Viewing biofilms within the larger context of bacterial aggregations

The ‘Microbial Cities’ vision of bacterial biofilms has dominated our understanding of the development and functioning of bacterial aggregations for the past 20 years, during which active sludge, clumps, colonies, flocs, mats, pellicles, rafts, slimes, zooglea, etc. have been largely forgotten or ignored. Although the medically inspired developmental model of human pathogen biofilms has merits including providing a rationale for the development of anti-biofilm therapeutics, it fails to provide links to other types of bacterial aggregation that are commonly found in a wide range of natural and man-made environments. Possibly as a result, applied and environmental microbiologists tend to avoid the term ‘biofilm’ and use others such as ‘microbial mats’ instead. Here we challenge the simplistic planktonic (independent and free-swimming bacteria)-biofilm (sessile and co-operative bacteria) dichotomy, and consider biofilms within the larger context of bacterial aggregations. By placing biofilms into context, which we see as a continuum of aggregations or communities with varying abiotic and biotic properties, fundamental physical, biological, and evolutionary ecological processes that effect community development and function can no longer be considered unique to biofilms, but may also be important in other aggregations that develop over time and change in nature depending on prevailing conditions. By doing this, we will be better able to distinguish those processes which govern bacterial colonisation and ecological success in a wider sense from those that are unique to particular environments and specialised strategies.

The ecology and evolution of invasive Potamopyrgus antipodarum in Australia

The spread of invasive organisms is one of the greatest threats to ecosystems and biodiversity worldwide. Understanding the evolutionary and ecological factors responsible for the transport, introduction, establishment and spread of invasive species will assist the development of control strategies. The New Zealand mudsnail, Potamopyrgus antipodarum (Gray 1843) (Gastropoda: Hydrobiidae), is a global freshwater invader, with populations established in Europe, Asia, the Americas and Australia. While sexual and asexual P. antipodarum coexist in the native range, invasive populations reproduce by parthenogenesis, producing dense populations that compete for resources with native species. Potamopyrgus antipodarum is a natural model system for the study of evolutionary and ecological processes underlying invasion. This thesis assesses the invasion history, genetic diversity and ecology of P. antipodarum in Australia, with particular focus on: a) potential source populations, b) distribution and structure of populations, and c) species traits related to the establishment, persistence and spread of invasive P. antipodarum. Genetic analyses were carried out on specimens collected for this study from New Zealand and Australia, along with existing museum samples. In combination with published data, the analyses revealed low genetic diversity among and within invasive populations in south-eastern Australia, relative to New Zealand populations. Phylogenetic relationships inferred from mitochondrial sequences indicated that the Australian populations belong to clades dominated by parthenogenetic haplotypes that are known to be present in Europe and the US. These ‘invasive clades’ are likely to originate from the North Island of New Zealand, and suggest a role for selection in determining genetic composition of invasive populations. The genotypic diversity of Australian P. antipodarum was low, with few, closely related clones distributed across south-eastern Australia. The pattern of clone distribution was not consistent with any assessed geographical or abiotic factors; instead a few, widely-distributed clones were present in high frequencies at most sites. Differences in clone frequencies were found, which may indicate differential success of clonal lineages. A range of traits have been proposed as facilitators of invasion success, and within-species variation in these traits can promote differential success of genotypes. Using laboratory-based experiments, the performance of the three most common Australian clones was tested across a suite of invasion-relevant traits. Ecologically-relevant variation in traits was found among the clones. These differences may have determined the spatial distribution of clones, and may continue to do so into the future. This thesis found that the P. antipodarum invasion of Australia is the result of few introductions of a small number of globally-invasive genotypes that vary in ecologically-relevant traits. From a source of considerable genetic diversity in the native range, very few genotypes have become invasive. Those that are invasive appear to be very successful at continental scales. These findings highlight a capacity in asexual invaders to successfully invade, and potentially adapt to, a broad range of ecosystems. The P. antipodarum invasion system is amenable to research using combinations of field-based studies, molecular and laboratory approaches, and is likely to yield significant, broadly-applicable insights into invasion.

Evaluating conservation and fisheries management strategies by linking spatial prioritization software and ecosystem and fisheries modelling tools

Well-designed marine protected area (MPA) networks can deliver a range of ecological, economic and social benefits, and so a great deal of research has focused on developing spatial conservation prioritization tools to help identify important areas. However, whilst these software tools are designed to identify MPA networks that both represent biodiversity and minimize impacts on stakeholders, they do not consider complex ecological processes. Thus, it is difficult to determine the impacts that proposed MPAs could have on marine ecosystem health, fisheries and fisheries sustainability. Using the eastern English Channel as a case study, this paper explores an approach to address these issues by identifying a series of MPA networks using the Marxan and Marxan with Zones conservation planning software and linking them with a spatially explicit ecosystem model developed in Ecopath with Ecosim. We then use these to investigate potential trade-offs associated with adopting different MPA management strategies. Limited-take MPAs, which restrict the use of some fishing gears, could have positive benefits for conservation and fisheries in the eastern English Channel, even though they generally receive far less attention in research on MPA network design. Our findings, however, also clearly indicate that no-take MPAs should form an integral component of proposed MPA networks in the eastern English Channel, as they not only result in substantial increases in ecosystem biomass, fisheries catches and the biomass of commercially valuable target species, but are fundamental to maintaining the sustainability of the fisheries. Synthesis and applications. Using the existing software tools Marxan with Zones and Ecopath with Ecosim in combination provides a powerful policy-screening approach. This could help inform marine spatial planning by identifying potential conflicts and by designing new regulations that better balance conservation objectives and stakeholder interests. In addition, it highlights that appropriate combinations of no-take and limited-take marine protected areas might be the most effective when making trade-offs between long-term ecological benefits and short-term political acceptability.

Spatial behavior of two coral reef fishes within a Caribbean Marine Protected Area

A better understanding of the key ecological processes of marine organisms is fundamental to improving design and effective implementation of marine protected areas (MPAs) and marine biodiversity. The movement behavior of coral reef fish is a complex mechanism that is highly linked to species life-history traits, predation risk and food resources. We used passive acoustic telemetry to study monthly, daily and hourly movement patterns and space use in two species, Schoolmaster snapper (Lutjanus apodus) and Stoplight parrotfish (Sparisoma viride). We investigated the spatial overlap between the two species and compared intra-specific spatial overlap between day and night. Presence-absence models showed different diel presence and habitat use patterns between the two species. We constructed a spatial network of the movement patterns, which showed that for both species when fish were detected by the array of receivers most movements were made around the coral reef habitat while occasionally moving to silt habitats. Our results show that most individuals made predictable daily crepuscular migrations between different locations and habitat types, although individual behavioral changes were observed for some individuals across time. Our study also highlights the necessity to consider multiple species during MPA implementation and to take into account the specific biological and ecological traits of each species. The low number of fish detected within the receiver array, as well as the intraspecific variability observed in this study, highlight the need to compare results across species and individuals to be used for MPA management.

Phytoplankton versus macrophyte contribution to primary production and biogeochemical cycles of a coastal mesotidal system. A modelling approach

This study presents an assessment of the contributions of various primary producers to the global annual production and N/P cycles of a coastal system, namely the Arcachon Bay, by means of a numerical model. This 3D model fully couples hydrodynamic with ecological processes and simulates nitrogen, silicon and phosphorus cycles as well as phytoplankton, macroalgae and seagrasses. Total annual production rates for the different components were calculated for different years (2005, 2007 and 2009) during a time period of drastic reduction in seagrass beds since 2005. The total demand of nitrogen and phosphorus was also calculated and discussed with regards to the riverine inputs. Moreover, this study presents the first estimation of particulate organic carbon export to the adjacent open ocean. The calculated annual net production for the Arcachon Bay (except microphytobenthos, not included in the model) ranges between 22,850 and 35,300 tons of carbon. The main producers are seagrasses in all the years considered with a contribution ranging from 56% to 81% of global production. According to our model, the -30% reduction in seagrass bed surface between 2005 and 2007, led to an approximate 55% reduction in seagrass production, while during the same period of time, macroalgae and phytoplankton enhanced their productions by about +83% and +46% respectively. Nonetheless, the phytoplankton production remains about eightfold higher than the macroalgae production. Our results also highlight the importance of remineralisation inside the Bay, since riverine inputs only fulfill at maximum 73% nitrogen and 13% phosphorus demands during the years 2005, 2007 and 2009. Calculated advection allowed a rough estimate of the organic matter export: about 10% of the total production in the bay was exported, originating mainly from the seagrass compartment, since most of the labile organic matter was remineralised inside the bay.

DIFFERENTIATION OF ARBOREAL VEGETATION IN THREE SECTORS OF A FOREST FRAGMENT RELATED TO ITS HISTORICAL DISTURBANCES

Forest fragmentation is one of the main causes of biodiversity loss, directly affecting the ecological processes. This study aimed to evaluate tree diversity, structure, and composition parameters in three sectors of a forest fragment with distinct disturbance records. The arboreal vegetation was evaluated in twenty-four 10 × 10 m plots, sampling a total of 1,228 living individuals. We calculated Shanon’s diversity index, Pielou’s equability, and jackknife estimators of first and second orders. The sampled individuals were distributed in diameter classes and the importance value (VI) was calculated for each species. It was made a Detrended Correspondence Analysis (DCA) to verify whether there were significant distinctions between the sectors. It was noticed that the sector where there was clear cutting and vegetation burning in a recent past had higher abundance and richness but also the worst equability. That corresponds to the effects of perturbation as confirmed by the tree diameters and the presence of species of greater importance value. The sector that had no record of disturbance, situated in a location with greater variety of microenvironments, presented diversity, structure, and composition consistent with a no disturbance scenario. The other sector, which did not have clear cutting, was subjected to cattle trampling presented ecological parameters consistent with the absence of major disturbances. On the other hand, this third sector had the smallest environmental diversity, which puts this last sector in an intermediate situation.

Applied evolution: An integrated approach to studying life history traits in response to drug selection

The use of chemical control measures to reduce the impact of parasite and pest species has frequently resulted in the development of resistance. Thus, resistance management has become a key concern in human and veterinary medicine, and in agricultural production. Although it is known that factors such as gene flow between susceptible and resistant populations, drug type, application methods, and costs of resistance can affect the rate of resistance evolution, less is known about the impacts of density-dependent eco-evolutionary processes that could be altered by drug-induced mortality. The overall aim of this thesis was to take an experimental evolution approach to assess how life history traits respond to drug selection, using a free-living dioecious worm (Caenorhabditis remanei) as a model. In Chapter 2, I defined the relationship between C. remanei survival and Ivermectin dose over a range of concentrations, in order to control the intensity of selection used in the selection experiment described in Chapter 4. The dose-response data were also used to appraise curve-fitting methods, using Akaike Information Criterion (AIC) model selection to compare a series of nonlinear models. The type of model fitted to the dose response data had a significant effect on the estimates of LD50 and LD99, suggesting that failure to fit an appropriate model could give misleading estimates of resistance status. In addition, simulated data were used to establish that a potential cost of resistance could be predicted by comparing survival at the upper asymptote of dose-response curves for resistant and susceptible populations, even when differences were as low as 4%. This approach to dose-response modeling ensures that the maximum amount of useful information relating to resistance is gathered in one study. In Chapter 3, I asked how simulations could be used to inform important design choices used in selection experiments. Specifically, I focused on the effects of both within- and between-line variation on estimated power, when detecting small, medium and large effect sizes. Using mixed-effect models on simulated data, I demonstrated that commonly used designs with realistic levels of variation could be underpowered for substantial effect sizes. Thus, use of simulation-based power analysis provides an effective way to avoid under or overpowering a study designs incorporating variation due to random effects. In Chapter 4, I 3 investigated how Ivermectin dosage and changes in population density affect the rate of resistance evolution. I exposed replicate lines of C. remanei to two doses of Ivermectin (high and low) to assess relative survival of lines selected in drug-treated environments compared to untreated controls over 10 generations. Additionally, I maintained lines where mortality was imposed randomly to control for differences in density between drug treatments and to distinguish between the evolutionary consequences of drug treatment versus ecological processes affected by changes in density-dependent feedback. Intriguingly, both drug-selected and random-mortality lines showed an increase in survivorship when challenged with Ivermectin; the magnitude of this increase varied with the intensity of selection and life-history stage. The results suggest that interactions between density-dependent processes and life history may mediate evolved changes in susceptibility to control measures, which could result in misleading conclusions about the evolution of heritable resistance following drug treatment. In Chapter 5, I investigated whether the apparent changes in drug susceptibility found in Chapter 4 were related to evolved changes in life-history of C. remanei populations after selection in drug-treated and random-mortality environments. Rapid passage of lines in the drug-free environment had no effect on the measured life-history traits. In the drug-free environment, adult size and fecundity of drug-selected lines increased compared to the controls but drug selection did not affect lifespan. In the treated environment, drug-selected lines showed increased lifespan and fecundity relative to controls. Adult size of randomly culled lines responded in a similar way to drug-selected lines in the drug-free environment, but no change in fecundity or lifespan was observed in either environment. The results suggest that life histories of nematodes can respond to selection as a result of the application of control measures. Failure to take these responses into account when applying control measures could result in adverse outcomes, such as larger and more fecund parasites, as well as over-estimation of the development of genetically controlled resistance. In conclusion, my thesis shows that there may be a complex relationship between drug selection, density-dependent regulatory processes and life history of populations challenged with control measures. This relationship could have implications for how resistance is monitored and managed if life histories of parasitic species show such eco-evolutionary responses to drug application.

Análise da eficiência de indicadores da restauração ecológica em Mata Ripária no Cerrado, Planaltina - DF

Dissertação (mestrado)—Universidade de Brasília, Departamento de Engenharia Florestal, Programa de Pós-Graduação em Ciências Florestasi, 2015.

Sources de variation intra-populationelle de la morphologie des otolithes: asymétrie directionnelle et régime alimentaire

Otoliths are calcified structures located in Osteichthyes’ inner ear that are involved in audition and balance. Their morphology is used as an indicator of various ecological processes or properties. This application requires identifying the endogenous and exogenous factors that act simultaneously as sources of shape variation. This thesis aims at detecting and quantifying the relative contributions of directional asymmetry and diet to otolith shape variation at the intra-population level. Directional asymmetry between left and right otoliths was found in flat-fishes, the blind-side otolith being always longer and larger, whereas it was negligible in round-fishes. However, asymmetry amplitude never exceeded 18 %, which suggests evolutionary canalization of otolith shape symmetry. A correlation between global diet and otolith was detected in 4 species studied in situ. Diet composition contributed more than food amount to morphological variation and affected otolith shape both globally and locally. An experimental study on sea bass (Dicentrarchus larbrax) showed that diet composition in terms of essential polyunsaturated fatty acids at larval stage affects otolith morphogenesis during juvenile stage without impacting on individuals’ somatic growth. This result suggests a direct effect of diet on otolith shape and not an indirect one through the somatic-otolith growth relationship. This effect disappeared at later stages, morphogenetic trajectories converging back to a similar shape, which suggests ontogenetic canalization of otolith shape.

Use of acoustic telemetry techniques to understand the individual variability in movement ecology of juvenile lemon sharks, Negaprion brevirostris, in natural conditions, around Bimini Islands, Bahamas: a comparison study with preliminary personality traits observed in mesocosms

Dissertação de Mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2016

Abundance of sedentary consumers and sessile organisms along the wave exposure gradient of subtropical rocky shores of the south-west Atlantic

Sedentary consumers play an important role on populations of prey and, hence, their patterns of abundance, distribution and coexistence on shores are important to evaluate their potential influence on ecosystem dynamics. Here, we aimed to describe their spatio-temporal distribution and abundance in relation to wave exposure in the intertidal rocky shores of the south-west Atlantic to provide a basis for further understanding of ecological processes in this system. The abundance and composition of the functional groups of sessile organisms and sedentary consumers were taken by sampling the intertidal of sheltered and moderately exposed shores during a period of one year. The sublittoral fringe of sheltered areas was dominated by macroalgae, while the low midlittoral was dominated by bare rock and barnacles. In contrast, filter-feeding animals prevailed at exposed shores, probably explaining the higher abundance of the predator Stramonita haemastoma at these locations. Limpets were more abundant at the midlittoral zone of all shores while sea urchins were exclusively found at the sublittoral fringe of moderately exposed shores, therefore, adding grazing pressure on these areas. The results showed patterns of coexistence, distribution and abundance of those organisms in this subtropical area, presumably as a result of wave action, competition and prey availability. It also brought insights on the influence of top-down and bottom-up processes in this area.

APPLICATION OF REMOTE SENSING IN AQUATIC ECOSYSTEMS

I utilized state the art remote sensing and GIS (Geographical Information System) techniques to study large scale biological, physical and ecological processes of coastal, nearshore, and offshore waters of Lake Michigan and Lake Superior. These processes ranged from chlorophyll a and primary production time series analysies in Lake Michigan to coastal stamp sand threats on Buffalo Reef in Lake Superior. I used SeaWiFS (Sea-viewing Wide Field-of-view Sensor) satellite imagery to trace various biological, chemical and optical water properties of Lake Michigan during the past decade and to investigate the collapse of early spring primary production. Using spatial analysis techniques, I was able to connect these changes to some important biological processes of the lake (quagga mussels filtration). In a separate study on Lake Superior, using LiDAR (Light Detection and Ranging) and aerial photos, we examined natural coastal erosion in Grand Traverse Bay, Michigan, and discussed a variety of geological features that influence general sediment accumulation patterns and interactions with migrating tailings from legacy mining. These sediments are moving southwesterly towards Buffalo Reef, creating a threat to the lake trout and lake whitefish breeding ground.

Does Landscape Context Affect Habitat Value? The Importance of Seascape Ecology in Back-reef Systems

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created in various seascape contexts in Abaco, Bahamas. I found that the amount of seagrass at large spatial scales was an important predictor of community assembly on these reefs. Additionally, seascape context had differing effects on various aspects of habitat quality for the most common reef species, White grunt Haemulon plumierii. The amount of seagrass at large spatial scales had positive effects on fish abundance and secondary production, but not on metrics of condition and growth. The second part of my dissertation focused on how foraging conditions for fish varied across a linear seascape gradient in the Loxahatchee River estuary in Florida, USA. Gray snapper, Lutjanus griseus, traded food quality for quantity along this estuarine gradient, maintaining similar growth rates and condition among sites. Additional work focused on identifying major energy flow pathways to two consumers in oyster-reef food webs in the Loxahatchee. Algal and microphytobenthos resource pools supported most of the production to these consumers, and body size for one of the consumers mediated food web linkages with surrounding mangrove habitats. All of these studies examined a different facet of the importance of seascape context in governing ecological processes occurring in focal habitats and underscore the role of connectivity among habitats in back-reef systems. The results suggest that management approaches consider the surrounding seascape when prioritizing areas for conservation or attempting to understand the impacts of seascape change on focal habitat patches. For this reason, spatially-based management approaches are recommended to most effectively manage back-reef systems.

Enzymatic activity on sediments and nematode assemblage responses during seagrass beds habitat recovery following the disturbance of the traditional digging activity of bivalves harvesting.

Sediment digging is an anthropogenic activity connected to the exploitation of living resources in estuarine and marine environments. The knowledge on the functional responses of the benthic assemblages to the physical disturbance is an important baseline to understand the ecological processes of the habitat recovery and restoration and to develop tools for the management of the harvesting activities. To investigate the effects of the digging activity of the bivalves on Zostera noltii seagrass beds a manipulative field experiment was conducted that included the enzymatic activity of sediments and the associated nematode assemblages. Four plots (two undisturbed serving as control and two dug to collect bivalves - treatment) with 18 subplots were randomly located at seagrass beds in the Mira estuary at the SW coast of Portugal. Samples were randomly and unrepeatably collected from three subplots of each plot in five different occasions, before sediment digging (T0) up to six months after disturbance (T5). Microbial activity in sediments was assess by determining the extracelular enzymatic activity of six hydrolytic enzymes (sulfatase, phosphatase, b -N-acetilglucosaminidase, b-glucosidase, urease, protease) and two oxidoreductases (phenol oxidase and peroxidase). The microbial community status was also assessed through the measurement of dehydrogenase, which reflects microbial respiration. The nematode assemblages composition, biodiversity and trophic composition at different sampling occasions were also analyzed. The fluorometric and biochemical parameters analysed of the Z. noltii plants during the experimental period showed a recovery of the seagrass beds, and it was detected an increase of the enzymatic activity of the sediments after disturbance. The nematodes assemblages were similar in all sampling occasions. The seagrass beds and the nematodes assemblages associated showed a high resilience to the stress caused by the traditional bivalves digging activity. The obtained results allow the development of a management programme for the commercial fishing activity to maintain the good environmental status and minimized the secondary environmental effects on marine and estuarine habitats through the establishment of a baseline for the regulation of the harvesting frequency.

Marine palaeo-ecological and depositional processes on the shallow-waters of the Azores archipelago: the mobile Ostracoda (Crustacea) and the sessile Bryozoa as case-studies

Tese de Doutoramento, Biologia (Taxonomia Zoológica), 11 de Outubro de 2013, Universidade dos Açores.