[Truncated abstract] The role of marine microzooplankton in aquatic food webs has been studied in most regions of the world’s oceans, with the exception of the subtropical/temperate eastern Indian Ocean. This thesis addresses this gap in knowledge by investigating microzooplankton from five stations on a cross continental shelf transect and in two mesoscale features ∼300 km offshore of south west Western Australia. My primary focus was to measure and evaluate microzooplankton community change over space and time and their impact on phytoplankton on a cross shelf transect, sampling five stations from February 2002 December 2004 as part of a large multidisciplinary investigation into the pelagic ecosystem on the shelf (Chapter 2). This transect was named the Two Rocks transect. I also investigated an eddy pair (Chapter 5), which had originated from water in the vicinity of the Two Rocks transect, also undertaken as part of a larger study, investigating biophysical coupling within mesoscale eddies off south west Western Australia . . . The distribution of mixotrophic cells differed across the transect. Those mixotrophs that use photosynthesis as their primarily energy source exploited nutrient limited conditions inshore consuming particles, while mixotrophs that are primarily heterotrophic survived low prey conditions offshore by photosynthesizing. In the eddies, the grazing behaviour of microzooplankton was dependent on the specific phytoplankton assemblage in each eddy. The warm core eddy had a resident population of diatoms that were consumed by heterotrophic dinoflagellates present in high numbers. The cold core eddy had a warm cap which prevented upwelled water reaching the surface, resulting in stratification and a very active microbial food web, particularly in the surface.

Οι κρατήρες διαφυγής ρευστών (pockmarks) είναι βυθίσματα σε μαλακά ιζήματα του βυθού, στα παράκτια και πελαγικά οικοσυστήματα. Μελετώνται παγκοσμίως τις τελευταίες τέσσερις δεκαετίες και στον ελληνικό χώρο έχουν εντοπιστεί κυρίως στη Δυτική Ελλάδα. Εξ αυτών, οι περισσότεροι είναι κρατήρες μεθανίου και μόνο στον Ελαιώνα Αιγίου και στον όρμο του Πρίνου έχουν βρεθεί κρατήρες γλυκού νερού. Έως τώρα, η μελέτη της βιολογίας των κρατήρων έχει εστιάσει κυρίως την περίπτωση των κρατήρων μεθανίου. Για τους κρατήρες γλυκού νερού δεν υπάρχουν εργασίες σχετικά με τη βιολογία τους, εκτός από μια η οποία αφορά τη μικροβιακή δράση στο ίζημα. Στον Ελαιώνα οπτική παρατήρηση έδειξε την ύπαρξη πληθώρας βενθικών οργανισμών, οι οποίοι απουσιάζουν από τον ευρύτερο πυθμένα. Το φαινόμενο αυτό έχει παρατηρηθεί σε πολλούς κρατήρες παγκοσμίως και θεωρείται ότι σχετίζεται κυρίως με τη φύση του υποστρώματος στο εσωτερικό της δομής των κρατήρων. Γενικά, υπάρχει πολύ περιορισμένη πληροφορία για το αβιοτικό και βιοτικό περιβάλλον των κρατήρων, ιδιαίτερα στη στήλη του νερού, ενώ δεν είναι σαφές το αν οι δομές αυτές μπορούν να αποτελέσουν διαταραγμένα περιβάλλοντα ή οάσεις οργανισμών. Η παρούσα εργασία διερευνά το πλαγκτικό στοιχείο στους κρατήρες γλυκού νερού του Ελαιώνα και αποτελεί την πρώτη σχετική αναφορά σε διεθνές επίπεδο, τουλάχιστον σε ότι σχετίζεται με το ζωοπλαγκτόν. Για τη μελέτη συλλέχθηκε μικρο- και μεσοζωοπλαγκτόν, έτσι ώστε να διερευνηθεί όλο το εύρος μεγέθους των οργανισμών από 50 μm έως 20 mm. Οι κρατήρες που μελετήθηκαν παρουσίασαν μικρή εκροή γλυκού νερού. Μετρήσεις θρεπτικών ιόντων και χλωροφύλλης -α έδειξαν ότι οι κρατήρες δεν επηρέασαν φυσικοχημικά το θαλάσσιο περιβάλλον. Ωστόσο, παρατηρήθηκε αύξηση της Chl-a κοντά στο στόμιο του κρατήρα και της φαιοφυτίνης (προϊόν αποδόμησης της Chl-a) και των θρεπτικών στο εσωτερικό του κρατήρα. Ως προς το ζωοπλαγκτόν, οι κρατήρες βρέθηκαν να συγκεντρώνουν μεγαλύτερες αφθονίες πελαγικών προνυμφών βενθικών οργανισμών που εγκαθίστανται στο εσωτερικό τους, όπως έχει επιβεβαιωθεί με οπτική παρατήρηση, καθώς και ειδών Αρπακτικοειδών και Ποικιλοστοματοειδών Κωπηπόδων (ενηλίκων, κωπηποδιτών, ναυπλίων). Τα εν λόγω κωπήποδα πιθανόν να σχετίζονται με την παρουσία αυξημένου αιωρούμενου οργανικού υλικού στους κρατήρες και ζελατινοειδών διηθηματοφάγων οργανισμών (κωπηλατών, βυτιοειδών) σε αυτούς. Επιπλέον, η αυξημένη συγκέντρωση ναυπλίων και κωπηποδιτικών σταδίων υποθέτουμε ότι μπορεί να σχετίζεται με την αυξημένη παρουσία αυγών κωπηπόδων, εφόσον η δομή του κρατήρα μπορεί να τα συγκεντρώνει. Επειδή η παρούσα μελέτη πραγματοποιήθηκε σε μια περίοδο ανάμιξης του νερού και μια περίοδο ασθενούς θερμοστρωμάτωσης, θεωρούμε ότι οι παρατηρήσεις μας για το ζωοπλαγκτόν δεν εμφανίζουν έντονο ‘’σήμα’’ και προτείνεται επανάληψη της έρευνας σε περίοδο έντονης θερμοστρωμάτωσης. / Pockmarks are seabed depressions on soft sediments, found in coastal and pelagic ecosystems. They have been studied for the last four decades and in Greece they can be found mainly in the western parts of the country. Most of the pockmarks are methane formatted, while groundwater formatted pockmarks have been found in Greece only in Elaionas bay and Prinos bay. So far, only methane pockmarks have been studied, concerning their biological components, and there are no references for the groundwater formatted ones, except one that focused on the microbial activity in the sediments. In Elaionas bay optical observations revealed the presence of an extensive benthic community that lacks from the surrounding seabed. This has been observed in a number of pockmarks worldwide and is believed to be co occurring with the presence of hard substrates in the pockmarks. Generally, there is little information of the biotic and abiotic environment of the pockmarks, especially in the water column, while it is not yet clear if these depressions should be considered as disturbed environments or local oasis for the organisms in the area. This study is focusing on the planktonic component of the pockmark field at Elaionas bay and to our knowledge it is the first attempt internationally, at least when it comes to zooplankton. Mesozooplankton and microzooplankton samples were collected in order to investigate the whole basic size range of the zooplankton community (50 μm to 20 mm). The studied pockmarks exhibited slight groundwater flow. Nutrient and chlorophyll a concentrations showed no physicochemical ‘’signal’’ in the pockmarks. However, there was a trend of increase of Chl –a near the opening of the pockmark and of phaeophytin and nutrients inside the pockmark. As for zooplankton, there is evidence that greater abundances of pelagic larvae of benthic organisms are concentrated in the pockmarks (the presence of the adults has been confirmed by divers and ROV), as well as some species of the Order Harpacticoida and Poecilostomatoida (adults, copepodites, nauplii). These copepods may be related to the increase of dissolved organic matter in the pockmark and the presence of tunicates (appendicularians, doliolids) also found concentrated in the pockmarks. Increased abundance of nauplii and copepodite stages in the pockmark is believed to result from the increase of copepod eggs, assuming that the pockmark can gather and retain them. Repetition of the sampling procedure at the pockmark field on a different season is necessary, because the lack of a strong thermocline suggests that any strong differences between the pockmark and the surrounding environment are being less detectible.

O objetivo desta tese foi o estudo da variabilidade temporal, crescimento e produção do zooplâncton metazoário, com ênfase sobre estágios imaturos de copépodes, na região costeira de Ubatuba (SP, Brasil). Para tal, a comunidade zooplanctônica foi estudada durante as estações de verão e inverno em regime de dias alternados, para os anos de 2009 a 2011, através de coletas realizadas com redes de malha de 20 e 100 m. Índices ecológicos como densidade, diversidade e equitabilidade foram calculados. Os estágios imaturos de copépodes foram submetidos a experimentos de coortes artificiais em quatro classes de tamanho (50-80, 80-100, 100-150 e 150-200 m) para a determinação das taxas de crescimento de 14 táxons em diferentes estágios de desenvolvimento. A biomassa foi estimada através de equações de regressão comprimento-peso para o posterior cálculo da produção secundária. A incidência e possíveis efeitos de um protista alveolado parasita (Ellobiopsis sp.) sobre o crescimento de copépodes hospedeiros, com ênfase sobre a família Paracalanidae, também foi avaliada. A comunidade de copépodes esteve representada por 66 espécies e caracterizada por valores relativamente altos de diversidade e equitabilidade em relação aos demais trabalhos na plataforma interna da região sudeste do país. Os copépodes foram o grupo dominante, sendo que estágios naupliares foram os mais comuns para a rede de 20 m, enquanto que copepoditos juvenis dominaram para a rede de 100 m. A densidade do zooplâncton foi altamente variável, sendo os maiores valores registrados para o inverno de 2011 para a malha de 20 m (33.160 ± 23.136 org. m-3) e os menores para o inverno de 2009 para a malha de 100 m (5.393 ± 2.264 org. m-3). As famílias dominantes de copépodes foram Oithonidae, Oncaeidae, Paracalanidae e Acartiidae, sendo a primeira dominante também em termos de biomassa. Os estágios juvenis dos copépodes representaram uma biomassa entre 1,06 a 3,47 mg C m-3 para o inverno de 2010 e verão de 2009 respectivamente. Taxas de crescimento foram obtidas para sete táxons de Calanoida (0,41 ± 0,21 d-1), cinco de Cyclopoida (0,27 ± 0,17 d-1) e dois de Harpacticoida (0,31 ± 0,16 d-1). Os valores de crescimento foram semelhantes entre as diferentes classes de tamanho e as estações do ano, mas foram substancialmente diferentes entre as ordens, sendo geralmente maiores para os Calanoida. A produção média estimada para os estágios imaturos dos táxons dominantes de copépodes foi igual a 0,45 mg C m-3, valor conservativo por não contemplar as espécies de menor densidade e frequência. O crescimento de copépodes da família Paracalanidae, principalmente Parvocalanus crassirostris, foi afetado pelo protista parasita Ellobiopsis sp., uma vez que as fêmeas adultas infectadas foram significativamente menores do que as normais. Cerca de 5% das fêmeas da espécie estiveram infectadas pelo parasita, que provavelmente afeta o crescimento somático e reprodutivo de P. crassirostris, com efeitos ainda desconhecidos em termos de biomassa e produção. As taxas calculadas de crescimento e a produção são semelhantes às de outros trabalhos em regiões tropicais. A abordagem experimental através de coortes artificiais forneceu os primeiros resultados sobre o crescimento de estágios juvenis de copépodes para uma região subtropical do Atlântico Sul Ocidental e demonstrou que a concentração da clorofila-a não foi um fator limitante. Este é um dos poucos trabalhos a disponibilizar dados de crescimento, biomassa e produção de tais estágios em ecossistemas marinhos tropicais e que padroniza o método de coortes artificiais para obtenção do crescimento / This thesis aimed to evaluate the temporal variability of the metazoan zooplankton density, growth, and production, with emphasis on copepod immature stages in the coastal area of Ubatuba (São Paulo, Brazil). The zooplankton community was studied during summer and winter from 2009 to 2011, by means of sampling with 20 and 100 m mesh-sized nets. Ecological indexes such as density, diversity and evenness were calculated. Growth rates for 14 taxa of copepod juvenile stages were determined by the artificial cohort method, in four size classes and different developmental stages (50-80, 80-100, 100-150 and 150-200 m). Biomass was estimated by the use of length-weight regressions followed by secondary production estimates. The incidence and possible effects of the alveolate parasite Ellobiopsis sp. on the growth of the copepod hosts was also investigated, with emphasis on the Paracalanidae family. The copepod assemblage was represented by 66 species and displayed relatively high diversity and evenness, in comparison to other studies in the inner shelf of the Brazilian southeastern coast. Copepod was the dominant group; nauplii in the 20 m net, and juvenile copepodids in the 100 m net. The zooplankton density was highly variable: the highest densities occurred during winter 2011 in the 20 m samples (33,160 ± 23,136 org. m-3) and the lowest for the winter 2009 in the 100 m samples (5,393 ± 2,264 org. m-3). The dominant copepod families were Oithonidae, Oncaeidae, Paracalanidae and Acartiidae, the former being the main taxa in terms of biomass as well. Juvenile copepod biomass varied between 1.06 and 3.47 mg C m-3 in the winter 2010 and summer 2009, respectively. Growth rates were recorded for seven Calanoida (0.41 ± 0.21 d-1), five Cyclopoida (0.27 ± 0.17 d-1) and two Harpacticoida (0.31 ± 0.16 d-1) taxa. Growth values were similar between the different size classes, seasons and years, but were substantially different between copepod orders (higher rates for the Calanoida). The mean production for all immature copepod stages was 0.45 mg C m-3, a conservative value, since rare species were not accounted for. The growth of the Paracalanidae copepod Parvocalanus crassirostris, was affected by the parasite protist Ellobiopsis sp., since infected adult females were significantly smaller than normal individuals. About 5% of adult females were infected by the parasite, which probably reduced somatic and reproductive growth of P. crassirostris, with potential consequences for biomass accumulation and, consequently, production. Growth and production rates were similar to those found in other studies carried out in tropical regions. The artificial cohort method has been applied here for the first time on the tropical and subtropical Southwest Atlantic, where clorophyl-a concentration was not considered a limiting factor for growth rates. This is one of the few studies providing data on growth, biomass and production for copepod juvenile stages in tropical marine ecosystems and standardizing the artificial cohort method to measure the growth rates