The status of the Irish freshwater fish fauna: a review

The status of the Irish freshwater fish fauna is reviewed. Of the 25 Irish species, 11 are introduced and five are considered as endangered or vulnerable. Agriculture through eutrophication, farm wastes and overgrazing, and afforestation and introductions are the main threats to the native fauna.     

Direct extraction of microbial community DNA from humified upland soils

This paper describes a protocol effective at extracting high yields of high-purity microbial community DNA from humified soils. DNA was extracted from soil by lysozyme, SDS and freeze–thaw lysis, precipitated and then subjected to a double caesium chloride density gradient centrifugation stage before concentrating and washing. Evaluation using three soils yielded up to 30 μg DNA g⁻¹ dry soil, with absorbance ratios at 260 : 230 nm and 260 : 280 nm of 1·6–2·0. The DNA extracted from the three soils was digested by four restriction enzymes and a 16S rDNA eubacterial product was amplified by PCR. These tests indicated that the DNA obtained by the protocol was sufficiently pure for molecular biological analysis.     

Structural and chemical defenses of echinoderms from the northern Gulf of Mexico

The feeding deterrent effects of echinoderm body-wall tissues and ethanolic extracts containing mid-polarity compounds were evaluated utilizing generalist fish and crabs as model predators. The body-wall tissues of the echinoderms examined ranged 10-fold from 0.9–9.4 mm in thickness, and four and a half-fold in level of mineralization (17.8–82.7% ash content). Holothuroids had the thickest body-wall tissues and contained the lowest levels of mineralization in their body-walls. Crinoids and ophiuroids had high levels of mineralization in their arms. Asteroid body-wall tissues varied the most in thickness and ash content (0.9–3.9 mm in thickness and 29.2–55.5% in ash content). Body-wall tissues of 19 species of echinoderms were tested for their feeding deterrent properties against the marine fishes Lagodon rhomboides (Linnaeus) and Cyprinodon variegatus (Lacepede), as well as the decapod crustacean Libinia emarginata (Leach). Equivalent sized pieces of fresh body-wall tissue of 16 species of echinoderms caused observable feeding deterrence responses in at least two of the three model predators. There was no significant correlation between body-wall thickness or percent ash and its palatability to any of the three model predators. Agar pellets containing ethanolic body-wall extracts of 12 of 18 echinoderm species caused observable feeding deterrence responses in the fish L. rhomboides. In similar experiments with the arrow crab Stenorhyncus seticornis (Herbst), using carrageenan fish-meal blocks as food models, no differences in consumption of control fish-meal and experimental body-wall extract blocks were detected. Our findings indicate that invertebrate and vertebrate predators may respond quite differently to echinoderm body-wall extracts.     

On the Mechanism of Reinitiation of Endogenous Crassulacean Acid Metabolism Rhythm by Temperature Changes

Under continuous light the endogenous Crassulacean acid metabolism (CAM) rhythm of Kalanchoe daigremontiana Hamet et Perrier de la Bathie disappears at high (>29.0[deg]C) or low (<8.0[deg]C) temperatures. We investigated the reinitiation of rhythmicity when temperature was reduced from above the upper and increased from below the lower threshold level via measurements of (a) short-term changes in carbon-isotope discrimination to illustrate shifts between C3 and C4 carboxylation in vivo, and (b) the malate sensitivity of phosphoenolpyruvate carboxylase (PEPC) in vitro. When the net CO2-exchange rhythm disappears at both temperatures, the instantaneous discrimination indicates low PEPC activity. Leaf malate concentration and osmolarity attain high and low values at low and high temperatures, respectively. After small temperature increases or reductions from the low and high temperatures, respectively, the rhythm is reinitiated, with phases shifted by 180[deg] relative to each other. This can be related to the contrasting low and high leaf malate concentrations due to direct inhibition of PEPC and possibly also of the phosphorylation of PEPC by malate. The experimental results were satisfactorily simulated by a mathematical CAM-cycle model, with temperature acting only on the passive efflux of malate from the vacuole. We stress the important role of the tonoplast in malate compartmentation and of malate itself for the reinitiation and generation of endogenous CAM rhythmicity.     

Discrimination Processes and Shifts in Carboxylation during the Phases of Crassulacean Acid Metabolism

The magnitude and extent of Crassulacean acid metabolism (CAM) activity in two Clusia species was manipulated to investigate the regulation of the distinct CAM phases. First, in response to leaf-air vapor pressure deficit at night, changes in leaf conductance altered on-line carbon-isotope discrimination throughout the theoretical range for dark CO2 uptake during CAM. These ranged from the limit set by phosphoenolpyruvate carboxylase (PEPc) (-6[per mille (thousand) sign], [delta]13C equivalent of -2[per mille (thousand) sign]) to that imposed by diffusion limitation (+4[per mille (thousand) sign], [delta]13C equivalent of -12[per mille (thousand) sign]), but the lowest carbon-isotope discrimination occurred when P[square root]pa was only 0.7. Second, when the availability of external or internal sources of CO2 was reduced for both field- and greenhouse-grown plants, CO2 uptake by day via PEPc during phase II largely compensated. Third, by reducing the dark period, plants accumulated low levels of acidity, and CO2 uptake occurred throughout the subsequent light period. Discrimination switched from being dominated by PEPc (phase II) to ribulose 1,5-bisphosphate carboxylase/oxygenase (phase III), with both enzymes active during phase IV. Under natural conditions, photochemical stability is maintained by extended PEPc activity in phase II, which enhances acid accumulation and delays decarboxylation until temperature and light stress are maximal at midday.     

Manipulating freezing tolerance in transgenic plants

Winterhardiness is a composite of tolerances to freezing, desiccation, ice-encasement, flooding and diseases. From one point of view, winterhardiness may not be easily manipulated by genetic engineering technology because many different genes are involved in the tolerance of these diverse stresses. However, these various stresses have similarities. They promote formation of activated forms of oxygen, promote membrane lipid and protein degradation, cause similar biophysical changes in membrane structure, and culminate with increased leakage of cytoplasmic solutes and loss of cellular membrane functions. These similarities led to the hypothesis that winter injury might be reduced in crop plants if their tolerance of oxidative stress was increased. Towards that objective we created transgenic alfalfa (Medicago sativa L.) plants that overexpress either Mn-SOD or Fe-SOD cDNA (provided by Dirk Inzé, Universiteit Gent). Petiole explants were transformed using Agrobacterium tumefaciens and plants were regenerated by somatic embryogenesis. The primary transgenic plants were screened using PCR (polymerase chain reaction), Southern hybridization and native PAGE for SOD activity. Greenhouse and laboratory studies showed a minimal difference in stress tolerance between the primary transgenic and non-transgenic plants. In the first field trial, four primary transgenic plants expressing two forms of the Mn-SOD cDNA had greater survival after two winters than the non-transgenic RA3. Similar results were obtained in a second field trial, comparing 18 independent transformants with Mn-SOD targeted to the mitochondria, 11 independent transformants with Mn-SOD targeted to the chloroplast and 39 independent transformants with Fe-SOD targeted to the chloroplast, expressed in three different non-transgenic plants. The transgenic plants averaged over 25% higher survival than the non-transgenic controls after one winter. There was no effect of subcellular targeting or SOD type on field survival, but there was variation among independent transformants containing the same SOD construct. Activated oxygen therefore appears to be one of the possible causes of winter injury, and it should be possible to reduce winter injury in transgenic plants by constitutive overexpression of SOD.     

Gradation in Nutrient Composition and Photosynthetic Pathways Across the Restinga Vegetation of Brazil

The restinga comprises coastal vegetation formations which dominate the Atlantic seaboard of Brazil. Exposed sand ridges and associated lagoon systems have poorly developed soils subject to pronounced water deficits. Distinct vegetation zones support a high diversity of life forms, and a comparative study has been undertaken to investigate interactions between degree of exposure, nutrient supply and photosynthetic pathway (C₃, or CAM) in selected species across the restinga. A number of species occurring throughout the restinga were chosen as representative species of different life forms, comprising C₃ pioneer shrubs (Eugenia rotundifolia and Erythroxylum ovalifolium), impounding (tank) terrestrial bromeliad (Neoregelia cruenta: CAM) and the atmospheric epiphyte (Tillandsia stricta: CAM). Comparisons of plant and soil nutrient composition, and airborne deposition were conducted for each zone. Soil nutrient content and organic matter were closely related, reaching a maximum in zone 4, the seaward face of the inner dune. Salt concentration in leaves was independent of atmospheric deposition for the terrestrial species, in contrast to the atmospheric epiphyte T. stricta. In the slack area, vegetation formed characteristic “islands” with the soil beneath enriched in nutrients, suggesting a complex interplay between plants and soil during the development of vegetation succession. Here, two additional trees were investigated, C₃ and CAM members of the Clusiaceae, respectively Clusia lanceolata and C. fluminensis. Stable isotope composition of nitrogen (δ¹⁵N) was generally more negative (depleted in ¹⁵N) in plants with low total nitrogen content. This was exemplified by the atmospheric bromeliad, T. stricta, with an N content of 2.91 g/kg and δ¹⁵N of ?12.3 per mil. Stable isotopes of carbon (δ¹³C) were used to identify the distribution of photosynthetic pathways, and while the majority of bromeliads and orchids were CAM, analysis of the soil organic matter suggested that C₃ plants made the major contribution in each zone of the restinga. Since δ¹³C of plant material also suggested that water supply was optimal in zone 4, we conclude that succession and high diversity in the restinga is dependent on exposure, edaphic factors, and perhaps a critical mass of vegetation required to stabilize nutrient relations of the system.     

A method for the estimation of parameters for natural stage-structured populations

A relatively simple method is proposed for the estimation of parameters of stage-structured populations from sample data for situation where (a) unit time survival rates may vary with time, and (b) the distribution of entry times to stage 1 is too complicated to be fitted with a simple parametric model such as a normal or gamma distribution. The key aspects of this model are that the entry time distribution is approximated by an exponential function withp parameters, the unit time survival rates in stages are approximated by anr parameter exponential polynomial in the stage number, and the durations of stages are assumed to be the same for all individuals. The new method is applied to four Zooplankton data sets, with parametric bootstrapping used to assess the bias and variation in estimates. It is concluded that good estimates of demographic parameters from stagefrequency data from natural populations will usually only be possible if extra information such as the durations of stages is known.