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Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state-of-the-art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the wocDNA metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long-term integrative potential of wocDNA COI metabarcoding for biodiversity science.

Orientadores: Ivan Sazima, Carlos Eduardo Leite Ferreira Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: O Parque Estadual Marinho da Laje de Santos localiza-se na costa sudeste do Brasil a 36 km da cidade de Santos, Estado de São Paulo. O Parque consiste uma pequena ilha (Laje de Santos) com vários parcéis rochosos submersos. O substrato é composto por rochas graníticas cobertas por algas e várias espécies de invertebrados. Desde 1993, foi declarada como área de proteção marinha e desde então o local é de particular interesse, pois é a única área totalmente fechada para a pesca na região mais povoada e desenvolvida do país. Uma lista com 196 espécies de peixes recifais registradas é apresentada para o Parque Estadual Marinho da Laje de Santos. A maioria das espécies tem ocorrência comum a todo o Atlântico Ocidental tropical ou ocorre nos dois lados do Oceano Atlântico. Uma parte menor das espécies tem distribuição em comum com os recifes rochosos temperados da Patagônia ou é endêmica ao Sudeste do Brasil. Moringua edwardsi, Antennarius multiocellatus, Scorpaena dispar, Aulostomus strigosus, Lutjanus buccanella, Mulloidichthys martinicus and Halichoeres penrosei tem aqui seu limite merional de distribuição estendido ao Estado de São Paulo. Há uma clara diferença na contribuição dos fatores abióticos para a estruturação da comunidade de peixes recifais. A profundidade foi o fator que mais influenciou a riqueza de espécies e abundância de indivíduos, apresentação uma clara distinção ambiental entre raso e fundo, com um decréscimo da riqueza e abundância conforme o aumento da profundidade. A complexidade do habitat também foi um fator de influência na comunidade, sendo a riqueza e abundância correlacionada com maior complexidade. Entretanto, esta relação só foi significativa na menor profundidade avaliada. A exposição às ondas não se correlacionou com nenhum dos descritores da comunidade utilizados neste estudo. Aparentemente os efeitos do hidrodinamismo em recifes rochosos se manifesta em escalas espaciais maiores entre a costa e ilhas com diferentes distâncias da costa. Espécies de diferentes categorias tróficas não respondem da mesma maneira a estes fatores. Herbívoros vagueadores são afetados pela profundidade, herbívoros territoriais pela complexidade e pela exposição a ondas, enquanto que planctívoros são afetados pela complexidade do habitat e em menor extensão pela profundidade. Análises de espécies filogeneticamente relacionadas sugerem que ocorre partição de nicho, aparentemente mediada pela capacidade de natação em resposta ao grande dinamismo que ocorre nas zonas rasas. A água fria oriunda de eventos de reesurgência foi um fator de redução da abundância e número de espécies capazes de extender sua distribuição batimétrica para as zonas mais fundas, desencadeando respostas comportamentais específicas em algumas espécies como a formação de densos cardumes na camada superficial durante os eventos de ressurgência. Herbívoros vagueadores e onívoros foram os grupos tróficos que foram particularmente afetados pela intrusão de água fria. Em geral, espécies com alta capacidade de mobilidade evitam a camada de água fria abaixo da termoclina durante o verão e espécies de pequena capacidade de mobilidade ou extremamente territoriais não alteram sua abundância em resposta estes eventos Abstract: The Laje de Santos State Marine Park is located on the southeastern coast of Brazil, 36 km off the city of Santos, São Paulo State. It consists of an uninhabited islet and several sparse rocky reefs with extensive sand bottoms in between. The subtidal substrate is composed of granitic boulders of varying sizes and shapes. The rocky substrate is mainly covered with patches of algae and several species of sessile invertebrates. Since 1993 the Laje de Santos Island was declared a protected area. The area is of particular interest as this is the only Marine Protected Area totally closed to fishing in the most populated and developed region of Brazil. A check-list containing 196 species of reef fishes recorded at the Laje de Santos Marine State Park is presented. Most of them occur along the tropical western Atlantic or occur on both sides of the Atlantic Ocean. A minor part ranges to the temperate rocky reefs of Patagonia or are endemics to southeastern Brazil. Moringua edwardsi, Antennarius multiocellatus, Scorpaena dispar, Aulostomus strigosus, Lutjanus buccanella, Mulloidichthys martinicus and Halichoeres penrosei have here their ranges extended southward to the São Paulo coast. There is a clear difference among the contributions of each abiotic factors analyzed in the reef fish community structure. Depth was the most influent factor on species richness and abundance, presenting a clear distinction between shallow and deep zones with a decrease of both factors with depth increase. Habitat complexity also had an influence in the community, being species richness and abundance correlated with higher complexity. However, this relationship was significant on the shallower evaluated depth only. Exposition to wave surge does not correlate with any of the community descriptors used in this study. Apparently, hydrodynamics effects on rocky reefs manifest only at larger spatial scales like between the shore and islands. Species on different trophic categories do not respond the same way to these factors. Vagrant herbivores are affected by depth; territorial herbivores by habitat complexity and marginally by exposition, and planktivorous are affected mostly by habitat complexity and in less extension by depth. Analyses of phylogenetically related species suggest that niche partitioning occur, apparently mediated by swimming capacity in response to higher hydrodynamic forces occurring in shallow water. Cold water derived from upwelling events was a further factor reducing species richness and abundance, triggering specific behavioral responses in some species such as the formation of tight packed schools in the surface layer during upwelling. Vagrant herbivores and omnivores were the trophic groups most affected by upwelling. In general, species with high mobility capacity avoid the cold-water layer below the thermocline during summer and species with limited mobility capacity do not change their abundance is response to these events Mestrado Ecologia Mestre em Ecologia

[eng] The alarming rate of marine biodiversity loss calls for new strategies of understanding and accounting for human-nature relationships. Anthropogenic impacts are the main drivers of changes in coastal and marine systems (hereafter coastal systems), where more than 50% of the world’s human population lives. Such cumulative anthropogenic impacts are leading to a dangerous decline in the ecosystem functions and resilience of coastal systems. However, the lack of knowledge about how the social and ecological dimensions interrelate in the coastal systems may lead to failure in protecting, not only nature but also the society that relies on it. This thesis aims to contribute to the social-ecological knowledge of coastal systems by assessing the social-ecological associations of the Spanish coastal and marine communities. In doing so, it develops a methodological approach for defining and spatially identifying coastal and marine social-ecological systems, assesses the relationship between marine biodiversity and the socio-economic and marine environmental characteristics of the social-ecological systems, and detects the hotspots of social-ecological vulnerability in the Spanish temperate coastal system. The findings presented in this thesis show that applying innovative methods, it is possible to untangle the complexity of social-ecological interactions. This thesis identifies the associations between the socio-economic and marine environmental aspects that form the coastal marine social-ecological systems of the Mediterranean coast of Andalusia, and how these social-ecological aspects relate to biodiversity metrics. Deeping in these associations, the results of this thesis identify the most social-ecological vulnerable areas in the Spanish coastline, which require immediate sustainable management actions. Within the context of global changes and biodiversity loss, this thesis challenges conventional studies with an innovative perspective that advance the understanding of social-ecological associations, and provide the needed knowledge to identify sustainable management strategies for building more resilient temperate coastal systems., [spa] El alarmante ritmo de pérdida de la biodiversidad marina exige nuevas estrategias para comprender las relaciones entre el hombre y la naturaleza. Los impactos antropogénicos son los principales impulsores de cambio en los sistemas costeros y marinos (en adelante, sistemas costeros), donde vive más del 50% de la población humana del mundo. La acumulación de estos impactos antropogénicos está provocando una peligrosa disminución de las funciones de los ecosistemas y de la capacidad de recuperación de los sistemas costeros. Sin embargo, la falta de conocimientos sobre la forma en que las dimensiones sociales y ecológicas se interrelacionan en los sistemas costeros, puede conducir a un fracaso en la protección no sólo de la naturaleza sino también de la sociedad que depende de ella. Esta tesis doctoral tiene por objeto contribuir al conocimiento socio-ecológico de los sistemas costeros mediante la evaluación de las asociaciones socio-ecológicas de las comunidades costeras y marinas españolas. Para ello, desarrolla un enfoque metodológico para definir e identificar espacialmente los sistemas socio-ecológicos costeros y marinos, evalúa la relación entre la biodiversidad marina y las características socioeconómicas y ambientales marinas de los sistemas socio- ecológicos y detecta focos de vulnerabilidad socio-ecológica en el sistema costero templado español. Los resultados presentados en esta tesis doctoral muestran que aplicando métodos innovadores es posible desenredar la complejidad de las interacciones socio- ecológicas. En esta tesis doctoral se identifican las asociaciones entre los aspectos socioeconómicos y ambientales marinos que conforman los sistemas socio-ecológicos marinos costeros de la costa mediterránea de Andalucía, y cómo estos aspectos socio- ecológicos se relacionan con la biodiversidad. Profundizando en estas asociaciones, los resultados de esta tesis doctoral identifican las zonas más vulnerables socio- ecológicamente del litoral español, las cuales requieren de una gestión sostenible inmediata. En el contexto de cambio mundial y pérdida de biodiversidad, esta tesis desafía los estudios convencionales con una perspectiva innovadora que avanza en la comprensión de las asociaciones socio-ecológica, y proporciona el conocimiento necesario para identificar estrategias de gestión sostenible para construir sistemas costeros templados más resistentes.

Plants interact with many organisms around them, and one of the most important groups that a plant has to deal with, are the herbivores. Insects represent the most diverse group of herbivores and have many different ways of using the plant as a food source. Plants can, however, defend themselves against those herbivores, either by constitutive defences, or by traits that are induced upon herbivory. These traits, such as the formation of more trichomes or the production of secondary metabolites, can deter an insect herbivore in its decision to eat from the plant, can be toxic, or otherwise hamper the insect to feed, grow or reproduce. The way a plant responds to herbivory is very specific, depending on the feeding mode or the species of the attacking insect. Furthermore, plant responses to dual herbivory differ from the sum of responses to each herbivore alone. Also the time and order at which multiple insects arrive on a plant, influence the plant’s response. Finally, plant species or populations can show different responses to herbivory. Altogether these factors result in a plant phenotype that the attacking herbivore has to deal with. In addition to the attacker, also subsequently arriving insects will be affected by a change in plant phenotype. Because plants and insects can respond to each other in a continuous chain of interactions, an herbivore early in the season can indirectly affect the later-season community composition through the induced plant response. However, we know only little about the consequences of a dual-herbivore induced plant phenotype for subsequent feeders, and ultimately, the effects on the assembly and dynamics of an insect community as a whole. The aim of this thesis project was to study the consequences of feeding by multiple insects from the same plant, not only to a subsequent herbivore, but also to the dynamics of a whole insect community over the course of a growing season, and beyond. Furthermore, I studied how the order of herbivore arrival and timing of arrival affected both a next herbivore’s choice and performance in a greenhouse setting, as well as the development of the whole insect community in the field. In addition, I studied how plant populations vary in induced responses, have specific plant-mediated interactions among insect herbivores, and how long these induced responses influence the insect community and plant fitness. Finally, I identified non-additive effects of the history of insect attacks and plant ontogeny to the future insect community. In the first chapter of this thesis, I introduce the study system. For this project I used several populations of the wild cabbage plant, Brassica oleracea. This is an herbaceous perennial plant that flowers from the second growing season onwards, and supports a large and diverse above-ground arthropod community of more than thirty different species. The plant belongs to the family of Brassicaceae, which is known for the biosynthesis of a group of secondary metabolites, the glucosinolates. These metabolites may deter insects, although some insect species use it as a feeding cue. Two specialist insect herbivores from different feeding guilds, the caterpillar of the diamondback moth Plutella xylostella and the cabbage aphid Brevicoryne brassicae, were used to study their effect as early-season inducer of plant responses either alone or in combination. The caterpillar of the generalist cabbage moth, Mamestra brassicae, was used in bioassays to assess the effects of the induced plant phenotype by single or dual herbivory. Furthermore, in three chapters (Chapters 4, 6 and 7) I have closely studied the composition of the naturally occurring insect community throughout the season for one or two years in a common-garden field setting. In the last of these three chapters, I used the caterpillars of the specialist cabbage white, Pieris rapae, to induce plants at different moments of their ontogeny, while excluding the insect community for varying periods of time by a net or exposing plants to their natural insect community. In an elaborate literature review, I and my collaborators concluded in chapter 2 that plant responses to dual herbivory evoke different plant responses than the sum of each herbivore alone. This has consequences at all levels from arthropod community assembly to the choice and performance of individual insects. The mechanisms of plant responses to dual herbivory are found in gene expression, hormone production and other molecular processes within the plant. All these aspects of interactions between insects and plants occur and are connected at different time scales. To follow up on the question how timing plays a role in dual herbivory, we varied the time between, as well as the order of arrival of aphids and/or caterpillars on a plant. We observed that both affected the preference and performance of a subsequently feeding caterpillar (Chapter 3). Mamestra brassicae performed better on plants with a longer time interval between the first and second feeder. Also in a field setting (Chapter 4), the order of herbivore arrival early in the season affected the insect community composition later in the season in two different years, likely through a chain of indirect insect interactions. In this field study, the plant population influenced the outcome of early-season herbivory to later community dynamics. In chapter 5 we found that three plant populations in response to simultaneous aphid and caterpillar attack differed in the expression of two genes that are important for the regulation of herbivore-induced responses. Also, the production of one of two important plant hormones, salicylic acid, responded differently to single or dual herbivory in a unique pattern for each of the plant populations. These different plant responses subsequently negatively affected a next caterpillar on the same plant; M. brassicae growth was impaired on plants which had been fed upon by both aphids and caterpillars, in comparison to control plants. These field and greenhouse studies thus show the implications of dual herbivory beyond effects in the plant; it affects subsequent herbivory, and through a chain of plant-mediated insect interactions, the dynamics of a whole insect community. In the sixth chapter we show that variation in insect community dynamics can last beyond the moment that the insects were present, even across years. In this field study, the naturally occurring carnivore community influenced the carnivore community composition a year later. Importantly, the herbivore community affected plant fitness across years (but not within years). We propose that such legacy effects are mediated by plant traits, which vary upon insect induction in the first year, and affect the insect community in the next year. Finally, the history of all insect attacks to a plant up until that moment shape the future insect community by influencing the colonisation of insect species on the plant. Moreover, also plant ontogeny plays a role in shaping the insect community; plant-mediated responses to herbivory at different plant ages resulted in different insect colonisation rates. The most important conclusion from this last data chapter (Chapter 7) is that the two processes, insect community history and plant ontogeny, are non-additive and affect the colonisation of insect species in the same (synergistic) or opposite (antagonistic) direction. By framing my study results in a time line from minutes to months to years, I show in the general discussion (Chapter 8) that the consequences of dual herbivory for subsequently arriving insects are connected at different time scales. Plant responses to herbivory can occur within hours to days, which affect herbivore choices and performance in the following days and weeks. In their turn, variation of a few days in arrival time of insects may change how plants respond and prioritize their responses to insects throughout the rest of the season. The insects that subsequently arrive on a dual-herbivore induced plant may change the plant phenotype even further and through a chain of insect-plant interactions, the effects on the insects and the plant can last throughout the season, and even across seasons. Furthermore, various factors such as the species of the attacking insect and its feeding guild, the timing after previous attack and the plant age at which herbivory occurs, as well as the genotypic background of the plant, all affect the outcomes of dynamic insect-plant interactions. The results presented in this thesis thus contribute to the knowledge and interpretation of plant interactions with multiple herbivores. As plants are seldom attacked by a single herbivore, this implies that we have to take into account that multiple herbivory is not the same as the additive effects of single herbivores, and that this has long-lasting consequences for the insect community and the plant. To further understand how plants and insects have adapted to such a dynamic environment, I suggest future research to focus even more on the kinetics of plant physiological responses to dual attack, and to aim at answering the question of how predictable insect communities on a plant really are.

A study on the population and habitat of oriental hard clam (Meretrix meretrix Linnaeus, 1758) along coast of Tarakan City had been conducted from februari to april 2009. Oriental hard clam and associated macrozoobenthic animals were sampled (10 m x 10 m) at 6th fixed stations with 3 replicates which were spred along the coast of Tarakan. The abiotic enviromental factors measured are water temperature, dissolved oxygen, visibility, depth, pH, turbidity, total suspended solid, total dissolved solid and sediment properties (particle composition and sediment pH). During this study we have discover the density, diversity and distribution of oriental hard clam. The results show that the density of oriental hard clam is very low and indicates the over-exploitation on this species. We also discover by the Wilhm criteria that the low mark for diversity of makrozoobenthic community indicates that the waters are polluted at medium level.

Animals have to eat a certain amount of food every day to survive. Since trophic resources are usually found in exposed locations, animals are in risk of predation while feeding, and face the well known trade-off between predation and starvation risks. Animals may reduce predation risk by scanning for predators. However, an increase in vigilance entails an increase in exposure time to predators. Therefore, animals may increase food intake to reduce foraging bouts at the cost of vigilance or may do the opposite. Animals may also reduce predation risk without increasing vigilance by joining groups. However, when food items are concentrated in some defendable patches, individuals will fight to access them, leading to interference competition. Birds have developed different vigilance and foraging strategies to cope with all these trade-offs. These strategies can be adapted to the environmental conditions and type of predators, and will highly differ according to the genetic, phenotypic and ecological characters of the individuals. In this thesis I investigated how wintering Eurasian siskins (Carduelis spinus) adjusted their vigilance and foraging behaviour to predation risk and competition, and how this adjustment varied according to conspicuousness, residence status and personality of focal birds. I also studied how resident and transient siskins regulated their body mass to predation risk. In order to determine the differential effects of predation risk and competition on the behaviour of siskins, I designed an experiment with three feeders differing in predation risk and interference competition. I captured the siskins every week and marked them with aluminium rings (at first capture) and colour rings (if residents). From each bird, I measured body mass, wing length and plumage coloration cues. I filmed the siskins foraging at feeders from a hide. Then I analyzed the video recordings and selected a sample of birds at each feeder to study the effect of environmental factors, and selected pairs of birds belonging to different cohorts of sex, residence and personality to compare their vigilance and foraging behaviour. I also compared body mass of a large sample of residents and transients in two periods with and without avian predators. I found that siskins adjusted their vigilance behaviour specifically to the environmental conditions. Vigilance to predators, achieved by reducing inter-scan durations, was less costly in terms of food intake rate than vigilance to flockmates, achieved by increasing scan durations. Siskin males were more brightly coloured and detectable than females, and showed a vigilance system more oriented to predator detection, supporting (together with the correlation between coloration and vigilance in males) the view of a predation cost to conspicuousness. Resident and transient siskins showed a different vigilance and foraging strategy. Residents were more confident in vigilance to reduce predation risk while transients preferred to reduce foraging bout lengths. Transient siskins were in higher predation risk because of their vigilance and foraging behaviour, and this was related both to their unfamiliarity with the area and their subordination to residents. Proactive male siskins showed a vigilance system that improved their ability to detect predators as compared with reactive males, supporting the view of a behavioural compensation for their personality trait (and not the existence of behavioural carryovers). Resident siskin males adjusted their body mass to the presence of predators at the foraging area, something that transients could not do because of their site unfamiliarity. In general, dominant individuals (whether males, residents or proactive birds) showed a foraging behaviour that prioritized the reduction in predation risk and not the increase in food intake rate, as compared to subordinates. Dominance alone cannot account for our results, although it probably had some effect in all the comparisons., En aquesta tesi vaig estudiar el comportament de vigilància i d'alimentació de lluers hivernants a tres menjadores que diferien en risc de depredació i competència. Vaig determinar com els ocells ajustaven la vigilància a aquestes variables, i vaig comparar el comportament dels ocells pertanyents a diferents classes de sexe, estatus de residència i personalitat, per veure si adoptaven diferents estratègies. Els lluers van ajustar de manera diferent el seu comportament al risc de depredació i la competència. La vigilància dirigida als depredadors, assolida tot reduint la durada dels intervals entre vigilàncies, va resultar ser menys costosa en termes d'ingesta d'aliment que la vigilància a companys d'estol, assolida mitjançant l'increment de la durada de les vigilàncies. Els mascles de lluer van ser més brillants i fàcils de detectar que les femelles, i van mostrar un comportament més orientat a la detecció de depredadors, cosa que dóna suport (junt amb la correlació entre coloració i vigilància en mascles) a l'existència d'un cost de depredació associat a la conspicuïtat del plomatge. Els lluers residents van adoptar un sistema de vigilància que els exposava a menor risc de depredació que els transeünts. A més, a diferència d'aquests, van confiar sobretot en la vigilància a l'hora de reduir el risc de depredació. Aquestes diferències estarien relacionades tant amb el grau de coneixement de la zona com amb la dominància. Els mascles proactius van mostrar un sistema de vigilància que millorava la seva capacitat per detectar aviat els depredadors en comparació amb els mascles reactius, cosa que dóna suport a la idea d'una compensació comportamental del tret de personalitat. Els mascles residents van ajustar la seva massa corporal a la presència d'un depredador aeri a la zona, cosa que no van fer els transeünts segurament pel seu desconeixement del risc de depredació. En general, els individus dominants (mascles, residents o individus proactius) van mostrar un comportament d'alimentació que prioritzava la reducció del risc de depredació i no l'increment en la ingesta d'aliment. La dominància per sí sola no pot explicar els resultats de les comparacions, malgrat que pot tenir un cert efecte en totes elles.

[eng] This thesis focuses on the study of the meiofaunal community in streams and rivers of the Mediterranean region. It approaches to a community level from a functional point of view, studying their response as a whole to different processes occurring in those systems. The thesis is divided into 5 chapters, in which we sampled various substrates in order to study the small-scale processes affecting them and the interactions with other organisms. We focused essentially on the main lotic ecosystem determinants: hydrology and nutrient inputs (organic and inorganic). In Chapter 1, we studied the meiofaunal community over 2 years. Its structure reflected high intra- and inter-annual variability, which coincided with the alternating periods of hydrological stability and disturbances. Since flow is a major abiotic determinant of invertebrate distribution patterns in streams and its impact on meiofauna is relatively well known (see Swan and Palmer, 2000 and references therein), the study addressed mainly the adaptive responses of organisms to spates and droughts in a Mediterranean context. These adaptations were measured in terms of advantageous traits (either structural or life strategies) that could confer resistance or resilience to organisms. Results from that study pointed out that the resilient response of meiofauna in downstream reaches of the study site had a slower recovery given that heavy rainfall events resulted in higher discharges (as a consequence of higher water run-off from catchments). In that system, previous hydrological history also appeared to modulate invertebrate response to floods, diminishing recovery response of the community in that reaches. In contrast, this effect was not observed in the most upstream reach which also showed a fast recovery after spates caused by higher habitat heterogeneity and complexity that served as a refuge to fauna. Organic matter input and its availability to consumers is one of the major processes in headwater streams. In Chapter 2, we analysed the colonisation pattern of experimentally disposed riparian leaves, including all organisms (bacteria, fungi, protozoa, meiofauna and macroinvertebrates) involved to trace the fate of carbon during the process. The experiment showed a clear energy transfer from bacterial to faunal compartments modulated by differences in temperature and discharge that naturally occurred in the stream. Eutrophication of lotic systems is one of the negative results of human activity. Therefore we paid special attention to the effects of nutrient availability to meiofauna because their small size and high turnover rates can provide information of interest about their rapid response to these kinds of disturbances. In Mediterranean systems scarcity can potentiate the negative effects of eutrophication. Therefore, we also explored the interaction of hydrology and nutrient inputs. In Chapter 3 we analysed the meiofaunal response to an experimental addition of nutrients in an almost pristine headwater stream. For this purpose, we focused on differences in community assemblages and secondary production of microcrustaceans, finding that hydrological stability and even water scarcity could potentiate the effects of the nutrient addition. In that system, hydrological disturbances were the “background noise”. In contrast, in Chapter 4 we explored a nematode community in a eutrophic system and we focused on the stability of substrate. We found a different pattern of fauna inhabiting the same biofilm depending on the mobility (attached vs. free-floating cyanobacterial mats). Nematodes were found to be an active part of this detachment though their activity and adapted their life strategies to those changes. In Chapter 5, using a laboratory experiment, we analysed the fast response of two nematode species to eutrophication and examined life strategies adopted to adapt to increased nutrient availability. We could observe a clear bottom-up effect in microcosms and also that small differences in behavioural attributes may shape the successional pattern of recolonisation after a disturbance., [cat] L’objectiu principal d’aquesta tesi doctoral és caracteritzar la comunitat de la meiofauna en sistemes mediterranis i integrar-la com a baula dins dels processos funcionals d’ambients lòtics. Tot i que el coneixement sobre la meiofauna d’aigua dolça és encara escàs, aquesta tesi no ha pretès tenir un caire descriptiu de la comunitat des d’un punt de vista taxonòmic sinó emprar classificacions funcionals que permetin integrar la meiofauna en processos i contextos més amplis. La tesi esta articulada en 5 capítols i en cadascun s’ha mostrejat diferents substrats en funció de les interaccions entre organismes i les característiques dels processos a petita escala. En aquests experiments, s’han adreçat diferents qüestions depenent de l’hàbitat o de les característiques del lloc. Essencialment, aquesta tesi s’ha centrat en els processos lòtics més influents: la hidrologia i les entrades de nutrients (ja siguin orgànics com inorgànics). La resposta general de la meiofauna trobada al llarg d’aquesta tesi ha estat sempre molt vinculada als factors climàtics, ja fos analitzant l’efecte de les avingudes o de les sequeres sobre la comunitat de meiofauna o sobre processos de descomposició, o bé la variabilitat intranual sobre comunitats de cianobacteris i nematodes. Al llarg d’aquesta tesi doctoral, els trets adaptatius de la meiofauna en front a pertorbacions hidrològiques o d’entrada de nutrients han demostrat ser nombroses i merèixer una investigació mes exhaustiva en la recerca futura.

In this paper a simple model is used to study the dispersal of earthworm populations into new habitats. Simple models do not describe processes accurately, but can help gain insight into the functioning of ecosystems or processes in ecosystems. Using information on reproduction, survival and dispersal at the level of the individual, the velocity of earthworm population expansion was calculated. Dispersal of earthworms can be active or passive. The parameters of active and passive dispersal were calculated from field experiments in one of the Dutch polders. Parameters of reproduction and survival were estimated from published data. The effects of processes at the individual level on the velocity of population expansion were studied for two species (Aporrectodea caliginosa and Lumbricus rubellus). The model shows that passive transport has a major influence on the velocity of population expansion, which is strongly increased even if this transport involves only a very small part of the population. At a high level of passive transport, however, death induced by this mode of dispersal can have a negative influence on population expansion. In the discussion it is indicated that optimising growth conditions of the earthworms might be the easiest way to promote population expansion. However, promoting dispersal by passive mechanisms can also be very important.

Leaf litter inputs and retention play an important role in ecosystem functioning in forested streams. We examined colonization of leaves by microbes (bacteria, fungi, and protozoa) and fauna in Fuirosos, an intermittent forested Mediterranean stream. Black poplar (Populus nigra) and plane (Platanus acerifolia) leaf packs were placed in the stream for 4 mo. We measured the biomasses and calculated the densities of bacteria, fungi, protozoa, meiofauna, and macroinvertebrates to determine their dynamics and potential interactions throughout the colonization process. Colonization was strongly correlated with hydrological variability (defined mainly by water temperature and discharge). The 1st week of colonization was characterized by hydrological stability and warm water temperatures, and allocation of C from microbial to invertebrate compartments on the leaf packs was rapid. Clumps of fine particulate organic matter (FPOM) were retained by the leaf packs, and enhanced rapid colonization by microfauna and meiofaunal collector-gatherers (ostracods and copepods). After 2 wk, an autumnal flood caused a 20-fold increase in water flow. Higher discharge and lower water temperature caused FPOM-related fauna to drift away from the packs and modified the subsequent colonization sequence. Fungi showed the highest biomass, with similar values to those recorded at the beginning of the experiment. After 70 d of postflood colonization, fungi decreased to nearly 40% of the total C in the leaf packs, whereas invertebrates became more abundant and accounted for 60% of the C. Natural flood occurrence in Mediterranean streams could be a key factor in the colonization and processing of organic matter This research was funded by the Spanish Ministry of Education and Science project CGL2005–06739-C02–01/02 and by the Fundacio´ n Banco Bilbao Vizcaya Argentaria project GLOBRIO

13 páginas, 4 figuras, 1 foto., The structure and dynamics of ecological communities can be determined by both top-down (e.g., predation) and bottom-up (e.g., energy inputs) processes, which can act synergistically and across spatial and temporal scales. Here we aimed at understanding the role of multiple controls in a Mediterranean rocky sublittoral marine community that harbors a diverse algal community and strongly interacting herbivores, and which is subject to marked seasonality in energy inputs. We conducted an experiment by manipulating densities of the major consumers of benthic algae (fishes and sea urchins) in ;100-m 2 enclosures in a marine reserve, and monitored algal assemblages over two and a half years. Most algae showed a marked annual cycle, with a biomass peak in late spring/summer and low biomass in winter, following seasonal fluctuations in resource availability, indicating the existence of bottom-up processes. Sea urchins reduced the abundance of most algal species, indicating the existence of top-down processes. The effect of fish grazing on algal abundances was significantly weaker. Sea urchin grazing was inhibited when predatory fish were present. Multivariate analysis showed that the interaction between seasonal resource inputs and herbivory induced the formation of algal assemblages characterized by different species abundances. The organization of algal assemblages was determined by the synergistic interaction between top-down and bottom-up processes: top-down control regulated total algal abundance, while bottom-up control determined seasonal fluctuations., This study was funded by grant MAR1999-0526 from the Spanish Department of Education and Science, and by the Department of the Environment of the Catalan Government.

S'ha estudiat l'estructura i dinàmica del sistema bentònic de llacunes costaneres de la maresma dels aiguamolls de l'Empordà (NE de la península Ibèrica) i els factors que les determinen. Amb aquesta finalitat es van prendre mostres d'organismes del bentos (mensualment), nutrients i pigments de l'aigua (setmanalment) i el sediment (mensualment), així com paràmetres físics de l'aigua (setmanalment), durant dos cicles d'inundació (1997-1998 i 1998-1999). En aquesta maresma els factors determinants per als organismes bentònics i el contingut en nutrients del sediment són principalment físics: el grau de permanència de l'aigua, el confinament i la granulometria. De manera que els factors tròfics tenen menys pes que els físics tal com es posa de manifest amb les associacions de nematodes. El règim hídric de les llacunes integra des del grau de permanència de l'aigua fins a la salinitat i el confinament, per la qual cosa a partir de la caracterització dels diferents tipus de règim hídric es poden discriminar les tres tipologies d'ambients amb comunitats bentòniques diferenciades en l'estructura, la composició i la dinàmica temporal. Així, les tres comunitats diferenciades són: (1) la d'aigües permanents caracteritzada per una riquesa i diversitat elevades i constants en el temps, i per un nombre més elevat de tàxons sense adaptacions per passar situacions adverses; (2) la d'aigües semipermanents i temporànies d'inundació pulsativa, caracteritzada per una menor riquesa i diversitat, i per la dominància d'organismes amb estructures de resistència per passar la fase seca i aguantar condicions desfavorables, i (3) la d'aigües temporànies d'inundació continuada, caracteritzada per una major variabilitat de la riquesa i diversitat al llarg del cicle i per una singularitat taxonòmica més elevada, ja que s'observen cladòcers i una major representació taxonòmica dels insectes. Durant la realització d'aquest estudi els dos cicles d'inundació van suposar entrades d'aigua en el sistema diferents, per això es va diferenciar un cicle humit (1997-1998) i un de sec (1998-1999). En relació amb la major importància de les entrades d'aigua en el sistema, es va observar un contingut en nutrients de l'aigua significativament superior durant el cicle humit. Pel que fa al sediment, la seva major inèrcia explicaria la manca de diferències significatives en el contingut en nutrients del sediment del cicle humit i del sec. Ara bé, sí que s'observa diferència en la composició d'organismes. Així, la variabilitat interanual en l'estructura de la comunitat bentònica de la maresma es pot atribuir a una situació d'estrès provocada pel cicle sec. Aquesta situació va comportar un augment de la diversitat per disminució de la dominància a totes les llacunes estudiades, determinada, en gran manera, per la disminució de l'abundància original de poblacions dominants i característiques d'ambients permanents, Corophium orientale, o temporànies, Gammarus aequicauda. No existeix un patró estacional en les comunitats estudiades, sinó que els principals canvis en el plàncton i el bentos són deguts a pertorbacions hídriques. Aquestes pertorbacions provoquen que s'estableixi una situació en què dominen uns tàxons característics en el plàncton (Synchaeta i Eutintinnus) i, en canvi, que en el bentos es perdi l'estructura pròpia de les comunitats característiques dels diferents ambients (comunitats dominades per Corophium orinetale en aigües permanents i per Chironomus salinarius en temporànies). La severitat és diferent en funció del grau de permanència de l'aigua, i és més alta en ambients permanents i més baixa en els temporanis. La major severitat en ambients permanents ve determinada per la menor adaptació del bentos d'aigües permanents a les fluctuacions ambientals i a l'efecte de la predació sobre el plàncton. A més, tant en el bentos com en el plàncton es donen fenòmens d'histèresi, segons els quals l'efecte de la pertorbació no solament depèn de la causa pertorbadora sinó també de l'estat en què es troba la comunitat en el moment de la pertorbació., The structure and dynamic of the benthic system, and the main factors that control this system have been studied in coastal basins of the Empordà wetlands (NE Iberian Peninsula). During two hydroperiods (1197-1998; 1998-1999) organisms and sediment samples (nutrient and pigment analysis) have been taken monthly, and water samples (nutrient and pigment analysis) and physic and chemical parameters (Tª, Conductivity, Oxygen and pH) have been taken weekly. In these wetlands benthic organisms and sediment nutrient content were mainly determined by physics factors as water permanence, confinement and granulometry. Trophic factors were less important for the benthic communities than physics ones, as it has been shown by the nematodes associations. Based on the hydrological pattern, three types of basins are distinguished: permanent waters (type 1), temporary waters with pulse water inputs (type 2), and temporary waters with continuous water inputs (type 3). These three types are in agreement with the classification resulting from the benthic communities composition. The type 1 basins, where the more stable environemental conditions were found, had a community characterized by a high density of individuals, total biomass and diversity. The community of type 2 basins had lower richness and diversity values with little temporal variability. Organisms with resistant structures to pass the dry phase and survive adverse conditions were dominant in these community. The high frequency of freshwater inputs in type 3 basins causes a high taxonomic singularity and high temporal variability of species richness and diversity in these basins.The water input in the wetlands was significantly different for the two hydroperiods studied, so we can distinguish a wet hydroperiod (1197-1998) and a dry hydroperiod (1998-1999). Significantly higher nutrient content in the water was observed related to more important water entrance during the wet hydroperiod. The lack of significant differences on nutrient content of sediment between hydroperiods could be explained by a higher inertia in the benthic system. Differences in faunal composition were observed between hydroperiods. Thus, the interannual variability in the benthic community structure could be attributed to the stress situation caused by the dry hydroperiod. This situation implies a diversity increase due to a highest evenness because the dominant species decrease its relative abundance. The main plankton and benthos changes were due to hydrological perturbations, so seasonal patterns did not have any relevance to the studied communities. In the plankton community hydrological perturbations caused a new situation (situation dominated by Synchaeta and Eutintinnus), while in the benthos communities provokes a lost of the characteristic structure (characteristic structure were communities dominated by Corophium orientale in permanent waters, and by Chironomus salinarius in temporary waters). The severity varied depending on water permanence, so it was higher in permanent systems and lower in temporary ones. The higher severity in permanent systems was conditioned by the low adaptation to environmental fluctuations of the benthos which lives in permanent waters, and to the effect of predation on the plankton community. Moreover, histeresy phenomenons were observed, since the effects of perturbation were not only caused by the perturbation but also by the community status when the perturbation started.

82 pages.-- REGHAB Project: Report on Workpackage 2 – Deliverable no 7., The objectives of this workpackage are to synthesise the available data on the effects of gamebird management and hunting on biodiversity. In particular, the objectives of WP2 are to review available information on the effect of habitat management and species management (reinforcement of gamebird populations, predator control) on gamebird populations and on species other than gamebirds., Additionally, in order to evaluate whether quantitative estimates of the impact of hunting practices on biodiversity are currently possible at any scale, we review the available information on the extent of the implementation of the main management practices in each country/area. In particular, we review and discuss levels of implementation of different measures of habitat management, predator control, and restocking., REGHAB Project is funded by European Union Contract No. EVK2-CT-2000-200004 within the 5th Research Framework Program.