialist predator (B _i  = 0.37). The mean δ¹⁵N and δ¹³C values were 13.07 ± 0.52 and −16.34 ± 0.37, respectively. No significant difference was found in the δ¹⁵N values from the sea lion rookeries, but differences were found inter- and intra-population in δ¹³C values for pups from different groups (ANOVA P < 0.05). Our results indicate that diet diversification is present in the Galapagos sea lion and may play important role to the survival of the species in a habitat where pinniped populations are limited.     

The three-dimensionality of obstructed shear flows

Obstructed shear flows (i.e. those over permeable media) are common in the environment. An archetypal example, flow over a submerged vegetation canopy, is investigated here. Like any flow through complex geometry, canopy flows are characterised by strong spatial gradients. The focus of this experimental study is the three-dimensionality of aquatic canopy flow, in particular that of the coherent interfacial vortices that govern mixing into and out of the canopy. It is shown here that the vortices have a finite lateral scale that is comparable to their vertical scale; both are of the order of the drag length scale of the canopy, (C _D a)⁻¹, where a is the frontal area density and C _D is a bulk drag coefficient. The finite lateral extent of the vortices generates strong lateral hydrodynamic gradients, both instantaneously and in the long-term. The instantaneous gradients, which can contribute greatly to the dispersion of dissolved and particulate species, are far more pronounced. Finally, the potential for canopies to generate differential roughness secondary circulation is examined. In the consideration of vertical scalar transport, this circulation can be of the same order as turbulent diffusion.     

Persistence models for mark-recapture

The stable of models available for analyzing mark-recapture data (Otis et al. Wild Momogr 66:135, 1978) includes those having behavioral characteristics, time variation, heterogeneity, along with combinations of those characteristics. This paper proposes use of a series of models based on the persistence model of Ramsey and Usner (Biometrics 59:331–339, 2003). We show that persistence can be modeled in combination with behavior and with time variation. We apply the persistence model to situations in which capture occasions are not equally-spaced in time. Two case studies illustrate the use of these extended persistence models.     

Geochemical and microbial effects on the mobilization of arsenic in mine tailing soils

Arsenic (As) contamination has become a serious environmental problem in many countries. We have performed batch-type leaching experiments on mine tailing soils collected from three abandoned mine areas in South Korea with the objective of evaluating the effect of indigenous bacterial activity on As mobilization. The analysis of physicochemical properties and mineralogical compositions of the samples indicated that the secondary minerals or phases formed as a result of the oxidation or alteration of primary minerals were associated with the labile and bioleachable fractions of As. Compared to simulated abiotic processes using sterilization, the indigenous bacteria activated using a carbon source were able to enhance the dissolution of As under both aerobic and anaerobic conditions. The bacterial dissolution of iron (Fe) and manganese (Mn) was found to occur simultaneously with the dissolution of As, suggesting that the main bacterial mechanism was via the dissimilatory reduction of Fe(III), Mn(IV), and As(V). An anaerobic environment was more favorable for the prominent dissolution of As in the tailing soils. These results indicate that the mobilization of As can be enhanced in the oxygen-depleted part of the tailing dump, particularly with the infiltration of organic substrates. The difference in the degree of As lixiviation between the three tailing soils was found to be related to the bioavailability of As as well as the original biomass in the tailing soils.     

The potential impacts of sea level rise along the coastal zone of Kanyakumari District in Tamilnadu,India

Climate change associated with sea level rise (SLR) is one of the major environmental concerns of today. This paper presents an assessment of the impacts of sea level rise on the coastal zone of Kanyakumari District in Tamilnadu, India. Digital Elevation Model (DEM) combined with overlay techniques in GIS are used in determining the inundation zones along the coastal region. The analysis evaluated the impact on coastal fishing villages, landuse, tourist spots and sensitive areas under threat. The vulnerability of the coastal areas in Kanyakumari to inundation was quantified, based on the projected sea level rise scenarios of 0.5 and 1 m. Our findings reveal that approximately 13 km² of the land area of Kanyakumari would be permanently inundated due to SLR. This would result in loss of land, alteration of the coastal zone and affects coastal ecosystem. From the study, the mitigation measures (engineering measures) and Coastal Zone Management practices that can be taken to protect human life and property from sea level rise are suggested.     

Trophic diversity of idoteids (Crustacea, Isopoda) inhabiting the Posidonia oceanica litter

The coexistence of three idoteid species in Posidonia oceanica litter raises the question of trophic diversity and their role in the litter degradation process. Hence, diet composition of Idotea balthica, Idotea hectica and Cleantis prismatica was studied using a combination of gut contents and stable isotopes analysis. Gut content observations indicate that P. oceanica dead leaves are an important part of the ingested food for the three species, although their tissues are constituted of only a small to medium fraction of P. oceanica carbon. Our results also underlined the potential role of these species in the degradation of P. oceanica litter by mechanically fragmenting the litter and by assimilating a small to medium fraction of carbon. Moreover, we showed that there were considerable inter- and intra-specific differences in diet composition. Diet differed between juveniles and adults for I. balthica. Crustaceans are an important food source for adults of I. balthica, while I. hectica indicated a major contribution of algal material. C. prismatica showed an intermediate diet. This trophic diversity is probably one of the factors allowing these species to coexist in the same biotope.     

Analytical survey of arsenic in geothermal waters from sites in Kyushu,Japan, and a method for removing arsenic using magnetite

The objective of this study was to survey the cation and anion contents of geothermal waters to gather fundamental information on geographical variations. Sixteen sites in hot spring areas on the island of Kyushu in Japan were studied. The study focused on the arsenic content of the samples. Very high arsenic concentrations (more than 0.1 mg/l) were detected in most of the geothermal waters sampled. High contents of boron and fluoride (more than 1.0 mg/l) were also detected in some samples. Arsenic removal was performed on a laboratory scale using columns packed with a magnetite-type adsorbent. The reduction of arsenic contamination to a concentration of less than 0.01 mg/l could be achieved in the early stages of adsorption (bed volume = 200).     

Anthropogenic influence on surface water quality of the Nhue and Day sub-river systems in Vietnam

In order to investigate the temporal and spatial variations of 14 physical and chemical surface water parameters in the Nhue and Day sub-river systems of Vietnam, surface water samples were taken from 43 sampling sites during the dry and rainy seasons in 2007. The results were statistically examined by Mann–Whitney U-test and hierarchical cluster analysis. The results show that water quality of the Day River was significantly improved during the rainy season while this was not the case of the Nhue River. However, the river water did not meet the Vietnamese surface water quality standards for dissolved oxygen (DO), biological oxygen demand (BOD₅), chemical oxygen demand (COD), nutrients, total coliform, and fecal coliform. This implies that the health of local communities using untreated river water for drinking purposes as well as irrigation of vegetables may be at risk. Forty-three sampling sites were grouped into four main clusters on the basis of water quality characteristics with particular reference to geographic location and land use and revealed the contamination levels from anthropogenic sources.     

Biosecurity threats: the design of surveillance systems,based on power and risk

We consider the problem of designing a surveillance system to detect a broad range of invasive species across a heterogeneous sampling frame. We present a model to detect a range of invertebrate invasives whilst addressing the challenges of multiple data sources, stratifying for differential risk, managing labour costs and providing sufficient power of detection. We determine the number of detection devices required and their allocation across the landscape within limiting resource constraints. The resulting plan will lead to reduced financial and ecological costs and an optimal surveillance system.