Rozprawy doktorskie na temat „Marine Benthos”

The last two decades have seen a shift of emphasis in ecology; from a focus on the drivers of biodiversity change toward a consideration for its effects on ecosystem functioning. Ecosystem functioning is affected by individual species (i.e. species with functionally dominant biological traits), but can also be influenced by other factors, such as interspecific interactions. Current evidence suggests that biotic influence over marine ecosystem functioning is largely underpinned by the effects of individual species. However, there are indications that this might not constitute a complete understanding of the link between marine biodiversity and ecosystem function (BEF). For this thesis, I applied our current understanding of marine BEF relationships (i.e. the causal link between particular biological traits and particular ecological functions) to long-term benthic community time series and investigated the causes of ecological change and its consequences for ecosystem functioning. A shift in the taxonomic composition of the species assemblage was explained by underlying variation in extrinsic drivers. However, the long-term conservation of trait composition suggests that functioning can be sustained in the face of environmental and ecological change. Experiments conducted to test BEF relationships in intertidal marine benthos reaffirmed the functional importance of the biological traits of species, but also showed that interactions among species can influence the delivery of ecological functions in various ways, including facilitation (i.e. function delivery is enhanced) and antagonism (i.e. function delivery is reduced). The results suggest that biotic influence over marine ecosystem functioning is more complex than previously suggested, and that the impacts of biodiversity change (e.g. species extinctions or shifts in species densities) could be either exacerbated or mitigated depending on the composition of the affected assemblage and the ecological function considered. To produce more realistic results, future indirect assessments of ecosystem functioning would benefit from incorporating interactions among species as well as their biological traits.

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Briozoários são organismos sésseis e coloniais, que dependem de uma superfície firme para assentamento larval e crescimento da colônia. Entre os diferentes substratos disponíveis para briozoários, as esponjas podem oferecer uma superfície favorável, trazendo muitas vantagens como a presença de compostos químicos que inibem a predação. Este estudo verificou a presença de briozoários em seis espécies de esponjas, com finalidade de avaliar a abundância e riqueza desses briozoários em diferentes esponjas. Três espécimes das esponjas, Amphimedon compressa Duchassaing & Michelotti, 1864, Amphimedon viridis Duchassaing & Michelotti, 1864, Desmapsamma anchorata (Carter, 1882), Dysidea etheria de Laubenfels, 1936, Haliclona implexiformis (Hechtel, 1965) e Tedania ignis (Duchassaing & Michelotti, 1864) foram coletadas mensalmente entre setembro de 2014 e fevereiro de 2016, em Pontas de Pedra, Pernambuco, Brasil. Os briozoários encontrados foram identificados até o menor nível taxonômico possível e quantificados. Um total de 324 espécimes de esponjas foi analisado, no qual destas 88 apresentavam briozoários em sua superfície (27%). Onze espécies de briozoários pertencentes à Classe Gymnolaemata foram encontrados nas esponjas, sendo quatro pertencentes à Ordem Ctenostomata, Amathia distans Busk, 1886, Amathia verticillata (delle Chiaje, 1822), Amathia vidovici Heller,1867 e Nolella stipata Gosse, 1855, sete da Ordem Cheilostomata, Beania klugei Cook, 1968, Catenicella uberrima (Harmer, 1957), Caulibugula dendograpta (Waters, 1913), Licornia sp., Savignyella lafontii (Audoin, 1826), Synnotum aegyptiacum Canu & Bassler, 1928 e Thalamoporella floridana Osburn, 1940. Briozoários foram abundantes nas esponjas Te. ignis e De. anchorata e pouco frequentes em Ap. compressa e Ap. viridis. Desmapsamma anchorata e Te. ignis apresentaram a maior riqueza de espécies (nove espécies em cada esponja), seguida por Dy. etheria (sete espécies). Uma baixa riqueza de espécies foi observada em Ap. compressa, com apenas três espécies de briozoários, Ap. viridis com quatro espécies, e H. implexiformis com cinco espécies. Apenas o briozoário N. stipata foi encontrado em todas as espécies de esponjas, enquanto que At. distans e At. vidovici não foram encontradas apenas em Ap. compressa. Uma maior riqueza e abundancia de briozoários foram encontradas em De. anchorata e Te. ignis, que apresentam superfície lisa e aveludada, e lisa e vilosa, respectivamente. Por outro lado, superfície lisa também é característica das espécies Ap. compressa e Ap. viridis, que apresentaram a menor frequência e diversidade de briozoários. Adicionalmente, as esponjas De. anchorata e Dy. etheria que apresentam superfície lisa e conulosa, respectivamente, compartilharam grande parte das espécies encontradas. A presença de metabólitos secundários nas esponjas do gênero Amphimedon que apresentam toxicidade já descrita na literatura, pode ter influenciado na ocorrência dos briozoários. Enquanto que as esponjas Te. Ignis, De. anchorata e Dy. Etheria, que apresentaram uma grande abundância de briozoários, podem ter provido um microhabitat adequado para os briozoários da região. O padrão temporal de ocorrência dos briozoários nas esponjas durante os 18 meses de coleta foi aleatório. O presente trabalho permite identificar alguns padrões da ocorrência dos briozoários, relacionado a composição química das esponjas e sua posição no substrato.
Bryozoans comprise sessile, colonial organisms that require a hard surface for settlement and growth. Among different substrata for bryozoans, sponges may provide suitable substrata, with advantages such as presence of compounds against predators. This study analyses the bryozoan community on six sponges species throughout 18 months, to evaluate the presence of bryozoans on its surface. Three specimens of each sponges, Amphimedon compressa Duchassaing & Michelotti, 1864, Amphimedon viridis Duchassaing & Michelotti, 1864, Desmapsamma anchorata (Carter, 1882), Dysidea etheria de Laubenfels, 1936, Haliclona implexiformis (Hechtel, 1965) and Tedania ignis (Duchassaing & Michelotti, 1864), were taken monthly betweem September 2014 to February 2016, in Pontas de Pedra, Pernambuco State, Brazil. Bryozoans were identified to the lowest taxonomic level, and quantified. Total of 324 specimens of sponges were analysed, 88 from those were found bryozoans on its surface (27%). Eleven gymnolaemate bryozoans were found on sponges being four of the Order Ctenostomata, Amathia distans Busk, 1886, Amathia verticillata (delle Chiaje, 1822), Amathia vidovici Heller,1867 and Nolella stipata Gosse, 1855, and seven species Cheilostomata, Beania klugei Cook, 1968, Catenicella uberrima (Harmer, 1957), Caulibugula dendograpta (Waters, 1913), Licornia sp., Savignyella lafontii (Audoin, 1826), Synnotum aegyptiacum Canu & Bassler, 1928 and Thalamoporella floridana Osburn, 1940. Bryozoans were considered abundant on the sponges Te. ignis and De. anchorata, but few frequents on Ap. compressa and Ap. viridis. On De. anchorata and Te. ignis were found the highest bryozoan richness (9 species of bryozoan per sponge species), followed by Dy. etheria (7 bryozoan species). A low species richness was observed in Ap. compressa, Ap. viridis and H. implexiformis with respectively three, four and five species of bryozoans on their surface. Only N. stipata was found on the six sponge species, while At. distans and At. vidovici were not found only on Ap. compressa. Higher richness and abundance of bryozoans were found in De. anchorata and Te. ignis, with smooth and velvety surface, smooth and villous surface, respectively. Smooth surface is also characteristic of Ap. compressa and Ap. viridis, with the lowest frequency and diversity of bryozoans. Additionally, on sponges De. anchorata and Dy. etheria, with smooth and conulose surface respectively, were shared the majority of bryozoan species. We suggest the presence of secondary metabolites may have interfered the bryozoans on sponges of Amphimedon genus. Sponges Te. ignis, De. anchorata and Dy. etheria, have an abundance of bryozoans; thus, we suggest these sponges may allow a suitable substratum for the bryozoans. The temporal variation of bryozoans on sponges was random. In present work some patterns of occurrence of bryozoans are presented, with relation to the chemical composition and position of sponge.

This study examined the relationship between sediment structure and infaunal polychaete communities off the southern coast of Namibia from two separate sets of data, and a total of ninety-two samples. It also examined whether a selected group of organisms (polychaetes) could provide the same level of information regarding community structure, as the entire fauna, at a number of taxonomic resolutions.

Microplastics have become ubiquitous pollutants in the marine environment. Ingestion of microplastics by a wide range of marine organisms has been recorded both in laboratory and field studies. Despite growing concern for microplastics, few studies have evaluated their concentrations and distribution in wild populations. Further, there is a need to identify cost-effective standardized methodologies for microplastics extraction and analysis in organisms. In this thesis I present: (i) the results of a multi-scale field sampling to quantify and characterize microplastics occurrence and distribution in 4 benthic marine invertebrates from saltmarshes along the North Adriatic Italian coastal lagoons; (ii) a comparison of the effects and cost-effectiveness of two extraction protocols for microplastics isolation on microfibers and on wild collected organisms; (iii) the development of a novel field- based technique to quantify and characterize the microplastic uptake rates of wild and farmed populations of mussels (Mytilus galloprovincialis) through the analysis of their biodeposits. I found very low and patchy amounts of microplastics in the gastrointestinal tracts of sampled organisms. The omnivorous crab Carcinus aestuarii was the species with the highest amounts of microplastics, but there was a notable variation among individuals. There were no substantial differences between enzymatic and alkaline extraction methods. However, the alkaline extraction was quicker and cheaper. Biodeposit traps proved to be an effective method to estimate mussel ingestion rates. However their performance differed significantly among sites, suggesting that the method, as currently designed, is sensible to local environmental conditions. There were no differences in the ingestion rates of microplastics between farmed and wild mussels. The estimates of microplastic ingestion and the validated procedures for their extraction provide a strong basis for future work on microplastic pollution.

Thesis (M.Phil.)--City University of Hong Kong, 2009.
"Submitted to Department of Biology and Chemistry in partial fulfillment of the requirements for the degree of Master of Philosophy." Includes bibliographical references (leaves 144-191)

Virtually all marine conservation planning and management models in place or proposed have in common the need for improved scientific rigour in identifying and characterising the marine habitats encompassed. An emerging central theme in the last few years has been the concept of representativeness, or representative systems of Marine Protected Areas (MPAs). The habitat classification and mapping needed to incorporate considerations of representativeness into MPA planning must logically be carried out at the same scale at which management occurs. Management of highly protected areas occurs almost exclusively at local scales or finer, independent of the reservation model or philosophy employed. Moreton Bay, on Australia’s east coast, was selected for studies at the local scale to map and classify macrobenthic habitats. In a site scale (1 km) trial for the major habitat classification study, remote underwater videography was used to map and characterise an unusual assemblage of epibenthic invertebrates on soft sediments. The assemblage included congregations of the comatulid crinoid Zygometra cf. Z. microdiscus (Bell) at densities up to 0.88 individuals.m-2, comparable to those found in coral reef habitats. There was no correlation between the distribution of this species and commonly used abiotic surrogates depth (6 – 18 m), sediment composition and residual current. This site scale trial is the first quantitative assessment of crinoid density and distribution in shallow water soft-sediment environments. The high densities found are significant in terms of the generally accepted picture of shallow-water crinoids as essentially reefal fauna. The findings highlight the conservation benefits of an inclusive approach to marine habitat survey and mapping. Assemblages such as the one described, although they may be of scientific and ecological significance, would have been overlooked by common approaches to marine conservation planning which emphasise highly productive or aesthetically appealing habitats. Most habitat mapping studies rely solely or in part on abiotic surrogates for patterns of biodiversity. The utility of abiotic variables in predicting biological distributions at the local scale (10 km) was tested. Habitat classifications of the same set of 41 sites based on 6 abiotic variables and abundances of 89 taxa and bioturbation indicators were compared using correlation, regression and ordination analyses. The concepts of false homogeneity and false heterogeneity were defined to describe types of errors associated with using abiotic surrogates to construct habitat maps. The best prediction by abiotic surrogates explained less than 30% of the pattern of biological similarity. Errors of false homogeneity were between 20 and 62%, depending on the methods of estimation. Predictive capability of abiotic surrogates at the taxon level was poor, with only 6% of taxon / surrogate correlations significant. These results have implications for the widespread use of abiotic surrogates in marine habitat mapping to plan for, or assess, representation in Marine Protected Areas. Abiotic factors did not discriminate sufficiently between different soft bottom communities to be a reliable basis for mapping. Habitat mapping for the design of Marine Protected Areas is critically affected by the scale of the source information. The relationship between biological similarity of macrobenthos and the distance between sites was investigated at both site and local scales, and for separate biotic groups. There was a significant negative correlation between similarity and distance, in that sites further apart were less similar than sites close together. The relationship, although significant, was quite weak at the site scale. Rank correlograms showed that similarity was high at scales of 10 km or less, and declined markedly with increasing distance. There was evidence of patchiness in the distributions of some biotic groups, especially seagrass and anthozoans, at scales less than 16 km. In other biotic groups there was an essentially monotonic decline in similarity with distance. The spatial agglomeration approach to habitat mapping was valid in the study area. Site spacing of less than 10 km was necessary to capture important components of biological similarity. Site spacing of less than 2.5 km did not appear to be warranted. Macrobenthic habitat types were classified and mapped at 78 sites spaced 5 km apart. The area mapped was about 2,400 km2 and extended from estuarine shallow subtidal waters to offshore areas to the 50 m isobath. Nine habitat types were recognised, with only one on hard substrate. The habitat mapping characterised several habitat types not previously described in the area and located deepwater algal and soft coral reefs not previously reported. Seagrass beds were encountered in several locations where their occurrence was either unknown or had not previously been quantified. The representation of the derived habitat types within an existing marine protected area was assessed. Only two habitat types were represented in highly protected zones, with less than 3% of each included The study represents the most spatially comprehensive survey of epibenthos undertaken in Moreton Bay, with over 40,000 m2 surveyed. Derived habitat maps provide a robust basis for inclusion of representative examples of all habitat types in marine protected area planning in and adjacent to Moreton Bay. The utility of video data to conduct a low-cost habitat survey over a comparatively large area was also demonstrated. The method used has potentially wide application for the survey and design of marine protected areas.

Virtually all marine conservation planning and management models in place or proposed have in common the need for improved scientific rigour in identifying and characterising the marine habitats encompassed. An emerging central theme in the last few years has been the concept of representativeness, or representative systems of Marine Protected Areas (MPAs). The habitat classification and mapping needed to incorporate considerations of representativeness into MPA planning must logically be carried out at the same scale at which management occurs. Management of highly protected areas occurs almost exclusively at local scales or finer, independent of the reservation model or philosophy employed. Moreton Bay, on Australia’s east coast, was selected for studies at the local scale to map and classify macrobenthic habitats. In a site scale (1 km) trial for the major habitat classification study, remote underwater videography was used to map and characterise an unusual assemblage of epibenthic invertebrates on soft sediments. The assemblage included congregations of the comatulid crinoid Zygometra cf. Z. microdiscus (Bell) at densities up to 0.88 individuals.m-2, comparable to those found in coral reef habitats. There was no correlation between the distribution of this species and commonly used abiotic surrogates depth (6 – 18 m), sediment composition and residual current. This site scale trial is the first quantitative assessment of crinoid density and distribution in shallow water soft-sediment environments. The high densities found are significant in terms of the generally accepted picture of shallow-water crinoids as essentially reefal fauna. The findings highlight the conservation benefits of an inclusive approach to marine habitat survey and mapping. Assemblages such as the one described, although they may be of scientific and ecological significance, would have been overlooked by common approaches to marine conservation planning which emphasise highly productive or aesthetically appealing habitats. Most habitat mapping studies rely solely or in part on abiotic surrogates for patterns of biodiversity. The utility of abiotic variables in predicting biological distributions at the local scale (10 km) was tested. Habitat classifications of the same set of 41 sites based on 6 abiotic variables and abundances of 89 taxa and bioturbation indicators were compared using correlation, regression and ordination analyses. The concepts of false homogeneity and false heterogeneity were defined to describe types of errors associated with using abiotic surrogates to construct habitat maps. The best prediction by abiotic surrogates explained less than 30% of the pattern of biological similarity. Errors of false homogeneity were between 20 and 62%, depending on the methods of estimation. Predictive capability of abiotic surrogates at the taxon level was poor, with only 6% of taxon / surrogate correlations significant. These results have implications for the widespread use of abiotic surrogates in marine habitat mapping to plan for, or assess, representation in Marine Protected Areas. Abiotic factors did not discriminate sufficiently between different soft bottom communities to be a reliable basis for mapping. Habitat mapping for the design of Marine Protected Areas is critically affected by the scale of the source information. The relationship between biological similarity of macrobenthos and the distance between sites was investigated at both site and local scales, and for separate biotic groups. There was a significant negative correlation between similarity and distance, in that sites further apart were less similar than sites close together. The relationship, although significant, was quite weak at the site scale. Rank correlograms showed that similarity was high at scales of 10 km or less, and declined markedly with increasing distance. There was evidence of patchiness in the distributions of some biotic groups, especially seagrass and anthozoans, at scales less than 16 km. In other biotic groups there was an essentially monotonic decline in similarity with distance. The spatial agglomeration approach to habitat mapping was valid in the study area. Site spacing of less than 10 km was necessary to capture important components of biological similarity. Site spacing of less than 2.5 km did not appear to be warranted. Macrobenthic habitat types were classified and mapped at 78 sites spaced 5 km apart. The area mapped was about 2,400 km2 and extended from estuarine shallow subtidal waters to offshore areas to the 50 m isobath. Nine habitat types were recognised, with only one on hard substrate. The habitat mapping characterised several habitat types not previously described in the area and located deepwater algal and soft coral reefs not previously reported. Seagrass beds were encountered in several locations where their occurrence was either unknown or had not previously been quantified. The representation of the derived habitat types within an existing marine protected area was assessed. Only two habitat types were represented in highly protected zones, with less than 3% of each included The study represents the most spatially comprehensive survey of epibenthos undertaken in Moreton Bay, with over 40,000 m2 surveyed. Derived habitat maps provide a robust basis for inclusion of representative examples of all habitat types in marine protected area planning in and adjacent to Moreton Bay. The utility of video data to conduct a low-cost habitat survey over a comparatively large area was also demonstrated. The method used has potentially wide application for the survey and design of marine protected areas.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environmental and Applied Science
Full Text

The symbiotic lifestyle represents a fundamental contribution to the diversity of marine ecosystems. Sponges are ideal models to study symbiotic relationships from evolutionary and ecological points of view since they are the most ancient metazoans on Earth, are ubiquitous in the marine benthos, and establish complex symbiosis with both prokaryotes and animals, which in turn harbour their own bacterial communities. In this thesis, we aim to go deeper into the mechanisms by which sponges establish symbiotic associations with members of the three domains of life, combining taxonomical, ecological, and molecular approaches. We study how sponges acquire their symbiotic microbes and whether these microbes contribute to shape the ecological distribution of their hosts. Moreover, we use the sponge-polychaete relationship as an example of multi-partner symbiosis and study the eukaryotic association from the microbial perspective. Finally, we focus on the less studied domain of life, the archaea, to gain insights into the composition and stability of these symbionts in sponges. To assess these goals, we characterized the sponge assemblages in two contrasting environments (well-preserved and impacted) of Nha Trang Bay (Vietnam) and selected the most abundant species for the study of their microbiomes. Additionally, four sponge species harbouring thousands of polychaetes were sampled to analyse the relationships sponge-microbes-polychaetes. Sponges and polychaetes were identified and their respective microbiones and the seawater bacterial communities were analysed by high-throughput sequencing of the 16S rRNA gene (V4 region). We first describe and illustrate the sponges collected to facilitate further taxonomic and faunistic studies in the area. Our samples belonged to 60 species (9 orders, 22 families, and 36 genera) of demosponges. A total of 24 species were added to the already known sponge fauna of Vietnam, from which, 11 species likely represent new species to science. The described species represent an increase of 8 % in the already known sponge list of Vietnam. Our results show that sponge assemblages were more diverse and rich in the well-preserved environments, being dominated by Neofibularia sp. and Aaptos suberitoides in the reefs, and by Monanchora unguiculata, Antho (Antho) sp., and Amphimedon sulcata in rocky habitats. On the other hand, impacted coral reefs were mainly dominated by two abundant species: Clathria reinwardti and Amphimedon paraviridis. Similar ecological metrics were shown by the sponge microbiomes according to the type of habitat, being more diverse in the well-preserved environments. Morever, the sponge microbiomes of the sponge assemblages from the impacted habitats showed higher intra-species dispersion and lower core size (shared ZOTUs across species replicates) than microbiomes of sponges from the well-preserved environments. In this sense, we propose that the Anna Karenina concept, which states that intraspecific variability is higher in dysbiotic than in healthy individuals, can also be applied at the community level for the study sponge assemblages. In our study sponges, bacterial communities were highly stable regardless of the environment, whereas some of their associated polychaetes varied depending on the sampling location. Environmental resilience to different habitat conditions was certainly true for bacterial communities of A. sulcata, the solely species that was found abundant in the two contrasting habitats explored. Moreover, the high overlap in bacteria composition between sponges and seawater suggest microsymbiont acquisition from the environment. In a similar manner, polychaetes were also able to specifically select and enrich some bacteria from their food sponge. Overall, most sequences were shared between biotypes, but at differential abundances, leading to highly specific and stable invertebrate microbiomes, acquired from the environment. Our results support the tenet “Everything is everywhere, but the environment selects”.
La vida en simbiosi representa una contribució fonamental a la diversitat dels ecosistemes marins. Les esponges són models ideals per l’estudi de les relacions simbiòtiques des del punt de vista evolutiu i ecològic, ja que són els metazous més antics de la Terra, són ubiqüistes al bentos marí, i estableixen simbiosis complexes amb procariotes i animals, que al seu torn, contenen les seves pròpies comunitats bacterianes. En aquesta tesis, volem aprofundir en els mecanismes pels quals les esponges estableixen associacions amb membres dels tres dominis de vida, combinant eines taxonòmiques, ecològiques i moleculars. Estudiem com les esponges adquireixen els seus microbis simbionts i com aquests microbis contribueixen a modelar la distribució ecològica de les esponges. A més, utilitzem la relació esponja-poliquet com a exemple de simbiosis multi-organisme i estudiem les associacions eucariotes des de un punt de vista microbià. Finalment, ens centrem en el domini de vida menys estudiat, les arqueas, per aprofundir en la composició i estabilitat d’aquests simbionts en esponges. Per assolir aquests objectius, vam caracteritzar els grups d’esponges de dos ambients diferenciats (impactat i ben preservat) de la badia de Nha Trang (Vietnam), i vam seleccionar les espècies més abundants per l’estudi del seu microbioma. Addicionalment, vam mostrejar quatre espècies d’esponges que contenien milers de poliquets per l’anàlisi de les relacions esponja-microbis-poliquets. Els nostres resultats mostren que les comunitats d’esponges eren més riques i diverses en els ambients ben preservats, i els seus microbiomes mostraven variables ecològiques similars, en els dos tipus d’ambients. La majoria de simbiosis estudiades mostraven una gran especificitat i estabilitat, independentment de l’ambient on vivia l’esponja. El gran solapament entre els bacteris de l’aigua i de l’esponja suggereix que hi ha adquisició microbiana de l’ambient. De forma similar, els poliquets també eren capaços d’adquirir específicament bacteris de les esponges de les quals s’alimentaven. En resum, la majoria de seqüències microbianes eren compartides entre els tres habitats estudiats (aigua/esponge/poliquet), però a diferents abundàncies, donant lloc a microbiomes específics i estables adquirits de l’ambient en els dos grups d’invertebrats estudiats .

Aquest treball no pretén ser un estudi exhaustiu sobre la flora bentònica marina de Namíbia, sinó simplement una base per portar-lo a terme en un futur. El que sí pretén, en canvi, és oferir una recopilació de tota la informació que hi ha fins a aquest moment sobre el tema i contribuir al coneixement de la flora bentònica marina de Namíbia, proporcionant-ne noves dades sobre la composició i biogeografia, a part de descripcions detallades i valoracions crítiques de moltes de les especies que la integren. En una època en què les noves tecnologies fan orientar la botànica cap a l'estudi de les relacions filogenètiques entre les espècies, amb la consegüent reconsideració de la seva classificació taxonòmica, o cap a la realització de revisions sistemàtiques de grups concrets, potser resulta anacrònic presentar un treball de les característiques del que ara ens ocupa. No obstant això, el fet que la major part de les espècies de la flora marina de Namíbia no estiguin degudament documentades, cosa que obliga sovint a recórrer a les descripcions originals o a les obres clàssiques, creiem que ho justifica.

Les impacts des changements climatiques en Arctique sont de plus en plus présents et affectent davantage les écosystèmes marins. De plus, la fonte des glaces ouvre de nouvelles routes maritimes telles que le passage du Nord-Ouest dans la région marine du Kitikmeot. Ces problématiques croissantes soulèvent des préoccupations quant à l’état des organismes benthiques vivant dans cette région où peu d’études ont été menées. Les invertébrés benthiques sont primordiaux dans le recyclage des nutriments, l’oxygénation et la décomposition dans les sédiments et sont de très bons indicateurs de changement. Ce projet a comme objectif d’explorer et d’évaluer quels sont les paramètres environnementaux influents et de modéliser les assemblages d’espèces benthiques dans la région du Kitikmeot et le chenal de Parry dans l’Arctique canadien. Pour ce faire, plusieurs échantillons provenant d’un chalut Agassiz (épibenthos) et d’un carottier à boîte (endobenthos) ont été récoltés à bord du NGCC Amundsen de 2010 à 2018. En outre, 19 variables environnementales ont été considérées lors des analyses statistiques. Nous avons observé que l’endofaune est dominée par les annélides (principalement les polychètes) tandis que l’épifaune par les arthropodes. Les résultats démontrent aussi que les différents types de communautés benthiques se succèdent un après l’autre formant ainsi une zone de transition (écotone) entre la mer de Beaufort et la baie de Baffin. Les eaux qui ont comme origine l’océan Pacifique ont une influence majeure sur la distribution et la composition des communautés. Il en est de même pour les apports d’eaux douces d’origine terrestre. Ce sont deux paramètres qui sont actuellement de plus en plus présents en Arctique, ce qui laisse présager d’importants changements dans la distribution des communautés dans l’Archipel canadien central pour les années à venir. De plus, deux autres facteurs explicatifs de la composition taxonomique sont la profondeur et la concentration de pigments associés à la production primaire locale. Cette étude a aussi démontré que la profondeur, l’oxygène ainsi que le ratio N/P sont les paramètres ayant le plus d’influence sur le nombre de taxons retrouvé. Elle a aussi permis de modéliser la répartition de la diversité benthique pour la première fois dans l’Archipel canadien. De tels modèles peuvent ensuite servir dans une optique de gestion d’aires marines.
The impacts of climate change in the Arctic are increasingly present and affect marine ecosystems. In addition, the associated sea ice melt opens up new shipping routes such as the Northwest Passage in the Kitikmeot marine region. These growing issues raise concerns about the state of benthic organisms living in this region where few studies have been carried out. Benthic invertebrates are essential in nutrient recycling, oxygenation and de composition in sediments and are very good indicators of change. The objective of this project is to exploreand assess the influential environmental parameters and model benthic species assemblage distributions in the Kitikmeot region and Parry Channel in the Canadian Arctic. For this, a number of samples from an Agassiz trawl (epifauna) and a box corer (infauna) were collected on board the CCGS Amundsen between 2010 and 2018. In addition, 19 environmental variables were considered for the statistical analyses. It was observed that infauna is dominated by annelids (mainly polychaetes) and epifauna by arthropods. The results also show that the different types of benthic communities succeed one another, thus forming a transition zone (ecotone) between the Beaufort Sea and Baffin Bay. Waters originating from the Pacific Ocean have a major influence on the distribution and composition of communities, as do freshwater inputs from land. These are two parameters whose volumes are currently increasing in the Arctic, which suggests significant changes in the distributionof communities in the central Canadian Archipel ago for years to come. Moreover, two other significant factors explaining the taxonomic composition are the depth and the pigment concentrations associated with local primary production. This study also demonstrated that depth, oxygen and N/P ratio are the parameters having the most influence on the number of taxa found. Moreover, it is the first time the distribution of benthic diversity is modeled inthe Canadian Archipelago. The models developed here can be used by decision makers forspatial marine management purposes.

All marine ecosystems in the Mediterranean Sea are highly threatened by anthropogenic stressors that can alter their structure and function, especially in rocky shores. Moreover, extreme climate events are becoming more frequent and intense in our times. To detect the potential impacts and the vulnerability of any ecosystem, the combination of experimental and observational studies in the field is vital. In addition, long-term monitoring programs carried out simultaneously on human-protected and human- impacted environments may be crucial to discern the nature of the impacts. Macroalgal beds dominate the shallow benthic Mediterranean habitats where they play a pivotal role. Among them, the canopy-forming Cystoseira sensu lato species represent the highest structural complexity level and provide unique habitats with ecological services comparable to terrestrial forests. Canopy-forming algae are in decline in many coastal areas where, among other impacts, overgrazing by herbivorous can lead to the loss of these diverse habitats shifting towards degraded sea urchin barren grounds. Conservation tools such as marine reserves or No-take zones (NTZs) have the potential to reduce some of the anthropogenic threats and to restore benthic habitats through trophic cascade effects caused by the major abundance of predator. Besides, active ecosystem restoration strategies may speed up the recovery of impacted ecosystems. Nevertheless, there is an important lack of continuous and long-term studies providing robust ecological data of the natural dynamic and vulnerability of macroalgal assemblages while integrating the role of marine conservation. In this dissertation, different methodological approaches were combined to explore the long-term dynamics of macroalgal communities and the role of different conservation strategies (NTZs and active restoration) in the Montgrí, Medes Islands, and Baix Ter (MIMBT) Natural Park (NW Mediterranean Sea). In the first two chapters, the analysis of long-term monitoring datasets provided essential information to understand how macroalgal assemblages and sea urchin populations respond to natural fluctuations and anthropogenic disturbances, mainly overfishing. In the third chapter, field monitoring and sampling were combined with genetic analyses to increase the ecological knowledge of the canopy-forming alga Treptacantha elegans as well as to describe their recent expansion. In the fourth and last chapter, active restoration actions as seeding experiments were conducted in aquaria and in the field to optimize restoration techniques to recover degraded shallow ecosystems. In addition, different restoration strategies were combined in the field inside and outside the Medes Islands NTZ to evaluate the role of marine protection on restoration activities. The results of this thesis showed that the abundance and structure of the main macroalgal assemblages in the MIMBT Natural Park were stable at large over the last fifteen years. Overall, any effect of marine protection was observed on the most representative species of this habitat but we found a higher abundance of canopy- forming algae inside the NTZ than in unprotected areas. Contrarily, sea urchin populations were deeply affected by a severe storm in 2008 which caused the almost depletion of its populations in all the studied areas. Although similar trajectories of sea urchin abundance have been observed over the years between both protection regimes due to the large stability of the sea urchin high-density state, clear differences in the recovery of sea urchin populations were found after the storm linked to marine protection. The sea urchin populations inside the NTZ recovered slowly than the populations outside the NTZ inside due to the higher predatory fish abundance inside the NTZ. In contrast to the global widespread decline of canopy-forming macroalgal assemblages across many regions during the last decades, Treptacantha elegans has increased their distributional range and has shown an extraordinary expansion along the Catalan northern coast over the last two decades. The results of this thesis contributed to explaining this geographical and depth range extension, which could be linked to some ecological attributes such as their relative fast-growing dynamics, early fertile maturity, and high turnover rate. Besides, the molecular analyses have shown that all the populations of T. elegans in the Catalan coast constitute a single genetic group that could be originated in the MIMBT Natural Park under the marine protection benefit. Given the fast and stable population dynamics of T. elegans, this species was selected as a potential species to actively restore degraded shallow rocky ecosystems (e.g., sea urchin barren grounds) turning them into productive marine forests. In this way, the effectiveness of active restoration actions combined with passive strategies such as marine protection (e.g., NTZs) was experimentally demonstrated. This thesis addressed marine vegetation changes in the shallow rocky shores of the MIMBT Natural Park integrating the macroalgal and sea urchin dynamics in front of natural and human-related impacts, and the role and effectiveness of Marine Protected Areas and restoration actions as conservation tools at lower trophic levels. Besides, since most of this thesis is based on long-term monitoring data, a valuable baseline of the algal community’s structure and functioning was provided here which could be vital to predict and detect ecological changes that could jeopardize the preservation of marine forests.
Els ecosistemes bentònics mediterranis es troben fortament amenaçats per pressions, tant a nivell local com global, que poden alterar la seva estructura i funcionament, especialment en els fons rocosos litorals. A més, els episodis climàtics extrems esdevenen cada vegada més freqüents i intensos. Per a detectar els possibles impactes sobre qualsevol ecosistema així com la seva vulnerabilitat, la combinació d’estudis observacionals i experimentals al camp és primordial. En aquest sentit, els estudis a llarg termini realitzats simultàniament en zones impactades i en zones protegides de l’acció humana, poden ser crucials per a identificar la naturalesa dels impactes. Al mar Mediterrani, les comunitats de macroalgues dominen els hàbitats bentònics soms, on tenen un paper primordial. D’entre elles, les algues de tipus arborescent del gènere Cystoseira representen el nivell més elevat de complexitat estructural i proporcionen hàbitats amb serveis comparables als boscos terrestres. Aquestes algues es troben en declivi en diverses zones costaneres. És aquí on, entre altres impactes, la sobrepastura dels herbívors pot portar a la pèrdua d’aquests hàbitats rics i diversos i la seva transició cap a fons degradats dominats pels eriçons. Les eines de conservació, així com ara les reserves marines o les àrees on està prohibida completament l’extracció (NTZs), tenen el potencial de reduir algunes de les amenaces derivades de l’acció humana i de restaurar els hàbitats bentònics gràcies als efectes dels depredadors a través de les cascades tròfiques. A més de la restauració passiva a través de la creació d’aquestes àrees protegides, la restauració activa dels ecosistemes impactats pot accelerar la seva recuperació. No obstant això, hi ha una manca important d’estudis continuats i a llarg termini que proporcionin dades ecològiques robustes sobre la dinàmica natural i la vulnerabilitat dels hàbitats de macroalgues i que alhora integrin el paper de les diferents eines de conservació marina. En aquesta tesi, s’han combinat diferents metodologies per explorar la dinàmica de les comunitats de macroalgues juntament amb el paper de diferents estratègies de conservació (NTZs i restauració activa) al Parc Natural del Montgrí, les Illes Medes i el Baix Ter (MIMBT), situat al Nord-oest del mar Mediterrani. En els primers dos capítols, les anàlisis de dades d’estudis a llarg termini han proporcionat informació essencial per millorar la nostra comprensió sobre com les comunitats de macroalgues i les poblacions d’eriçons responen a les fluctuacions naturals i a les pertorbacions d’origen antròpic, principalment, la sobrepesca. En el tercer capítol, mostrejos en el camp s’han combinat amb anàlisis genètics per augmentar el coneixement ecològic de l’alga arborescent Treptacantha elegans i per descriure la seva recent expansió. Al quart i últim capítol, s’han realitzat accions de restauració activa, com ara experiments de sembra en aquaris i al camp per optimitzar les tècniques de restauració dels ecosistemes poc profunds degradats. A més, s’han combinat diferents estratègies de restauració a camp, dins i fora de la NTZ de les Illes Medes, per avaluar el paper de la protecció en les activitats de restauració. Els resultats d’aquesta tesi mostren que la abundància i la composició de les principals comunitats algals del Parc Natural del MIMBT s’han mantingut estables al llarg dels darrers quinze anys. En general, no es va observar cap efecte de la protecció en les espècies d’algues més representatives, tot i que si que es van trobar abundàncies més elevades de l’alga T. elegans a dins de la NTZ que a les zones no protegides de l’acció humana. Al contrari, les poblacions d’eriçons es van veure profundament afectades per una forta tempesta l’any 2008, el que va provocar el declivi gairebé total d’aquestes poblacions a les zones estudiades. Tot i que s’havien observat trajectòries similars en l’abundància d’eriçons al llarg del temps, tant a dins com a fora de la NTZ, degut a la gran estabilitat de les poblacions d’eriçons quan les poblacions presenten elevades densitats, en aquesta tesi es van trobar clares diferències en la recuperació d’aquestes poblacions després de la tempesta que estarien vinculades a l’efecte de la protecció marina. Les poblacions d’eriçons a dins de la NTZ es van recuperar més lentament que les de les zones no protegides degut a la major abundància de peixos depredadors a dins de la NTZ. Davant de la davallada generalitzada de les macroalgues arborescents que s’ha pogut observar a moltes regions al llarg de les darreres dècades, l’alga Treptacantha elegans ha demostrat una extraordinària expansió a la costa nord catalana al llarg de les dues darreres dècades, augmentat considerablement la seva distribució. Els resultats d'aquesta tesi contribueixen a explicar aquesta expansió, tant en fondària com a nivell geogràfic, que podria estar relacionada amb alguns trets ecològics, com ara la seva dinàmica de creixement relativament ràpid, la maduresa reproductiva precoç i la seva elevada taxa de renovació poblacional. A més, les anàlisis moleculars mostren que totes les poblacions de T. elegans a la costa catalana constitueixen un únic grup genètic que podria tenir el seu origen al Parc Natural del MIMBT com a conseqüència de la protecció marina. Atesa la dinàmica ràpida i estable de les poblacions de T. elegans, es va seleccionar aquesta com a potencial espècie per restaurar activament els ecosistemes rocosos poc profunds degradats (els blancalls originats per la sobrepastura d’eriçons) convertint-los en productius boscos marins. Gràcies a això, també s’ha demostrat experimentalment l’èxit de combinar accions de restauració activa amb estratègies passives com la protecció marina (p.e. NTZs). Aquesta tesi aborda els canvis de vegetació marina als fons soms i rocosos del Parc Natural del MIMBT integrant la dinàmica de les macroalgues i els eriçons enfront dels impactes naturals i humans, i, el paper i l’eficàcia de les zones marines protegides i de les accions de restauració com a eines de conservació per als nivells tròfics més basals. A més, atès que la major part d’aquesta tesi es basa en dades d’estudis a llarg termini, aquesta tesi proporciona una valuosa referència de la dinàmica i de l’estat actual de les comunitats infralitorals dominades per algues, el que podria ser vital per predir i detectar canvis ecològics que puguin posar en perill la preservació dels boscos marins.

Benthic animals have been widely used as health indicators of the marine benthic ecosystems in temperate regions. My PhD thesis mainly aimed to understand the responses of benthic ecosystem in tropical Hong Kong waters to the two management measures - pollution control and trawling ban. My study was based on sediment grab samples collected from 28 stations in three territory-wide surveys conducted in 2001, 2012 and 2015 in Hong Kong waters. I compared the spatial and temporal changes in macrobenthic community structure as well as physical and chemical characteristics of benthic habitats between surveys conducted before and after the pollution control measures in 2001 and 2012, as well as surveys before and after the fishery management measure in 2012 and 2015. The impacts of sewage pollution to benthic ecosystems had been noted in many studies, which included deteriorated water quality and bottom sediment, and disturbed, less diverse macrobenthic community dominated by opportunistic small-sized species. Therefore, sewage treatment and cessation of sewage effluent discharge were expected to lead to notable improvement in benthic habitats, biodiversity and macrobenthic communities; besides, responses of benthic ecosystems to pollution control may be hydrologically varied. In Hong Kong, a series of sewage treatment schemes, e.g. Stage 1 of Harbour Area Treatment Scheme (HATS), Tolo Harbour Action Plan (THAP), Tolo Harbour Effluent Export Scheme (THEES) and a number of sewage treatment works had been conducted in different areas of Hong Kong. Changes in the community structure were noted in the three focal areas with pollution control measures, i.e. Victoria Harbour, Deep Bay and Tolo Harbour; while apparent recoveries were noted inside the Victoria Harbour, the changes in benthic communities inside the Tolo Harbour and Deep Bay could not be attributed to the pollution control measures. Specifically, a decline in nutrient input to the eastern part of Victoria Harbour due to the implementation of HATS might have led to declined sedimentary total organic matter and the disappearance of the opportunistic species, and hence a recovery of benthic ecosystem therein. But in the sheltered Tolo Harbour and Deep Bay, neither improvement in sediment quality nor biodiversity were noted, thus indicating a longer duration is needed for the recovery of benthic ecosystems to take place in these land-locked bays. Degraded marine fishery resources and destruction in marine ecosystems had been noted since the introduction of modern trawling vessels had into Hong Kong since the 1950s and 1960s. Currently, most reports of benthic ecosystem responses to cessation of trawling originate from temperate regions, while it is not well understood for the situation in tropical areas. The territory-wide trawling ban in tropical Hong Kong waters was implemented by the Hong Kong government since December 31, 2012. Although improvement in benthic ecosystems was anticipated after the ban, it was unknown when this would happen and how different parts of the Hong Kong waters would respond to the trawling ban. My study showed that, around 3 years after the trawling ban, sedimentary organic matter content had increased significantly, and bottom water suspended solid loads had decreased in most of the survey stations, indicating territory-wide improvement in the benthic environment. Moreover, significant increases in richness, abundance and functional diversity of macrobenthos, as well as a more aggregated, fewer but larger station groups of macrobenthic communities were also detected after the trawling ban, indicating rapid recovery of the benthic communities. In conclusion, my study indicates that benthic communities in tropical Hong Kong can be used as bioindicators of environmental changes. Due to their restricted mobility, benthic organisms should be an integral part of the ecosystem monitoring aiming to detect the consequences of management measures to the marine environment. Environmental data including habitat complexity and hydrology are also required to fully understand the spatial and temporal dynamics of benthic ecosystems. Besides, my study has provided two territory-wide baseline data on the biodiversity and macrobenthic community structure in the tropical Hong Kong waters, which will be valuable for detecting future changes in the benthic ecosystems. My benthic ecology studies have resulted in a published paper and a manuscript ready for submission for publication. Besides focusing on benthic ecology, I have conducted taxonomic studies on benthic polychaetes, resulting in two published papers. As good taxonomy is the basis of high-quality data in benthic ecology, the training I received from studying these benthic polychaetes has enhanced my understanding of the biology of benthos, which is also important for my career development. However, since these papers do not fall into the main theme of my thesis, they are included in the thesis as appendixes only.

Marine renewable energy developments (MRED) will result in large quantities of infrastructure being deployed in coastal habitats, and the localised exclusion of fishing. The ecological consequences of this scale of deployment are largely unknown, particularly for benthic species. Infrastructure has the capacity to act as artificial reefs (ARs), providing novel habitat, and this may viewed as a benefit of MRED, or a means to mitigate the exclusion of fishing. At present, the functioning of AR ecosystems remains poorly understood. As a measure of ecosystem function, secondary productivity can be used to assess the implications of MRED. The lack of suitable methodology, deployable at relevant scales within time and/or cost constraints, has limited benthic secondary productivity (BSP) quantifications on ARs. Techniques to measure potential BSP and particle flux were developed and applied to the Loch Linnhe Artificial Reef (functionally similar to scour protection material). Variations in BSP and mobile epifaunal densities on, and between, structures in different environments were quantified. Reefs exposed to intermediate current had the highest potential productivity. The BSP on internal areas of structures contributed to the total productive output, but the relative contribution varied according to reef location and design. BSP was primarily determined by particle supply, but the response was not consistent among locations. Mobile epifaunal densities related to reef location, but not reef design, and were highest on reefs in the deepest water and exposed to the fastest currents. The evidence presented in this thesis highlights the need to account for the receiving environment when predicting the ecological consequences of MRED, or when modelling the productive capacity of structures. Such information can be used to suggest modifications to proposed or existing structures in order to maximise their benefit to coastal ecosystems.

Hypoxia and ocean acidification (OA) are amongst the major environmental threats to marine ecosystems worldwide. Biofilms, the signpost to guide larval settlement of many benthic invertebrates, are known to be responsive to environmental changes and thus can become the crucial factor for the response of benthic invertebrate communities. This study aimed at investigating the individual and interactive effects of hypoxia and OA on biofilms and the subsequent effects on larval settlement. Biofilms collected from two sites (clean, hypoxic) were treated with a factorial design of low dissolved oxygen and/or low pH conditions in microcosms and the bacterial cell density and viability (by LIVE/DEAD® cell viability assays) were analyzed. Larval settlement preference was tested with the marine invertebrate, Crepidula onyx. The total bacterial cell densities of biofilms of the hypoxia and hypoxia and OA combination treatment were lower than that of the control biofilms for both sites. There was generally no significant difference in cell viability among control and different treatments for both sites. While the larval settlement rate on hypoxia and hypoxia and OA combination treated biofilms was significantly lower. In conclusion, this study revealed that hypoxia and OA are likely to affect larval settlement by alteration of biofilms, and this may lead to alterations in future coastal communities.

Previous pulse-chase experiments have revealed a wide diversity of benthic response patterns to organic matter (OM) input depending on environmental setting, benthic community structure and experimental conditions i.e. quantity and quality of the added OM.  However, the mechanisms and interaction of environmental and biological factors that produce an observed response pattern are poorly understood. The present thesis set out to improve our current understanding on the set of parameters that determine benthic response patterns.  The core of this study was based on two pulse-chase experiments in two bathyal settings: the Faroe-Shetland Channel (FSC) and the SW Cretan slope in the E. Mediterranean (E. Med).  The sub-zero temperatures in the FSC enabled the observation of the benthic response in “slow-motion” and showed that the response is not static but instead might go through various “phases”.  In the warm E. Med, C processing rates were considerably lower compared to previous measurements in adjacent regions.  The discrepancy was attributed to the particularly refractory sedimentary OM at the sampling station with apparent consequences for the physiological state of the bacterial community.  Both experiments showed that bacterial metabolism and its regulation is a key factor determining the reaction of the benthic community to OM inputs.  This thesis provided further understanding on the short-term fate of organic C in deep-sea sediments but also raised certain issues that could be addressed in future studies.

A wave energy park has been established on the Swedish west coast outside Lysekil and pioneer work about its interactions with the marine environment has been conducted. So far, little is known about the effects of offshore energy installations on the marine environment, and this thesis assists in minimizing environmental risks as well as in enhancing potential positive effects on the marine environment. The Lysekil research site is situated about two kilometres offshore and has been under development since 2005. During this time 26 “environmental devices”, without generators, consisting of a steel buoy attached via a wire to a foundation on 25 m depth have been placed out for ecological studies on macrofauna in surrounding sediments and on colonization of the foundations and the buoys. Sediment samples to examine macrofauna in the seabed have been taken during five seasons. Biomass, abundance and diversity of infauna in the test site were generally low, but higher than in a nearby control site. The species composition was typical for the area and depth. In addition to sediment analysis, the effect of wave power concrete foundations on the marine environment has been investigated by scuba diving. The surface orientation and its effect on colonization by sessile organisms was examined on the first five foundations, placed out in 2005, and observations of habitat use by fish and crustaceans were made. The results show a succession of colonization over time (three years of investigation) with a higher cover by sessile organisms on vertical surfaces. Mobile fauna abundance on and around the foundations was generally low. Three months after the deployment of the 21 new foundations in 2007, assemblages of mobile organisms were examined visually. Also here, mobile species exhibit a low density, but still higher than on surrounding soft bottoms. The edible crab used artificial holes in the foundations frequently. The foundations were placed in two different clusters, north and south, and the degree to which early recruits covered the foundations and the succession of epibenthic communities were documented during two years. Sessile organisms colonized the northern foundations more rapidly, producing a higher diversity which suggests that the placement of wave energy devices affects colonization patterns. Biofouling on buoys was examined and blue mussels, Mytilus edulis, dominated with a cover about 90%. Wave exposed buoys were particularly favoured by M. edulis which there had a higher biomass and larger shells compared to those on sheltered buoys. Biofouling on wave power buoys, independent whether these had a cylindrical or toroidal shape, was insufficient to markedly affect their energy production. Finally, the thesis incorporates a review describing wave power projects in general pointing out the need of future research on for instance no-take zones, marine bioacoustics and electromagnetic fields. The main conclusions are that large-scale renewable wave energy conversion will cause ecological impact primarily by adding new hard substrate to an area but not by harming organisms or decreasing biodiversity within wave power parks.

Studies were conducted to broadly describe and understand the sediment benthos of a shallow-water coastal area (Aramoana Beach - Heyward Point - Blueskin Bay) near the entrance to Otago Harbour, a system largely representative for southeastern New Zealand. Benthic assemblages were examined in relation to gradients of wave exposure and disturbance, sediment type and bathymetry, and dredge-spoil disposal. Sediment and macrofaunal surveys in autumn and spring 2003 found little change in sediment texture gradients from historical studies and a lack of vertical stratification. Macrobenthic samples from spring produced significantly higher abundances of three numerically dominant phyla (Arthropoda, Annelida, and Mollusca) and higher taxon richness compared to autumn. Within water depths of 6-30 m, abundance, richness, and diversity increased with depth. Multivariate analyses identified similar assemblages among deeper sites, despite sediment textural differences, whereas distinct assemblages were found in the shallow portions of the three areas. Meiofaunal abundance patterns did not reflect those of macrofauna, possibly indicating greater vertical penetration of sediments in these hydrodynamic environments. Several new kinorhynch taxa were found. In a field manipulation, part of the Aramoana dredge-spoil dumpground was protected from spoil disposal for an extended period followed by experimental dumping of sandy and muddy spoil. Macrofaunal samples were collected before dumping and at nine sites < 119 d after disposal. Water velocities at the sediment-water interface were compared to a local sediment disturbance model. Dumpground samples were depauperate in individuals and taxa compared to an area protected from dumping for > 180 d. A drop in abundance and a dissimilar community coincided with muddy spoil, but fine sediments were dispersed within 26 d and macrofaunal assemblages recovered to the pre-existing state. Sandy spoil, while not altering native sediment textures, had a more prolonged impact due to transplantation of macrofauna from the dredged area that persisted for < 41 d after disposal. Side-scan sonar mapping indicated that the disposal footprint model used approximated the extent of sandy spoil impacts well, while local conditions spread muddy sediments beyond the initial impact site. A novel sediment profile imaging device was constructed that has many advantages over existing devices for spoil mound studies and habitat mapping: it is smaller, can be manually deployed from small boats, is cheaper, and can be modified to work in almost any soft sediment. Studies of one dominant taxon, the gastropod Zethalia zelandica, showed it was better able to survive sand burial than mud burial, did not vary in overall activity through a range of 5-14� C, and contributed a large proportion of biomass of its community. The spoil disposal strategy used does not appear as environmentally neutral as originally thought. Only muds are effectively dispersed whereas coarser sediments accumulate, affecting physical and biological benthic processes of a wider area. Two mitigation strategies were evaluated using a heuristic model. Reducing the disposal area and spreading mud disposal events over a longer time span may be an effective interim strategy. Overall, the studies will help guide management of the area.

Coastal ecosystems are highly threatened worldwide by multiple anthropogenic stressors that act at a range of spatial scales, from local to the global, and adversely affect their ecological functions and associated biodiversity. Global warming is one of the most pervasive stressors, and the assessment of how the species (or other levels of biological organization) react to it is an urgent need in a rapidly warming world. Moreover, thermal stress rarely acts in isolation from other stressors. The potential synergies among global warming and local stressors is of particular concern in what it regards foundation species, such as the case of seagrasses, due to their crucial role in maintaining the structure and function of coastal ecosystems. The main objective of this PhD thesis is to improve the knowledge of how warming alone and in combination with different local factors can affect seagrasses. This research has been conducted based upon mesocosm experiments submitted to different temperatures (and, in some cases, to other agents), and plants responses measured from biochemical to population levels. The results obtained are considered an approach to what may occur in the real world, always acknowledging the limitations of our methodology. Chapter 1 revealed different tolerance to warming among the two main Mediterranean seagrass species, Cymodocea nodosa and Posidonia oceanica. C. nodosa tolerates temperature increases much better than P. oceanica probably due to its life story (opportunistic), habitat (from confined waters to the open sea) and biogeographical affinity (tropical and subtropical). This will potentially cause changes in the distribution area of these two species in the Mediterranean under a future scenario of warming. As shown in Chapter 2, an increase in nutrient concentration in water does not modify the response of C. nodosa to warming. However, the increase of organic matter in sediment clearly worsens, synergistically in some plant traits, the effects of warming, entailing a hazardous combination for plant survival. P. oceanica, in turn, is severely affected by conditions of high nutrient content and high temperatures (Chapter 3), again displaying synergistic effects, and confirming not only a thermal sensitivity in this species greater than in C. nodosa, but also a greater vulnerability to the exacerbation of thermal effects by other local stressors. Finally, the interactive effects of warming and salinity (Chapter 4) in an estuarine seagrass species, Halophila ovalis, in southwestern Australia resulted beneficial for plant survival, as the negative effect of warming was buffered by concomitant salinity increases. Overall, this research highlights the complexity of global warming effects in at least two aspects. Firstly, the multiplicity of biological levels at which those effects act and, secondly, the importance of studying not only isolated effects of temperature increases but also their joint effect with other stressors. Advances in these two directions will yield more realistic predictions concerning global warming and seagrass ecosystems and help to develop management policies to protect seagrass ecosystems in a changing world.

This thesis presents the first intensive community-level investigation of the mesozooplankton from a biogeographical transition zone estuary. The Mgazana Estuary is located along a rural, semi-undeveloped part of South Africa’s east coast, believed to represent a transition zone between the subtropical and warm-temperate biogeographical zones. The research represented in this thesis involves data collected over a five year period between 2002 and 2006, with additional data collection made in 2008. The study focussed on five areas of investigation, the first of which investigated the physico-chemical dynamics of the Mgazana Estuary. The Mgazana Estuary exhibited marked vertical, horizontal and regional structures in the hydrological environment. Prominent vertical and horizontal stratification characterised summer months. A substantial turbidity front was observed in the lower estuary during summer and winter. The upper estuary was marked by considerable variation in multiple variables but especially salinity. These structures appeared to have shifted in position over the horizontal plane, which was attributed to variation in freshwater flow. The second study focused on the spatial dynamics of mesozooplankton in the Mgazana Estuary. The zooplankton was rich and in terms of composition typical of mangrove systems. The Copepoda were dominant, numerically and in terms of taxonomic representation. Calanoids Acartiella natalensis and Pseudodiaptomus hessei characterised middle and upper reaches in summer and mostly upper reaches in winter. On community level, a highly structured assemblage arrangement was observed during summer and winter months. These trends were further scrutinised under the theoretical framework of ecological boundaries. In so doing, an agreeable spatial association emerged between specific assemblages and their environments. These trends were concluded to reflect ecoclinal as well as ecotonal properties, the latter describing interactions over narrow spatial bands of marked changes in turbidity. The third study investigated flooding events as short-lived extreme meteorological events and the influence on zooplankton. Within this regard, second-stage multivariate statistics was used to assess year-to-year variability in assemblage structures on whole-system and regional scales. The impact of two major flooding events that flushed the estuary some days prior to sampling could clearly be elucidated. Flooding emerged as a significant source of inter-annual variability in the zooplankton of the Mgazana Estuary. Second-stage multivariate analysis proved to be an effective analytical strategy for investigating inter-annual variability in species assemblage structures. Results from the preceding study prompted a detailed investigation into the spatio-temporal dynamics of Acartiella natalensis, the most important zooplankton species of the system aimed at elucidating flood responses. Acartiella natalensis showed indication of temporal arrest in association with flooding events in a similar fashion as is observed in seasonal variation trends in estuaries towards its geographical distribution limit south of the study area. It was concluded that A. natalensis was severely affected by floods and the possibility exist for entrainment of entire populations from the estuary during flooding events. The final study tested the hypothesis of post-flood propagation from a resting egg bank in the sediments of the Mgazana Estuary. Preliminary data revealed that numerous eggs were present in the sediments. Nauplii hatched from eggs under laboratory conditions were identified as belonging to the family Acartiidae. The preliminary mode of diapause is presented as a schematic model, emphasising the role of freshwater flow and specific environmental variables. This was the first discovery of resting eggs from a subtropical estuary from South Africa. It is hoped that the findings of this study would give rise to new research initiatives investigating the importance of resting stages in estuarine and coastal Copepoda species and the role such reproductive strategies may play in estuarine functioning.

Submarine canyons are major topographic structures forming deep incisions in shelfs and continental margins around the globe. Due to their topographic characteristics, canyons influence both local hydrodynamic conditions and the transfers of organic material and sediment from shelfs to deep seafloor. This leads to changes in sediment characteristics and organic enrichment that play a key role in deep-sea the functioning, and particularly affect benthic communities. Metazoan meiobenthos are the most abundant deep-sea infauna, with nematodes being dominant. Due to their small size, meiofauna is intimately related with the sediment so that the physical properties are highly influencing the assemblages harbored by a given ecosystem. Therefore, habitat heterogeneity, a particularly relevant canyons feature plays a key role in shaping meiofaunal distribution and biodiversity. Blanes canyon (NW Mediterranean) has been intensively explored during the last years, mostly in relation with the fishery activities in the area. However, as in many other canyons, the meiobenthic component had been almost neglected. Within this context and in the frame of the Spanish research project Dos Mares, the present thesis, focus on the metazoan meiofauna in the Blanes Canyon system. Samples were obtained by the multicore deployments from 500 to 2,000 m depth during four oceanographic campaigns (spring and autumn in 2012-2013). The main objective was to increase the knowledge and further understanding of the patterns and trends of meiofaunal density, diversity and community composition, as well as on its main environmental drivers, with a particular emphasis on the dominant nematode assemblages. Our results indicate that Blanes Canyon exhibits: marked sediment variability, high food availability (i.e., Organic Carbon, Chlorophyll a, Chloroplastic Pigments Equivalents) compared to the adjacent slope, together with higher density, and diversity, and more marked differences in community composition and distribution, both at higher (i.e., meiofauna) and lower (i.e., nematodes and kinorhynchs) taxon level. The observed temporal variability is only partly explained by the seasonal patterns of food input, derived from phytoplanctonic production, where major oceanographic processes such as recurrent dense shelf water cascading events; seem to play a key role. Moreover, the topographically heterogeneous environment associated to the canyon bathymetric gradient, combined with the existence of recurrent, non-seasonal food pulses, are better explaining the observed meiofaunal trends, particularly those concerning nematodes. However, among all gradients analysed, the greatest effect on nematode communities occurred at small-scale (cm), both in the canyon and on the slope, with the highest abundance at the surface sediment layer leading to a marked diversity decrease along the vertical sediment profile. This Thesis includes the first known study on Mediterranean deep-sea kinorhynchs, which contributes to increase the current knowledge on its diversity and distribution, as seven over the nine species found in the canyon system turned to be undescribed. Our results allowed us to avoid suggesting generalizations in the description of meiofauna patterns in the canyon, highlighting those different taxa may show different bathymetric-related responses, this being particularly relevant in the case of the rare taxa (e.g., the kinorhynchs). They also support the consideration of submarine canyons as hotspots of faunal density, biomass and diversity, confirming its key role in shaping the patterns and trends shown by benthic fauna. Finally, the overall results of this Thesis strongly suggest that the Blanes Canyon system is not functioning as a purely natural environment. The high sedimentation rates in the canyon axis suggest that the indirect but regular effects of bottom trawling are driving the structure, and possibly the functioning, of the associated meiobenthos, all along the axis down to at least, 1,750 m depth.
Los cañones submarinos son una de las principales estructuras geomorfológicas del margen continental y un recurso de heterogeneidad del fondo marino. Su abrupta topografía influye en el régimen hidrodinámico local, interrumpiendo y amplificando las corrientes e incrementando los flujos de partículas. Juegan un papel importante en el transporte entre plataforma y océano profundo atrapando, acumulando y canalizando sedimentos y materia orgánica con importantes consecuencias para la diversidad, funcionamiento y dinámica del bentos. La meiofauna es un componente importante del bentos. Dado su pequeño tamaño, está íntimamente relacionada con el sedimento y sus posibles alteraciones (p. ej., alteración de las tasas de sedimentación, resuspensión). Esta Tesis se centra en el Cañón de Blanes (NO Mediterráneo), lugar de importante actividad pesquera. Partiendo de muestras recogidas en primavera y otoño de 2012 y 2013, el principal objetivo ha sido incrementar el conocimiento y las pautas y tendencias de las comunidades de meiofauna (densidad, biomasa, diversidad y estructura) del Cañón de Blanes, así como de su talud adyacente con especial énfasis en los nematodos. Las elevados tasas de sedimentación detectados en el cañón (hasta los 1,750 m), sugieren un efecto indirecto de la pesca de arrastre, que estaría afectando a la meiofauna, sugiriendo la parcial antropogenización de los ambientes profundos del cañón. La variabilidad temporal observada obedece a: entradas estacionales de materia orgánica (derivadas de la producción primaria), procesos de formación de aguas profunda y heterogeneidad topográfica, combinados con entradas recurrentes no estacionales de materia orgánica. Sin embargo, la variabilidad a pequeña escala (cm) causa un mayor efecto en la estructura y diversidad de la comunidad de nematodos, principalmente debido a la disminución en diversidad a lo largo del perfil vertical del sedimento. El Cañón de Blanes muestra mayor variabilidad en el sedimento y disponibilidad de materia orgánica que el talud adyacente, así como una mayor variabilidad en la composición y estructura de las comunidades meiofaunales. Nuestros resultados apoyan la relevancia del papel de los cañones submarinos en la distribución de la fauna bentónica, así como su consideración como hot spots de densidad, biomasa y diversidad.

Numerous ecological studies have used lipids to determine trophic pathways in aquatic systems, as fatty acid profiles provide time-integrated information on an organism’s assimilated diet. Many of these studies have, however, been based on sample collections with a limited temporal scale. The trophic ecology of pelagic systems has been studied intensively using fatty acid analyses, but very little work has been directed toward benthic communities, with the intertidal being especially neglected. The investigation of trophic pathways within rocky shore communities will help us to better understand system responses to environmental changes. The determination of long term temporal variation of the food web within a community could reveal the type, magnitude, duration and frequency of highly seasonal productivity. Changes in fatty acid profiles through time in primary consumers of intertidal rocky shores are poorly understood, but represent an important step towards a more comprehensive understanding of rocky shore food webs, compared with those derived from snapshot or short-term studies. The aim of this thesis was to clarify the temporal variability in the diets of rocky shore intertidal suspension-feeders (the brown mussels Perna perna and the Cape reef worm, Gunnarea gaimardi) and grazers (the Cape sea urchin Parencinus angulosus and the Goat-eye limpet, Cymbulus oculus) on the south east coast of South Africa using fatty acid profiles, and to investigate the effects of life style (e.g. feeding mode) and life cycle on temporal variations in tissue fatty acid profiles. I had three hypotheses: firstly, that suspension-feeders experience high levels of variability in their diets through time because water quality has the potential to change quickly and drastically, whereas grazers experience less variability in their diets over time since their food sources are more constant. Secondly, the reproductive cycles of the suspension-feeder P. perna and the grazer P. angulosus affect the fatty acid composition of their gonads, with temporal variations in lipid composition reflecting changes in reproduction investment. Thirdly, the total amount of energetic reserves available for reproduction are different for each gender (females allocate more energy to egg production than males allocate to gamete production). To address these aims, fatty acid profiles of suspension-feeders and grazers were investigated over a period of twelve months (from July 2010 to June 2011) at a single site on the south east coast of South Africa. The results showed high variability in the fatty acid composition of both the suspension-feeders strongly related with changes in their food source (suspended particulate material). Furthermore, similar temporal changes in fatty acid profiles of the two suspension-feeders were observed over time, reflecting their common diet and life style. There were some inter-specific differences in the suspension-feeders, likely originating from differences in their particle capturing mechanisms. Grazers showed less variability through time compared with the suspension-feeders, with the limpets being more consistent than the sea urchins. The temporal variability in the sea urchin diets may have resulted from the highly diverse and heterogeneous food sources available to them, whereas limpets may be more selective and have a limited range of diet items. Differences between the two grazer species may have arose from differences in their feeding strategies and intertidal zonation. The fatty acid compositions of gonad tissues in both P. perna and P. angulosus showed temporal variability strongly related to reproductive cycle. Differences in the fatty acid values between females and males were apparent, with females richer in total and polyunsaturated fatty acids than males. Spawning and gametogenesis influenced the variability of fatty acids through time in both species, suggesting the importance of considering the reproductive cycle when studying lipids in rocky shore species. Little evidence of lipid transfer between muscles and gonads was seen, suggesting the importance of direct lipid storage into the reproductive tissues. The influence of diet and life history of intertidal consumers on the temporal variability of their fatty acid compositions is important to understand, as it provides us with a better understanding of the functioning of rocky shore systems. There is an enormous potential for future research in this field of study.

Climate changes effects include ocean acidification and, possibly, the alteration of frequency and magnitude of climate events, such as El Niño. All environmental global changes are supposed to be a major threat to ecosystem, both terrestrial and marine. Despite the amazing bulk of literature on these last, few efforts have been devoted to polar regions, which are actually likely to be the most fragile environments on the Earth. In this work we want to elucidate the response, to environmental modifications, of three Antarctic benthic macroinvertebrates: the scallop Adamussium colbecki, the sea urchin Sterechinus neumayeri and the sea star Odontaster validus, inhabiting the littoral area of Terra Nova Bay (Ross Sea, Victoria Land). Using long term series, we investigated potential correlation between A. colbecki recruitment and environmental variables (sea ice cover duration and El Niño events), reporting that A. colbecki recruitment is not affected by these variables. We also performed a manipulative experiment in the Mario Zucchelli Station to understand the effects of three pH levels (8.16, 7.8 and 7.6) on the three species, investigating the response of hard tissues and of the reproductive system. Results show that S. neumayeri spines are affected by low pH only at nanoscale and only in hardness property, while the shell of A. colbecki is not altered at all. As far as reproductive system, we found a significant effect in the gonado-somatic index and on stage development of A. colbecki, in addition to some damages in the gonad tissue, although not statistically significant. S. neumayeri shows the same disrupt tissue all over ovary and testes, although differences from the control are not statistically significant. Conversely, O. validus does not show any effect of low pH exposure at all. Further investigations are necessary to understand the energy costs of maintenance of the polar organisms and its potential consequence on individual life history and, thus, populations dynamic.

The current thesis covers two important and poorly known aspects of Antarctic bryozoans: biodiversity and chemical ecology. The comparative analyses of diversity carried out here (Chapters 1 and 2) between Antarctica and the last separated fragments of Gondwana support the hypothesis of the sequential separation of Gondwana. We discuss that the high number of species from the Argentine Patagonian (AP) region shared with Antarctica found in our study question the real extent of Antarctic isolation for cheilostome bryozoans. The presence of shared common bryozoan species between these two regions may also be explained by the free migration of marine organisms in and out of the Polar Front, via the deep abyssal plains and the potential passive northwards transport of larvae (or perhaps even adults) to considerable distances, via the branch of the Antarctic Circumpolar Current (ACC) flowing northward along the continental shelf of Argentina, the Falkland/Malvinas Current. The role of the Scotia Arc and other dispersal pathways, like eddies of ACC, and human dispersal mechanisms, may increase the bryozoan connection found between the Antarctica and the AP region. Also, our studies (Chapters 1 and 2) are among the first characterizations of the bryozoan communities, mainly at the slope, from the AP region, and from the Southern Ocean (SO), specially the Weddell Sea. The bathymetric distribution from the AP region and the SO found in our studies fits well with the limits of the continental shelf, the slope and the deep sea. Interestingly, our research also shows an expansion in the known distribution of diverse bryozoan species from the AP region and the SO. Our results stress the importance of taxonomical studies in these scarcely explored regions, reporting a high number of new genera and species, and new records too. Among the new species found in our study, a bryozoan of the genus of Reteporella characterized by rare giant spherical avicularia is described in Chapter 3, leading us to discuss which are the potential roles of the avicularia. Since the studied bryozoan communities, below areas affected by local disturbances (iceberg scours and anchor ice), are mainly subject to biotic factors such as competence and predation, the evolution has favoured the development of chemical mechanisms in benthic organisms, which have also been investigated here (Chapters 4 and 5). Our studies are among the first reports on chemical ecology of Antarctic bryozoans. In order to study these chemical interactions, new adapted protocols were designed using sympatric and abundant predators. Our findings demonstrate the importance of diverse chemical ecology mechanisms against competence and predation in Antarctic bryozoans. Most bryozoan species tested here display cytotoxicity and/or repellent activity against the sea urchin Sterechinus neumayeri and the amphipod Cheirimedon femoratus, respectively (Chapter 4). In Chapter 5, our results demonstrate that bryozoans seem to be readily defended against at least one of the two abundant predators, Odontaster validus and C. femoratus. The intra- and interspecific variability in bioactivity suggest an adaptive response to diverse abiotic and biotic factors, presence of microorganisms and/or genetic variability. The general trend in our study indicates the presence of a combination of both chemical and physical defensive mechanisms in most bryozoan species, suggesting complementary traits. In general, these results lead to the conclusion that this phylum is very active with extended repellent activities.
Aquesta tesi cobreix dos aspectes importants i poc coneguts dels briozous antàrtics: la biodiversitat i l'ecologia química. L'anàlisi comparatiu de diversitat realitzat aquí (Capítol 1 i 2) entre l'Antàrtida i altres zones geogràficament properes recolzen la hipòtesi de la separació seqüencial de Gondwana. Es discuteix que l'elevat nombre d'espècies de la regió de la Patagònia argentina (PA) compartides amb l'Antàrtida qüestiona el grau real d'aïllament de l'Antàrtida en briozous queilostòmats. Els nostres estudis (Capítols 1 i 2) són també una de les primeres caracteritzacions de les comunitats de briozous, principalment del talús, de la regió de la PA, i de l' Oceà Austral, especialment el Mar de Weddell. Els nostres resultats remarquen la importància dels estudis taxonòmics en aquestes regions escassament explorades, incloent un gran nombre de nous gèneres i espècies, i noves cites. Entre les noves espècies trobades en el nostre estudi, es descriu un briozou del gènere Reteporella caracteritzat per una rara aviculària esfèrica i gegant, portant-nos a reconsiderar quines són les possibles funcions de l'aviculària (Capítol 3). Com les comunitats estudiades de briozous, per sota de les zones afectades per pertorbacions locals (erosió per icebergs), estan subjectes principalment a factors biòtics com la competència i la depredació, l'evolució ha afavorit el desenvolupament de mecanismes químics de protecció (Capítols 4 i 5). Els nostres estudis són dels primers en ecologia química de briozous antàrtics. Els nostres resultats demostren la importància de diversos mecanismes d'ecologia química contra la competència i la depredació en briozous antàrtics. La majoria de les espècies de briozous mostraven activitat citotòxica i/o repel•lent contra l'eriçó de mar Sterechinus neumayeri i l'amfípode Cheirimedon femoratus, respectivament (Capítol 4). En el capítol 5, totes les espècies de briozous estudiats mostraven activitat de repel•lència alimentària contra almenys un dels dos depredadors abundants considerats, l'estrella de mar Odontaster validus i l'amfípode Cheirimedon femoratus. La tendència general en el nostre estudi indica la possessió d'una combinació de mecanismes físics i químics en la majoria de les espècies, fet que suggereix estratègies complementàries.

Os estudos de ecologia descritiva de comunidades marinhas bentônicas, tanto as de substratos consolidados (costões rochosos, recifes de corais, recifes de arenitos e bancos de algas calcárias) como as de substratos inconsolidados (areia, silte e sedimentos de baixa granulação), apontam para uma busca, ainda não finalizada, por padrões de distribuição que possam apresentar-se como modelo recorrente, sendo capazes de predizer sobre a composição de uma comunidade local. Como exemplos bem sucedidos, na busca de padrões, sendo marcos históricos no desenvolvimento da ecologia descritiva de comunidades marinhas bentônicas, temos as abordagens da zonação e de níveis de fundo, que buscaram encontrar um meio prático para descrições generalistas em larga escala que se apresentassem universais. No Brasil são caracterizados 3 momentos históricos sobre ecologia descritiva de comunidades marinhas bentônicas de substrato consolidado, que se caracterizam pelo uso de espécies como unidade operacional, recorrendo pouco a abordagens alternativas para ganho de conhecimento sobre grandes áreas. Neste estudo foi utilizado o método alternativo Caracterização fisionômica de comunidades marinhas de substrato consolidado para descrição dessas comunidades no infralitoral e busca por padrões de estruturação gerais visualmente evidentes. Este estudo foi realizado no Parque Estadual da Ilha Anchieta, Ubatuba SP, no infralitoral do costão oeste da Enseada das Palmas, compreendido entre as coordenadas 23°31\'44.37\"S / 045° 3\'38.07\"O e 23°32\'1.62\"S / 045° 3\'39.17\"O. Como principais resultados foram encontrados 24 povoamentos descritos na Abordagem 1, 20 povoamentos no inverno e 23 no verão . Na Abordagem 2, 19, povoamentos no inverno e, na Abordagem 3., 22 no verão. Os resultados quantitativos mostram, discriminados no costão estudado, a formação de 2 grupos gerais, que se mantiveram os mesmos no inverno e no verão, permitindo a conclusão de que há um padrão geral de estruturação da comunidade visualizada. Os povoamentos determinantes na divisão dos 2 grupos foram: Colônia de Palythoa, Tapete de Amphiroa e Jania, Banco de Dichotomaria e Região de Substrato Inconsolidado. Constata-se o mundo natural como um lugar desigual, que se manifesta em manchas ou remendos distintos, apresentando-se de muitas formas e com uma ampla gama de escalas. Os resultados foram vistos sob uma perspectiva exploratória, uma vez que se buscou encontrar padrões de distribuição das comunidades apenas a partir da unidade visual povoamento, sem o registro de dados de condições ambientais. Nessa busca, visualizando tal mosaico de distribuição de formas, cores, estrutura e composição em diferentes escalas encontramos padrões gerais de distribuição da comunidade, aqui representados por 2 grandes grupos, caracterizados por estarem em um nível acima de povoamentos ou supra povoamentos
The studies on descriptive ecology of marine benthic communities, hard bottom (Rocky Shores, Coral Reefs, Sandstone Rock Reefs and Rodolith Beds) as much as soft bottom communities (sand, silt and soft substrate of low granular material), lead to a non finished search for distribution patterns that may present it as a model able to predict about the local communities composition. As successful examples on searching for patterns as historical reference on the developing of descriptive ecology of marine benthic communities we have the zonation and bottom level approaches, that seek for a practical way to describe on a general and large scale universal patterns of distribution. In Brazil we found 3 historical moments about studies dealing with descriptive ecology of hard bottom marine benthic communities, which are characterized by the use of species as an operational unit, taking advantage of few alternative approaches to acquire knowledge about the communities in large areas. In this study the alternative methodology Physiognomic characterization of hard bottom marine benthic communities was applied, to describe such communities in infra-littoral regions and to search for general structural patterns visually evident. This study was made in Anchieta Island State Park, Ubatuba SP, Brazil, on the west rocky shore of Palmas Bay, located between the geographical positions 23°31\'44.37\"S / 045° 3\'38.07\"W and 23°32\'1.62\"S / 045° 3\'39.17\"W. As main results, 24 settlements described by the first approach were found; 20 settlements in winter season and 23 in summer season by the second approach ; 19 settlements in winter season e 22 in summer season by the third approach. The quantitative results show 2 general groups found on the studied rocky shore that were the same both in winter and summer seasons, allowing that we come to the conclusion that there is a general structural pattern visualized in the communities. The determinant settlements to the formation of the 2 groups were Palythoa Colony, Amphiroa and Jania Turf, Dichotomaria Bed and Soft Bottom Region. We face the fact that nature is an unequal place, which manifests this visual difference on patches of different sizes, showing many forms and colors on a huge range of scales. The results were reviewed under an exploratory perspective, searching first for structural patterns of these communities only from the visual unit called settlement, without the data of environmental conditions. On this search, visualizing the distribution of forms, colors, structure and composition mosaic on different scales we found general patterns of communities distribution that here are represented by 2 large groups, characterized by being on a higher level than the one of the settlement

Cold seep ecosystems in the deep sea are fuelled by chemosynthetic processes based on methane emission to the sediment surface from gas hydrate disassociation, methanogenesis or thermogenic processes. While cold seep ecosystems have been studied in the last three decades worldwide, little is known about New Zealand’s cold seep habitats and associated fauna. A joint German-New Zealand cruise to the Hikurangi Margin in early 2007 enabled biological and sediment sampling to investigate the biological and sedimentological relationships and variability of seeps and their faunal diversity. Multi-disciplinary approaches were employed that included Xray radiography, stratigraphic descriptions, lebensspuren traces analysis, sediment grain size analysis, determination of total organic content, carbonate content and its stable isotopic composition, and analysis of benthic invertebrate assemblages of seep habitats. The results of this study revealed three distinctive habitats and associated fauna based on the sediment characteristics and faunal type. Habitat 1 includes all sites pertaining to Omakere Ridge, a seep-related habitat comprised of layers of very poorly sorted, sandy silt, shell hash and bands of methane-derived authigenic aragonitic carbonate nodules with low total organic content (TOC). Due to the characteristics of the sediments and death assemblages of molluscs, it is inferred that Habitat 1 methane seepage is actively diffusive, waning or dormant. Habitat 2 describes sites that are either non-seep or relic and applies to those at Bear’s Paw and Kaka. Habitat 2 constituted of shell hash overlain with very poorly sandy silt, and low carbonates content and low to medium TOC. Habitat 3 describes non-seep related habitats, and includes all sites of the Wairarapa region and one reference site from Kaka also falls into this category. Sediments for Habitat 3 constituted poorly sorted silt with high TOC and low carbonate content which can be explained by their close proximity to land and converging sea currents. The mineral components of the background siliciclastic sediments for all sites studied originated in the Tertiary mudstone of the East Coast Basin. The characteristics of seep habitats of the Hikurangi Margin were comparable to that of the Northern Hemisphere modern seep counterparts, although the abundance and distributions of seep fauna were low. Results from this research have enhanced our understanding on the spatial and variability of methane fluxes and their affects on the duration of cold seep ecosystems, especially for New Zealand. However, more such studies are essential to increase our understanding of seep sediments and explain disturbance-sediment-benthic invertebrate interactions.

With the marine environment subjected to ever increasing anthropogenic pressures resulting in biodiversity and habitat losses, there is an urgent need to implement effective management and conservation strategies to limit these losses. One such strategy is the designation of Marine Protected Area (MPA) networks, with the central concept that individual MPAs are connected to its neighbours within the network However, determining scales of connectivity in an environment that varies considerably both spatially and temporally is inherently difficult. Larval dispersal is a main driver of population connectivity, and planktonic larval duration (PLD) is frequently used to infer dispersal distance. Thus far studies have predominantly focused on fish and tropical species, using approaches such as larval dispersal modelling, otolith microchemistry or genetic estimates of connectivity. This thesis aimed to assess the levels of connectivity in a range of benthic invertebrates characteristic of offshore shelf seas of the Northeast Atlantic, at a range of spatial and temporal scales. This was achieved by: (1) examining the variation in PLDs of a typical benthic assemblage, then using this information to examine the variation in realised dispersal at multiple locations using particle tracking software; (2) assessing habitat preferences for the same species, and exploring how the distribution of broad habitats would affect connectivity of species; and (3) using microsatellite markers to determine the genetic structure of the exploited scallop Pecten maximus at both a localised scale (Isle of Man) and a regional scale covering over half its range. While biological variation, in the form of PLD, did affect dispersal potential of common benthic invertebrates, it was the physical factors of hydrographic regime and substrate type within a species given dispersal range that played the most important role in determining ultimate dispersal distance and location. Additionally, the scale of genetic structure of the scallop Pecten maximus, with Norway genetically distinct from Scotland, Ireland and Isle of Man but weaker or no structure within those regions, highlighted the interaction of biological and physical factors. Ultimately, this thesis has provided valuable insight into the drivers of connectivity in the marine benthos, but further work, particularly more collaborative studies across multiple fields, is required if MPAs are to achieve their aims in the face of a changing environment.

Las zonas costeras son uno de los ecosistemas que sufre mayor impacto antrópico a nivel mundial. La sobreexplotación de los recursos marinos es una de las actividades humanas que genera mayor impacto, reduciendo la abundancia y tamaño de las especies objetivo. Una de las medidas para proteger estos ecosistemas consiste en el establecimiento de áreas marinas protegidas. En Chile, el sistema actual de manejo de las pesquerías artesanales de especies bentónicas está basado en áreas parcialmente protegidas, las Áreas de Manejo y Explotación de Recursos Bentónicos (AMERBs), lo que ha supuesto una mejora en la sostenibilidad de una actividad de larga tradición en el país. Estas áreas entregan derechos de usos territoriales, conocidos mundialmente como TURF (sigla en inglés de Territorial Use Right for Fisheries). Sin embargo, actualmente estas áreas se gestionan de forma individualizada, de tal manera que la escala espacial de manejo no está acoplada a la escala de la dinámica de las poblaciones de invertebrados bentónicos. El objetivo de esta tesis es identificar áreas de alto valor para la producción, exportación y llegada de larvas en base a los patrones de historia de vida temprana, considerando variables y/o condicionantes relevantes de la fase adulta bentónica, como (a) la inversión reproductiva, (b) la densidad y talla de los adultos reproductores, variables determinantes de la distribución espacial de la producción de huevos y larvas, así como también variables que intervienen en la fase larval planctónica, como (c) los rasgos biológicos larvales, para acoplarlo con los patrones de circulación costera con el fin de contribuir a un mejor entendimiento de la dispersión y conectividad larval. Para este fin se seleccionaron dos especies relevantes social, comercial y ecológicamente: el erizo rojo (Loxechinus albus) y la lapa (Fissurella latimarginata). En primer lugar, se evaluó mediante muestreos de campo el efecto de la protección (relacionada con el régimen de explotación) y afloramiento costero sobre la inversión reproductiva y la condición individual de los adultos reproductores. Esta información sumada a los datos empíricos de distribución de tallas, densidad de individuos y fecundidad de las hembras reproductoras se utilizó para desarrollar un modelo de producción potencial de huevos en la costa central de Chile. Para el estudio del reclutamiento y dispersión se desarrolló un modelo biofísico de dispersión larvaria que permite evaluar el efecto de la variabilidad oceanográfica y los rasgos biológicos (migración vertical de las larvas y desarrollo dependiente de la temperatura) en la distancia de dispersión, el éxito del reclutamiento, y los patrones de conectividad larval. Los resultados sugieren que, para ambas especies, la protección y el afloramiento costero no tienen un efecto sobre la inversión reproductiva y la condición de los individuos. Sin embargo, la protección sí tuvo un efecto sobre la talla y densidad de individuos generando claros patrones espaciales de producción de gametos. Se observó que la variación geográfica y temporal de los procesos de circulación dominaneltransportey la dispersióndelas larvas enlaregión, independientemente de los rasgos biológicos evaluados. La mayoría del reclutamiento fue alóctono, con niveles bajos de auto-reclutamiento y retención local, incluso para la especie con un tiempo de vida planctónica corto (F. latimarginata). Los patrones geográficos de salida y llegada fueron similares para ambas especies, observándose una mayor importancia relativa de la región norte del dominio de estudio. Estos resultados permiten identificar los principales determinantes de la producción de huevos, el éxito del reclutamiento y la distancia de dispersión para dos especies de gran interés comercial en Chile, información que podría guiar recomendaciones para el manejo y la conservación en una de las regiones costeras más productivas pero también más explotadas del mundo.
Coastal zones are one of the ecosystems receiving higher anthropic impact. Fishing is a major source of human impact, reducing density and size of exploited species. Marine protected areas are one of the strategies established to control fishing impacts. The current artisanal fisheries management system in Chile is based on partially protected areas, TURFs (Territorial Use Right for Fisheries). This system enhances sustainability of one of the traditional activity in the country. However, these areas are individually managed so the scale of resource management is not coupled with the scale of exploited population dynamics. The objective of this thesis dissertation is to identify areas of high value for propagule production as well as source and sink areas based on early life history patterns, considering variables relevant for the adult phase such as (a) reproductive output, (b) density and size of reproductive adults as both variables define the spatial distribution of eggs and larvae, as well as variables that affect the larval phase such as (c) larval biological traits, coupling these pieces of information with coastal circulation models to reach a better understanding of dispersal and larval connectivity. Two benthic invertebrates species exploited by artisanal fisheries in Chile, the red sea urchin (Loxechinus albus) and keyhole limpet (Fissurella latimarginata) were used as models. First, I evaluated the effect of protection and coastal upwelling on reproductive output and individual condition of reproductive adults. Based on size distribution, density of individuals and fecundity data I developed an egg production model along the central coast of Chile. Finally, I developed a biophysical larval dispersal model to assess the effect of oceanographic variability and larval biological traits (larval diel vertical migration and temperature-dependent larval development) on dispersal distance, recruitment success and connectivity patterns. These results showed that fishing regime and coastal upwelling did not affect individual reproductive output either individual condition for both species. However, fishing regime had an effect on size and density of individuals. I found that the geographic and temporal variation in circulation processes dominate transport and effective dispersal of larvae in the study region, regardless of larval biological traits. Most recruitment to local population was allochthonous, with low levels of self-recruitment and local retention even for the species with short planktonic larval duration. Similar geographic patterns of source and destination strengths were observed in both species, with the northern region of the studied domain showing relatively higher importance. These findings allow identifying primary determinants of recruitment success and dispersal distance for two important exploited species in Chile, and to provide the bases to advance recommendations for management and conservation in one the most productive, but also exploited, coastal regions in the world.

With the advent of an ecosystem approach to marine management, the importance of developing methods to investigate ecological functioning is receiving increasing attention. This thesis develops a novel approach for describing ecological functioning in marine benthic systems. Biological traits analysis (BTA) uses a suite of life history, morphology and behaviour characteristics of species to describe aspects of their functioning. Comparison of BTA with two other approaches proposed for describing functioning in marine ecosystems established that BTA identified a range of biological attributes important for differentiating benthic communities and was better able to describe spatial patterns in assemblage composition than the other measures. Appraisal of the analytical tools proposed for use in BTA revealed they provided similar views of assemblage functioning, with the nonparametric tool being appropriate for providing a general picture of functioning, while the more complex parametric tools had greater power to detect anthropogenic impacts. Evaluation of the type and number of traits included in BTA showed it was sensitive to the number of traits selected for analysis, with optimal results being gained by maximising trait number. Examination of the relationship between functioning and environmental variability revealed that trait composition was related to changes in a number of environmental factors, although this relationship was complex and the nature of associations between traits and specific environmental factors varied depending on the location of assemblages. Further analyses focussed on the impacts of anthropogenic activities on benthic assemblage functioning. These revealed that assemblage functioning was impacted by fishing disturbance in both subtidal and intertidal assemblages. A number of traits were impacted by fishing, including some associated with vulnerability to physical stress and others related to resistance to disturbance, while other aspects of functioning remained unaffected. The thesis has increased our understanding of biological traits analysis as a tool for describing functioning in marine benthic systems. It has also contributed to some interesting ecological and management issues, such as the relationship between species and functioning and the importance of, information required for, and strategies available for conservation of ecological functioning in marine ecosystems.

Macrobenthic assemblages and sedimentary conditions of five areas were described and compared; the role of abiotic factors in shaping benthic distributions was also examined. Two of the study sites were actively dredged at the time of sample collection and the effects of this aggregate extraction were investigated. It was concluded that trailer dredging (at the level intensity employed at these sites) was not associated with any significant disruption to benthic community structure, despite the differences in abiotic and biotic characteristics of the two dredged areas. A meta-analysis of findings from published dredging impact studies revealed a differential response to dredging that was related to habitat type. Full recovery of the benthos following the cessation of dredging was not observed in any of the habitat types suggesting that dredging is associated with a long-term alteration of macrobenthic resources.

A low content of organic matter, which is largely refractory in nature, is characteristic of most sediments, meaning that aquatic deposit-feeders live on a very poor food source. The food is derived mainly from sedimenting phytodetritus, and in temperate waters like the Baltic Sea, from seasonal phytoplankton blooms. Deposit-feeders are either bulk-feeders, or selective feeders, which preferentially ingest the more organic-rich particles in the sediment, including phytodetritus, microbes and meiofauna.

The soft-bottom benthos of the Baltic Sea has low species biodiversity and is dominated by a few macrobenthic species, among which the most numerous are the two deposit-feeding amphipods Monoporeia affinis and Pontoporeia femorata, and the bivalve Macoma balthica. This thesis is based on laboratory experiments on the feeding of these three species, and on the priapulid Halicryptus spinulosus.

Feeding by benthic animals is often difficult to observe, but can be effectively studied by the use of tracers. Here we used the radioactive isotope ¹⁴C to label food items and to trace the organic matter uptake in the animals, while the stable isotopes ¹³C and ¹⁵N were used to follow feeding on aged organic matter in the sediment.

The abundance of M. balthica and the amphipods tends to be negatively correlated, i.e., fewer bivalves are found at sites with dense populations of amphipods, with the known explanation that newly settled M. balthica spat are killed by the amphipods. Whether the postlarvae are just accidentally killed, or also ingested after being killed was tested by labelling the postlarvae with ¹⁴C and Rhodamine B. Both tracer techniques gave similar evidence for predation on and ingestion of postlarval bivalves. We calculated that this predation was likely to supply less than one percent of the daily carbon requirement for M. affinis, but might nevertheless be an important factor limiting recruitment of M. balthica.

The two amphipods M. affinis and P. femorata are partly vertically segregated in the sediment, but whether they also feed at different depths was unknown. By adding fresh 14C-labelled algae either on the sediment surface or mixed into the sediment, we were able to distinguish surface from subsurface feeding. We found M. affinis and P. femorata to be surface and subsurface deposit-feeders, respectively.

Whether the amphipods also feed on old organic matter, was studied by adding fresh ¹⁴C-labelled algae on the sediment surface, and using aged, one-year-old ¹³C- and ¹⁵N-labelled sediment as deep sediment. Ingestion of old organic matter, traced by the stable isotopes, differed between the two species, with a higher uptake for P. femorata, suggesting that P. femorata utilises the older, deeper-buried organic matter to a greater extent.

Feeding studies with juveniles of both M. affinis and P. femorata had not been done previously. In an experiment with the same procedure and treatments as for the adults, juveniles of both amphipod species were found to have similar feeding strategies. They fed on both fresh and old sediment, with no partitioning of food resources, making them likely to be competitors for the same food resource.

Oxygen deficiency has become more wide-spread in the Baltic Sea proper in the last half-century, and upwards of 70 000km² are now devoid of macrofauna, even though part of that area does not have oxygen concentrations low enough to directly kill the macrofauna. We made week-long experiments on the rate of feeding on ¹⁴C-labelled diatoms spread on the sediment surface in different oxygen concentrations for both the amphipod species, M. balthica and H. spinulosus. The amphipods were the most sensitive to oxygen deficiency and showed reduced feeding and lower survival at low oxygen concentrations. M. balthica showed reduced feeding at the lowest oxygen concentration, but no mortality increase. The survival of H. spinulosus was unaffected, but it did not feed, showing that it is not a surface deposit-feeder. We conclude that low oxygen concentrations that are not directly lethal, but reduce food intake, may lead to starvation and death in the longer term.