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The assemblage composition, biomass and dynamics of zooplankton and epibenthos were examined in a commercial prawn pond in southeast Queensland over two seasons. Physico-chemical characteristics of the pond water were measured concurrently. Numbers and biomass of zooplankton in the surface tows (140 micrometre mesh) varied from 8 ind. L-1 (44 micrograms L-1) to 112 ind. L-1 (324 micrograms L-1) in the first season, with peaks in biomass corresponding to peaks in numbers. In the second season the zooplankton numbers varied from 12 to 590 ind. L-1, but peaks in numbers did not correspond with peaks in biomass, which varied from 28 to 465 micrograms L-1. This was due to differences in the size of the dominant taxa across the season. Although this occurred in both seasons, the effect on biomass was more pronounced in the second season. In both seasons, immediately after the ponds were stocked with prawn postlarvae there was a rapid decline in zooplankton numbers, particularly of the dominant larger copepods. This was probably due to predation by the postlarvae. Subsequent peaks in zooplankton numbers were principally due to barnacle nauplii. The largest peaks in zooplankton numbers occurred before stocking in the first season, but the largest peaks were in the middle of the second season. While changes in abundance and biomass of the zooplankton assemblage were not correlated with physico-chemical characteristics in the first season, there were correlations between zooplankton numbers and temperature, dissolved oxygen, pH and secchi disk readings in the second season. No correlations were found with zooplankton biomass and physico-chemical characteristics in the second season. The correlations in the second season were mainly due to the high prevalence of barnacle nauplii through the middle part of the season, and may reflect suitable conditions for barnacle reproduction. Epibenthic faunal abundance in the beam trawls (1 mm mesh) peaked at 14 ind. m-2 and 7 ind. m-2 in the first and second seasons respectively and the biomasses at 0.8 g m-2 and 0.7 g m-2. Peaks in abundance of epibenthos did not correspond to peaks in biomass. This was due to large differences in the size of the taxa across the seasons. Sergestids (Acetes sibogae) and amphipods were the most abundant taxa in beam trawl samples. Amphipods were only abundant in the first season, with their numbers increasing towards the end of the grow out period. Acetes were abundant in both seasons, but were dominant in the second season. Correlations between physico-chemical parameters and epibenthos numbers were found to be strongly influenced by the dominant taxa in each season. In the first season, negative correlations were found between epibenthos abundance and pH and temperature. These relationships may reflect an effect on the growth of macroalgae in the pond, with which the amphipods were strongly associated, rather than a direct effect on the epibenthos. In the second season, a positive correlation existed between temperature and epibenthos abundance, however this was strongly influenced by the very high abundance of Acetes in the last sampling period. No correlations were found between epibenthic fauna biomass and physico-chemical parameters. Abundances of epibenthic fauna were not related to zooplankton densities indicating this source of food was not likely to be a limiting factor. Neither the pond water exchange regime nor moon phase could explain changes observed in abundances of zooplankton or epibenthos assemblages in the first season, however the sampling regime was not designed to specifically investigate these effects. In the second season water exchanges were sampled more rigorously. The density of zooplankton in the outlet water was from 2 to 59% of the density of zooplankton in the pond, and the zooplankton density of the inlet water was from 9 to 50% of the outlet water. The number of zooplankton recruited into the pond from the inlet water, after the prawns were stocked, was negligible and contributed little to changes observed in zooplankton assemblages. Reproduction of barnacles within the pond appeared to play the most important role in changes in the assemblage. Water exchange did, however, appear to play a greater role in the changes observed in epibenthic fauna assemblages. In the last season of sampling the feeding of the dominant epibenthic species, Acetes sibogae, was examined using a combination of gut content and stable isotope analysis. Acetes gained little nutrition directly from the pelleted feed, probably relying primarily on zooplankton as their direct food source. Other dietary items such as macroalgae also played a role in the nutrition of the Acetes. If Acetes numbers were high at the beginning of a season they may compete with the newly stocked prawns for the zooplankton resource. However, they will not compete with the prawns later in the season when the prawns are gaining most of their nutrition from the pelleted feed. Overall it appears that zooplankton are important to the nutrition of the prawns at the beginning of the season when the assemblage is usually dominated by copepods. Later in the season the assemblage is dominated by barnacle nauplii which are recruited from within the pond. The establishment of an abundant assemblage of suitable zooplankton species before stocking prawn postlarvae would appear to be beneficial, if not essential. The assemblage of epibenthic fauna changes throughout the season as new recruits are brought in from outside the pond. Epibenthic faunal assemblages in ponds from southeast Queensland are dominated by Acetes which are not likely to adversely affect the production of prawns unless they are particularly abundant early in the grow out season when the prawns would be utilising the same food resources as Acetes.

Orientadores: Fosca Pedini Pereira Leite, Giuliano Buzá Jacobucci / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-21T12:16:02Z (GMT). No. of bitstreams: 1 Siqueira_SilvanaGomesLeite_D.pdf: 2460624 bytes, checksum: 11cc560773d9117ec50e5c04d3f4ba0c (MD5) Previous issue date: 2012 / Resumo: O monitoramento dos ambientes marinhos pode ser feito avaliando a presença de poluentes em organismos que são capazes de acumular estas substâncias. Desta forma, este estudo avaliou a presença de hidrocarbonetos petrogênicos na alga parda Sargassum furcatum e em anfípodes ampitoídeos associados provenientes de costões rochosos do Canal de São Sebastião, o qual está sujeito à poluição por petróleo, devido às operações do Duto e Terminais Centro Sul (DTCS) e por efluentes domésticos. Identificou-se as espécies de ampitoídeos que ocorreram associadas ao S. furcatum estudando também a variação espacial e temporal da composição desta comunidade. A relação entre os hidrocarbonetos presentes em S. furcatum, a densidade e a estrutura populacional de Cymadusa filosa, espécie de ampitoídeo mais representativa da região, também foi investigada. Adicionalmente foi realizado o estudo do comportamento reprodutivo de C. filosa e avaliado o seu uso como bioindicador de qualidade da água, por meio de teste de toxidade aguda de curta duração. O material analisado foi proveniente de 7 coletas realizadas entre março de 2007 a novembro de 2008 em 7 costões rochosos. Foram quantificados os hidrocarbonetos alifáticos e policíclicos aromáticos derivados de petróleo tanto na alga como nos anfípodes, que compostos variaram em termos de concentração entre os meses amostrados. A alga possivelmente refletiu as concentrações de hidrocarbonetos presentes na água enquanto que os anfípodes podem ter assimilado via contato direto ou via alimentação. Foram identificadas seis espécies de anfípodes da Família Ampithoidae: Ampithoe sp., A. divisura, A. marcuzzi, A. ramondi, C. filosa e Sunampithoe pelagica que apresentaram diferenças significativas em termos de ocorrência, densidades e variação temporal. A população de C. filosa, de modo geral, foi dominada por jovens, possivelmente devido a elevada fecundidade das fêmeas. Ocorreu também desvio da razão sexual a favor das fêmeas, relacionado com o comportamento diferencial do macho ou devido a sua maior sensibilidade aos hidrocarbonetos presentes na alga. Tanto hidrocarbonetos alifáticos como policíclicos aromáticos influenciaram a densidade e estrutura de tamanho dos diferentes estádios de desenvolvimento de C. filosa. Foram observadas interações agonísticas entre machos e fêmeas de C.filosa, formação de tubos conjugais e a alimentação de filhotes ainda no marsúpio pela fêmea, caracterizando o cuidado parental desta espécie. Verificou-se ainda que o período de incubação dos ovos foi curto e a maturidade sexual ocorreu entre seis a sete semanas. Os resultados de toxidade aguda sugerem que C.filosa tem um potencial para uso em experimentos de ecotoxicologia marinha devido a elevada sensibilidade ao cobre e ao naftaleno, contudo estudos adicionais com outros xenobióticos são necessários para comprovação destes resultados e para validar o uso desta espécie no monitoramento dos ambientes marinhos / Abstract: The monitoring of marine environments can be made by evaluation of pollutant presence in organisms that are able to accumulate these substances. Thus, this study evaluated the occurrence of oil-derived hydrocarbons in the brown algae Sargassum furcatum and in its associated amphitoid amphipods found on rocky shores of the São Sebastião Channel, which is exposed to pollution by oil due to the operations of the Duct and Center Southern Terminal (DTCS) and domestic sewage. The species of amphitoid that occurred associated to S. furcatum were identified, and time and spatial variation of the composition of this community were also studied. The relationship between the hydrocarbons present in S. furcatum and the density and populational stucture of Cymadusa filosa, the most representative species of amphitoid in the area, was also investigated. Additionally a study on the reproductive behavior of C. filosa was conducted and its use as a bioindicator of water quality was evaluated through high toxicity test of short duration. The analysed material was obtained from 7 samples taken from march 2007 to november 2008 on 7 rocky shores. The oil-derived aliphatic and polycyclic aromatic hydrocarbons were quantified both in the algae and in the amphipods. Such compounds varied in concentration between the months of sampling. The algae possibly reflected the hydrocarbon concentrations present in the water while the amphipods may have assimilated hydrocarbons by direct contact or through the trophic chain. Six species of amphipods from the Ampithoidae family were identified: Ampithoe sp., A. divisura, A. marcuzzi, A. ramondi, C. filosa and Sunampithoe pelagica which presented significant differences in occurrence, density and temporal variation. The population of C. filosa in general was dominated by young individuals, possibly due to the high fecundity of the females, and there was a deviation of the sexual ratio favoring the females, related to the male?s differential behavior or due to its higher sensibility to hydrocarbons in the algae. Both aliphatic and polycyclic aromatic hydrocarbons influenced the density and size structure of the different stages of development of C. filosa. Agonistic interactions between male and female C. filosa were observed, formation of share tubes and feeding of the offspring still in the pouch by the female, characterizing parental care by this species. It was also verified that the egg incubation period was short and sexual maturity occurred between six and seven weeks. The results of high toxicity suggest that C. filosa has potential for use in experiments of marine ecotoxicology due to its high sensibility to copper and naphthalene, however, additional studies with other xenonbiotics are necessary to confirm these results and to validate the use of this species in marine environments monitoring / Doutorado / Ecologia / Doutora em Ecologia

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Currently there are 68 species of Hyalella gender described, whereas in South America, the largest diversity of species is observed, 52 record species. The State of Rio Grande do Sul has nine species of this gender recorded. Through an extensive sampling period, the current study objectives to described three new species of Hyalella observed at the Northwest Region of Rio Grande do Sul State, South region of Brazil. The specimens were sampled at a small spring, an artificial pond and a natural pond, in the municipality of Palmeira das Missões. The three species have a curved seta on the inner ramus of uropod 1 and an accessory seta for the males. Hyalella sp. nov. 1 has dactylus of gnathopod 2 shorter than the propodus palm, showing simple apical setae on outer ramus of uropod 3, in addition of having 9 serrate setae inner face of propodus of gnathopod 1 and a peculiar pattern of setae on peduncle of uropod 3 ramus. This species differs from H. montenegrinae and H. carstica by showing sternal gills on segments 2 to 7 and more than two apical setae on telson. The Hyalella sp. nov. 2 resembles the species H. bonariensis, H. castroi, H. curvispina, H. kaigang, H. pampeana e H. pleoacuta by having gills on sternum of segments 2 to 7. This specie differs from H. pleoacuta, H. kaingang and H. pseudoazteca by lacking dorsal flanges on pereions and pleonites. Finally, Hyalella sp. nov. 3 differs from others species found in the State of Rio Grande do Sul (H. bonariensis, H. castroi, H. kaigang, H. imbya, H. montenegrinae and H. pampeana) in type and number of setae on uropods, telson and inner face of gnathopod 1. Despite the resemblance with H. curvispina, Hyalella sp. nov. 3 has only two simple setae on telson, inner face of gnathopod 1 with five serrate setae and denticles in comb-scales only at the posterior distal margin, and also has sternal gills on segments 3 to 7. After this study, the number of Hyalella species found in Brazil raises to 26 and to 71 worldwide for the gender. / Atualmente existem 68 espécies descritas do gênero Hyalella, sendo que na América do Sul, tem-se a maior diversidade, com registro de 52 espécies. No Estado do Rio Grande do Sul, nove espécies do gênero foram registradas. Com base em amostragens de coletas durante um longo período, o objetivo do presente estudo foi descrever três novas espécies de Hyalella com ocorrência na Região Noroeste do Estado do Rio Grande do Sul, sul do Brasil. Os exemplares foram amostrados em uma nascente, um açude artifical e um açude natural, no municipio de Palmeira das Missões. As três espécies possuem uma seta curva no ramo interno do urópodo 1 com uma seta acessória nos machos. Hyalella sp. nov. 1 possui o dáctilo do gnatópodo 2 mais curto que o própodo, apresentando setas apicais simples no ramo externo do urópodo 3, além de possuir 9 setas serradas na face interna do própodo do gnatópodo 1 e um padrão peculiar de cerdas no pedúnculo do ramo do urópodo 3. Este espécie difere de H. montenegrinae e H. carstica apresentando brânquias no esterno nos segmentos de 2 a 7 e mais de duas setas apicais no télson. Já Hyalella sp. nov. 2 assemelha-se as espécies H. bonariensis, H. castroi, H. curvispina, H. kaigang, H. pampeana e H. pleoacuta por possuir brânquias no esterno nos segmentos de 2 a 7. No entanto, Hyalella sp. nov. 2 difere da H. pleoacuta, H. kaingang e H. pseudoazteca por ausência de flanges dorsal sobre péreon e pleonitos. Por fim, a Hyalella sp. nov. 3 difere de outras espécies encontradas no Estado do Rio Grande do Sul (H. bonariensis, H. castroi, H. kaigang, H. imbya, H. montenegrinae e H. pampeana) no tipo e número de setas nos urópodos, télson e face interna do gnatópodo 1. Apesar da semelhança com H. curvispina, Hyalella sp. nov. 3 possui apenas duas cerdas simples no télson, face interna do gnatópodo 1 com cinco setas serradas e dentículos em ―comb scales‖ apenas na margem disto-posterior e, especialmente, por possui brânquias esternais nos segmentos 3 a 7. A partir deste trabalho, o número de espécies de Hyalella encontradas no Brasil aumenta para 26 e para 71 espécies para o gênero.

Mesobenthic amphipods (2-15 mm) constitute an important faunal component of coastal ecosystems, and often represent a major trophic link between primary producers and fishes. However, obtaining basic demographic data on these taxa is often hindered by a lack of suitable non-destructive, quantitative, collection techniques. Although artificial substrates have been advocated for collecting data at these lower trophic levels, recent studies suggest that they may not accurately represent the natural benthic assemblage. This study evaluated how a structurally-complex artificial substrate (3-dimensional) simulated the natural substrate of a shallow Acropora reef environment. Assemblage development was followed on a series of artificial substrate units (ASUs) at 2-week intervals over a 14-week period; adjacent natural substrate was sampled monthly. Multivariate analyses were applied to determine the (dis)similarity of assemblages between the two substrate types. Statistical analyses showed significant differences in assemblage structure between artificial and natural substrates. However, no significant differences were found between sites or habitats within substrate type. Samples from the ASUs were dominated by Elasmopus balkomanus, Bemlos kunkelae, Neomegamphopus kalanii, and Ericthonius punctatus. Taxa abundant on the natural substrate, but numerically poor on the ASUs, included Chevalia carpenteri, Apolochus sp., Gammaropsis atlantica, and Globosolembos smithi. Assemblage dissimilarities depended chiefly on differences in species composition and relative abundance largely contributed to the dissimilarity between the two substrates.

Lake Baikal is the oldest, by volume, the largest, and the deepest freshwater lake on Earth. It is characterized by an outstanding diversity of endemic faunas with more than 350 amphipod species and subspecies (Amphipoda, Crustacea, Arthropoda). They are the dominant benthic organisms in the lake, contributing substantially to the overall biomass. Eulimnogammarus verrucosus, E. cyaneus, and E. vittatus, in particular, serve as emerging models in ecotoxicological studies. It was, then, necessary to investigate whether these endemic littoral amphipods species form genetically separate populations across Baikal, to scrutinize if the results obtained --~for example, about stress responses~-- with samples from one single location (Bolshie Koty, where the biological station is located), could be extrapolated to the complete lake or not. The genetic diversity within those three endemic littoral amphipod species was determined based on fragments of Cytochrome C Oxidase I (COI) and 18S rDNA (only for E. verrucosus). Gammarus lacustris, a Holarctic species living in water bodies near Baikal, was examined for comparison. The intra-specific genetic diversities within E. verrucosus and E. vittatus (13% and 10%, respectively) were similar to the inter-species differences, indicating the occurrence of cryptic, morphologically highly similar species. This was confirmed with 18S rDNA for E. verrucosus. The haplotypes of E. cyaneus and G. lacustris specimens were, with intra-specific genetic distances of 3% and 2%, respectively, more homogeneous, indicating no --or only recent disruption of-- gene flow of E. cyaneus across Baikal, and recent colonization of water bodies around Baikal by G. lacustris. The data provide the first clear evidence for the formation of cryptic (sub)species within endemic littoral amphipod species of Lake Baikal and mark the inflows/outflow of large rivers as dispersal barriers. Lake Baikal has provided a stable environment for millions of years, in stark contrast to small, transient water bodies in its immediate vicinity. A highly diverse endemic amphipod fauna is found in one but not the other habitat. To gain more insights and explain the immiscibility barrier between Lake Baikal and non-Baikal environments faunas, the differences in the stress response pathways were studied. To this end, exposure experiments to increasing temperature and a heavy metal (cadmium) as proteotoxic stressors were conducted in Russia. High-quality de novo transcriptome assemblies were obtained, covering multiple conditions, for three amphipod species: E. verrucosus and E. cyaneus -Baikal endemics-, and G. lacustris -Holarctic- as a potential invader. After comparing the transcriptomic stress responses, it was found that both Baikal species possess intact stress response systems and respond to elevated temperature with relatively similar changes in their expression profiles. G. lacustris reacts less strongly to the same stressors, possibly because its transcriptome is already perturbed by acclimation conditions (matching the Lake Baikal littoral). Comprehensive genomic resources are of utmost importance for ecotoxicological and ecophysiological studies in an evolutionary context, especially considering the exceptional value of Baikal as a UNESCO World Heritage Site. In that context, the results presented here, on the genome of Eulimnogammarus verrucosus, have been the first massive step to establish genomic sequence resources for a Baikalian amphipod (other than mitochondrial genomes and gene expression data in the form of de novo transcriptomes assemblies). Based on the data from a survey of its genome (a single lane of paired-end Illumina HiSeq 2000 reads, 3X) as well as a full dataset (two complete flow cells, 46X) the genome size was estimated as nearly 10 Gb based on the k-mer spectra and the coverage of highly conserved miRNA, hox genes, and other Sanger-sequenced genes. At least two-thirds of the genome are non-unique DNA, and no less than half of the genomic DNA is composed of just five families of repetitive elements, including low complexity sequences. Some of the repeats families found in high abundance in E. verrucosus seem to be species-specific, or Baikalian-specific. Attempts to use off-the-shelf assembly tools on the available low coverage data, both before and after the removal of highly repetitive components, as well as on the full dataset, resulted in extremely fragmented assemblies. Nevertheless, the analysis of coverage in Hox genes and their homeobox showed no clear evidence for paralogs, indicating that a genome duplication did not contribute to the large genome size. Several mate-pair libraries with bigger insert sizes than the 2kb used here and long reads sequencing technology combined with semi-automated methods for genome assembly seem to be necessary to obtain a reliable assembly for this species.

Aquaculture facilities involve mooring a large amount of artificial structures in offshore areas, which are colonised by a wide group of marine organisms, forming characteristic fouling communities. Many studies have focused on determining what sessile organisms are able to settle on nets, ropes and buoys, owing to the specific problems they cause and their economic cost to the aquaculture industry. Although sessile fouling communities are well-studied from the point of view of controlling this community on aquaculture facilities, little is known about the epifaunal mobile species inhabiting these artificial structures. This thesis addresses the study of crustacean amphipods, which have been scarcely studied regarding their species composition and relation to the habitats created by the sessile species and despite being detected in high abundances. After the general introduction, which sets the study framework, Chapter 1 is a preliminary study on the composition of fouling assemblages on aquaculture facilities in the Mediterranean Sea, comparing them with others such as those in harbours or offshore structures. Therein, it is shown that fouling communities are made up of mainly bivalves, algae, hydroids and bryozoans and amphipods usually represent more than 80 % of motile fauna associated with these organisms. Moreover, amphipod assemblages are characterised by seven frequent and dominant species: Elasmopus rapax, Jassa marmorata, Jassa slatteryi, Ericthonius punctatus, Stenothoe tergestina, Caprella equilibra and Caprella dilatata. A quantitative study of amphipod densities is carried out in Chapter 2, where mean amphipod densities observed in fish farm fouling amounted to 176,000 ind.m-2 and reached maxima up to 1,000,000 ind.m-2. There, the role of the macro- and microhabitat in supporting such amphipod communities is explored. The effect of the modification of marine currents on pelagic communities due to the introduction of coastal infrastructures is analysed in Chapter 3. Therein, it was detected a retention effect on planktonic amphipods near such facilities, noticeable in the increased abundance of hyperiids and migrating amphipods from different benthic and floating habitats. The influence of fouling amphipods on other habitats is analysed in Chapters 4 and 5, it is shown that fish-farm fouling acts as a source population of amphipods dispersing towards both defaunated sediments in soft-bottoms and surrounding floating habitats. Finally, in the last chapter, based on the possibility of using wild fauna already growing in fish farms, the applicability of amphipods as an accessory culture is tested in an offshore integrated multi-trophic aquaculture (IMTA) system with finfish as main fed species. Throughout this thesis it has been shown that fish-farming activities affect the amphipod assemblage in several ways such as the establishment of high population densities or the intimate connectivity between different subpopulations. As a result, a new potential commercial application arises from the possibility of using them as biofilters of aquaculture wastes, within an off-coast integrated multitrophic aquaculture system, promoting a more sustainable development of aquaculture in the marine environment. / Las estructuras artificiales que conforman las instalaciones de acuicultura en mar abierto suelen ser colonizadas por multitud de organismos marinos, que forman comunidades de fouling características en estas estructuras. Muchos estudios se han centrado en la descripción de los organismos sésiles que se desarrollan sobre cabos, redes y boyas de las instalaciones de acuicultura, debido a los problemas que generan para el cultivo y los costes adicionales que significan para la industria derivados de su necesaria eliminación. Sin embargo, aunque las comunidades de fouling sésiles han sido bien estudiadas desde el punto de vista de su control en las instalaciones de acuicultura, poco se sabe sobre la epifauna que habita estas estructuras artificiales. Esta tesis se centra en el estudio de los crustáceos anfípodos, los cuales aún no han sido estudiados en cuanto a la composición de especies y a su relación con los hábitats creados por los organismos sésiles, a pesar de haber sido detectados en grandes abundancias en las instalaciones de acuicultura. Después de una introducción general, que establece el marco de estudio, el capítulo uno es un estudio preliminar sobre las comunidades de fouling de las instalaciones de acuicultura en el Mediterráneo, comparándolas con las desarrolladas en otras estructuras artificiales como puertos o plataformas petrolíferas. En este capítulo, se demuestra que las comunidades de fouling están compuestas principalmente por bivalvos, algas, hidrozoos y briozoos y que más de un 80% de la fauna asociada a estos organismos son anfípodos. Además el poblamiento se caracteriza por la presencia de siete especies de anfípodos que son frecuentes y abundantes: Elasmopus rapax, Jassa marmorata, Jassa slatteryi, Ericthonius punctatus, Stenothoe tergestina, Caprella equilibra y Caprella dilatata. Un estudio cuantitativo de las densidades de estos anfípodos se lleva a cabo en el capítulo 2, donde se encuentra que la densidad media es de 176.000 ind.m-2, con máximos de más de 1.000.000 ind.m-2. Allí se explora también el papel de los macro y microhábitats en mantener dichas poblaciones de anfípodos. El efecto de la modificación de corrientes sobre las comunidades plantónicas debida a la instalación de las piscifactorías se analiza en el capítulo 3. En él, se detectó una retención de los anfípodos planctónicos cerca de las instalaciones, evidenciada por el incremento en las abundancias de hipéridos y de anfípodos migradores desde diferentes hábitats bentónicos flotantes. La influencia de las grandes densidades de anfípodos del fouling sobre otros hábitats se estudia en los capítulos 4 y 5, donde se observó que el fouling actúa como fuente de anfípodos migradores, exportando individuos que colonizan tanto sedimentos defaunados en el fondo marino como otros hábitats flotantes cercanos. Finalmente, en el último capítulo se analiza la posibilidad de aprovechar la producción natural y la conectividad observadas a través del cultivo de anfípodos como parte de un sistema de acuicultura multitrófica integrada (AMTI) en mar abierto con peces como especie principal. A lo largo de esta tesis, se demuestra que la acuicultura influencia las poblaciones de anfípodos marinos, tanto en el establecimiento de grandes densidades de población como en la conectividad entre las diferentes subpoblaciones. Como resultado, surge una nueva aplicación comercial de la posibilidad de usar los anfípodos del fouling como biofiltros, reciclando los residuos de la acuicultura dentro de un sistema de acuicultura multitrófica, garantizando así un desarrollo más sostenible de la acuicultura en el medio marino.

Chez les parasites à cycle complexe et à transmission trophique, des stratégies d’exploitation de l’hôte intermédiaire ont été sélectionnées. Notamment, de nombreux parasites sont capables d’altérer le comportement de leur hôte intermédiaire (manipulation comportementale). Cette manipulation n’intervient que lorsque le stade larvaire du parasite est infectieux pour l’hôte définitif. Avant d’atteindre cette infectivité, le développement du stade larvaire n’est pas suffisamment avancé pour lui permettre de s’établir dans l’hôte définitif (il est dit non-infectieux). La transmission prématurée d’un stade non-infectieux implique alors la mort du parasite. Les parasites capables de renforcer les défenses anti-prédateurs de leur hôte intermédiaire au stade non-infectieux (i.e. de le protéger vis-à-vis de la prédation), avant de manipuler leur comportement au stade infectieux (i.e. de les exposer à la prédation par l’hôte définitif) devraient avoir été sélectionnés. Dans ces travaux de thèse, j’ai pu montrer qu’au stade larvaire non-infectieux, le parasite acanthocéphale Pomphorhynchus laevis renforce les défenses anti-prédateurs de son hôte intermédiaire amphipode, ce qui a pour effet de diminuer ses risques de prédation. Cet effet protecteur de l’hôte intermédiaire affecte négativement l’approvisionnement de l’amphipode, bien que cela n’ait aucune incidence sur l’état des réserves énergétiques de l’hôte. De même, le comportement reproducteur de l’hôte mâle n’est pas affecté par l’infection par ce stade protecteur. Les origines de cette stratégie parasitaire sont discutées, et des perspectives écologiques à ce changement comportemental de l’hôte sont suggérées / In trophically-transmitted parasites, exploitation strategies of the intermediate host have been selected, in a way increasing parasites transmission probabilities to their definitive host. Particularly, numerous parasites are able to alter their intermediate host behaviour, a phenomenon called ‘behavioural manipulation’. This manipulation only occurs when the parasite developmental stage (or larval stage) is infective for the definitive host. Before reaching this stage, the development of parasite larvae is not sufficiently advanced to allow establishment in the definitive host (this stage is thus called ‘non-infective’). Early transmission of a non-infective stage therefore implies parasite death. Parasites able to reinforce their intermediate host anti-predatory defences when non-infective (i.e. protecting them from predation), before manipulating their intermediate host behaviour when infective (i.e. exposing them to predation by definitive hosts), should have been selected. In this thesis, I showed that, when non-infective, the acanthocephalan parasite Pomphorhynchus laevis strengthens its amphipod intermediate host anti-predatory defences, which diminishes its host predation risk. This protective-like strategy negatively affects the amphipod food intake, although it has no effect on host energetic reserves. Similarly, the male amphipod reproductive behaviour is not affected by infection with a non-infective stage of the parasite. The origins of such parasitic strategy are discussed, and ecological perspectives to this host behavioural change are suggested

Les proliférations nuisibles de la cyanobactérie filamenteuse benthique Lyngbya wollei qui forme des tapis déposés sur les sédiments ont augmenté en fréquence au cours des 30 dernières années dans les rivières, lacs et sources de l'Amérique du Nord. Lyngbya wollei produit des neurotoxines et des composés organiques volatils (géosmin, 2-méthylisobornéol) qui ont des répercussions sur la santé publique de même que des impacts d'ordre socioéconomiques. Cette cyanobactérie est considérée comme un habitat et une source de nourriture de piètre qualité pour les invertébrés en raison de sa gaine robuste et de sa production de toxines. Les proliférations de L. wollei ont été observées pour la première fois en 2005 dans le fleuve Saint-Laurent (SLR; Québec, Canada). Nous avons jugé important de déterminer sa distribution sur un tronçon de 250 km afin d'élaborer des modèles prédictifs de sa présence et biomasse en se basant sur les caractéristiques chimiques et physiques de l'eau. Lyngbya wollei était généralement observé en aval de la confluence de petits tributaires qui irriguent des terres agricoles. L’écoulement d’eaux enrichies à travers la végétation submergée se traduisait par une diminution de la concentration d’azote inorganique dissous (DIN), alors que les concentrations de carbone organique dissous (DOC) et de phosphore total dissous (TDP) demeuraient élevées, produisant un faible rapport DIN :TDP. Selon nos modèles, DOC (effet positif), TP (effet négatif) et DIN :TDP (effet négatif) sont les variables les plus importantes pour expliquer la répartition de cette cyanobactérie. La probabilité que L. wollei soit présent dans le SLR a été prédite avec exactitude dans 72 % à 92 % des cas pour un ensemble de données indépendantes. Nous avons ensuite examiné si les conditions hydrodynamiques, c'est-à-dire le courant généré par les vagues et l'écoulement du fleuve, contrôlent les variations spatiales et temporelles de biomasse de L. wollei dans un grand système fluvial. Nous avons mesuré la biomasse de L. wollei ainsi que les variables chimiques, physiques et météorologiques durant trois ans à 10 sites le long d'un gradient d'exposition au courant et au vent dans un grand (148 km2) lac fluvial du SLR. L'exposition aux vagues et la vitesse du courant contrôlaient les variations de biomasses spatiales et temporelles. La biomasse augmentait de mai à novembre et persistait durant l'hiver. Les variations interannuelles étaient contrôlées par l'écoulement de la rivière (niveau d'eau) avec la crue printanière qui délogeait les tapis de l'année précédente. Les baisses du niveau d'eau et l'augmentation de l'intensité des tempêtes anticipées par les scénarios de changements climatiques pourraient accroître la superficie colonisée par L. wollei de même que son accumulation sur les berges. Par la suite, nous avons évalué l'importance relative de L. wollei par rapport aux macrophytes et aux épiphytes. Nous avons examiné l'influence structurante de l'échelle spatiale sur les variables environnementales et la biomasse de ces producteurs primaires (PP) benthiques. Nous avons testé si leur biomasse reflétait la nature des agrégats d'habitat basées sur l'écogéomorphologie ou plutôt le continuum fluvial. Pour répondre à ces deux questions, nous avons utilisé un design à 3 échelles spatiales dans le SLR: 1) le long d'un tronçon de 250 km, 2) entre les lacs fluviaux localisés dans ce tronçon, 3) à l'intérieur de chaque lac fluvial. Les facteurs environnementaux (conductivité et TP) et la structure spatiale expliquent 59% de la variation de biomasse des trois PP benthiques. Spécifiquement, les variations de biomasses étaient le mieux expliquées par la conductivité (+) pour les macrophytes, par le ratio DIN:TDP (+) et le coefficient d'extinction lumineuse (+) pour les épiphytes et par le DOC (+) et le NH4+ (-) pour L. wollei. La structure spatiale à l'intérieur des lacs fluviaux était la plus importante composante spatiale pour tous les PP benthiques, suggérant que les effets locaux tels que l'enrichissement par les tributaire plutôt que les gradients amont-aval déterminent la biomasse de PP benthiques. Donc, la dynamique des agrégats d'habitat représente un cadre général adéquat pour expliquer les variations spatiales et la grande variété de conditions environnementales supportant des organismes aquatiques dans les grands fleuves. Enfin, nous avons étudié le rôle écologique des tapis de L. wollei dans les écosystèmes aquatiques, en particulier comme source de nourriture et refuge pour l'amphipode Gammarus fasciatus. Nous avons offert aux amphipodes un choix entre des tapis de L. wollei et soit des chlorophytes filamenteuses ou un tapis artificiel de laine acrylique lors d'expériences en laboratoire. Nous avons aussi reconstitué la diète in situ des amphipodes à l'aide du mixing model (d13C et δ15N). Gammarus fasciatus choisissait le substrat offrant le meilleur refuge face à la lumière (Acrylique>Lyngbya=Rhizoclonium>Spirogyra). La présence de saxitoxines, la composition élémentaire des tissus et l'abondance des épiphytes n'ont eu aucun effet sur le choix de substrat. Lyngbya wollei et ses épiphytes constituaient 36 et 24 % de l'alimentation in situ de G. fasciatus alors que les chlorophytes, les macrophytes et les épiphytes associées représentaient une fraction moins importante de son alimentation. Les tapis de cyanobactéries benthiques devraient être considérés comme un bon refuge et une source de nourriture pour les petits invertébrés omnivores tels que les amphipodes. / Harmful proliferations of the filamentous cyanobacterium L. wollei forming conspicuous benthic mats on the bottom sediment have been reported with increasing frequency in the last 30 years in rivers, lakes, and springs in North America. It is a known producer of neurotoxins and volatile organic compounds (geosmin, 2-methylisoborneol) thus exerting socioeconomic and public health impacts. Lyngbya wollei is also considered a poor nutritional source for invertebrates because of its robust sheath and toxin production. Proliferation of L. wollei in St. Lawrence River (SLR; Quebec, Canada) was first noticed in 2005. We deemed important to determine its distribution over a 250 km stretch of the SLR to elaborate predictive models of its presence and biomass based on chemical and physical characteristics. Lyngbya wollei was generally found downstream of the inflow tributaries draining farmlands. As enriched waters flowed slowly through submerged vegetation, dissolved inorganic nitrogen (DIN) concentration dropped but dissolved organic carbon (DOC) and total dissolved phosphorus (TDP) remained high, leading to a low DIN:TDP ratio. Models identified DOC (positive effect), TP (negative effect), and DIN:TDP (negative effect) as the most important variables explaining L. wollei distribution. The risk of L. wollei occurrence in the SLR was correctly forecasted in 72%-92% of all cases with an independent data set. We then examined if hydrodynamic conditions, namely currents generated by waves and river flow, control spatial and temporal variations of L. wollei biomass in a large river system. We measured L. wollei biomass together with meteorological, physical, and chemical variables over three years at 10 sites along a gradient of exposure to current and wind in a large (148 km2) fluvial lake of SLR. Wave exposure and current velocity controlled spatial and temporal biomass variations. Biomass increased from May to November and persisted during winter. Interannual variations were primarily controlled by river flow (water level) with spring discharge dislodging mats from the previous year. As anticipated under climate change scenarios, drops in water level and rising storm intensity may lead to an increase in the areas colonized by L. wollei, together with more frequent episodes of mat disruption and beach fouling. Additionally, we evaluated the relative importance of L. wollei with respect to macrophytes and epiphytes. We assessed the influence of the spatial scale in structuring environmental variables and biomass of these benthic primary producers (PP). We also test to which extent their biomass reflected the nature of patches based on ecogeomorphology or the river continuum. To address these two questions, we used a nested design at 3 spatial scales within the SLR: 1) along a 250-km-long upstream-downstream river stretch, 2) among three fluvial lakes located within that river stretch and 3) within each fluvial lake. Environmental factors (conductivity and TP) and spatial structure together explained 59% of the variability in biomass of all three benthic PP. Spatial variability of biomass was best explained by conductivity (+) for macrophytes, DIN:TDP ratio (+) and water extinction coefficient (+) for epiphytes and DOC (+) and NH4+ (-) for L. wollei mats. Within-lake structure was the most important spatial component for all benthic PP, suggesting that local effects, such as enrichment by the inflow of tributaries, rather than upstream-downstream gradients, determined the biomass and composition of benthic PP. Therefore patch dynamics represents a general framework which adequately covers the spatial variability and wide variety of environmental conditions experienced by aquatic organisms found in large rivers. Finally, we investigated the ecological role of L. wollei mats in aquatic ecosystems, especially as a food source and shelter for the amphipod Gammarus fasciatus. We offered amphipods a choice between mats of L. wollei and either chlorophytes or an artificial mat made of acrylic wool in laboratory experiment. Moreover, we reconstructed in situ amphipod diet using mixing model (δ13C and δ15N). Gammarus fasciatus selected the substratum offering the best light refuge (Acrylic > Lyngbya = Rhizoclonium > Spirogyra). Presence of saxitoxins, tissue elemental composition and epiphyte abundance had no significant effect on substratum choice. Lyngbya wollei and its epiphytes constituted 36 and 24% of the in situ diet of G. fasciatus whereas chlorophytes, macrophytes and associated epiphytes represented a less important fraction of its diet. Benthic cyanobacterial mats should be considered a good shelter and food source for small omnivorous invertebrates such as amphipods.