Improving fisheries management through spatio-temporal analysis of catches, discards, fishing effort and selectivity, across different métiers

I would first like to thank my advisers, especially Dr. Karim Erzini for helping me with the project change during the first of the PhD and for overall support since the beginning of my master’s project. I deeply admire your passion for fisheries research and the number of hours you have spent reviewing my writing. Thank you to Dr. Aida Campos for giving me an opportunity to expand my horizons in fisheries when I joined the TecPescas project and for support in and outside the PhD. Thank you to Dr. Jorge Gonçalves for the local support during the PhD, especially for helping me learn how to take care of the financial side of science. Finally, a thank you to Dr. Svein Løkkeborg in Norway for the original opportunity to collaborate with him prior to my change in the project and for the support during writing my first review. Thank you to all the fishers I worked with, and we interviewed for giving me the data that I needed to complete this PhD. A special thanks to the captain and crew of Mar Vivo, for a very wild experience on the sea and delicious fresh lunches. And to the captain and crew of Bartolomeu who worked with us on the trammel net project as I thoroughly enjoyed the dinners that I received from them and due to all of them being extremely friendly. A thank you to all my colleagues who worked with me at various periods of the PhD. Without your support I could not have finished my work. Thank you to Mariana Fernandes, Ana Marçalo and especially Pedro Monteiro for helping me grow as a researcher from the master’s until now. Thank you to all the people of Fisheries, Biodiversity and Conservation lab for all the help, for creating a general environment of friendliness and for making time to chat. Thank you so much to all my friends and to my husband that have also been there for me throughout the PhD. From getting coffees in the morning, to lunches in the afternoon, to those who were there from the beginning and to those I met later in the PhD program, as well as those who I’ve known from 6 to 15 years and have supported my dreams in science. Thank you to my parents who have supported my journey in science since I decided I was going to do a PhD in marine biology when I was only 13 years old. Thank you for the sacrifices you both made and for being role models in what hard and efficient work can mean, as well as taking pride in your work. Thank you to my sister who has been my cheerleader through the past years and especially during my periods of struggle, I am extremely thankful to have a sibling who cares so much to see me succeed. Thank you to my grandma for getting on skype almost every weekend and to my grandpa for making me laugh. (PL: Dziękuję mojej babci za to, że prawie w każdy weekend wchodziła na skype i słuchała mnie i mojemu dziadkowi za rozśmieszenie mnie.) Fishers in the Southern Portuguese multi-gear coastal fleet own licenses for a variety of fishing gears including static nets, longlines, and traps, and dredges. Information on the fishing gear being actively used is scarce and most vessels are not required to report geographic location, making the impact of the local environment difficult to evaluate. The first and main objective of this thesis was to identify métiers in the multi-gear coastal fisheries operating in the Portuguese south coast, including the type of gear being used to target specific species or assemblages in certain areas during a specific time of year in a three-step process. The first step was a review to understand the definition of fisheries métiers using static longlines due to their well-defined target species, little environmental impacts, and various characteristics that can be modified for improved fishing. This was followed by a cluster analysis on landing profiles for the fleet (2012-2016), followed by the second and third step in which validations using questionnaires and onboard observations, respectively. The main finding was the application of a low-cost analysis to identify métiers within a multi-gear fleet with limited data, and specific to this fleet, an increasing number of vessels active within the octopus (Octopus vulgaris) trap métier. The second objective was to assess a proposed raised trammel net (by insertion of a section referred to as “aranha”) to reduce by-catch and habitat impacts in the cuttlefish (Sepia officinalis) trammel net fishery. The results were promising as the modified net caught significantly less habitat forming organisms and similar target species’ amounts as the standard net. The results presented in this thesis can contribute to the management of this multi-gear fleet by presenting the necessary information to make decisions, especially for métiers with high number of vessels, and effort in highlighting the necessity for gear modifications in areas where the habitat is impacted.As embarcações da frota costeira polivalente que opera na costa sul portuguesa possuem geralmente várias licenças de pesca, incluindo redes de emalhar e de tresmalho, armadilhas, potes (alcatruzes), palangres de deriva e de fundo, e dragas. A informação existente sobre as artes efetivamente utilizadas e as áreas de operação é escassa, pois só um número muito reduzido de embarcações nesta frota está equipada com o sistema de monitorização das pescas (MONICAP e diários eletrónicos de pesca). Uma vez que a utilização de artes distintas resulta em grandes diferenças quer na composição das capturas, quer nos efeitos sobre os diferentes habitats, é difícil avaliar o impacte desta frota sobre o ecossistema onde opera. O primeiro e principal objetivo desta tese foi identificar os métiers desta frota, incluindo as artes de pesca utilizadas em determinadas áreas ao longo do ano e as espécies capturadas por estas artes. Para responder a este objetivo foi adotada uma abordagem em quatro etapas sequenciais (Capítulos 2 a 6). A primeira etapa visou melhorar a compreensão sobre o conceito de métier, através da revisão bibliográfica sobre os principais parâmetros operacionais que podem afetar as capturas em palangres de fundo e semi-pelágicos, artes de pesca consideradas altamente seletivas, ambas utilizadas pela frota polivalente costeira. A revisão bibliográfica (Capítulo 2) resultou na definição das características destas artes (tipo e tamanho do de anzol) e estratégias de pesca (tipo de isco e tempo de imersão) associadas a diversos métiers. Concluiu-se que a utilização de anzóis circulares melhora a seletividade e a eficiência de captura em diversas pescarias com esta arte, enquanto que o tempo de imersão não afetará de modo significativo estas características, embora isso possivelmente se deva ao fato de ser um parâmetro mascarado por outros parâmetros. Os resultados contribuem para futuros estudos que tenham como objetivo otimizar as estratégias de pesca com esta arte e melhorar a eficiência de captura. A segunda etapa (Capítulo 3) envolveu a utilização de técnicas de análise multivariada (Clustering Large Aplications, CLARA) com o objetivo de definir os perfis de desembarque para esta frota entre 2012 e 2016, identificando as principais espécies-alvo, bem como possíveis alterações sazonais na composição das capturas e ainda propondo, com base em conhecimento prévio, as artes de pesca utilizadas. A terceira etapa (Capítulo 4) foi dedicada à validação dos métiers propostos por meio de inquéritos/entrevistas nos portos, utilizando dois questionários, o primeiro contendo questões abertas sobre as características da viagem e das artes de pesca utilizadas, incluindo perguntas sobre as espécies-alvo, enquanto que o segundo visou a associação entre espécies-alvo e operações de pesca em perguntas fechadas. A comparação das respostas nos dois questionários permitiu avançar na identificação dos métiers. Na quarta etapa (Capítulo 5) procedeu-se a uma validação adicional dos métiers através de observações a bordo, onde foi registada a composição das capturas, juntamente com os detalhes e a localização geográfica das operações de pesca nos métiers amostrados. Os resultados dos Capítulos 3 a 5 apontam para a relevância de uma pescaria dirigida ao polvo (Octopus vulgaris) com alcatruzes e armadilhas, durante todo o ano, a profundidades até aos 100 metros, tendo sido definido um conjunto de espécies acessórias numa pescaria anteriormente conhecida como sendo mono-específica. Outros métiers importantes são a pescaria do tamboril (Lophius spp.) com redes de emalhar, no período do inverno ao verão, a profundidades até 400 metros; e da pescada branca (Merluccius merluccius) e a azevia (Microchirus spp.), também com redes de emalhar, durante todo o ano, a profundidades até 100 e 50 metros, respetivamente, com capturas acessórias mais reduzidas quando comparadas com as capturas reportadas em estudos anteriores sobre estes métiers. Os bivalves, incluindo o pé-de-burrinho (Chamelea gallina), a amêijoa-branca (Spisula solida) e as conquilhas Donax spp, são capturados com ganchorras, durante todo o ano. Por fim, o choco (Sepia oficinallis) e a canilha (Bolinus brandaris) são capturados com tresmalhos, o primeiro no inverno e na primavera e a segunda durante todo o ano. Estes resultados permitiram validar métiers propostos em estudos anteriores, embora os nossos resultados indiquem que mais de metade das embarcações se encontram envolvidas na captura de polvo, tendo alterado as suas licenças de pesca para incluir alcatruzes e armadilhas durante o período em análise. De um modo geral, as embarcações que operam redes alternam sazonalmente entre tresmalhos e redes de emalhar. No Capítulo 5, procedeu-se a uma caracterização mais aprofundada de alguns dos métiers propostos, tendo sido identificados alguns métiers adicionais envolvendo um número reduzido de embarcações. Um segundo objetivo desta tese (Capítulo 6) foi propor e testar modificações às artes para reduzir capturas acessórias e impactes negativos no ecossistema, concretamente na pesca de choco (Sepia officinalis) com redes de tresmalho, em áreas com fundos rochosos, onde as capturas acessórias de invertebrados são elevadas. As alterações à rede tradicionalmente utilizada consistiram na introdução de uma secção entre os panos de rede e o cabo dos chumbos, à qual os pescadores chamaram “aranha”, e que permitiu levantar a rede do fundo. Os resultados apontam para uma redução dos principais invertebrados (incluindo esponjas, corais, pepinos-do-mar e estrelas-do-mar), com alterações não significativas na captura das duas principais espécies-alvo, o choco e a azevia. As entrevistas que foram feitas após a análise permitiram recolher opiniões dos pescadores sobre a utilidade de uma futura implementação das alterações propostas, tendo oferecido uma solução que poderá ser testada no futuro. Os resultados apresentados nesta tese fornecem uma base para a identificação de métiers através de uma abordagem que envolve três etapas sequenciais. A informação obtida com a análise das atividades desta frota pode ser utilizada para avaliar o impacte no meio ambiente local de acordo com as artes de pesca efetivamente utilizadas. Os diferentes métodos de entrevista devem também ser considerados e, para fins futuros, os dois formulários utilizados podem ser reunidos num único formato. No entanto, reconheceu-se que a segunda rodada de questionários foi mais útil, pois forneceu respostas mais diretas às questões colocadas aos pescadores. Curiosamente, os resultados obtidos relativamente às rejeições ao mar foram diferentes daqueles esperados para as embarcações que operam com armadilhas e redes. Os resultados apresentados nesta tese podem ser utilizados na gestão desta frota polivalente, voltando potencialmente a atenção para o segmento da frota que visa o polvo, uma vez que este métier envolve mais de metade das embarcações ativas desta frota. Além disso, os ensaios de pesca experimental podem ajudar a gestão a avaliar os impactos das artes estáticas nas espécies formadoras de habitat e, ao apoiar futuros estudos com foco na captura acidental desses organismos, reduzir os impactos negativos da atividade da pesca.The primary data, landings by vessel, were provided by the Directorate-General for Natural Resources, Safety and Maritime Services (DGRM) and the DocaPesca Portos e Lotas SA of Portugal. The bottom sediment chart was accessed through Observation Data Network (EMODnet), Seabed Habitats initiative (www.emodnet-seabedhabitats.eu), financed by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund. The remainder of the data used in this thesis was collected by the author with her colleagues within the framework of the project “TecPescas – Tecnologia da Pesca e Seletividade” (Mar2020 16-01-04-FMP-0010 – IPMA)

Fishers, let us talk: validating métiers in a multi-gear coastal fishing fleet

In the multi-gear coastal fleet in the Algarve (South Portugal), fishers own licenses for various fishing gears. However, they generally do not use all these licenses, and therefore, it is difficult to estimate the impacts this fleet has on the local environment. In this study, two types of questionnaires were used directed to the local fishers from the multi-gear fleet during interviews carried out between November 2019 and July 2021 with the objective to validate the métiers proposed for this fleet in a previous study using multivariate analysis on past landing profiles. A total of 10 out of the 11 proposed métiers were validated, including four métiers with gillnets, three with dredges, two with trammel nets, and one with traps. Additional métiers were identified not found in the previous study. The results obtained with the two types of questionnaires are presented, and their usefulness in validating the gear used and the seasonality of fishing activities are discussed, as well as their contribution to a clearer distinction between target species and commercial by-catch.info:eu-repo/semantics/publishedVersio

Reducción de la captura secundaria y los descartes en la pesquería costera de pequeña escala del Algarve utilizando una red de trasmallo de monofilamento equipada con una red de protección

Experimental fishing was conducted off the port of Quarteira (southern Portugal) from October 2016 to February 2017 using standard trammel nets and modified nets rigged with a guarding net. The commercial catches of trammel nets rigged with a guarding net were 46.1% and 38.0% less than those of the standard net in numbers and economic value. However, there were significantly fewer commercial discards in biomass in the modified trammel nets (68.2%) and by-catch abundance and biomass were also lower in the modified nets (41.8% and 17.3% less, respectively). For the two main fish by-catch species, the modified net caught 62.2% fewer longfin gurnards (C. obscurus) and 33.1% fewer greater weever (T. draco) than the standard nets. Timing the removal from the nets of the main by-catch and discards species revealed savings in time associated with the use of modified nets. However, net damage occurred twice as much as in the modified net, probably contributing to the reduced commercial catches. The results indicate that trammel nets with the guarding net reduce by-catch and discards and save time, but are unlikely to be adopted by fishers targeting soles due to the higher costs of the modified nets and losses in commercial catches and earnings.European Commission's Horizon 2020 Research and Innovation Programme - 634495info:eu-repo/semantics/publishedVersio

Identificando metiers usando perfis de aterrissagem: uma frota costeira multi-engrenagem impulsionada por polvo

The multi-gear coastal vessels in the Algarve (South Portugal) own licenses for various fishing gears. However, it is generally uncertain what gears they use, which is problematic as each individual gear is responsible for unique impacts on the resources and the environment. In this study, landing profiles identified for the multi-gear coastal fleet (2012–2016) were used as support in defining potential métiers using k-mean clustering analysis (CLARA) along with information from past studies on métiers. The results showed that more than 50% of the vessels were engaged in the octopus fishery year-round, using traps, while a small percentage (~13%) were entirely dedicated to clam dredging. In general, gillnets (21%) were used to target monkfish, hake and bastard soles, while trammel nets (6%) were used to target cuttlefish, with some vessels alternating the fishing gears (either seasonally or annually) according to target species. The method for the initial characterization of this fleet’s métiers and its efficiency with limited data is discussed, as well as the utility of this segmentation in support of management advice.16-01-04-FMP-0010, UIDB/04326/2020, SFRH/BD/137818/2018info:eu-repo/semantics/publishedVersio

The Effects of Silica Nanoparticles on Apoptosis and Autophagy of Glioblastoma Cell Lines

Silica nanoparticles (SiNPs) are one of the most commonly used nanomaterials in various medical applications. However, possible mechanisms of the toxicity caused by SiNPs remain unclear. The study presented here provides novel information on molecular and cellular effects of SiNPs in glioblastoma LBC3 and LN-18 cells. It has been demonstrated that SiNPs of 7 nm, 5–15 nm and 10–20 nm induce time- and dose-dependent cytotoxicity in LBC3 and LN-18 cell lines. In contrast to glioblastoma cells, we observed only weak reduction in viability of normal skin fibroblasts treated with SiNPs. Furthermore, in LBC3 cells treated with 5–15 nm SiNPs we noticed induction of apoptosis and necrosis, while in LN-18 cells only necrosis. The 5–15 nm SiNPs were also found to cause oxidative stress, a loss in mitochondrial membrane potential, and changes in the ultrastructure of the mitochondria in LBC3 cells. Quantitative real-time PCR results showed that in LBC3 cells the mRNA levels of pro-apoptotic genes Bim, Bax, Puma, and Noxa were significantly upregulated. An increase in activity of caspase-9 in these cells was also observed. Moreover, the activation of SiNP-induced autophagy was demonstrated in LBC3 cells as shown by an increase in LC3-II/LC3-I ratio, the upregulation of Atg5 gene and an increase in AVOs-positive cells. In conclusion, this research provides novel information concerning molecular mechanisms of apoptosis and autophagy in LBC3 cells