Adverse consequences of stock recovery : European hake, a new “choke” species under a discard ban?

Date of Acceptance: 28/01/2014 Funded by Seventh Framework Programme as part of the European research project EcoFishMan. Grant Number: FP7-265401 The Marine Alliance for Science and Technology for Scotland Scottish Funding Council. Grant Number: HR09011

Using individual tracking data to validate the predictions of species distribution models

The authors would like to thank the College of Life Sciences of Aberdeen University and Marine Scotland Science which funded CP's PhD project. Skate tagging experiments were undertaken as part of Scottish Government project SP004. We thank Ian Burrett for help in catching the fish and the other fishermen and anglers who returned tags. We thank José Manuel Gonzalez-Irusta for extracting and making available the environmental layers used as environmental covariates in the environmental suitability modelling procedure. We also thank Jason Matthiopoulos for insightful suggestions on habitat utilization metrics as well as Stephen C.F. Palmer, and three anonymous reviewers for useful suggestions to improve the clarity and quality of the manuscript.

Comparative genome analysis of human bifidobacteria with commercial potential

This thesis describes two newly sequenced B. longum subsp. longum genomes and subsequent comparative analysis with publicly available B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis genomes (Chapter 2). The acquired data revealed a closed pan-genome for this bifidobacterial species and furthermore facilitated the definition of the B. longum core genome. The comparative analysis also highlights differences in the potential metabolic abilities of all three sub-species. Interestingly, phylogenetic analysis of the B. longum core genome indicated the existence of a novel B. longum subspecies. Characterisation of restriction-modification systems from two B. longum subsp. longum strains is described in Chapter 3. These defence mechanisms limit the uptake of genetic material, which was successfully demonstrated for some of the identified systems. When these systems were by-passed by methylation of DNA prior to the transformation procedure, the resulting transformation efficiency of both B. longum subsp. longum strains was increased to a level that allowed for the generation of mutants via homologous recombination. Arabinoxylan metabolism by B. longum subsp. longum NCIMB 8809 was investigated in Chapter 4 of this thesis. Transcriptome analysis allowed the identification of a number of genes involved in the degradation, uptake and utilisation of arabinoxylan. Biochemical analysis revealed that three of the identified genes encode arabinofuranosidase activity. Phenotypic assessment of a number of insertion mutants in genes identified by the transcriptome analysis revealed the essential role of two of these enzymes in arabinoxylan metabolism, and a third enzyme in the metabolism of debranched arabinan. Furthermore, this investigation revealed that B. longum subsp. longum NCIMB 8809 does not completely degrade arabinoxylan, but utilises the arabinose substitutions only, while leaving the xylan backbone untouched.Finally, Chapter 5 outlines that B. longum subsp. longum NCIMB 8809 is capable of removing ferulic and p-coumaric acid substitutions that originate from arabinoxylan. Analysis of the genome sequence led to the identification of a candidate gene for this activity, which was subsequently cloned and expressed in E. coli. Biochemical analysis revealed that the enzyme, designated here as FaeA, is indeed capable of releasing both ferulic and p-coumaric acid from arabinoxylan. Furthermore, it is shown that a derivative of B. longum subsp. longum NCIMB 8809 carrying an insertion mutation in faeA had lost the ability to release ferulic and p-coumaric acid from arabinoxylan, and that growth of this mutant strain is negatively affected when cultivated on growth-limiting levels of arabinoxylan.

Diagnostic Tests and their Application in the Management of Soil- and Water-borne Oomycete Pathogen Species

Oomycete diseases cause significant losses across a broad range of crop and aquaculture commodities worldwide. These losses can be greatly reduced by disease management practices steered by accurate and early diagnoses of pathogen presence. Determinations of disease potential can help guide optimal crop rotation regimes, varietal selections, targeted control measures, harvest timings and crop post-harvest handling. Pathogen detection prior to infection can also reduce the incidence of disease epidemics. Classical methods for the isolation of oomycete pathogens are normally deployed only after disease symptom appearance. These processes are often-time consuming, relying on culturing the putative pathogen(s) and the availability of expert taxonomic skills for accurate identification; a situation that frequently results in either delayed application, or routine ‘blanket’ over-application of control measures. Increasing concerns about pesticides in the environment and the food chain, removal or restriction of their usage combined with rising costs have focussed interest in the development and improvement of disease management systems. To be effective, these require timely, accurate and preferably quantitatve diagnoses. A wide range of rapid diagnostic tools, from point of care immunodiagnostic kits to next generation nucleotide sequencing have potential application in oomycete disease management. Here we review currently-available as well as promising new technologies in the context of commercial agricultural production systems, considering the impacts of specific biotic and abiotic and other important factors such as speed and ease of access to information and cost effectiveness

The effect of ecological changes in Lake Victoria on the present trophic characteristics of Oreochromis niloticus in relation to the species' role as a stabilizing factor of biomanipulation

The Lake Victoria ecosystem has experienced such a profound ecological change that Oreochromis niloticus - an introduced species, is the only important cichlid (out of the original 250 + spp) left in the lake. It is the basis of an important commercial fishery which is intensely exploited by sophisticated methods. An investigation of its feeding habits at present indicates that the species could also playa major role in the energy flux of the lake. Fisheries management in Lake Victoria will thus require multi-disciplinary studies which reflect a total ecosystem approach.

Seed and vegetative propagation methods for the rare Florida native species Chionanthus pygmaeus (pygmy fringetree)

Chionanthus pygmaeus Small (pygmy fringetree) (Oleaceae) is an endemic and rare Florida species, which has an attractive, small habit giving it great potential for use in managed landscapes. Members of the genus Chionanthus are difficult to propagate via cuttings and possess complex seed dormancies that are not well understood. Conservation of pygmy fringetree and its potential for commercial propagation for use in managed landscapes is contingent on a better understanding of its complex seed dormancy and enhancement of its propagation. I conducted two experiments to assess sexual and asexual propagation methods for pygmy fringetree. The first experiment was conducted to determine what factors are involved in overcoming seed dormancy. Various scarification treatments, which mimicked conditions seeds are exposed to in the wild, were investigated to determine their effects on germination of 20-year-old seeds originally collected from the species’ native range. Treatments included endocarp removal, sulfuric acid, boiling-water, and smoke-water treatments. Prior to treatment initiation, seed viability was estimated to be 12%. Treated seeds went through two cold- and two warm-stratification periods of 4°C and 25°C, respectively, in a dark growth chamber. After 180 days, none of the treatments induced early germination. Seeds were then tested for viability, which was 11%. Seed dormancy of the species is apparently complex, allowing some of the seeds to retain some degree of viability, but without dormancy requirements satisfied. The second experiment was conducted to assess if pygmy fringetree could be successfully propagated via hardwood or root cuttings if the appropriate combination of environmental conditions and hormones were applied. Hardwood and root cuttings were treated with either 1000 ppm IBA talc, 8000 ppm IBA talc, or inert talc. All cuttings were placed on a mist bench in a greenhouse for 9 weeks. Hardwood cuttings were supplemented with bottom heat at 24 °C. No treatments were successful in inducing adventitious root formation. I conclude that pygmy fringetree seeds possess complex dormancy that was not able to be overcome by the treatments utilized. However, this result is confounded by the age of the seeds used in the experiment. I also conclude that vegetative propagation of pygmy fringetree is highly dependent on the time of year cuttings are harvested. Further research of both seed and asexual propagation methods need to be explored before pygmy fringetree can be propagated on a commercial scale.

Development of a simple and fast “DNA extraction kit” for sea food identification and marine species

Seafood products fraud, the misrepresentation of them, have been discovered all around the world in different forms as false labeling, species substitution, short-weighting or over glazing in order to hide the correct identity, origin or weight of the seafood products. Due to the value of seafood products such as canned tuna, swordfish or grouper, these species are the subject of the commercial fraud is mainly there placement of valuable species with other little or no value species. A similar situation occurs with the shelled shrimp or shellfish that are reduced into pieces for the commercialization. Food fraud by species substitution is an emerging risk given the increasingly global food supply chain and the potential food safety issues. Economic food fraud is committed when food is deliberately placed on the market, for financial gain deceiving consumers (Woolfe, M. & Primrose, S. 2004). As a result of the increased demand and the globalization of the seafood supply, more fish species are encountered in the market. In this scenary, it becomes essential to unequivocally identify the species. The traditional taxonomy, based primarily on identification keys of species, has shown a number of limitations in the use of the distinctive features in many animal taxa, amplified when fish, crustacean or shellfish are commercially transformed. Many fish species show a similar texture, thus the certification of fish products is particularly important when fishes have undergone procedures which affect the overall anatomical structure, such as heading, slicing or filleting (Marko et al., 2004). The absence of morphological traits, a main characteristic usually used to identify animal species, represents a challenge and molecular identification methods are required. Among them, DNA-based methods are more frequently employed for food authentication (Lockley & Bardsley, 2000). In addition to food authentication and traceability, studies of taxonomy, population and conservation genetics as well as analysis of dietary habits and prey selection, also rely on genetic analyses including the DNA barcoding technology (Arroyave & Stiassny, 2014; Galimberti et al., 2013; Mafra, Ferreira, & Oliveira, 2008; Nicolé et al., 2012; Rasmussen & Morrissey, 2008), consisting in PCR amplification and sequencing of a COI mitochondrial gene specific region. The system proposed by P. Hebert et al. (2003) locates inside the mitochondrial COI gene (cytochrome oxidase subunit I) the bioidentification system useful in taxonomic identification of species (Lo Brutto et al., 2007). The COI region, used for genetic identification - DNA barcode - is short enough to allow, with the current technology, to decode sequence (the pairs of nucleotide bases) in a single step. Despite, this region only represents a tiny fraction of the mitochondrial DNA content in each cell, the COI region has sufficient variability to distinguish the majority of species among them (Biondo et al. 2016). This technique has been already employed to address the demand of assessing the actual identity and/or provenance of marketed products, as well as to unmask mislabelling and fraudulent substitutions, difficult to detect especially in manufactured seafood (Barbuto et al., 2010; Galimberti et al., 2013; Filonzi, Chiesa, Vaghi, & Nonnis Marzano, 2010). Nowadays,the research concerns the use of genetic markers to identify not only the species and/or varieties of fish, but also to identify molecular characters able to trace the origin and to provide an effective control tool forproducers and consumers as a supply chain in agreementwith local regulations.

Trophic niche overlap of sprat and commercial small pelagic teleosts in the Gulf of Lions (NW Mediterranean Sea)

Increasing abundance of non-commercial sprats and decreasing biomass and landings of commercial anchovies and sardines justify the need to study the feeding ecology and trophic niche overlap of these planktivorous species in the Gulf of Lions. Their diet has been investigated on the basis of stomach content and stable isotope analyses in 2011 and 2012 according to different depths and regions in the study area. The main prey were Corycaeidae copepods, Clauso/Paracalanus, Euterpina acutifrons and Microsetella, for sprats and small copepods, such as Microsetella, Oncaea and Corycaeidae, for anchovies and sardines. This is the first time that the diet of sprats is described in the Gulf of Lions. Sprats fed on a larger size spectrum of prey and seem to be more generalist feeders compared to anchovies and sardines. Ontogenetic changes as well as spatial and temporal variations of the diet occurred in the three species. Stable isotope analysis revealed mobility of sardines and sprats among feeding areas while anchovies exhibited preferred feeding areas. Sprats showed a higher relative condition assessed by C/N ratios than sardines and anchovies. Our results showed an overlap of the trophic niches for the three species, indicating a potential trophic competition in the Gulf of Lions.

Stout Whiting Fishery Summary : Commercial Quota Setting for 2017

This fishery assessment report describes the commercial stout whiting fishery operation along Australia’s east coast between Sandy Cape and the Queensland-New South Wales border. The fishery is identified by a T4 symbol. This study follows methods applied in (O'Neill & Leigh, 2016a) and extends the results of that study by using the latest data available up to end of March 2016. The fishery statistics reported herein are for fishing years 1991 to 2016. This study analysed stout whiting catch rates from both Queensland and New South Wales (NSW) for all vessels, areas and fishing gears. The 2016 catch rate index from Queensland and NSW waters was 0.86. This means that the 2016 catch rate index was 86% of the mean standardised catch rate. Results showed that there was a stable trend in catch rates from 2012 to 2016, as in the previous study (O'Neill & Leigh, 2016a), with the 2015 and 2014 catch rates 85% of the mean catch rate. The fish-length frequency and age-length-otolith data were translated using two models which showed: • Where patterns of fish age-abundance were estimated from the fish-length frequency and age-length data, there were slightly decreased estimated measures of fish survival at 38% for 2014, compared to fish survival estimates in 2013 at 40%. The 2014 and 2015 estimated age structure was dominated by 1+ and 2+ old fished, with a slightly higher frequency of age 2 - 3 fish for 2015. • Where only the age-length data were used, estimates showed that from 2011 to 2014 the survival index increased. The estimated survival index increased from 35% in 2013 to 64% in 2014, indicating stronger survival of fish as they recruited and aged. Together the stout whiting catch rate and survival indicators showed the recent fishery harvests were sustainable. Since 1997, T4 management (Stout Whiting Fishery) is centred on annual assessments of total allowable commercial catch (TACC). The TACC is assessed before the start of each fishing year using statistical assessment methodologies, namely evaluation of trends in fish catch rates and catch-at-age frequencies measured against management reference points. The TACC has been under-caught in many years. For setting the 2017 T4 stout whiting TACC, the calculations covered a range of settings to account for the variance in the data and provide options for quota change. The overall (averaged) results suggested: • The procedure where the quota was adjusted based on previous TACC setting in year 2016 gave a recommended TACC for 2017 of between 1100 and 1130 t. • The procedure that focussed directly on optimising the average harvest to match target reference points gave a recommended TACC for 2017 of between 860 and 890 t. Use of these estimates to set TACC will depend on management and industry aims for the fishery.

Variation in susceptibility among macadamia genotypes and species to Phytophthora root decay caused by Phytophthora cinnamomi

Phytophthora cinnamomi is a major pathogen of cultivated macadamia (Macadamia integrifolia, Macadamia tetraphylla and their hybrids) worldwide. The susceptibility of the two non-edible Macadamia species (Macadamia ternifolia and Macadamia jansenii) to P. cinnamomi is not well-understood. Commercial macadamia trees are established on grafted seedling (seed propagation) or own-rooted cutting (vegetative propagation) rootstocks of hybrids of the cultivated species. There is little information to support the preferential use of rootstock propagated by either seedling or own-rooted cutting methods in macadamia. In this study we assessed roots of macadamia plants of the four species and their hybrids, derived from the two methods of propagation, for their susceptibility to P. cinnamomi infection. The roots of inoculated plant from which P. cinnamomi was recovered showed blackening symptoms. The non-cultivated species, M. ternifolia and M. jansenii and their hybrids were the most susceptible germplasm compared with M. tetraphylla and M. integrifolia. Of these two species, M. tetraphylla was less susceptible than M. integrifolia. Significant differences were observed among the accessions of their hybrids. A strong association (R2 > 0.75) was recorded between symptomatic roots and disease severity. Root density reduced with increasing disease severity rating in both own-rooted cuttings (R2 = 0.65) and germinated seedlings (R2 = 0.55). P. cinnamomi severity data were not significantly (P > 0.05) different between the two methods of plant propagation. The significance of this study to macadamia breeding and selection of disease resistant rootstocks is discussed.

An examination of the usefulness of single-species biomass models for the management of Lake Victoria fisheries

Nile perch (Lates niloticus), tilapia (Oreochromis spp), dagaa (Rastrineobola argentea, silver cyprinid), and haplochromines (Tribe Haplochromini) form the backbone of the commercial fishery on Lake Victoria. These fish stocks account for about 70% of the total catch in the three riparian states Uganda, Kenya, and Tanzania. The lake fisheries have been poorly managed, in part due to inadequate scientific analysis and management advice. The overall objective of this project was to model the stocks of the commercial fisheries of Lake Victoria with the view of determining reference points and current stock status. The Schaefer biomass model was fitted to available data for each stock (starting in the 1960s or later) in the form of landings, catch per unit effort, acoustic survey indices, and trawl survey indices. In most cases, the Schaefer model did not fit all data components very well, but attempts were made to find the best model for each stock. When the model was fitted to the Nile perch data starting from 1996, the estimated current biomass is 654 kt (95% CI 466–763); below the optimum of 692 kt and current harvest rate is 38% (33–73%), close to the optimum of 35%. At best, these can be used as tentative guidelines for the management of these fisheries. The results indicate that there have been strong multispecies interactions in the lake ecosystem. The findings from our study can be used as a baseline reference for future studies using more complex models, which could take these multispecies interactions into account.

Recent development and commercial adoption of legumes for heavy clay soils in Queensland

In previous chapters of this volume, various authors describe the development of herbaceous legumes for pastures on clay soils in Queensland until about the 1980s. Emphasis is on the collection and evaluation of the genus Desmanthus, given its relatively recent addition to agriculture and considerable potential for providing useful pasture legumes for clay soils, particularly in the seasonally dry areas of northern Australia. Other genera are also discussed, including early assessments of herbaceous legumes that were later developed for clay soils (Clitoria, Macroptilium and Stylosanthes). This chapter provides a summary of the development of herbaceous legumes for clay soils in Queensland from these earlier assessments until present. Beef cattle farming is the principal agricultural enterprise in seasonally dry areas of northern Australia, including large areas of clay soils in Queensland. Sown and naturally occurring grasses provide the key feed resource, and the inclusion of sown legumes can significantly improve live-weight gain and reproductive performance per unit area. Queensland has been the centre of development for legumes for clay soils in tropical and subtropical areas of Australia, mostly through assessing and developing plants held in the Australian Tropical Forages Genetic Resource Collection (ATFGRC) (now a component of the Australia Pastures Genebank (APG)). The systematic appraisal of genetic material for clay soils was a focus of well-resourced government research up to the early to mid-1990s, but declined thereafter as sown pasture research teams were dismantled and funding to maintain the ATFGRC declined. Cultivar development is now conducted by small government, private enterprise and university research teams that collaborate where possible. In recent studies the use of experienced researcher knowledge and old plant evaluation sites has been particularly valuable for identifying potentially useful material. Cultivars for long- and short-term pastures on clay soils have been developed to the level of commercial seed production for Desmanthus (five cultivars from four species with two cultivars (one composite) in current use), Clitoria ternatea (one cultivar), Macroptilium bracteatum (two) and Stylosanthes seabrana (two). Other potential cultivars of these species are currently in various stages of development. Each species has different production niches depending on climate, clay soil type and grazing strategy. Adoption of these cultivars is occurring but has variously been impeded by limited promotion, mismatch of seed supply and demand, and difficulty establishing legumes in pastures of some key grass species. Recent renewed investment by the Australian Beef Industry has seen revived government research into pasture legumes in Queensland and rejuvenation of the APG.

Ethanolic extracts from three commercial edibe mushrooms: determination of ergosterol contente and evaluation of bioactives properties

Mushrooms are rich in several bioactive metabolites among them are phenolic compounds, terpenoids, polysaccharides, lectins, and steroids including mycosterols, namely ergosterol [1]. Ethanolic extracts prepared by maceration of several mushroom species have been recently described as having antiinflammatory properties [2]. In the present work, ethanolic extracts of Agaricus bisporus L., Lentinus edodes (Berk.) Pegler and Pleurotus ostreatus (Jacq. ex Fr.) P.Kumm., purchased from a local supermarket in the Northeast of Portugal, were obtained by Soxhlet and chemically characterized in terms of ergosterol content by HPLC-UV. The antioxidant properties of these extracts were evaluated through DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity (RSA), reducing power (RP), p. carotene bleaching inhibition (CBI) and lipid peroxidation inhibition in TBARS (thiobarbituric acid reactive substances) assay (LPI); the antioxidant activity of ergosterol was also evaluated by the DPPH assay. The anti-inflammatory activity of the same extracts and ergosterol was evaluated in LPS (lipopolysaccharide) stimulated RAW 264.7 macrophages, through the inhibition of NO production. A. bisporus revealed the highest content in ergosterol (44.8 ± 0.4 mg/ g extract) followed by P. ostreatus (34 ± 3 mg/ g extract) and finally L. edodes (8.9 ± 0.1 mg/ g extract). A. bisporus showed the highest RSA, RP and CBI (EC50 values= 7.0 ± 0.8, 2.3 ± 0.1 and 1.4 ± 0.1 mg/mL, respectively), while L. edodes presented the highest LPI (2.5 ± 0.1 mg/mL ); ergosterol revealed higher RSA (0.46±0. 0 I mg/mL) than the extracts. Concerning the anti-inflammatory potential, the most efficient species was L. edodes (lC50 value = 164 ± 16 J.lg/mL), followed by A. bisporus (185 ± 16 J.lg/mL) and finally P. ostreatus (290 ± 10 J.lg/mL). However, ergosterol presented lower activity (338 ± 23 J.lg/mL) due to its low solubility in the culture medium. The higher antioxidant properties displayed by A. bisporus can be related with its higher ergosterol content, while in the anti-inflammatory activity this relation cannot be established also due to the low solubility of ergosterol in the cells culture medium, decreasing the ergosterol availability. More studies are being conducted regarding the ergosterol solubility. Several compounds have been implicated in the bioactivity of mushrooms and in this study we have found that ergosterol can give an important contribution.

Recruitment patterns and processes of coastal fish species in a temperate rocky reef

Tese de Doutoramento, Ciências do Mar, da Terra e do Ambiente, Ramo: Ciências do Mar, Especialização em Ecologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2016