Yes / Marine plastic pollution has a range of negative impacts for biota and the colonization of plastics in the marine environment by microorganisms may have significant ecological impacts. However, data on epiplastic organisms, particularly fungi, is still lacking for many ocean regions. To evaluate plastic associated fungi and their geographic distribution, we characterised plastics sampled from surface waters of the western South Atlantic (WSA) and Antarctic Peninsula (AP), using DNA metabarcoding of three molecular markers (ITS2, 18S rRNA V4 and V9 regions). Numerous taxa from eight fungal phyla and a total of 64 orders were detected, including groups that had not yet been described associated with plastics. There was a varied phylogenetic assemblage of predominantly known saprotrophic taxa within the Ascomycota and Basidiomycota. We found a range of marine cosmopolitan genera present on plastics in both locations, i.e., Aspergillus, Cladosporium, Wallemia and a number of taxa unique to each region, as well as a high variation of taxa such as Chytridiomycota and Aphelidomycota between locations. Within these basal fungal groups we identified a number of phylogenetically novel taxa. This is the first description of fungi from the Plastisphere within the Southern Hemisphere, and highlights the need to further investigate the potential impacts of plastic associated fungi on other organisms and marine ecosystems. / Conselho Nacional de Desenvolvimento Científico e Tecnológico. Grant Numbers: 407889/2013‐2, PQ 310597/2018‐8, PQ 312470/2018‐5, SWE 206250/2017‐7. Programa de Excelênca Acadêmica – PROEX. University of Salford Career Development Fellowship. Chevron Brasil Upstrem Frade Ltda. Brazilian Interministerial Commission for the Resources of the Sea (CIRM).

Doctor of Philosophy / Department of Biology / David A. Haukos / The lesser prairie-chicken (Tympanuchus pallidicinctus) is 1 of 3 prairie-grouse species in North America. Prairie-grouse have undergone local or widespread declines due to a loss of habitat through conversion to row crop agriculture, anthropogenic development, and alteration of ecological drivers that maintain quality grasslands. For lesser prairie-chickens, habitat loss and declines were deemed significant for listing as threatened under the Endangered Species Act in 2014. Despite a judge vacating the listing decision in 2015, the lesser prairie-chicken remains a species of concern. Conservation plans are currently being implemented and developed. To maximize the effectiveness of efforts, knowledge of the distribution of lesser prairie-chickens, regional demography, foods used during critical life-stages, and where to prioritize management is needed. To guide future conservation efforts with empirical evidence, I captured, marked with transmitters, and monitored female lesser prairie-chickens in Kansas and Colorado during 2013–2016 (n =307). I used location data to predict the distribution of habitat. Encounter data from individuals were used to estimate vital rates and integrated into a matrix population model to estimate population growth rates (λ). The matrix model was then decomposed to identify life-stages that exert the greatest influence on λ and vital rate contributions to differences in λ among sites. After assessing demography, I examined the diet of adults and chicks during critical brood rearing and winter periods using a fecal DNA metabarcoding approach. Overall, potential habitat appears to compromise ~30% of the presumed lesser prairie-chicken range in Kansas with most habitat in the Mixed-Grass Prairie Ecoregion. Within occupied sites, populations were most sensitive to factors during the first year of life (chick and juvenile survival), however, the persistence of populations through drought may rely on adult survival. Among regional populations, breeding season, nest, and nonbreeding season survival rates contributed most to differences in λ among sites, breeding season survival contributed to differences in λ among more and less fragmented sites. During critical life-stages, diets were comprised of arthropod and plant foods. Among 80 readable fecal samples, 35% of the sequences were likely from Lepidoptera, 26% from Orthoptera, 14% from Araneae, and 13% from Hemiptera. Plant sequences from 137 fecal samples were comprised of genera similar to Ambrosia (27%) Latuca or Taraxacum (10%), Medicago (6%), and Triticum (5%). Among cover types, lesser prairie-chickens using native grasslands consumed a greater diversity of foods. Last, promising conservation options include the conversion of cropland to grassland through the Conservation Reserve Program (CRP) and tree removal in mixed-grass prairie landscapes. Lesser prairie-chickens mostly used CRP during nesting and the nonbreeding season, during drier periods, and in drier portions of their distribution. Strategic CRP sign-up and tree removal could recover >60,000 ha and~100,000 ha of habitat respectively. In summary, conservation that targets management in areas within broad scale habitat constraints predicted will be most beneficial. In areas occupied by lesser prairie-chickens, management that increases brood survival in large grasslands having optimal nesting structure will elicit the strongest influence on population growth and will likely be the most resilient to stochastic drought-related effects.

Cette thèse s'inscrit dans le cadre du traitement des données issues de séquençage haut débit, et en particulier des données produites en metabarcoding ADN. Le metabarcoding ADN consiste à identifier des taxons ou des groupes taxinomiques à partir de l'ADN présent dans des échantillons environnementaux (eau, sol, fèces...). Après extraction de l'ADN, de courtes séquences utilisées comme marqueurs taxinomiques sont amplifiées par PCR puis séquencées en utilisant les nouvelles techniques de séquençage haut débit. De très importants volumes de données sont ainsi générés, le plus souvent, de plusieurs milliers à plusieurs centaines de milliers de séquences par échantillon. L'objectif principal de cette thèse était le développement de méthodes d'analyse de ces séquences. Les méthodes de classification permettent de traiter de nombreuses problématiques en metabarcoding ADN. La classification supervisée est utilisée pour assigner les séquences à des taxons en les comparant aux séquences de bases de données de référence. Les méthodes de classification non supervisée permettent de créer des groupes taxinomiques (MOTU) à partir des séquences, afin de faire des estimations de biodiversité. Ces méthodes sont aussi employées pour identifier les séquences erronées produites par la PCR et le séquençage notamment, où les séquences erronées dérivent souvent des vraies séquences et leur sont très similaires. Les méthodes de classification demandent une méthode de comparaison des séquences qui soit idéalement à la fois très rapide et exacte. Une telle méthode a été développée, en utilisant un algorithme d'alignement global de type Needleman-Wunsch calculant la longueur de la plus longue sous-séquence commune entre les séquences à aligner, associé à un filtre sans perte permettant d'éviter l'alignement de certaines paires de séquences n'ayant aucune chance de présenter une similarité supérieure à un seuil choisi. L'utilisation d'instructions Single Instruction, Multiple Data, de même que le multithreading optionnel des calculs, permettent d'associer rapidité et exactitude. Cette méthode de comparaison est implantée dans SUMATRA, un programme calculant toutes les similarités deux à deux d'un jeu de données ou entre deux jeux de données, avec possibilité de fixer un seuil de similarité en dessous duquel les similarités ne sont pas rapportées. Elle est aussi utilisée dans SUMACLUST. SUMACLUST est un programme regroupant les séquences en utilisant un algorithme de clustering en étoile, où chaque groupe possède une séquence représentative. Il peut être utilisé pour créer des MOTU, ou pour détecter les séquences erronées dérivant de vraies séquences. Plus spécialisé, le programme SUMACLEAN a été développé pour détecter les séquences contenant des erreurs ponctuelles de PCR. Pour cela, des graphes orientés acycliques sont générés, dont la topologie correspond parfaitement aux cascades d'erreurs générées par les erreurs ponctuelles de PCR. Par ailleurs, une réflexion a été menée pour le développement d'une nouvelle approche de classification supervisée pour l'assignation taxinomique des séquences. Aujourd'hui, la plupart des approches d'assignation utilisent des méthodes mal adaptées au polymorphisme important des marqueurs, et ne considèrent pas suffisamment l'incomplétude et les erreurs inhérentes aux bases de données de référence. Une nouvelle approche a été testée, basée sur l'idée d'un départ depuis la racine de l'arbre taxinomique, suivi d'une descente jusqu'à un arrêt possible lorsque descendre à un niveau taxinomique plus précis semble irraisonnable. Cela permettrait en théorie de mieux gérer les problèmes inhérents aux bases de données de référence, mais pose le problème de la représentation des séquences aux différents niveaux de l'arbre, et du modèle de choix du chemin à prendre, pour lesquels aucune solution complètement satisfaisante n'a été trouvée à ce jour. / This thesis positions itself in the context of the processing of high-throughput sequencing data, and specifically DNA metabarcoding data. DNA metabarcoding consists of the identification of taxa or taxonomic groups from DNA extracted from environmental samples (water, soil, animal feces). After extraction of the DNA, short sequences used as taxonomic markers are amplified by PCR, then sequenced using high-throughput sequencing technologies. Important volumes of data are produced that way, usually from several thousands to several hundreds of thousands sequences per sample. This thesis aimed for the development of methods for the analysis of these sequences. Classification methods allow the treatment of numerous problems in DNA metabarcoding. Supervised classification is used for the taxonomic assignment of sequences to taxa, by comparing them to the sequences of a reference database. Unsupervised classification methods are used to create taxonomic groups (MOTUs) from the sequences, in order to estimate biodiversity. They are also used to identify the erroneous sequences generated during the PCR and sequencing steps in particular, where erroneous sequences often derive from true sequences and remain very close to them. Classification approaches used in the context of DNA metabarcoding necessitate a sequence comparison method that should be both fast and exact. Such a method was developed, using a Needleman-Wunsch type global alignment algorithm computing the length of the longest common subsequence between the two sequences being aligned, associated with a lossless filter allowing to avoid the alignment of some pairs of sequences that have no chance to present a similarity superior to a chosen threshold. The use of Single Instruction, Multiple Data instructions, as well as the availability of multithreading speed up the calculations. This comparison method is implanted in SUMATRA, a program computing all the pairwise similarities of a dataset or between two datasets, with the possibility to set a threshold under which similarities are ignored. It is also used in SUMACLUST, a program grouping sequences using a star clustering algorithm, where each cluster possesses a representative sequence. This algorithm can be used to generate MOTUs, or to identify erroneous sequences deriving from true sequences, by using the fact that true sequences tend to end up as the representative sequences of their cluster. More specialized, the SUMACLEAN program was developed to identify sequences containing ponctual PCR errors. To that end, directed acyclic graphs are created, whose topology matches perfectly the successions of errors generated by ponctual errors during PCR. A new approach for the taxonomic assignment of sequences with a supervised classification method was also studied. Nowadays, most taxononomic assignment approaches use methods that are badly suited for the important polymorphism of markers, and don't take in account enough the incompleteness and errors inherent to reference databases. A new approach was tested, based on the idea of a start from the root of the taxonomic tree, and a descent in it with a possible stop before reaching a leaf, if descending to a more precise taxonomic level seems unreasonable. This approach would theoretically allow for a better handling of the problems inherent to reference databases, but poses a few issues, such as the representation of sequences at intermediate tree levels, and the model used to make choices regarding the path to take in the tree, for which no satisfying solutions have been found yet.

Analysis of soil-derived DNA has been shown to minimize problems seen during traditional vegetation surveys, e.g. by matching the eDNA to a reference database for taxonomic identification rather than relying solely on taxonomic expertise. However, it has been debated to what extent and how accurately eDNA acts as a proxy for biodiversity. The reliability on eDNA and the awareness on influencing factors is also important for palaeoenvironmental reconstructions where above-ground vegetation cannot be used. This study aimed to investigate how well modern soil-derived eDNA reflects the contemporary vascular vegetation communities in a subarctic environment, and if the efficiency of the taxonomic identification differed between spatial scales. Near-surface soil samples at altitudinal gradients along numerous transects were collected in combination with vegetation surveys. The eDNA was amplified through metabarcoding using the P6 loop region of the chloroplast trnL intron, followed by a high-throughput sequencing. No difference in the number of identified taxa between eDNA and vegetation survey was seen at landscape scale. In contrast, the number of identified taxa was consistently higher in the vegetation survey at smaller spatial scales. The efficiency of identified taxa per scale remained stable for the vegetation survey, whereas for eDNA, a decreasing trend was seen. This study highlights the variations on taxa identification between both methods and which factors might cause it. Combining the methods allows for a more precise modern biodiversity estimation, as well as to minimize wrongful conclusions. This allows for a more accurate palaeoenvironmental reconstructions, which in turn can improve future species conservation decisions.

Despite over four decades of research on deep-sea hydrothermal vent ecosystems, major gaps remain in our understanding of these systems. Knowledge of microeukaryote diversity, abundance, and involvement in ecosystem function lags far behind that of prokaryotes, and contributions of the non-endosymbiotic microbiome in faunal assemblages to ecosystem processes and overall hydrothermal vent microbial diversity are not known. This research addresses these gaps using high-throughput sequencing of 16S/18S rRNA genes and metagenomes from vent and surrounding non-vent habitats encompassing diffuse hydrothermal fluids, plumes, deep seawater, and microbes in assemblages of the foundation tubeworm species Ridgeia piscesae. Co-occurrence/covariance is a central method used, first, between prokaryotes with known extreme habitat preferences and microeukaryotes to infer potential endemism in the latter, and then between microbes and fauna in R. piscesae assemblages to infer interspecies interactions. Microeukaryote distribution and abundance suggest potential vent endemic microeukarya are infrequently encountered, potentially in low abundance, and belong to novel lineages of Rhizaria and Stramenopila. Potential endemism is inferred for relatives of known apusomonads, excavates, and some clades of Syndiniales. R. piscesae assemblages are shown to be hotspots of microbial taxonomic richness and exhibit a robust temperature-driven distinction in assemblage composition above and below ~25°C spanning micro, meio and macro size classes and microbial domains (Bacteria, Archaea, and micro-Eukarya). Likely interacting faunal and microbial taxa among R. piscesae assemblages are identified as ‘core communities’, which included eight macro- and meiofaunal taxa and members of the Bacteroidetes and Epsilonbacteraeota in highT communities (>25°C) and more meiofaunal species in addition to Alpha- and Gammaproteobacteria, and Actinobacteria in lowT communities (<25°C). Core communities were used to guide metagenomic investigations of microbial functional potential. Exploratory metagenomic analysis required development of new methods to deal with compositional data. ‘Enrichment leanings’ were developed to prioritize in-depth functional comparisons between sample types, which revealed clades within core community microbes with differing functional potential between highT and lowT assemblages and between assemblages and fluids. The balance of autotrophy-heterotrophy genes and patterns of genes for different carbon, nitrogen, and sulfur-cycling processes were tested as potential metrics of community-level function but did not distinguish assemblages by highT/lowT designations. This research brings us closer to understanding hydrothermal vent ecosystem function and suggests sizeable continued discovery potential. / Graduate / 2022-06-08

The global aquaculture industry is expanding to support increased demand in global markets and supplement traditional fisheries. The rapid increase of aquaculture production relies on introducing and using species outside their native range, posing significant regional environmental and socio-economic risks. Non-native species are selected based on transferable large-scale production protocols, fast growth, and existing market demand. Aquaculture is an important sector within Saudi Arabia’s Vision 2030 (anticipated >400% production increase by 2030). Barramundi (Lates calcarifer) was introduced into the Red Sea for open sea-cage farming in 2008, with large-scale production beginning in 2014. Regionally, there are numerous anecdotal reports of escape events of this species, including an incident in 2015 involving the release of ~300,000 fish. Since then, local fishers have caught up to 15 wild individuals per month in Al Lith, central Saudi Arabia. This study presents the first biological information on L. calcarifer aquaculture escapees in the Saudi Arabian Red Sea. Wild-caught L. calcarifer (n=5) were collected from a local fish landing and measured up to 10 kg, eight years of age, were sexually mature, and consumed benthic and coral reef fishes. In contrast, individuals in aquaculture facilities are harvested at < 1 kg and < 400 mm. In their native range, L. calcarifer can reach up to 200 cm and 60 kg. To assist in detecting and monitoring escapees within the Red Sea, I designed and validated a species-specific SYBR-based environmental DNA quantitative PCR assay targeting a 16S mitochondrial region of L. calcarifer rRNA (Barramundi_16S assay). Preliminary results, using DNA metabarcoding and environmental (seawater) samples, detected L. calcarifer near active/historical aquaculture farms and north/south of areas where this species has not been reported previously in the Red Sea (10–250 km from aquaculture facilities). In the future, the Barramundi_16S assay can screen additional eDNA samples (n=250) collected for this study to delineate the geographic range of barramundi in the Red Sea. Cumulatively, this study highlights the need to consider the ecological impacts of aquaculture escapees and provides managers and industry with valuable information and a novel molecular monitoring tool for detecting aquaculture escapees.

Understanding factors that influence a species' distribution and abundance across their annual cycle is needed for range-wide conservation planning. Every year during spring migration, thousands of federally threatened (U.S.A.) and endangered (Canada) migratory Western Atlantic red knots (Calidris canutus rufa, 'red knot') use Virginia's barrier islands as stopover habitat to regain the fat required to continue flights to breeding grounds. Because the red knot completes one of the longest avian migrations in the world and relies on variable prey resources at its stopover grounds, the red knot exemplifies the challenges faced by long-distance migrant shorebirds. These challenges may be exacerbated by climate change, as long-distance migrants may be unable to adapt quickly to changing prey ranges and abundances, resulting in spatial and temporal mismatches between predators and prey. More specifically, as climate change causes ocean temperatures near Virginia's barrier islands to rise, organisms that live within the intertidal zone, like blue mussels (Mytilus edulis), are experiencing range shifts. Here, we 1) confirmed what prey red knots select in Virginia, 2) addressed the factors that affect red knot site selection, red knot flock size, and prey abundances across Virginia's barrier island intertidal shoreline during 2007 – 2018, and 3) predicted the origin of juvenile blue mussels, a key prey resource for red knots in Virginia. To determine which prey are most available to red knots in Virginia, we collected sand and peat substrate core samples from Virginia's ocean intertidal zone and counted the number of prey in each sample. We compared these prey availability data to prey DNA data obtained from fecal DNA metabarcoding analyses on red knot feces (n = 100) collected on peat and sand substrates between 2017 – 2019. Red knots consumed prey from Orders Veneroida (clams), Mytiloida (mussels), Diptera (flies), and Amphipoda/Calanoida (crustaceans). While crustaceans were the most abundant prey on both sand (70.80% of total prey counted) and peat (74.88%) substrates, red knots selected crustaceans less than expected given their availability. Red knots selected clams and mussels, supporting their status as bivalve specialists in Virginia. After determining which prey red knots consumed and selected in Virginia, we predicted the number of red knots using Virginia's barrier island stopover during their migratory stopover (May 14 – 27, 2007 – 2018) annually. We used confirmed prey, tide, distance to known roosts, and red knot winter counts from Tierra del Fuego to inform zero-inflated negative binomial mixed-effects regression models of red knot site selection and flock size in Virginia. We also used generalized linear mixed-effects regression models to determine how climatic and geomorphological factors affected prey abundances. Modeled red knot peak counts were highest in 2012 (11,644) and lowest in 2014 (2,792; x̄ = 7,055, SD = 2,841); the trend over time was variable but there was no evidence of a linear increase or decrease. Red knots selected foraging locations with more prey, though red knot flock size did not consistently relate to prey abundance. Tide, substrate, and water temperature affected prey availability. While different prey responded to these covariates in variable ways, prey generally were most abundant on peat banks at low tide. Given the importance of blue mussels in the red knot's diet and distribution in Virginia, if the blue mussel's range continues to contract northward, red knots could be faced with additional fat replenishment challenges. We analyzed the variation in blue mussels from 2010 – 2018 by collecting core samples on peat banks in Virginia and counting the number of blue mussels in the cores. To approximate the origin of Virginia's juvenile blue mussels and determine how continued ocean temperature warming may further affect the blue mussel's range contraction, we conducted oxygen stable isotope (δ¹⁸O_c) analyses on 74 blue mussel shell umbos (the first portion of the shell precipitated) and shell edges (the most recently precipitated shell) to compare and predict where different portions of the shell were formed. We compared blue mussel shell compositions to δ¹⁸O_c calculated in equilibrium with regional ocean water using recorded δ¹⁸O_w data and sea surface temperature data from ocean buoys between New Hampshire and Virginia. Blue mussel abundance/core sample declined over the duration of our study (Spearman's rank correlation coefficient: ρ(rho) = -0.31, p < 0.001), with the highest abundance in 2010 (x̄ blue mussels/core sample = 537.88, SE = 85.85) and lowest in 2016 (x̄ = 34.08 blue mussels/core sample, SE = 6.96). Blue mussel umbos (x̄ δ¹⁸O_c = -0.23‰, SE = 0.12) contained more positive δ18Oc than shell edges (x̄ δ¹⁸O_c = -0.53‰, SE = 0.20), suggesting that Virginia's blue mussels originated from ocean populations in more saline and/or colder water than that within Virginia's intertidal zone. Blue mussel umbo δ¹⁸O_c were not different than δ¹⁸O_c calculated in equilibrium with regional ocean water off the Virginia and Delaware coasts, suggesting that Virginia's blue mussels originated in ocean waters between Delaware and Virginia; however, they may have originated in waters as far north as New York in some years, potentially decreasing the risk of blue mussels being completely extirpated from Virginia in the near future. While red knots currently use spring migratory stopovers across the United States' Atlantic Coast, from Florida to New Jersey, the largest spring concentrations of knots are confined to the Delaware Bay and Virginia's barrier islands. Because these stopover grounds support large proportions of the red knot's migratory population, any changes in the factors that affect red knots at these stopover sites could have lasting implications for red knots. The blue mussel's range contraction and decline over time in Virginia, for example, is concerning from a conservation perspective. Red knots require easily accessible and abundant prey resources to efficiently replenish fat-stores needed for continued migration and breeding. Additionally, because red knots breed within a narrow period, any delays on stopover grounds could prevent red knots from breeding, even if they survive migration. Our research demonstrates that red knots use prey abundance as a determinant when selecting foraging locations, and that peat banks, while only sporadically available across the barrier islands at mid- to low-tides, contain higher prey abundances than sand. Thus, to continue maximizing the availability of prey in Virginia, measures should continue to be taken to allow natural island migration processes that encourage the presence of both sand and peat substrates. Beach nourishment and stabilization projects are often used on coastal beaches to prevent shoreline erosion; however, such actions prevent the formation of peat banks by blocking island migration processes. A reduction in peat banks could decrease the abundance of prey available to red knots, making weight gain during the critical stopover period more challenging for red knots. Additionally, beach nourishment through sand replenishment buries invertebrate prey, potentially causing mass prey mortality and reducing shorebirds' ability to access deeply buried prey. To prevent the loss of important peat banks on these islands, and to prevent disrupting predator-prey interactions, managers should continue their ongoing focus on allowing natural processes to occur on Virginia's barrier islands. / Doctor of Philosophy / Red knots (Calidris canutus rufa) are imperiled shorebirds that migrate thousands of kilometers each year from wintering grounds as far south as Argentina to breeding grounds in the Canadian Arctic. To migrate such long distances, red knots use stopover habitat, like Virginia's barrier islands, to regain the fat required to continue flights to breeding grounds. Climate change is causing the ranges of important red knot prey, such as blue mussels (Mytilus edulis), to shift. Red knots may be unable to quickly adapt to changes in prey abundances on stopover grounds, making it more challenging for them to gain the weight required for successful migration and breeding. Thus, understanding the factors that may affect red knots in Virginia are important for successful management of this shorebird. Here, we determined what prey red knots consume in Virginia, addressed the factors that affect red knots in Virginia, and predicted the origin of blue mussels, an important prey resource for red knots in Virginia. We collected sand and peat substrate samples from Virginia's ocean intertidal zone to determine what prey were available to red knots and collected red knot feces to determine what prey red knots consume. Red knots consumed clams, mussels, fly larvae, and crustaceans in Virginia and showed preference for clams and mussels over the more abundant crustaceans. Red knots selected foraging locations that had higher prey abundances than unused sites. The relationship between red knots and prey was affected by the tidal cycle, with the highest abundance of prey available and most birds foraging at low tide when peat banks were exposed. After confirming that red knots preferentially consume blue mussels, which is experiencing a northward range contraction due to increasing ocean temperatures, we analyzed how blue mussel numbers have changed over time in Virginia. Blue mussel numbers declined over the duration of our study. We also analyzed blue mussel shells to help determine where the blue mussels were spawned, as shells contain environmental clues that relate to the conditions within which the shell forms. The juvenile blue mussels red knots consumed on Virginia's peat banks likely originated in ocean waters between Delaware and Virginia, but potentially in waters as far north as New York, possibly using ocean currents to travel to Virginia's intertidal zone. Because migratory stopovers, like Virginia's barrier islands, support a large percentage of the total red knot migratory population, any changes in factors that affect red knots during their spring stopover, like prey availability, may negatively affect red knots. Because red knots need to quickly consume large quantities of prey to gain the weight needed for continued migration and breeding, managers should continue to prevent factors that negatively affect prey in Virginia. For example, we found that peat banks support high quantities of red knot prey; thus, continuing to ensure that peat banks are able to form on the islands is paramount. However, peat banks form through shoreline erosion and overwash, two natural processes which are often portrayed negatively. Beach nourishment and stabilization projects are commonly used in other coastal areas to prevent shoreline erosion and overwash along coastal beaches. If Virginia's barrier island beaches are nourished, natural processes like shoreline erosion may be less likely to occur. The absence of shoreline erosion on Virginia's barrier islands would preclude the formation of peat banks, likely decreasing prey availability for red knots. Beach nourishment also buries invertebrate prey, as sand is deposited along the beaches' intertidal zone. The disturbance caused by nourishment combined with the reduction in prey caused by it could negatively affect red knots in Virginia. Managers should continue to protect both peat and sand substrates by further allowing natural processes, like shoreline erosion, to occur on Virginia's barrier islands.

No description available.

Dans les agroécosystèmes, les réseaux trophiques sont souvent structurés à partir de la plante d’intérêt agronomique, qui permet aux herbivores qui lui sont associés de se développer, notamment les bioagresseurs. La monoculture de bananiers a permis au charançon du bananier (Cosmopolites sordidus) de prospérer. Les larves de C. sordidus se nourrissent exclusivement de bananiers et provoquent leur chute, réduisant fortement le rendement dans la plupart des régions de production. Cette thèse a cherché à élucider la structure et le fonctionnement du réseau trophique de la bananeraie et particulièrement les interactions trophiques qui lient le C. sordidus aux autres espèces. L’objectif appliqué en ligne de mire était de favoriser les prédateurs généralistes pour augmenter la régulation naturelle de C. sordidus.1. Quel est l’effet de l’ajout d’une plante de couverture sur la prédation de C. sordidus ? En utilisant une variété de méthodes – isotopes stables, piégeage, infestation artificielle de bananiers, nous avons testé avec succès l’hypothèse selon laquelle l’enherbement induit, via le développement de proies alternatives, un changement de régime alimentaire des prédateurs généralistes, une augmentation de leurs abondances et une plus forte prédation des oeufs de C. sordidus.2. Quel est la structure du réseau trophique ? Nous avons combiné le séquençage haut-débit (technologie 454) avec le concept de codes-barres à ADN pour identifier les proies présentes dans le contenu stomacal des consommateurs. Nous avons utilisé un marqueur chloroplastique (boucle P6 trnL) pour identifier le bol alimentaire des herbivores, et un marqueur mitochondrial (mini-CO1) pour les prédateurs. Cette approche a permis de détecter des espèces qui n’avaient pas été échantillonnées, d’identifier les prédateurs naturels de C. sordidus au champ, et de quantifier les interactions à l’échelle des populations.3. Comment la structure du réseau trophique peut-elle influencer la régulation de C. sordidus ? Nous avons cherché les différents éléments structuraux (motifs) présents dans le réseau trophique de deux agroécosystèmes bananiers (sur sol nu et sur sol enherbé), et analysé leurs fonctions. Nous avons notamment décelé un motif composé de 4 espèces (2 ressources et 2 consommateurs) qui est représenté en grand nombre par rapport à un modèle neutre de réseau trophique. Ce motif s’est révélé systématiquement déséquilibré en faveur d’une proie, ce qui démontre qu’une distribution asymétrique des forces d’interactions permet de structurer le réseau. L’analyse de la position de C. sordidus dans les motifs décelés a permis de révéler ses interactions préférentielles avec les autres espèces de la communauté.Cette thèse montre comment le couplage de méthodes innovantes et complémentaires permet d’avoir une approche globale du fonctionnement trophique de l’agroécosystème. Les résultats montrent l’importance des ressources primaires (autres que la plante cultivée) sur la structuration du réseau trophique des arthropodes et sur le potentiel de régulation des bioagresseurs. Ce travail illustre également le lien entre la structure globale d’une communauté et l’évaluation des fonctions qui y sont associées / In agroecosystems, food webs are often structured from the crop, which enables the associated herbivores, including pests, to develop. For instance, monoculture in banana fields allowed the development of the banana weevil (Cosmopolites sordidus) populations. Borrowing larvae of C. sordidus cause banana plants topple over, which dampens the yield in most production areas. In this Ph.D. thesis, we attempted to disclose the structure and function of the banana food web, and particularly the trophic interactions that link banana weevil to others species. The applied perspective was to enhance population of generalist predators in order to increase the natural regulation of the pest.1. What is the effect of adding a cover crop on the predation of the pest?By using a variety of methods - stable isotopes analyses, trapping, artificial infestation of banana trees, we successfully tested the hypothesis according to which the addition of a cover crop, by enabling population of alternative preys to develop in the system, induces a change in predator diet, an increase of predator densities, and a greater predation rate on the eggs of C. sordidus.2. How is structured the food web?We combined next generation sequencing (454 technology) with the DNA barcoding concept to identify prey into gut contents of consumers. We used a chloroplastic marker (trnL) to identify the diet of herbivores, and a mitochondrial marker (CO1) for predators. This approach enabled the detection of unexpected species, the identification of the natural enemies of the pest, and the weighting of trophic interactions at the population scale.3. How can food web structure influence pest regulation?We searched structural elements (network motifs) occurring in the food webs of two banana agroecosystems (on bare soil and with cover crop), and we inferred the system functions. We detected the “bi-fan” size-4 motif, which occurred more frequently in the cover cropped food web than in random food webs. Interestingly, this motif was unbalanced for one of the two resources, illustrating the asymmetrical distribution of interaction strengths that shapes food web structure. The analysis of the position of C. sordidus within key motifs revealed its preferential interactions with other species of the community.This Ph.D. thesis emphasizes how linking innovative and complementary methods provides a comprehensive approach of the trophic functioning of the banana agroecosystem. Our results show the importance of primary resources (other than the cultivated crop) on the structure of arthropods’ food webs and on the pest regulation potential. This work also illustrates the link between the community structure and the evaluation of associated functions (i.e. pest regulation)

>Magister Scientiae - MSc / Aims DNA metabarcoding has recently emerged as a valuable supplementary tool to ensure food authenticity within the global food market. However, it is widely known that highly processed food samples are one of DNA metabarcoding’s greatest shortfalls due to high DNA degradation, presence of PCR inhibitors and the incomplete removal of several undesirable compounds (such as polysaccharides) that makes the amplification of desired DNA challenging. This project has two main aims, the first of which was to determine and develop a cost and time effective DNA metabarcoding system that could successfully describe to species level the ingredient composition of highly processed vegetarian food products. The DNA metabarcoding system was thoroughly evaluated and tested by combining well-researched primers with varying concentrations into a multiplex reaction. The combination of plant and animal primers selected that yielded the best results were used to determine the species composition in the samples. The second aim is to determine the possible presence of meat contaminants within the highly processed vegetarian food samples. Numerous studies have shown that food adulteration is a wide-spread phenomenon throughout the world due to the economic gains it can provide. Animal primers were introduced into the multiplex reaction to aid in the identification of any meat products that could have been inserted into the vegetarian products to lower the overall cost to company. Methodology Thirty-two highly processed vegetarian food samples were collected in the Cape Town area from local and franchised supermarkets. DNA was extracted using the Chloroform/Isoamyl alcohol method best suited for plant-based samples followed by amplification of the following mini-barcoding regions: the mitochondrial 16S ribosomal rRNA, cytochrome B, tRNALeu – trnL – UAA intron and the ribosomal internal transcribed spacer region – ITS2 for plant and fungi identification. The PCR products were purified using the Qiaquick kit and library preparation and building was conducted using the TruSeq DNA PCR-free Library kit. Final purification was completed using AMPure XP kit and the pooled libraries were sequenced on an Illumina Miseq using 300bp paired-end run. Statistical and bioinformatic analysis on the NGS raw sequence reads was performed in R version 3.6.3. Results The results of the data analysis showed that the cytochrome B primer couldn’t detect any animal DNA in the vegetarian samples, however animal-derived sequences were detected in the positives present, validating the efficacy of the multiplex reaction. Mitochondrial 16S ribosomal rRNA was only able to detect plant-based DNA due to the structural homology between chloroplast and mitochondrial DNA. The fungal ribosomal internal transcribed spacer region – ITS2 detected sequences deriving from “Viridiplantae”. This result could have been due to the fungal and plant ribosomal internal transcribed spacer region – ITS2 sharing a reverse primer during amplification. The trnL region was able to detect the presence of undeclared coriander, mustard and wheat in 8 (29%), 6 (21%) and 5 (18%) samples respectively. Additionally, trnL was able to detect the presence of tobacco in 11 (35%) samples. This could have been due to cross-contamination between samples being co-extracted and amplified at the same time for separate studies. The PITS2 region was able to detect the presence of undeclared barley, mustard and wheat in 8 (25%), 4 (14%) and 4 (14%) samples respectively. Our results show the possibility of DNA metabarcoding for the authentication of a wide range of species present in highly processed vegetarian samples using a single assay. However, further optimization of the technique for the identification of both plant and animal species within vegetarian samples needs to be performed before the wide-spread implementation of this technology would be both feasible and viable. Eliminating primer biases, decreasing the risk of homology between different primers in the same assay as well as preventing the amplification of sequencing of undesirable DNA need to be further explored and ultimately mitigated before DNA metabarcoding can be widely seen as an effective and cost-effective method for authentication and food control.