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Thesis (MScAgric (Conservation Ecology and Entomology)--University of Stellenbosch, 2005. / Benthic macroinvertebrates (sampled using South African Scoring System, SASS5) and adult male Odonata (sampled with close-focus binoculars) were recorded on two streams and a river of Soutpansberg, with the aim of determining the effect of invasion and removal of alien riparian vegetation on their assemblages. A secondary aim was to establish the importance of dragonflies as indicators of degree of disturbance in rivers. Forty two aquatic macroinvertebrate families and 33 adult Odonata species were recorded at a total of 71 sampling units. Three distinct riparian vegetation types were selected (natural, alien and cleared). Cleared vegetation refers to clearing of invasive alien trees, allowing regrowth of natural vegetation. Natural and cleared vegetation supported more benthic macroinvertebrate families compared to alien vegetation. Certain families that were lost to alien vegetation were recorded from natural vegetation. The highest SASS5 score was recorded from natural vegetation, followed by cleared vegetation, and the lowest was from alien vegetation. The highest number of adult Odonata was recorded at cleared vegetation, with alien and natural vegetation supporting the least number of Odonata species. Vegetation type, stream flow and microhabitats were statistically identified as the most influential variables for benthic macroinvertebrate assemblages. For adult Odonata assemblages, vegetation type, shade and temperature were the most important environmental variables. Species assemblages of adult Odonata can be used as indicators of environmental condition of rivers. The clearing of alien riparian vegetation clearly benefits the indigenous benthic macroinvertebrates as conditions are restored to their natural state. It also benefits dragonfly species richness, but if natural succession proceeds to a shaded tree canopy, the effect becomes similar to that of habitat shaded by alien vegetation. The impact of alien vegetation is to reduce sun-loving invertebrate species, especially dragonflies, with lesser impact on shade-loving species.

A ciclagem de matéria orgânica (MO) no ambiente marinho é um processo-chave para o ciclo global de carbono. Os sedimentos costeiros são de suma importância para a ciclagem de carbono pois atuam como receptores de grandes quantidades de MO alóctone (i.e. terrestre) e autóctone (i.e. marinho). A miríade dos componentes orgânicos e suas diferentes características dificultam o entendimento das fontes de MO em ambientes costeiros. Este trabalho visou entender a origem e a composição da MO (através de biomarcadores lipídicos) e a dinâmica da comunidade microbiana (método ATP) em sedimentos superficiais de diferentes ecossistemas marinhos da costa sudeste do Brasil: (i) margem continental de Cabo Frio; (ii) sistema lagunar de Saquarema; (iii) áreas costeiras e a plataforma continental de Ubatuba; (iv) e a plataforma adjacente ao estuário de Santos. Os resultados apontaram uma origem predominantemente autóctone para a MO nestes sistemas, com contribuição terrestre reduzida e limitada à áreas próximas à costa. Processos oceanográficos e forçantes ambientais são cruciais para a composição da MO sedimentar e são discutidas para cada um dos ecossistemas estudados. / The cycling of the organic matter (OM) in the marine environment is a key process in the global carbon cycle. Coastal sediments are important to the global carbon cycle, since they receive large inputs from both marine and terrestrial OM. The myriad of organic compounds and their spectrum of reactivity complicate the understanding of OM sources in coastal environments. In this work, we aimed to access the origin and composition of the OM (through lipid biomarkers) and the microbial dynamics (ATP method) in surface sediments of diverse marine ecosystems from the SE Brazilian coast: (i) the continental margin off Cabo Frio; (ii) the lagoonal system of Saquarema; (iii) coastal and shelf areas from Ubatuba; and (iv) the continental shelf adjacent to Santos estuary. The results showed a dominance of autochthonous OM, with a minor fraction of the OM derived from terrestrial sources and restricted to areas close to the coast. Oceanographic processes and environmental forces are crucial to the composition of sedimentary OM and are discussed for each of those ecosystems.

published_or_final_version / abstract / toc / Ecology and Biodiversity / Master / Master of Philosophy

A travers le monde, les zones côtières abritent une grande diversité d’ingénieurs de l’écosystème accomplissant des fonctions clés comme le recyclage de la matière organique et des nutriments. Les habitats résultants de l’activité biologique de ces espèces sont exposés à de nombreuses perturbations comme la surpêche, le piétinement ou via l’aménagement des côtes. Dans ce contexte, il est urgent de comprendre le fonctionnement de ces habitats ingénieurés et comment ils sont affectés par des perturbations croissantes. Pendant ma thèse, j’ai utilisé l’habitat récifal construit par le polychète grégaire tubicole Sabellaria alveolata comme cas d’étude. Tout d’abord, les changements environnementaux et biotiques associés à la mise en place d’un récif à S. alveolata et à sa perturbation croissante ont été évalué, se concentrant sur les paramètres du sédiment (e.g. granulométrie, contenu en matière organique) ainsi que la diversité taxonomique et les assemblages d’espèces. De manière similaire, le troisième article se penche sur le fonctionnement trophique de la communauté récifale et d’une communauté contrôle afin de comprendre les effets de la mise en place de l’espèce ingénieur sur les transferts de carbone, s’intéressant successivement à l’ensemble de la communauté des consommateurs, aux consommateurs primaires et à l’importance des sources de nourriture autochtones (microphytobenthos et Ulva sp.) vs allochtone (phytoplancton). Dans cette partie, j’ai utilisé les isotopes stables du carbone et de l’azote ainsi que différentes approches analytiques telles que des mesures de la niche isotopique et des modèles de mélange. L’article 2 a pour but de comprendre les interactions entre complexité de l’habitat récifal, hétérogénéité des sources de nourriture autochtones et échelles spatiales dans l’explication des variations du rapport isotopique du carbone de S. alveolata et d’un suspensivore associée. Dans les deux derniers chapitres, j’ai traité la question du fonctionnement de l’habitat ingénieuré de manière directe, en utilisant des incubations de carottes benthiques pour mesurer des flux biogéochimiques (e.g. demande en oxygène), ou indirecte, en utilisant des indices de diversité fonctionnelle et isotopique intégratifs. Cette dernière partie révèle l’existence d’un optimum de densité de S. alveolata, utilisée comme proxy des perturbations, où la niche trophique et le fonctionnement biogéochimique du récif sont tous les deux maximaux. / Coastal zones worldwide are home to a large diversity of ecosystem engineers that perform key functions such as the recycling of organic matter and nutrients. The habitats resulting from the biological activity of these species are exposed to numerous disturbances such as over harvesting and trampling or via coastal modification. In this context, it is becoming key to understand the functioning of these engineered habitats and how they are affected by increasing disturbances. During my PhD, I used the reef habitat built by the gregarious tubiculous polychaete Sabellaria alveolata as a study case. First, the environmental and biotic changes associated with the establishment of a S. alveolata reef and its increasing disturbance were assessed, focusing on sediment characteristics (e.g. grain-size distribution, organic matter content) along with taxonomic diversity and species assemblage. In the same vain, the third article looks into the trophic functioning of the reef community and a control community to understand the effects of the establishment of the engineer species on carbon transfers, successively looking at the whole consumer community, the primary consumers and the importance of autochthonous (microphytobenthos and Ulva sp.) vs allochthone (phytoplankton) food sources. In this part, I used carbon and nitrogen stable isotopes and different analytical approaches such as isotopic niche metrics and mixing models. Article 2 aims towards understanding the interactions between reef habitat complexity, autochthonous food source heterogeneity and spatial scales in explaining the carbon isotopic ratio variations of S. alveolata and an associated suspension-feeder. In the last two chapters, I address the functioning of the engineered habitat either directly, using benthic core incubations to measure biogeochemical fluxes (e.g. oxygen demand) or indirectly, through the use of integrative functional and isotopic diversity indices. This last part reveals the existence of an optimum value of S. alveolata density, used as a disturbance proxy, where the trophic niche and the biogeochemical functioning of the reef are both maximal.

Rapid Bioassessment Protocols integrate a suite of community, population, and functional metrics, determined from the collection of benthic macroinvertebrates or fish, into a single assessment. This study was conducted in Dallas County Texas, an area located in the blackland prairie eco-region that is semi-arid and densely populated. The objectives of this research were to identify reference streams and propose a set of metrics that are best able to discriminate between differences in community structure due to natural variability from those caused by changes in water quality due to watershed impacts. Using geographic information systems, a total of nine watersheds, each representing a different mix of land uses, were chosen for evaluation. A total of 30 metrics commonly used in RBP protocols were calculated. Efficacy of these metrics to distinguish change was determined using several statistical techniques. Ten metrics were used to classify study area watersheds according to stream quality. Many trends, such as taxa presence along habitat quality gradients, were observed. These gradients coincided with expected responses of stream communities to landscape and habitat variables.

Coral reefs are being negatively impacted by various causes worldwide, and direct intervention is often warranted following disturbance to restore or replace lost ecosystem structure and function. An experimental coral reef restoration study involving standardized artificial reef modules (ReefballsTM) was conducted in Mexico’s Yucatan Peninsula in the towns of Puerto Morelos and Akumal. The purpose was to explore the use of artificial structure for restoration and mitigation applications in a highly diverse and dynamic Caribbean coral reef environment by applying and evaluating the performance of select experimental treatments hypothesized to accelerate development of the associated biota. The first treatment consisted of invertebrate enhancing artificial substrate padding material, which provided structurally complex refuge space for mobile epifaunal/infaunal invertebrates and other benthic organisms. The second treatment consisted of coral transplants, intended to provide additional structural complexity and kick-start development of stony coral populations. The third treatment consisted of settlement plates which were intended to provide data on coral recruitment and survival rates. Multiple hypotheses relating to the interactions between experimental treatments and the resulting macroalgal, non-coral invertebrate, stony coral, and coral reef fish assemblages were examined, and comparisons were made between natural and artificial substrates. In Puerto Morelos there were 40 modules; 10 controls and 10 of each of 3 treatments: substrate pads, coral transplants, and settlement plates. In Akumal there were 12 modules; 6 controls and 3 of each of 2 treatments: substrate pads and settlement plates. Following module deployment, 6 biannual monitoring trips were made over the course of three years to assess the development of the biota, with a final 7th trip made six years post-deployment. Divers conducted non-destructive visual surveys to evaluate total abundance, species richness, size class distribution, and assemblage structure of coral reef fishes. Other monitoring work included coral recruit surveys, mobile epifaunal invertebrate collections from substrate pads, and digital imaging of coral transplants, natural reef reference corals, and benthic quadrat areas. Hurricane Dean compromised the Akumal study site during the first year of the study, but Puerto Morelos was unaffected. There the modules developed biotic assemblages that differed from what was found on the natural reef, and the data suggests that the substrate pads may have had an effect on the development of faunal assemblages. Lobophora variegata macroaglae and Desmapsamma anchorata sponge were the major contributors to benthic community composition, and both had significantly greater coverage on the substrate pads treatment modules. Lobophora grew rapidly and peaked within the first year, while sponges increased steadily throughout the first three years of the study, surpassing the coverage of macroalgae before the end of the second year, much to the detriment of coral transplants and many coral recruits. By the end of the study, over 75% of the transplants were overgrown by D. anchorata, and density of new coral recruits on the Pads treatment modules was lower than the other treatments and controls. Coral recruitment was dominated by Porites astreoides on all treatments and controls, and the number of corals increased steadily throughout the study. The controls had consistently greater numbers of corals than the treatments, as well as lower percent coverage of macroalgae and sponges. Total abundance and species richness of reef fishes was generally unaffected by the treatments. However, at the family and species level, several differences were detected, particularly for the substrate pads treatment and to a lesser extent for the coral transplants treatment. For future restoration or mitigation efforts utilizing similar or identical treatments to artificial substrates, this study suggests that, in the absence of routine maintenance, greater success may be achieved after waiting several years post-deployment for the initial wave of unchecked growth by benthic organisms (i.e., macroalgae and sponges) to reach a balance point before a large investment of resources is devoted to coral transplanting. Further recommendations include routine monthly or quarterly on-site maintenance to enhance transplant survival, as well as a longer monitoring window to assess community development in response to experimental treatments. The results of this study suggest that the experimental treatments did indeed have an effect on the biota, but whether or not the effect was beneficial largely depends upon perspective. The Pads treatment in particular had the greatest effect on both reef fish and benthic community development, however, it was not beneficial for stony coral recruitment. Additional research is needed to fully understand the long-term performance and effects of the padding material on biotic assemblage development for future restoration or mitigation projects.