Three approaches were employed to examine the effects of elevated sediment trace metal concentrations on estuarine/marine macrobenthic invertebrate assemblages. The initial study examined macroinvertebrate communities along a known polymetallic gradient, Lake Macquarie, NSW (gradient study). The second study experimentally tested if sediments sourced from different locations within Lake Macquarie differentially influenced the recolonisation of benthic invertebrates. The third study investigated the different recolonisation patterns of benthic invertebrates into sediments spiked with increasing concentrations of sediment-bound cadmium. In the Lake Macquarie gradient study, four locations (Cockle Bay, Warner's Bay, Kooroora Bay and Nord's Wharf) were sampled in winter 2000 and summer 2003 using a hierarchical design (location > site > plot). On both sampling occasions, the sediments showed strong gradients in lead, cadmium and zinc concentrations emanating from the Cockle Bay industrialised region in the lake's north, with concentrations being significantly lower in the most southern and less urbanised location (Nord's Wharf). In general, concentrations of lead, cadmium and zinc in the sediments increased among locations in the following order: Nord's Wharf > Kooroora Bay > Warner's Bay > Cockle Bay. AVSJSEM analyses indicated that in some sites in Cockle Bay, and to a lesser extent Warner's Bay, SEM concentrations exceeded their molar equivalence of AVS, indicating the potential for trace metals to be labile within the porewaters. Granulometry also changed along the gradient, with a higher proportion of silt/clay occurring in the locations with high metal concentrations. Conversely, the percentage of total organic carbon was higher in the less contaminated locations. In winter 2000, changes in benthic communities along the gradient supported the a priori hypotheses, with diversity and richness being greater in locations with lower concentrations of metals. Polychaetes were most numerous in Cockle Bay and Warner's Bay, whilst bivalves and gastropods were more abundant in Nord's Wharf and Kooroora Bay. Crustaceans were more numerous in Nord's Wharf; with all other locations having similar, lower, abundances. Ordination maps of the assemblages provided relatively clear separation of the assemblages among locations, with nonparametric multivariate analysis of variance (NPMANOVA) and subsequent pair-wise comparisons finding significant differences among the assemblages from all locations. SIMPER analyses found the highest level of dissimilarity was between the Nord's Wharf and Cockle Bay assemblages - primarily attributable to differences in the relative contributions of isopods; tellenid bivalves; and the polychaete families Spionidae, Opheliidae and Nephytidae. Weighted Spearman rank correlations (BIOENV) identified cadmium (Pw =0.74) as the strongest environmental (single or combination) variable to correlate with biotic assemblages. Benthic patterns along the gradient were less defined in summer 2003 due to a dramatic reduction in the abundance and diversity of fauna in Nord's Wharf. This decline was possibly attributable to a sustained reduction in salinity caused by a prolonged rainfall event. With the exception of Nord's Wharf, trends in the community indices and abundances of key taxa among the other locations were similar to those reported in winter 2000. Multivariate analyses discriminated the benthic assemblages from the four locations, with the findings from the NPMANOVA pair-wise comparisons indicating that the assemblages from all four locations were significantly different. SIMPER analyses showed the highest level of dissimilarity was between Nord's Wharf and Warner's Bay, with these differences being primarily attributable to their relative abundances of amphipods and polychaetes from the families Spionidae, Cirratulidae, Opheliidae and Capitellidae. BIOENV found that the combination of the sedimentary concentrations of cadmium and iron provided the best correlation (Pw =0.73) with biotic patterns, with similar correlations occumng with the addition of lead and its covariate, zinc (Pw =0.72). The combined findings from the gradient study established a strong correlation between trace metal concentrations within the sediments and suite of univariate and multivariate measurements. The low abundance and diversity of fauna in Nord's Wharf in the summer of 2003 highlighted the dynamic changes which can occur in the distributions of macrobenthic invertebrates. Although the study indicated that there was a strong relationship between trace metal concentrations and benthic community structure, the study was correlative, and requires subsequent experimental testing to confirm the causality of the observed relationships. The second component of the research was a translocation experiment using benthic recolonisation as an end-point. The experiment was performed to identify if the sediments, and not location, were influencing the composition of benthic assemblages in Lake Macquarie. Sediments were collected from three locations (Cockle Bay, Warner's Bay and Nord's Wharf), defaunated, and transplanted in three new locations along the south-east edge of the lake. At each location, 10 containers of each treatment were randomly placed in the sediment and allowed to recolonise for 22 weeks. Upon retrieval, the benthic communities were sampled and enumerated in conjunction with a variety of chemical and sedimentary measurements. Ten replicate invertebrate samples were also collected in the sediments adjacent to the experiment (ambient samples) at the completion of the experiment. Due to human interference, the containers from only two locations were analysed. Upon retrieval, pH and redox profiles of the sediments were similar to those expected in natural sediments. In general, concentrations of metals were low in the porewaters; however, iron precipitation on the porewater collection devices may have artificially increased the diffusion of metals, increasing concentrations near the sediment-water interface. Concentrations of SEM exceeded their AVS equivalence in some samples taken from the Cockle Bay and Warner's Bay treatments. Two-way ANOVAs found significant interactions between location and sediment treatments in diversity, evenness and the number of polychaetes, as well as significant differences in the number of capitellids and crustaceans among locations. Post-hoc comparisons of means found the Nord's Wharf sediment contained a higher mean number of individuals than the other treatments, including the ambient samples. nMDS ordination plots for both locations provided poor graphical discrimination of the assemblages among treatments; however, NPMANOVA detected significant location and treatment interactions. In both locations, pair-wise comparisons indicated that the assemblages within the Nord's Wharf treatments were significantly different to the Cockle Bay, Warner's Bay and ambient assemblages. No significant differences were detected between the Cockle Bay and Warner's Bay assemblages at either location. SIMPER analyses found the highest level of dissimilarity occurred between the ambient assemblages in Location 2 and the Nord's Wharf treatment, primarily due to the relative difference in the abundances of Capitellidae, Spionidae, Oweniidae, Nereididae and isopods among the assemblages. The findings from the translocation experiment suggest that the sediments are influencing the recolonisation of benthos. However, because differences were not detected between the Cockle Bay and Warner's Bay treatments, the approach used in the study shows potential as an in situ technique which could be used to assess the potential ecological risks of sediments fiom specific locations. Excluding cost and time considerations, the technique's primary disadvantage is the lack of a true control. As a result, the technique can only identify if the sediments are modifying benthic recolonisation, and not causality. The final component of the research experimentally tested if elevated concentrations of sediment-bound cadmium affected benthic invertebrate recolonisation. Sediments from the south coast of New South Wales (Durras Lake) were defaunated, and spiked with cadmium under anaerobic conditions to obtain three targeted cadmium concentrations: control (<O.1 ug/g), Low-Cd (15 Cd ug/g) and High-Cd (150 Cd ug/g). The physio-chemical properties of the waters and porewater concentrations of cadmium were monitored over a 28-day equilibration period, with declines in pH mediated with the addition of NaOH(aq). At the end of the equilibration period, porewater concentrations of cadmium were low in the Low-Cd and High-Cd treatments (maximum <l.5 ug/L in High-Cd), and below the detection limit in the control. Cadmium was not detected in the control sediments, with concentrations in the Cd-Low and Cd-High sediments exceeding their targeted concentrations, with final mean concentrations of 17 ug/g and 183 ug/g, respectively. The experimental design was similar to that employed in the translocation experiment, with 10 containers from each treatment transplanted into the sediments at three locations within Lake Macquarie. After 20 weeks, the containers were collected, along with benthic invertebrate samples from the ambient sediments. Data was not used from Location C due to extensive sediment deposition on the transplanted treatments. Significant declines occurred in the concentrations of cadmium in both the Low-Cd and High-Cd sediments, with the greatest loss occumng in the surficial sediments. The loss of cadmium was probably due to the differential loss of the fine fraction through physical means (hydrodynamic) rather than fluxing, as it assumed that the cadmium was primarily sediment-bound and relatively insoluble under anoxic conditions. Mean porewater concentrations of cadmium were below the detection limit in the control treatments; < 1 ug/L in the Low-Cd treatment, and generally < 2ug/L in the High-Cd, with the exception of some samples in Location B (maximum 5.6 ug/L) Concentrations of ammonia were low in the porewaters from the surficial sediments, with concentrations being significantly higher, and potentially toxic, in the anoxic porewaters (7 cm depth). In comparison to the previous recolonisation experiment, the number of individuals which recolonised the cadmium-spiked treatments was low, and significantly lower than the mean number of individuals sampled in the ambient sediments. No significant differences were detected among the treatments or locations (and their interactions) in diversity (H'), richness (d) or evenness (J). The number of polychaetes and molluscs significantly differed among the treatments, with post-hoc analyses indicating these differences were not among the cadmium-spike treatments, but were due to a greater mean abundance of these taxa in the ambient sediments. A significant interaction between treatment and location was detected in the mean abundance of crustaceans, with the ambient sediments having significantly lower mean abundances in both Location A and B. Ordination plots of the experiments in Location A and B provided poor graphical discrimination among the spiked treatments, although the ambient assemblages appear to be separated from the cadmium-spiked assemblages. NPMANOVA detected a significant interaction between treatments and locations, as well as among treatments. In both Location A and B, pair-wise analyses found the assemblages in the ambient sediments to be significantly different to the assemblages in all three cadmium treatments, with no differences being detected among the latter. SIMPER analyses found the highest levels of dissimilarity occurred between the spike-treatments and the ambient sediments, with these differences being primarily due to the relatively higher abundance of decapods in the spiked treatments, and capitellids in the ambient sediments. The cadmium-spiking component of the experiment clearly illustrated that artificially increasing the trace metal concentrations of metals in estuarine sediments is a complex process which needs to be performed in a methodological manner in order to obtain homogenous treatments with low porewater concentrations, and minimal artefacts. Furthermore, the results confirmed that the equilibration time for sediments can be extensive (several weeks), even in the case of organically rich sediments. The timing of the experiment (commenced late summer, February, 2003) appears to the major factor for the relatively low recolonisation rates, with the experiment missing the main larval recolonisation period between spring and early summer. Even in the highest treatment, elevated concentrations of cadmium did not appear to affect benthic recolonisation. This finding is supported by other experimental studies which suggest that concentrations of a single isolated metal must considerably exceed current guideline values (or contain high porewater concentrations) in order to elicit a biological effect. Nevertheless, as trace metals generally co-occur with other contaminants - with the response of multiple contaminants being possibly additive or synergistic - a conservative guideline value may be suitable in the interim as a precautionary measure. The findings of this thesis suggest that elevated concentrations of trace metal mixtures in estuarine sediments can affect the structure and composition of benthic communities; however, identifying causality is difficult. Although there has been an increase in the use of manipulative field experiments as a means of reducing the confounding influence of covariables found in field studies, this approach also has limitations, e.g. spatial and temporal scale issues, container effects, cost and biogeochemical changes to the sediments. Measuring stress at a community level is a fundamental component of estuarine risk assessment programs; and in isolation this approach can produce subjective and confounded findings. In order to accurately assess the risks associated with trace metal contaminated sediments, an integrated approach (e.g. weight of evidence) is required, one which uses multiple lines of evidence sourced from various chemical, environmental biological measurements.

Manmade radionuclides have been introduced to the environment for almost a century. The main source has been the nuclear weapons testing programmes, but accidental releases from the nuclear power production industries have also contributed. The risk to humans from potential releases from nuclear facilities is evaluated in safety assessments. Essential components of these assessments are exposure models, which estimate the transport of radionuclides in the environment, the uptake in biota, and transfer to humans. Recently, there has been a growing concern for radiological protection of the whole environment, not only humans, and a first attempt has been to employ model approaches based on stylised environments and transfer functions to biota based exclusively on bioconcentration factors. They are generally of a non-mechanistic nature and involve no knowledge of the actual processes involved, which is a severe limitation when assessing real ecosystems. The research presented in this thesis attempts to introduce a methodology for modelling exposure of biota that is based on systems ecological theories and concepts. All presented papers concern bioaccumulation and circulation of radionuclides in coastal areas of the Baltic Sea, which is a sea surrounded by several nuclear power plants, waste repositories and reprocessing facilities. Paper I illustrates how an ecosystem model can be used to predict the fate of C-14 in a bay, and to explore the influence of uptake route and water exchange on the concentrations in biota. Due to the longevity of many radionuclides, time spans of thousands of years need to be considered in assessments of nuclear waste facilities. In Paper II, the methodological problems associated with these long timescales are discussed and a new modelling approach is proposed. An extension and generalisation of the C-14 flow model into a generic model for other radionuclides is described and tested in Paper III. This paper also explores the importance of three radionuclide specific mechanisms (plant uptake, excretion and adsorption to organic surfaces) for the concentrations in biota. In Paper IV, the bioaccumulation kinetics of three radionuclides in three key benthic species of the Baltic Sea is studied experimentally. Paper V considers remobilisation and redistribution of sediment-associated radionuclides due to biological mixing, in a microcosm study. The findings in this thesis show both that it was possible to use an ecosystem approach to assess the exposure to biota, and that this approach can handle many of the problems identified in the use of traditional exposure models for radionuclides. To conclude, frameworks for the protection of the environment from ionising radiation would benefit from implementing methodologies based on ecologically sound principles and modelling techniques.

This thesis aims to increase our understanding of mechanisms that influence larval dispersal in marine benthic invertebrates, particularly in the absence of strong oceanographic features (e.g. estuarine plumes, upwelling events, or markedly different water masses). Laboratory experiments identified behavioural mechanisms that regulate the vertical distribution of larvae in response to thermal stratification, and field studies in St. George’s Bay, Nova Scotia (NS), Canada, examined the relationship between larval abundance and physical variables (temperature, salinity, fluorescence, etc) and identified mechanisms that regulate larval distributions in situ. In the laboratory, I demonstrated that thermal stratification affects the vertical distribution of larvae by acting as a barrier to migration, or through temperature-dependent vertical swimming velocities. I also developed a random walk based model which highlighted that the key to successfully simulating larval response to temperature was 1) determining the temperature-dependent distribution of vertical swimming velocities and 2) the temporal autocorrelation in these velocities. In the field, the most striking pattern was that the larval distributions for species with similar swimming abilities were significantly correlated to one another at all scales (0.5 to 40 km). This suggests a common mechanism, related to larval swimming ability, which greatly influences the horizontal larval distribution. I found that the spatial scale of variability in larval distributions (~ 3 km) matches that in both the environmental variables and of coherent structures in current velocities (i.e. the tidal excursion). Results from an aggregation-diffusion model suggest that horizontal larval swimming could not be responsible for the observed level of aggregation in the larval horizontal distributions. I suggest that these horizontal patterns are the result of 1) an aggregative process (i.e. larvae swimming against a vertical current and maintaining their vertical position) and 2) a diffusive process which scales the aggregations to the scale of the coherent structures in current velocity (i.e. tidal excursion). In conclusion, this thesis increases our understanding of larval behaviour and its effects on larval dispersal. The results will be particularly useful to those who are interested in mechanisms regulate population connectivity, particularly those using bio-physical models to model dispersal trajectories.

La production sonore biologique, étudiée par acoustique passive, doit être évaluée comme méthode complémentaire pour l’étude des effets des perturbations anthropiques sur les milieux côtiers.Alors que les sons émis par les mammifères marins et les poissons sont largement documentés, ceux issus des invertébrés benthiques restent peu décrits, même si ces derniers peuvent assurer des fonctions-clés dans les systèmes marins. L’enjeu principal de cette thèse était d’évaluer la pertinence de l’utilisation de l’acoustique passive comme outil écologique en s’appuyant sur la biophonie des invertébrés benthiques d’habitats côtiers tempérés et plus particulièrement en prenant comme habitat-modèle les bancs de maërl de la rade de Brest. Nous avons mis en évidence l’existence d’espèces sonifères remarquables qui constituent de bons candidats pour leur suivi en milieu naturel. Ces travaux ont de plus montré l’importante contribution de certains invertébrés benthiques dans le paysage sonore sous-marin, encourageant à ne plus imputer systématiquement les sons benthiques uniquement aux « crevettes claqueuses ». Le deuxième volet de cette thèse a montré que les variations de production sonore des invertébrés benthiques, à l’échelle individuelle ou collective, offrent des informations précieuses sur la mise en évidence de stress tels qu’un bloom d’algues toxiques ou l’impact du dragage. Ainsi, le nombre de mouvements sonifères des coquilles Saint-Jacques est doublé en présence de fortes concentrations d’algues toxiques, et le paysage sonore des bancs de maërl fortement pêchés est trois fois plus silencieux et moins complexe que celui du maërl préservé. Les résultats de ce travail de thèse, discutés dans un contexte de développement d’outils pour l’évaluation de l’état de santé des écosystèmes marins, permettent l’émergence de nouvelles hypothèses de travail en écologie marine. / Biological sound production, as studied by passive acoustics, should be considered as a complementary method to study the effect of anthropogenic disturbances on coastal systems. While sounds emitted by marine mammals and fish are well documented, those from benthic invertebrates are poorly described, although they can play key roles in marine ecosystems. The main goal of this PhD work was to evaluate the suitability of passive acoustics as an ecological tool based on sound production by benthic invertebrates living in temperate coastal habitats, and particularly in maerl beds of the Bay of Brest.We highlighted the existence of interesting soniferous species that appear to be good candidates to monitor in the field. This work also showed the important contribution of some benthic invertebrates to the underwater soundscape, suggesting that benthic sounds should not be attributed only to snapping shrimps. The second part of this PhD thesis emphasized that changes in benthic invertebrate sound production, at individual or collective scales, provides valuable information on the detection of stress such as a toxic algal blooms or the impact of dredging. Thus, the number of soniferous movements made by the great scallop doubles in the presence of high concentrations of toxic algae, and the soundscape of heavily fished maerl beds is three times quieter and less complex than preserved ones. The results of this PhD thesis, which are discussed in the context of tool development for the assessment of marine ecosystem health, raise new working hypotheses in marine ecology.

The inhabitants of marine benthos must combat the ecological pressure caused by predation, competition and fouling through a series of mechanisms, one of which is chemical defense. This type of protection is particularly extended among sessile and/or sluggish organisms, such as sponges, soft corals or ascidians. The strategies to prevent predation are related to bad taste rather than to toxicity. Moreover, they must be considered along with nutritional quality, since the more nutritious the prey, higher quantities or more potent repellents are needed to gain protection. The production of defensive secondary metabolites is energetically expensive. For this reason, the Optimal Defense Theory (ODT) predicts that defenses must be allocated in the most valuable or more exposed structures or body-regions. In Antarctic communities, the main predators are asteroids, and defensive agents are hence expected to accumulate in superficial layers of potential prey. But dense populations of amphipods, which associate opportunistically with biosubtrata, obtaining both refuge and direct or indirect sources of nutrition, are also very influencing on these bottoms. It has been reported that chemical defenses are very common in Antarctic organisms, in accordance with our results. However, the research effort has not been the same for all the groups, and there are still many aspects to learn on the chemical ecology, like the identification of the implicated products, their mode of functioning or their localization and origin. This PhD has focused on three relevant groups of the Antarctic benthos, quite understudied: hexactinellid sponges, soft corals and colonial ascidians. Two influencing sympatric predators were selected, the sea star Odontaster validus, which is a known model predator, and for the first time, the amphipod Cheirimedon femoratus, used to perform feeding experiments for the detection of repellent chemical defenses. We designed a new protocol which provided numerous methodological profits, as well as a remarkable discriminatory potential for unpalatable activities. In a survey with 31 species of Antarctic organisms, a larger incidence of unpalatable activities was recorded towards C. femoratus than against the asteroid, especially in algae and sponges, in which amphipods may particularly influence defenses distribution for representing potential host-preys. Some organisms instead, seemed to exploit alternative defensive strategies. The ecological success of the three studied groups is probably related to the presence of chemical defenses. In hexactinellid sponges these are weak, yet compensated with a low energetic content, and derive from primary metabolites, such as steroid derivates. Some glucosphingolipids instead, could have a chemotaxonomical value as chemical markers in rossellid sponges. In soft corals, chemical protection is obtained from products originating from both, primary (wax esters) and secondary metabolism (sesquiterpenoids), which seem to cooperate in an additive way, and are likely exuded within the coral mucus in living specimens. The use of primary metabolites for defense represents an effective energy saving strategy. In colonial ascidians, defensive secondary metabolites of terpenoid and alkaloid nature with potent bioactivities predominate, and in some species these are accumulated in internal tissues. Presumably, this distribution is related to the production of chemically defended lavae. Some bioactive secondary metabolites isolated from various sources, like the meridianins, may suggest a broad evolutionary retention, or a symbiotic origin. Regarding bacterial antifouling, ascidians exhibited poor activity, while some soft corals did display inhibition. With this work we provide the identification, localization, and possible origin of several defensive agents in three relevant groups of Antarctic benthic invertebrates. / Los habitantes del bentos antártico combaten la depredación, la competencia y el recubrimiento desarrollando mecanismos como la defensa química. Ésta estrategia está particularmente extendida entre organismos sésiles y organismos de cuerpo blando. Las defensas repelentes contra depredadores han de considerarse junto con la calidad nutricional, pues las dietas muy energéticas enmascaran la repelencia. La producción de metabolitos secundarios defensivos es costosa. Por ello, la Teoría de Defensa Optimizada (ODT) prevé que han de localizarse en las regiones corporales más valiosas o expuestas. En las comunidades antárticas los principales depredadores son las estrellas de mar y se postula la concentración de defensas en áreas superficiales en las presas. Pero también influyen las poblaciones de anfípodos asociados a los biosustratos, obteniendo en ellos refugio y fuente de alimentación. Esta tesis se centra en las defensas químicas de tres grupos relevantes del bentos antártico relativamente poco estudiados: esponjas hexactinélidas, corales blandos y ascidias coloniales. Se seleccionaron dos depredadores simpátricos, la estrella Odontaster validus y, por primera vez, fue utilizado el anfípodo Cheirimedon femoratus. Diseñamos un nuevo protocolo con numerosas ventajas metodológicas además de un gran potencial discriminatorio, y observamos que en 31 especies hubo mayor repelencia hacia el anfípodo que hacia la estrella, sobretodo en algas y esponjas, que podrían representar potenciales huéspedes-presa. A partir de aquí estudiamos muestras de los tres grupos seleccionados. En hexactinélidas, las defensas químicas son más débiles y derivadas del metabolismo primario, pero compensadas con un bajo valor nutricional. Algunos glucoesfingolípidos, podrían tener valor quimiotaxonómico como marcadores de la familia Rossellidae. En corales blandos existen metabolitos de defensa primarios y secundarios operando sinérgicamente, y probablemente forman parte del mucus superficial. En ascidias coloniales, los metabolitos defensivos son secundarios y muy potentes; además, en algunas especies éstos tienden a acumularse en tejidos internos, presumiblemente para producir larvas protegidas químicamente. Las ascidias mostraron poca actividad antibacteriana, pero algunos corales exhibieron respuestas inhibitorias. Esta Tesis proporciona la estructura, distribución y posible origen de los metabolitos responsables de las actividades defensivas en tres grupos relevantes de invertebrados antárticos.

Processes during the meroplanktonic phase regulate population dynamics for many marine benthic invertebrates. I examined changes in vertical distribution of different meroplanktonic larvae in a coastal embayment during a stable period, at high temporal frequencies and spatial resolutions. Plankton samples were collected at 6 depths (3, 6, 9, 12, 18, 24 m) using a pump, every 2-h over a 36- and a 25-h period, during a spring and neap tide, respectively, concurrently with measures of temperature, salinity, fluorescence and current velocity. For 10 gastropod taxa, larval vertical distribution was mostly related to the thermal structure of the water column. Each of 7 taxonomic groups was found either exclusively near the surface, associated with the fluorescence maximum, or showed diel changes in distribution. These larvae that occupy different depths in the water column exhibit different dispersal potentials. / Biogeographical data contained in this thesis will be submitted to the Oceanographic Biogeographic Information System (OBIS) and may be accessed on-line at http://www.iobis.org

Abstract Human activities have increasingly altered freshwater ecosystems. Land use is a major driver of habitat loss and land use-related input of nutrients and other pollutants from agriculture, forestry and urbanization have deteriorated water quality. Freshwater research has mainly focused on lakes and streams while the effects of anthropogenic stressors on groundwater-dependent ecosystems (GDEs) are poorly known. Likewise, the effectiveness of ecological restoration in mitigating human disturbance in GDEs remains understudied. In this thesis, I studied the effects of two main anthropogenic stressors – land drainage and groundwater contamination – on boreal spring ecosystems and evaluated the recovery of spring biodiversity and ecosystem functioning after habitat restoration. I applied several structural (macroinvertebrates, bryophytes, leaf-decomposing fungi and groundwater bacteria) and functional (organic matter decomposition and primary productivity) measures to provide a comprehensive insight into these issues. Both stressors modified spring ecosystems. Land drainage reduced the key ecosystem processes. Long-term monitoring of drainage-impacted springs showed a marked biodiversity loss and change of spring-dwelling bryophytes, and no signs of recovery were observed after about 20 years since the intial land drainage. Groundwater contamination, indicated by elevated nitrate and chloride concentrations, altered the structure of spring biota, reduced their taxonomic diversity and suppressed primary productivity in the most severely contaminated springs. Spring restoration improved habitat quality by reducing drainage-induced inflow of surface water, thus re-establishing groundwater-dominated hydrological conditions. Restoration increased abundance of habitat-specialist bryophytes and shifted macroinvertebrate composition towards natural conditions, despite the restoration actions being fairly recent. Anthropogenic activities can thus cause severe structural and functional degradation of spring ecosystems, and their self-recovery potential from these stressors seems low. Habitat restoration bears great promise as a cost-effective approach to mitigate drainage-induced impacts on spring ecosystems, but protection and co-management of groundwater resources are urgently needed to secure the role of springs as biodiversity hotspots in the boreal forest landscape. / Tiivistelmä Ihmistoiminta muuttaa yhä enemmän vesiekosysteemejä. Maankäyttö on johtanut elinympäristöjen häviämiseen, ja siihen liittyvä ravinne- ja haitta-ainekuormitus maa- ja metsätaloudesta sekä kaupunkiympäristöistä on merkittävästi huonontanut veden laatua johtaen maailmanlaajuiseen vesiluonnon monimuotoisuuden heikentymiseen. Vesiekosysteemien tutkimus on keskittynyt pääasiassa järvi- ja jokiympäristöihin, kun ihmistoiminnan vaikutukset pohjavesiriippuvaisiin ekosysteemeihin tunnetaan edelleen huonosti. Samoin kunnostusten merkitys pohjavesiriippuvaisten ekosysteemien tilan parantamiseksi on selvittämättä. Väitöskirjassani tarkastelin kahden keskeisen ihmistoiminnan – metsäojituksen ja pohjaveden laadun heikkenemisen – vaikutuksia lähde-ekosysteemeihin sekä arvioin elinympäristökunnostusten vaikutuksia niiden rakenteeseen ja toimintaan. Sovelsin työssäni rakenteellisia (pohjaeläimet, sammalet, lehtikariketta hajottavat sienet ja pohjavesibakteerit) ja toiminnallisia (eloperäisen aineksen hajoaminen ja perustuotanto) mittareita tuottamaan kattavan käsityksen tutkimuskysymyksiini. Sekä metsäojitukset että pohjaveden laadun heikkeneminen aiheuttavat muutoksia lähteiden rakenteessa ja toiminnassa. Metsäojitukset hidastavat keskeisiä ekosysteemitoimintoja ja johtavat lähdesammallajiston muutokseen ja monimuotoisuuden taantumiseen. Pohjaveden pilaantuminen, jota työssä ilmennettiin kohonneilla nitraatti- ja kloridipitoisuuksilla, heikentää lähdelajiston monimuotoisuutta, muuttaa lajikoostumusta ja johtaa perustuotannon laskuun voimakkaimmin kuormitetuissa lähteissä. Kunnostus parantaa lähde-elinympäristön laatua vähentämällä metsäojien aiheuttamaa pintavesivaikutusta palauttaen pohjavesivaltaisen hydrologisen tilan. Lähdekunnostusten myötä lähdesammaleet runsastuvat ja pohjaeläinyhteisön rakenne palautuu luonnontilaisten lähteiden kaltaiseksi, vaikka kunnostuksista on kulunut vasta muutamia vuosia. Väitöskirjan tulokset osoittavat, että ihmisen toiminta voi aiheuttaa muutoksia lähde-ekosysteemien rakenteessa ja toiminnassa ja lähteiden luontainen palautuminen häiriöstä on hidasta. Lähde-elinympäristöjen kunnostus vaikuttaa lupaavalta suojelutoimenpiteeltä metsäojitusten vaikutusten vähentämisessä, mutta lähteiden säilyttäminen monimuotoisena ja suojelullisesti arvokkaana luontotyyppinä edellyttää pohjavesivarojen hallinnan ja tilan suojelun tehostamista.

La compréhension de la dynamique spatiale et temporelle des peuplements benthiques qu’elle soit naturelle et induite par des forçages anthropiques, nécessite de nouvelles méthodes d'observation du benthos avec des besoins affichés de haute résolution temporelle et de longues périodes de mesures. L'enregistrement et l’analyse des sons produits dans l’environnement marin donnent accès au paysage acoustique, et notamment à l’une de ses composantes biologiques la biophonie benthique. Observer les variabilités spatio-temporelles de cette biophonie benthique, afin de contribuer à l'évaluation de la structure, du fonctionnement, de l’état et des évolutions du compartiment benthique, constitue l'objectif principal de la thèse. Pour ce faire nous avons développé deux outils permettant d'évaluer la variabilité spatiale de ces émissions avec un ou plusieurs capteurs. Le premier est un descripteur de la forme des spectres des impulsions du benthos permettant de mieux caractériser la diversité de la biophonie benthique. Le second est une méthode de localisation tridimensionnelle des sources sonores benthiques et de cartographie de cette biophonie pour des échelles spatiales allant de 500 mètres jusqu’à 5 mètres. En utilisant ces deux outils, nous avons démontré la faisabilité de l'observation du benthos au travers de sa biophonie sur des sites spécifiques. Dans une partie applicative, nous nous sommes intéressés aux projets de site de production d’énergies marines renouvelables et à la compréhension et à l’observation de leurs impacts sur la faune marine. Sur un site atelier de géométrie similaire à celle d’une ferme d’éoliennes offshores, nous avons défini, réalisé et analysé une preuve de concept pour l’observabilité d’un effet de type binaire : présence ou absence de faune fixée dans une surface sentinelle de quelques mètres carré. Les travaux de thèse ont été conclus par une étude mesurant le niveau sonore rayonné par une hydrolienne en phase de production d’énergie (Paimpol-Bréhat) puis évaluant les impacts acoustiques sur trois compartiments biologiques : les mammifères marins, les poissons et les invertébrés. / Understanding the spatial and temporal dynamics of benthic populations, both natural and induced by anthropogenic pressures, requires new observation methods with high temporal resolution and long periods of measurement. The recording and analysis of sounds produced in the marine environment give access to the soundscape, and in particular to one of its biological components, the benthic biophony. Observing the spatiotemporal variability of this benthic biophony, in order to contribute to the evaluation of the structure, functioning, state and evolution of the benthic compartment, is the main objective of the thesis. To do this we have developed two tools to evaluate the spatial variability of these emissions with one sensor or more. The first is a descriptor of the shape of the spectra of the benthic snaps allowing to better characterize the diversity of benthic biophony. The second is a method of three-dimensional localization of the benthic sound sources and mapping of this biophony for spatial scales ranging from 500 meters to 5 meters. Using these two tools, we have demonstrated the feasibility of benthos monitoring through its biophony at specific sites. In an applicative part, we were interested in sites of production of marine renewable energies and the understanding and observation of their impacts on the marine fauna. On a workshop site of geometry similar to that of an offshore wind farm, we defined, realized and analyzed a proof of concept for the observability of a binary impact: presence or absence of fixed benthic fauna in a sentinel area of a few square meters. The thesis work was concluded by a study measuring the sound level radiated by a tidal current turbine in the energy production phase (Paimpol-Bréhat) and then evaluating the acoustic impacts on three biological compartments: marine mammals, fish and invertebrates.

Förändring av markanvändning i avrinningsområdet påverkar vattendrags karaktärer som vattenkvalitet och biodiversitet. Inom EU och Sverige utvecklas åtgärdsprogram för att förbättra ekologisk status av påverkade vattendrag. Det finns fortfarande osäkerheter när det kommer till effekten som jord- och skogsbruk har på bottenfauna. I studien användes data från ett nationellt miljöövervakningsprogram. Med dessa testades om proportionerna mellan jord- och skogsbruk påverkade på bottenfaunans diversitet och ekologisk status. 25 vattendrag i södra Sverige valdes med över 60% av någon av marktyperna inom avrinningsområdet inom tidserien 2007–2011. Statistiska analyserna gjordes i tre steg där det linjära sambandet mellan variabler testades. I första steget testades andelen jordbruksmark mot bottenfaunans diversitet och ekologisk status. I ett andra steg testades vattenkemi och vattenföring mot bottenfaunans diversitet och ekologisk status. I det sista steget testades andelen jordbruksmark mot vattenkemi och vattenföring. Resultaten visade att andelen jordbruksmark inte hade en effekt på bottenfaunans diversitet och ekologisk status, men hade en effekt på artsammansättningen. Specifikt, andelen jordbruksmark hade en effekt på vattendrags MISA-index, som indikerar vattnets surhetstillstånd. Ju mer jordbruksmark det fanns inom ett avrinningsområde desto mer surhetskänsliga arter hittades i vattendraget. Resultat visade därför att artsammansättningen skiljs mellan skogs- och jordbruksmark men inte antalet arter. För bättre utveckling av åtgärdsprogram behövs strandzons vegetationens betydelse undersökas mer. / Changes in catchment land-use affect stream morphology, water quality and biodiversity. In EU and Sweden measures are taken to improve the ecological status of streams. There are uncertainties about how land-use in terms of agriculture and forestry affect benthic invertebrates. In this study, data from national environmental monitoring programs was used. To test how the proportion of agricultural land-use in the catchment influence benthic invertebrate diversity and ecological status. In total 25 streams in southern Sweden with more than 60% of either land-use type in the catchment and data from 2007-2011 were selected. Statistical analyses were performed with simple linear regression in three steps. In a first step, the proportion of agriculture was tested against benthic invertebrate diversity and ecological status. In a second step, water chemistry and waterflow were tested against benthic invertebrate diversity and ecological status. In the final step, the proportion of agriculture was tested against water chemistry and waterflow. The results showed that the proportion of agricultural land-use did not influence benthic invertebrate diversity or ecological status. However, it influenced MISA, an index of stream acidification. The higher proportion of agricultural land-use there where in the catchment the more acid sensitive taxa where found. This can be explained by the fact that species composition alters between agriculture- and forestry land-use but not number of species or Simpson diversity-index. For better development of action programs, the importance of the riparian vegetation should be further investigated.

Il est de plus en plus clair que nos écosystèmes sont liés les uns aux autres de façons multiples et parfois complexes. De plus en plus nous identifions de nouvelles façons dont deux systèmes échangent des ressources et de l’énergie. Le rôle de ces échanges et transferts est encore difficile à quantifier. Nous en savons relativement peu sur les interactions de ceux-ci avec des processus locaux et spatiaux, ainsi que sur leur importance relativement à ces processus locaux et régionaux plus connus. À travers ce projet, nous cherchons à éclaircir l’importance relative des subsides particulaires de feuilles (et particulièrement de leur stoechiométrie) sur les communautés littorales d’invertébrés benthiques. Nous avons récolté des invertébrés et des feuilles mortes sur 23 sites à travers 7 lacs relativement isolés de l’influence humaine et avons comparé l’influence de la stoechiométrie de ces subsides à l’influence de facteurs locaux de qualité de l’eau et de facteurs spatiaux. Les résultats suggèrent que l’importance de la qualité nutritive (i.e. stoechiométrie) est secondaire aux facteurs locaux de qualité de l’eau dans des milieux naturels. L’importance des subsides particulaires de feuilles semble être grandement dépendante du contexte et pourrait gagner en importance dans des contextes de fortes perturbations. Les résultats indiquent que la qualité nutritive des subsides de feuilles, leur contenu relatif en azote et phosphore, est associée avec de plus grande abondance de plusieurs taxons. La richesse spécifique n’étant pas affecté, c’est à travers l’équitabilité (i.e. une distribution des abondances plus stable) que la qualité nutritive des feuilles pourrait promouvoir une plus grande biodiversité d’invertébrés benthiques. / It is clear now, more than ever before, that our ecosystems are linked to one another in multiples and sometimes complex ways. The role of these exchanges and transfers is still hard to quantify. We know little of the interactions of these fluxes with local and spatial processes happening in ecosystems, as well as their relative importance compared to local and regional drivers of ecosystem functions and community structure. With this project, we aim to untangle the relative importance of particulate subsidies of leaves (and specifically their stoichiometry) on littoral communities of benthic invertebrates in lakes. We collected invertebrates and leaf litter on 23 sites across 7 lakes somewhat isolated from human influence and compared the influence of leaf litter stoichiometry to the influence of local water quality and spatial variables. Results suggest that nutritive quality of leaf litter (i.e. stoichiometry) is secondary to water quality. Importance of leaf subsidies appears to be context dependant and could gain in importance in systems with higher degrees of disturbances. Results that nitrogen and phosphorus content of leaf subsidies is associated with higher abundances of several taxonomic groups. Species richness being unaffected, it is through higher evenness (i.e. even distribution of abundances) that higher quality of leaves may promote higher biodiversity of benthic invertebrates.