Phylogenetic analysis of bacterial communities in the shrimp and sea cucumber aquaculture environment in northern China by culturing and PCR–DGGE

In this study, we investigated the bacterial communities in the shrimp and sea cucumber culture environment, including shrimp ponds (SP), sea cucumber ponds (SCP), mixed-culture ponds (MCP) and the effluent channel (EC) in Qingdao, China. Bacteria cultivation showed that the counts of heterotrophic, nitrate-reducing and sulfate-reducing bacteria in the sediment of SP were higher than that in the sediment of SCP and MCP, varying between 8.7 × 10⁴ and 1.86 × 10⁶, 2.1 × 10⁴ and 1.1 × 10⁵, and 9.3 × 10¹ and 1.1 × 10⁴ CFU g^?1, respectively. In contrast, the counts of ammonium-oxidizing and nitrifying bacteria in the sediment of SP was lower than that in the sediment of SCP and MCP. Denaturing gradient gel electrophoresis (DGGE) of 16S rDNA gene and dendrogram analyses showed that bacterial diversity in the mixed-culture environment was higher than that in the monocultures. The similarity of bacterial community between EC and SCP or MCP was higher than that between EC and SP. These results indicated that sea cucumber culture played a significant role in influencing the environmental bacterial communities that were composed mainly of Flavobacteriaceae (64.3%), Bacteriodetes (21%) and delta proteobacteria (14.7%), including the genera of Croceimarina, Lutibacter, Psychroserpens and so on. The results explained the benefit of sea cucumber culture in shrimp ponds at the level of microbial ecology.     

Methods of assessing extinction risk in marine fishes

The decline and disappearance of species from large parts of their former geographical range has become an important issue in fisheries ecology. There is a need to identify which species are at risk of extinction. The available approaches have been subject to considerable debate – particularly when applied to commercially exploited species. Here we have compiled methods that have been used or may be used for assessing threat status of marine organisms. We organize the methods according to the availability of data on the natural history, ecology and population biology of species. There are three general approaches to inferring or assessing extinction risk: (i) correlative approaches based on knowledge of life histories and ecology; (ii) time‐series approaches that examine changes in abundance; and (iii) demographic approaches based on age‐ or stage‐based schedules of vital rates and fisheries reference points. Many methods are well suited to species that are highly catchable and/or have relatively low productivity, but theory is less well developed for assessing extinction risk in species exhibiting narrow geographical distributions or ecological specialization. There is considerable variation in both definitions of extinction risk and the precision and defensibility of the available risk assessment methods, so we suggest a two‐tiered approach for defining and assessing extinction risk. First, simple methods requiring a few easily estimated parameters are used to triage or rapidly assess large numbers of populations and species to identify potentially vulnerable populations or species. Second, the populations and species identified as vulnerable by this process can then be subject to more detailed and rigorous population analysis explicitly considering sources of error and uncertainty.     

Effects of salinity on the growth and lipid composition of Atlantic salmon (Salmo salar) and turbot (Scophthalmus maximus) cells in culture

The direct effects of osmotic pressure (salinity) on growth performance and lipid composition were investigated in fish cells in culture. Cell lines from a relatively stenohaline marine species, turbot (Scophthalmus maximus) (TF) and an anadromous species, Atlantic salmon (AS) were cultured in media supplemented with NaCl to produce osmotic pressures varying from 300 to 500 mOsm kg⁻¹. The growth rates of the two cell lines were affected in a similar manner by the salinity of the media with the rank order for both peak cell numbers and growth rates up to the day of peak cell number being 300 > 350 > 400 > 450 > 500 mOsm kg⁻¹. Cell death occurred in both cell lines in older cultures at all salinities with the greatest loss of viable cells in media of 300 and 350 kg⁻¹. However, there were quantitative and qualitative differences between the cell lines in their lipid metabolism in response to the salinity of the media. The lipid content expressed per cell showed a positive correlation between lipid per cell and salinity in TF cells, but this was less apparent in AS cells. The percentage of total polar lipid classes increased with increasing salinity in TF cells due mainly to graded increases in the percentages of choline phospholipids. In contrast, there were no significant differences in the proportions of polar and neutral lipid classes with salinity in AS cells. The only significant effect of salinity in AS cells was a decreased proportion of dimethylacetals in total lipid at the highest salinity. The same significant effect of salinity on dimethylacetal content of total lipid was observed in TF cells. However, in addition there was a graded decrease in the percentage of 18:2n-9 in TF cell total lipid with increasing salinity. This was accompanied by increased percentages of total n-3 and n-6 PUFA with higher proportions of both groups of PUFA at 450 and 500 compared with 300 mOsm kg⁻¹. The results show that environmental salinity, in the absence of hormonal or other physiological stimuli, has direct effects on the growth and lipid metabolism of fish cells and that these effects differ in cells from different fish species.     

Patterns and impacts of fish bycatch in a scallop dredge fishery

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Polygalacturonase and β-galactosidase activities in Hayward kiwifruit as affected by light exposure,maturity stage and storage time

Softening process and total antioxidant activity were evaluated in kiwifruit differently exposed to light intensity and harvested at two different times (October 10 and November 14). Fruit was stored for 2 months at 0 °C (S1) and then maintained for a week at ambient temperature (S2). The results showed that fruit harvested later presented a faster softening rate during storage than fruit harvested earlier, even if antioxidant activity did not change. Light-exposed fruit showed higher flesh firmness than that of shaded ones. Polygalacturonase activity was higher in kiwifruit maintained for a week at ambient temperature after cool storage and, in particular the highest value was recorded in fruit harvested later. The behaviour of β-galactosidase was different: it did not show changes in fruit harvested later and significantly decreased in light- and shade-exposed fruit harvested earlier.     

Drying half of the root-zone from mid fruit growth to maturity in ‘Hass’ avocado (Persea americana Mill.) trees for one season reduced fruit production in two years

We tested the effect of extended drying of half the root system on fruit yield and fruit Ca concentration, an indirect measure of fruit quality, in avocado (Persea americana Mill. cv Hass). In a field experiment on a sandy soil, withholding irrigation and plastic sheeting was used to dry the root-zone beneath the whole canopy (DD) or half the canopy (WD), compared with well-watered trees (WW). The irrigation water contained added nutrients and was slightly saline. Yield, shoot growth, leaf conductance, leaf and fruit water status and mineral concentrations of leaves and fruit were studied. The responses of treated trees were assessed in the following season during which normal irrigation practices were restored. With respect to yield, the WD treatment behaved the same as the DD treatment. It reduced yield by more than half and proportionately more than the reduction in water supply thus reducing irrigation efficiency. Re-watering did not restore yield of WD or DD-trees in the next season. The WD and DD treatments had no effect on the concentration of Ca in the fruit mesocarp and so are unlikely to affect fruit quality. The main impact of reduced water supply on the trees was fruit abscission and this was linked to dry soil around the roots rather than the water status of the leaves or fruits. We conclude that extended drying of half of the root-zone in one season reduced irrigation efficiency for two seasons by promoting the abscission of developing fruit to the same extent as occurred when the whole root system was exposed to extended drying.     

A SCAR marker linked to the N gene for resistance to root knot nematodes (Meloidogyne spp.) in pepper (Capsicum annuum L.)

The root-knot nematodes (Meloidogyne spp.) are important nematode pests and cause serious diseases in pepper in the world. No molecular markers linked to the nematodes resistance N gene have been reported. In this paper, ‘Carolina Wonder’ (Capsicum annuum L.), a sweet pepper line resistant to root-knot nematode with N gene, ‘20080-5-29’ (C. annuum L.), an inbred line susceptible to root-knot nematode with good horticultural characteristics, and their F₂ progeny with 320 individuals were used as materials. Evaluation of resistance and susceptibility of parental lines, F₁ and F₂ progeny inoculated with root-knot nematodes (Meloidogyne incognita) were carried out. ‘Bulked segregant analysis’ method was used to search for polymorphic markers from 512 pairs of AFLP primers. Based on the assessment of resistance and susceptibility and polymorphism of the AFLP marker in F₂ population, the genetic linkage distance between the AFLP marker and the N gene was estimated. One AFLP marker E39/M41-339 was obtained and transferred to a SCAR marker amplifying a 315 bp DNA fragment linked to the N resistant allele and a 331 bp fragment linked to the N⁺ susceptible allele. The distance between the molecular marker and the nematodes resistance N gene is 6.3 cM. This research delivered a valuable tool for the marker assisted selection of nematodes resistance in pepper.     

Floral induction (FI) in longan (Dimocarpus longan, Lour.) trees. III: Effect of shading the trees on potassium chlorate induced FI and resulting hormonal changes in leaves and shoots

Previous experiments demonstrated that treatment of longan trees with potassium chlorate (KClO₃) induces “off season floral induction” (FI) even in the absence of the naturally required cool temperature [Manochai, P., Sruamsiri, P., Wiriya-alongkorn, W., Naphrom, D., Hegele, M., Bangerth, F., 2005. Year around off season flower induction in longan (Dimocarpus longan, Lour.) trees by KClO₃ applications: potentials and problems. Sci. Hortic. 104, 379–390]. Potassium chlorate, however, cannot replace the presence of functional mature leaves and sufficient light intensity. Here we examined in more detail the effect of shade (about 10% of natural sunlight) on KClO₃ affected hormone concentrations/transport of leaves and shoot apical buds (SAB) and their interactions with FI.     

Condition assessment of lamprey populations in the Yorkshire Ouse catchment,north‐east England,and the potential influence of physical migration barriers

• 1. River lamprey (Lampetra fluviatilis) and sea lamprey (Petromyzon marinus) are designated features of the River Derwent Special Area of Conservation (SAC) and the Humber Estuary (a possible SAC). This study determined the condition of lamprey populations in the Yorkshire Ouse catchment by assessing the species composition, distribution, abundance and size‐structure of larval (ammocoete) populations in five major tributary rivers (Derwent, Swale, Ure, Nidd and Wharfe).
• 2. According to EU condition assessment criteria, Lampetra populations (assumed to be mostly river lamprey) are at present in favourable condition, with site mean (±SE) densities ranging from 2.7 (±1.2) to 160.3 (±50.5) individuals m^?2 (all river means >2 individuals m^?2), and at least two size (≈age) classes present in optimal microhabitats. By contrast, no sea lamprey larvae were recorded, suggesting that populations of this species are in unfavourable condition.
• 3. Actions to protect and enhance nationally or internationally important stocks must be implemented from at least a catchment perspective, because many of the issues affecting such species are not localized. With respect to lampreys, particular attention should be given to protecting spawning and nursery habitats, improving water quality, reducing impingement at abstraction points, preventing exploitation at spawning grounds and increasing passage at potential physical obstructions.

Copyright © 2007 John Wiley & Sons, Ltd.     

Comparison of three types of adhesives in attaching coral transplants to clam shell substrates

• 1. Nubbins from 12 coral species were transplanted onto dead giant clam shells at three sites in a lagoon near Bolinao, north‐western Philippines. Transplants were attached using three types of adhesives: cyanoacrylate glue (SG), epoxy putty (EP) and marine epoxy (ME) and were monitored over five months for detachment, in situ mortality and natural self‐attachment by tissue growth.
• 2. Corals attached with SG showed a significantly higher rate of detachment (logrank test) than those attached with either EP or ME (P<0.001 in each case). Also, those attached with EP showed a higher rate of detachment than corals attached with ME (logrank=6.46, P<0.05).
• 3. ANOVA (P>0.05) and survival analysis (logrank=2.85, P>0.05) showed no among‐adhesives differences in in situ mortality. Among the species used, Porites cylindrica, Pavona frondifera, Heliopora coerulea and Porites rus had the highest survivorship with 82%, 80%, 76% and 73%, respectively, of nubbins alive at the end of the experiment and also displayed the highest cumulative rates of self‐attachment. Species with the lowest survival rates included Acropora muricata and four pocilloporids.
• 4. Although there was no significant difference in the number of self‐attaching transplants among the adhesives, corals transplanted using ME and EP self‐attached earlier than those transplanted using SG (logrank=11.19, P<0.01).
• 5. Results from this study highlight the importance of selecting the appropriate means of attaching corals to substrates and carefully considering species‐specific traits of candidate corals for transplantation.

Copyright © 2008 John Wiley & Sons, Ltd.