Les herbivores invertébrés sont présents dans presque tous les habitats de la planète et peuvent grandement affecter la performance des plantes en nature. Que ce soit en communautés naturelles ou artificielles, une grande variation des taux d'herbivorie entre différentes espèces de plante [i.e. plantes] peut être observée. Ceci s'explique par le fait que les caractéristiques fonctionnelles des plantes, aussi appelées « traits », affectent les préférences des herbivores. Une espèce de plante, de par ces traits physiologiques, morphologiques ou phénologiques, peut donc décourager et/ou éviter l'herbivorie. La compréhension des relations entre les herbivores invertébrés et les traits des plantes est donc indispensable à la compréhension de l'assemblage des communautés herbivores-plantes. Cependant, les connaissances sur les liens entre les différents traits des plantes et la préférence des herbivores sont diffuses et incomplètes. Ce mémoire vise donc à quantifier et caractériser les effets de plusieurs traits fonctionnels de plantes herbacées sur la quantité de dommage foliaire faite par des herbivores invertébrés et à comparer ces effets entre monocultures et polycultures. Pour ce faire, j'ai participé au projet du Jena Experiment , une prairie expérimentale située en Allemagne visant à étudier la biodiversité. Cette prairie est exposée aux herbivores invertébrés naturels se trouvant sur le site de l'étude. Pour réaliser mon projet, les degrés d'herbivorie causés par les invertébrés ainsi que les valeurs de plusieurs traits fonctionnels des plantes ont été mesurés pour chacune de 51 espèces de plante [i.e. plantes] se trouvant sur le site d'étude. Travaillant d'abord avec des monocultures, sept traits sur 42 mesurés ont été sélectionnés dans une régression multiple en tant que prédicteurs importants de l'herbivorie. Le modèle est robuste et explique 63% de la variation en dommage subi par les espèces à l'étude. Parmi ces sept traits, deux sont physiologiques (concentration de lignine et d' azote dans les feuilles), deux sont morphologiques (architecture des racines et érection de la tige), un est phénologique (durée de vie du feuillage) et deux sont reliés aux herbivores (nombre d'espèces de coléoptère et d'hémiptère pouvant potentiellement prédater les plantes). Dans une seconde étape, à partir de l'herbivorie mesurée en monoculture et des sept traits sélectionnés dans le premier volet, trois modèles ont été développés pour prédire l'herbivorie dans des communautés formant un gradient de biodiversité de une à 60 espèces de plantes. Pour les trois différents modèles, le pouvoir de prédiction était faible; de 6 à 32% de variance en dommage foliaire expliquée. De plus, la déviation entre valeurs observées et valeurs prédites de l'herbivorie augmentait significativement avec l'augmentation du niveau de biodiversité dans les communautés. Les résultats de ce mémoire suggèrent que des patrons complexes de corrélation entre les différents traits des plantes existent et qu'il est donc nécessaire de travailler avec le plus de traits possibles pour identifier ceux qui contrôlent vraiment l'herbivorie. De plus, des interactions entre les différentes espèces de plante [i.e. plantes] d'une communauté semblent affecter de façon importante, directement ou pas, les dommages foliaires infligés par les herbivores invertébrés.Les conclusions de ce mémoire remettent en question l'importance relative des traits agrégés pour prédire des processus écologiques à facteur biotique tel que l'herbivorie et soulignent la complexité des relations entre deux niveaux trophiques.

Dissertação(mestrado)-Universidade Federal do Rio Grande, Programa de Pós-Graduação em Aqüicultura, Instituto de Oceanografia, 2009. / Submitted by Cristiane Silva (cristiane_gomides@hotmail.com) on 2012-07-27T00:36:17Z No. of bitstreams: 1 dissertao la costa.pdf: 778123 bytes, checksum: 5e1013f3ec79c5831a44cf3f91f24d2f (MD5) / Approved for entry into archive by Bruna Vieira(bruninha_vieira@ibest.com.br) on 2012-07-27T17:42:57Z (GMT) No. of bitstreams: 1 dissertao la costa.pdf: 778123 bytes, checksum: 5e1013f3ec79c5831a44cf3f91f24d2f (MD5) / Made available in DSpace on 2012-07-27T17:42:57Z (GMT). No. of bitstreams: 1 dissertao la costa.pdf: 778123 bytes, checksum: 5e1013f3ec79c5831a44cf3f91f24d2f (MD5) Previous issue date: 2009 / O presente experimento teve como objetivo avaliar o desempenho do camarão Litopenaeus vannamei e da tainha Mugil platanus em sistema de monocultivo e de policultivo. A criação dos organismos foi realizada em viveiros escavados, localizados no Laboratório de Aquacultura Continental da Universidade Federal do Rio Grande. Os viveiros com área aproximada de 200 m² foram previamente tratados com cal virgem e fertilizados com esterco bovino curtido. Os tratamentos, em triplicata, foram: monocultivo de camarão (CM); policultivo de camarão com tainha (P); e monocultivo de tainha (TM). As pós-larvas (PL) de camarão foram estocadas numa densidade de 10 PL m-2 com peso inicial de 0,02 g (± 0,003 g) e as tainhas na densidade de 0,67 peixes m-2, pesando inicialmente 1,67g (± 0,32 g). Peixes e camarões foram alimentados com ração comercial para camarão (38% PB) uma vez por dia. A quantidade de ração ministrada aos camarões inicialmente foi de 20% da biomassa total, decrescendo até 5% no final do experimento. Às tainhas, foi ofertada a quantidade de 5% da sua biomassa, durante todo o experimento. Os parâmetros físico e químicos da água foram registrados diariamente. O experimento teve duração de 79 dias durante o verão de 2007/2008. O acompanhamento do crescimento dos animais foi realizado por biometria semanal. No final do experimento foi verificado o ganho de peso, a taxa de crescimento específico, a conversão alimentar aparente, a sobrevivência e a produção dos animais cultivados, além do fator de condição para as tainhas. Os camarões em monocultivo apresentaram ganho de peso (15,59g), taxa de crescimento específico (8,40 % dia-1), conversão alimentar aparente (0,88), sobrevivência (91%) e produção (1.454 kg ha-1) significativamente maior (p < 0,05) do que no policultivo. As tainhas no policultivo apresentaram ganho de peso (42,72 g) e taxa de crescimento específico (3,99) significativamente maior (p < 0,05) que no monocultivo, enquanto seu fator de condição foi significativamente (p < 0,05) menor no policultivo (1,06). A conversão alimentar aparente das tainhas não apresentou diferenças significativas (p > 0,05) entre o monocultivo (2,50) e o policultivo (2,40). Os parâmetros físicos e químicos não foram significativamente diferentes (p > 0,05) entre os tratamentos adotados, com exceção da transparência que foi maior em viveiro de monocultivo de tainha. / The study objected to evaluate Litopenaeus vannamei (Boone, 1931) shrimp and Mugil platanus (Günther, 1880) mullet performance in monoculture and polyculture system. Culture of organisms was conducted in earthen ponds at Continental Aquaculture Laboratory of Rio Grande University. The ponds, with approximately 200 m², were early treated with lime and organic fertilization. The treatment were: shrimp monoculture (CM); shrimp and mullet polyculture (P); and mullet monoculture (TM), with three replicates. Shrimp post-larvae (PL) was stocked at a rate of 10 PL m-2 with mean initial weight of 0,02 g (± 0,003 g) and mullets were stocked at rate of 0,67 fish m-2, weighing 1,67g (± 0,32 g). The organisms have been fed with commercial meal to shrimp (38%PB) once a day at evening. Meal rate initially given to shrimp was 20% total biomass, it decreased until 5%, at the end of experiment. To mullets, it was given the same rate throughout experiment (5%). The water quality parameters were measured daily. Experiment had duration of 79 days in summer, from December, 5th, 2007 until February, 22th, 2008. Four biometry was done (at days 0, 30, 60 and 79) to accompany animals weight. At end experiment, gain weight, specific growth rate, feed conversion apparent rate, survival rate and yield of organisms cultured were analyzed. To mullets was analyzed too factor condition. Shrimp showed weight gain, specific growth, feed conversion apparent rate, survival rate and yield on monoculture significantly higher than on polyculture (p < 0,05). Mullet showed weight gain and specific growth rate significantly higher on polyculture (p < 0,05), while its condition factor was significantly higher (p < 0,05) on monoculture. There was no significant difference (p > 0,05) between feed conversion apparent rate of mullets among treatments. The water quality parameters had not significantly different between treatments, excepting transparency witch was biggest to mullet’s monoculture. The shrimp’s performance was suppressed in present mullets; it showed better zootechnic performance in monoculture.

L’aquaculture de la crevette bleue Litopenaeus stylirostris représente une activité profitable enNouvelle-Calédonie. Cependant, elle doit faire face à deux maladies bactériennes saisonnières quidiminuent les rendements et menacent le développement aquacole. D'après la littérature, lapolyculture avec des poissons pourrait diminuer l'occurrence des maladies, prévenir la dégradation del'environnement et au final augmenter la production des bassins. Cette étude porte sur la faisabilitéd'élever en bassins L. stylirostris avec Siganus lineatus. Les objectifs majeurs ont été 1) d’estimer lacapacité de S. lineatus à s’adapter aux bassins et d’évaluer les performances de croissance, 2)d’estimer la faisabilité technique de la polyculture de L. stylirostris avec S. lineatus et 3) d’estimer leseffets de cette polyculture sur les performances zootechniques des deux espèces et sur lefonctionnement écologiques des bassins par comparaison avec leur monoculture.Pour répondre au premier objectif, Siganus lineatus (5.7g) a été mis en culture à des densités de 7, 14et 21 poissons.m-2 en système clos. Après 8 semaines de culture, les performances de croissance de S.lineatus ont été similaires quelles que soient les densités. S. lineatus peut donc bien s’adapter etcroître dans ces systèmes clos, même à des températures basses, proches de 20°C, et à forte densité.Les fortes densités n’ont pas eu d’effets négatifs sur la croissance, mais sont à l’origine d’unedétérioration des conditions environnementales suite à un apport plus marqué en aliment générantdavantage de déchets organiques. En conséquence, une mortalité de S. lineatus peut apparaître lorsquela concentration en oxygène descend en dessous des 2 mg.L-1.Pour atteindre le 2ème et le 3ème objectif, une seconde expérience a montré que l’ajout de S. lineatus(25.5 g) à une culture de crevettes (2.9 g; 15 crevettes.m-2) à des densités de 0, 1.2 et 2.4 poissons.m-2n’a pas affecté les performances zooetchniques de L. stylirostris sur cette première phase d'élevage.La survie de S. lineatus a été de 100% et sa croissance a été similaire quelle que soit sa densité. Laproduction combinée totale pour les traitements polyculture a augmenté de 47 – 106 % et les indicesde conversions diminuent de 31.6 – 47.7% en comparaison avec le traitement "monoculture decrevettes". L'ajout de S. Lineatus n'a pas eu d'effets significatifs sur la production primaire, larespiration, les flux dissous et particulaires à l'interface eau-sédiment de l'écosystème bassin.Dans une troisième expérience, avec des biomasses initiales plus élevées de L. stylirostris (14 g) de156 g.m-2 en polyculture avec S. lineatus (19 g) (80 g.m-2) et de 237 g.m-2 en monoculture, nous avonsobservé une forte mortalité des crevettes. Inversement, avec des biomasses initiales de S. lineatus (19g) de 155 g.m-2 en polyculture avec L. stylirostris (14 g) (81 g.m-2) et de 235 g.m-2 en monoculture,nous avons montré une augmentation de la biomasse de S. lineatus. En utilisant l'aliment pour sapropre croissance non utilisé par les crevettes, S. lineatus est ainsi capable de limiter l'impact dû àl'eutrophisation de l'écosystème bassin.Les résultats des analyses isotopiques montrent que l'aliment n'est pas une source majeure de carbonepour L. stylirostris et S. lineatus alors qu'il l'est pour l'azote. Le biotope, en y incluant la matièreorganique des sédiments et la matière organique particulaire dans la colonne d'eau est la principalesource de carbone pour les deux espèces et une source secondaire pour l'azote.Pour conclure, S. lineatus est un candidat potentiel pour la culture commerciale / Blue shrimp Litopenaeus stylirostris farming is a major and profitable activity of aquaculture industryin New Caledonia. However, it is facing two seasonal bacterial diseases, which decrease rearedshrimp yield and threaten the sustainability of the aquaculture development. As reported by theliterature, polyculture with fish would have the potential to decrease the impact of these kind ofdiseases, prevent the deterioration of the environment and to increase the production of the ponds. Thefeasibility of L. stylirostris and Siganus lineatus polyculture in earthen ponds was carried out in thisstudy. The main objectives were 1) to estimate the adaptive capacity and growth performance of S.lineatus, and the environmental variations in a closed culture system, 2) to estimate the technicalfeasibility of L. stylirostris and S. lineatus polyculture, and 3) to estimate the effects of L. stylirostrisand S. lineatus polyculture on zootechnical performances and pond ecology in comparison withmonoculture of these species.To answer to the first objective, Siganus lineatus (5.7g) was stocked at 7, 14 and 21 fish.m-2 in aclosed culture system. After 8 weeks of culture period, S. lineatus growth performance was similarbetween all densities. S. lineatus could well adapt and grow in a closed system, even at lowtemperature, ca. 20oC and high stocking density, 21 fish.m-2. High stocking density did not havenegative effects on S. lineatus growth performance, but could cause the environmental deteriorationdue to increased nutrient input and accumulated organic wastes in the culture system. Asconsequence, S. lineatus could die when water oxygen depleted to below 2 mg.L-1.To reach the second and the third objective, a second experiment showed that adding S. lineatus (25.5g) to L. stylirostris (2.9 g) culture system (15 shrimp.m-2) at 1.2 and 2.4 fish.m-2 did not affect L.stylirostris zootechnical performance during the first stage of the rearing. S. lineatus gained 100% ofsurvival and similar growth performance in all densities. The polyculture system increased totalcombined production by 47 – 106 % and reduced FCR by 31.6 – 47.7% compared with those inshrimp monoculture. The addition of S. lineatus to the culture system did not have significantlyeffects on the gross primary productivity, the respiration, the nutrient and particulates fluxes at thewater-sediment interface of the pond ecosystem.In a third experiment, using higher stocking biomasses of L. stylirostris (14 g) at 156 g.m-2 in apolyculture with S. lineatus (19 g) (80 g.m-2) and at 237 g.m-2 in shrimp monoculture, we observed ahigh shrimp mortality. Conversely, stocking biomasses of S. lineatus (19 g) at 155 g.m-2 in apolyculture with L. stylirostris (14 g) (81 g.m-2) and at 235 g.m-2 in monoculture resulted in increasesof S. lineatus biomasses. This study showed that polyculture using S. lineatus is able to reduce organicwastes and nutrient release by consumption uneaten feed and retention input nutrients in biomass thatcontribute to limit the impact of the pond ecosystem eutrophication.Results of stable isotope analyses showed that the used pellet feed was not a major carbon source, butwas an important nitrogen source for both L. stylirostris and S. lineatus. Natural biota, includingsediment organic matter and particulate organic matter, was a main carbon source and represented asa secondary nitrogen source for both species.It may be concluded that S. lineatus is a suitable candidate for commercial culture in bothmonoculture and polyculture with L. stylirostris in earthen pond. Polyculture should be a properapproach that could partly contribute to sustainable development of aquaculture, but needs specificresearch to optimize the trophic status of the reared species.

Tilapia culture in Indonesia was started with the Mozambique Tilapia (Oreochromis mossambicus) in the 1930’s, and the Nile Tilapia (Oreochromis niloticus) the 1960’s. The genetic improvement program of the Nile Tilapia, has led Indonesia to be one of the main tilapia producers in the world. On the other hand, shrimp aquaculture in the country was not started until the 1960’s, it became more popular after the eye ablation technology for broodstock maturation was developed in the early 1980’s. The first experimental study was conducted to investigate the feasibility of low salinity shrimp farming in a polyculture system with tilapia. Polyculture increased the survival for shrimp (77% compared to 62%), but at the same time decreased the survival of tilapia (87% compared to 97%). Together, the data on survival, specific growth rates, and feed conversion ratios showed that the shrimp performed well at low salinity. The second experimental study investigated the feasibility of brackishwater shrimp farming in a polyculture system with tilapia. Polyculture increased the survival for shrimp (82% compared to 65%), and had higher survival for the tilapia (60% compared to 43%). The Red hybrid Tilapia strain used in the study experienced mortalities after one month, suggesting the need for a salt tolerant strain. The presence of tilapia stimulated the growth of microalgae (Chlorella dominance), promoted higher numbers of heterotrophic bacteria in the water, and had lower presumptive vibrios on TCBS agar. A challenge study was conducted by mixing pathogenic luminescent Vibrio harveyi UAZ-651 into shrimp and tilapia feed. The survival of shrimp in monoculture were significantly lower (20%) compared to in polyculture systems (75 - 95%). Mortality was not found in tilapia. Based on 16S rRNA gene sequence, shrimp monoculture water was dominated by marine Vibrio spp., while the polyculture system had Bacillus spp. and Vibrio spp. with high homology to V. cholerae. The presence of Bacillus spp. which produce a lactonase enzyme AiiA, seems to inhibit vibrio growth. While providing advantages, shrimp-tilapia polyculture might also contribute to streptococcosis transmission. Injecting shrimp with Streptococcus iniae and S. agalactiae resulted in mortalities. S. iniae caused higher mortality in the shrimp cultured in 20 ppt (40%) compared to 10 ppt (20%), and no mortality in 5 ppt. S. agalactiae caused higher mortality in 5 ppt (40%) compared to 10 ppt (20%) and 20 ppt (20%). Quorum sensing (QS) is a density dependent cell to cell communication process in bacteria. Based on challenge studies in shrimp, the luminescent Vibrio harveyi BB120 wild-type strain caused 75-90 % mortality through injection of 106 CFU/shrimp. The mortality patterns in the QS mutants suggest that QS defined, when specific virulence genes were expressed or repressed. As QS in V. harveyi consists of three different circuits, further experiments deployed six mutants lacking either a synthase or a receptor for each circuit. The highest survival in the CqsS (a receptor for CAI-1 circuit) mutant group indicates that the CAI-1 circuit is the most crucial for virulence, followed by the AI-2 and HAI-1 cascades. Chitin acquisition and oxygen scavenging may be two reasons for luminescence in V. harveyi evolution and why they infect shrimp.

There are currently numerous alternative food production models that may have potential to contribute substantially to improved environmental sustainability. However, such alternatives are not well studied, particularly within the context of the Canadian Prairies. To increase knowledge in this area, this thesis performed a preliminary agronomic trial for food grain production in intermediate wheatgrass (Thinopyrum intermedium), investigating the effects of legume intercropping and residue management. Mean grain yields were 520 and 447 kg/ha in 2014 and 2015, respectively, and a significant yield increase was observed following grazing with sheep. A series of farm case studies were also conducted in order to characterize ecological farming approaches on the Canadian prairies. The most consistent strategy among the farms was to increase diversity in multiple facets for both environmental and economic benefit, including more crop and livestock species, system and landscape components, and marketing strategies. / October 2016

Les exploitations de polyculture-élevage sont de plus en plus reconnues au plan international comme limitant les problèmes environnementaux tout en permettant une agriculture productive et économiquement viable. Les incitations à la spécialisation de la PAC et la diminution de la main d'oeuvre agricole les ont néanmoins marginalisées en Europe. Cette thèse vise à éclairer les conditions de maintien d'exploitations de polyculture-élevage durables. Un travail en partenariat avec des agriculteurs, maires et conseillers agricoles a été conduit sur un cas d'étude en zone défavorisée simple française, les Coteaux de Gascogne. Nos travaux ont montré que, malgré une forte variabilité entre exploitations, la polyculture-élevage locale était un bon compromis par rapport à la spécialisation pour une durabilité environnementale et économique. Une analyse des trajectoires passées des exploitations nous a permis d'éclairer quatre types de « chemins pour durer » en polyculture-élevage. Parmi ceux-ci, deux sont apparus pertinents pour le maintien de la polyculture-élevage en contexte incertain : « maximiser l'autonomie » et « diversifier les ateliers ». Sur la base de ces deux types de trajectoires, nous avons co-construit avec les partenaires deux scénarios techniques prospectifs. Pour le type « maximiser l'autonomie », implanter des intercultures fourragères basées sur des légumineuses permettrait de favoriser l'autonomie alimentaire du troupeau en maintenant la fertilité des sols. Pour le type « diversifier les ateliers », finir des génisses permettrait de les valoriser en circuit court. Ces scénarios ont été adaptés puis simulés sur des exploitations locales. Ce type de démarche a permis i) d'impliquer fortement les acteurs locaux via des réunions collectives et ii) une approche prospective originale fondée sur une étude rétrospective intégrant le temps long. / Mixed crop-livestock farms are again attracting worldwide interest, as they are considered to be a good way to limit environmental problems while allowing a productive and economically viable agriculture. The incentives of the Common Agricultural Policy and decreasing workforce availability nevertheless marginalized these farms in Europe. This thesis aims at understanding the conditions for a survival of sustainable mixed crop-livestock farms. A partnership process with farmers, mayors and technical advisers has been led in a French less favoured area, the Coteaux de Gascogne. Our work has shown that even if a wide variability existed between farms, local mixed crop-livestock farming was a good trade-off compared to farm specialization concerning an environmental and economic sustainability. An analysis of farm past trajectories allowed us to enlighten four “paths to last” in mixed crop-livestock farming. Two of these ones appeared to be suitable paths to maintain mixed crop-livestock farms in a uncertain context: “maximizing autonomy” and “diversification of production units”. On the basis of these two types of trajectories, we have co-constructed with local actors two technical prospective scenarios. In line with the type “maximizing autonomy”, forage legume intercropping could enable to autonomously feed the bovine herd while maintaining soil fertility. In line with the type “diversification of production units”, fattening heifers would allow a commercialization through short circuit. These scenarios have been adapted and then simulated on local farms. This type of approach allowed to i) strongly involve local actors through collective meetings and ii) an original future study based on a retrospective study integrating long time changes.

Research into the polyculture of finfish and crayfish has been conducted in Western Australia for over a decade now. This research was instigated out of a need to increase revenues from freshwater crayfish farmers wishing to diversify their income base with a view to increasing profitability and reducing risk. It has become clear that several key variables dictate how the polyculture system (i.e. polysystem) will perform. These include biological factors like: size of participating species, relative densities, gender, planktonic turbidity, natural feeds; and abiotic factors like: light intensity, clay turbidity, floating cages for segregation, water quality, and habitat/shelter complexity. Many of these factors can be controlled / adjusted by the manager of the polysystem to maximise performance, production and profitability.While much of the research to date has focussed on the marron (Cherax tenuimanus) industry, it is also important to realise that an understanding of these factors can also assist other crayfish polysystems, like integrated agri-aquaculture systems containing yabbies (Cherax albidus). Some of the factors that influence how the system will perform may become more prevalent, like suspended clay turbidity and the associated role of light intensity in species interactions, or shelter complexity and the resulting choice of shelter material. But overall, they are the same basic variables and we must understand how they affect the particular multi-species system that we are dealing with. There is a lot to be learned from the literature on how these variables affect multi-species aquatic environments in the wild. Perhaps aquaculturists have not considered this enough in the past. Some farmers seem to believe that these variables are different JUST because it is a culture system. This is not true. / The variables will take on different levels in a culture system (i.e. a manager will stimulate turbidity, provide artificial feeds, stock different sizes, and supply particular types of shelter) BUT the actual variables themselves (e.g. food, density, light, shelter) are basic to ALL aquatic ecosystems. Other researchers have looked at important factors like density, gender, and light intensity / turbidity in crayfish polysystems - but the issue of habitat complexity and the role of shelter has not been adequately addressed. This thesis will investigate some basic questions about shelter and endeavour to apply them to crayfish polysystems, with the emphasis on marron (C. tenuimanus) and yabbies (C. albidus) because these are the two most commercially important species of crayfish in Western Australia. Importantly, it should be noted that due to the invasive nature of yabbies, and their apparent ability to displace native marron in the wild, findings will be related to yabby-marron competition / displacement where relevant. We need to know many things about shelter: what type is best in a multi-species system? Should the shelter size match the crayfish size? Do marron have different requirements for shelter than yabbies? Does it matter who gets first use of a shelter (i.e. prior residence effect)? Can we learn about crayfish shelter requirements by examining the behaviour / plasticity of crayfish species? If crayfish are stocked with finfish and they retreat into shelter as a predator-avoidance measure, is the complexity important given that their densities will be higher? If densities of crayfish inside shelters are higher in polysystems, will cannibalism be a concern, particularly when conditions are right for moulting? Does visual recognition and / or chemo-detection of a predator affect the shelter usage by marron or yabbies? / Does temperature affect shelter usage behaviour for a burrowing species like yabbies? Shelter is an important factor in the life history of a freshwater crayfish and an understanding of its influence on different species is important for maximising system performance. Crayfish are categorised depending on their ability to construct shelters (i.e. burrows). Yabbies have evolved in systems with fluctuating water quality and many predators and, as such, have learned to burrow (to escape drought and also to escape predators). Marron, on the other hand, are a non-burrowing native crayfish species that have existed with relatively few predators in the South-West. As a result, marron are less capable of modifying their behaviour when confronted with a predator (i.e. low behavioural plasticity). Species with high plasticity, like yabbies, are more capable of adapting to new environments, because they can change their behaviour to increase their chance of survival. Therefore we can expect yabbies and marron to utilize habitats differently and we should compare these behaviours as a basis to developing management strategies. This type of knowledge may also assist with managing the translocation and spread of yabbies in the wild and their displacement of native marron.Within multi-species systems, the physical structure of shelter plays an important role inprotecting crayfish and the perfect shelter would not only provide safety from co-stocked finfish, but also from conspecific cannibalism. Given the different life histories and behaviours, it is probable that both species of crayfish will have different refuge requirements.Over the course of this four-year investigation, trials were conducted in four culture systems (72L aquariums, 300L circular tanks, 80t mesocosm tank, and 720m2 earthen ponds) using marron and yabbies as the species of interest. / Silver perch and Murray cod were chosen as the finfish species of interest as they appear to have the highest aquaculture potential for native freshwater finfish in Australia at the present time. Further, both of these fish have been documented as potential predators of crayfish, resulting in a challenge to understand the role of shelter in minimising the negative effects of fish-crayfish interactions within a polysystem. This study has confirmed that shelter plays a critical role in multi-species system dynamics. In the case of polysystems, it will affect both interspecific and intra-specific interactions, ultimately governing production and profitability, along with the other, previously defined factors. This means that the manager of a polysystem can influenceproductivity by understanding: a) the behavioural characteristics and biology of the crayfish; b) the feeding biology of the finfish; and c) the system variables (both biotic and abiotic) that will affect the overall well being of the fish and crayfish. In the case ofshelter, the manager should understand the available shelter types, the appropriatedensities, the importance of matching complexity to the crayfish size, and the prior residence effect when choosing a timing strategy for stocking and harvesting. Prior residence increased resource holding potential for both marron and yabbies in the short term. In fact, prior residence was a stronger determinant of successful sheltering than crayfish gender or species. However, in longer-term trials the physical size of the crayfish (larger animals evicted smaller animals) and reproductive status (berried females were successful at evicting all other crayfish) were more important factors in determining successful shelter acquisition, although the temporal variations (i.e. growth and release of young) complicate the issue. / When stocking crayfish of different sizes, and in polysystems, the correct size of shelter becomes critical, as smaller individuals will be forced to leave over-sized shelter and locate a shelter commensurate with their own body size to avoid predators. This is relevant to crayfish nurseries where complex habitat is paramount for juvenile cohorts that display variation in sizes and gender. The expansion of crayfish polyculture holds considerable promise; however, furtherinvestigations are required into shelter complexity within floating fish cages, shelter types and arrangement of shelters within ponds (for increased production and ease-of-harvesting), potential of yabbies in polyculture (comparison of monosex and hybrid strains), and the impact of shelter on escape behaviour of marron in a polysystem.

abstract: ABSTRACT Sustainable global energy production is one of the grand challenges of the 21st century. Next-generation renewable energy sources include using photosynthetic microbes such as cyanobacteria for efficient production of sustainable fuels from sunlight. The cyanobacterium Synechocystis PCC 6803 (Synechocystis) is a genetically tractable model organism for plant-like photosynthesis that is used to develop microbial biofuel technologies. However, outside of photosynthetic processes, relatively little is known about the biology of microbial phototrophs such as Synechocystis, which impairs their development into market-ready technologies. My research objective was to characterize strategic aspects of Synechocystis biology related to its use in biofuel production; specifically, how the cell surface modulates the interactions between Synechocystis cells and the environment. First, I documented extensive biofouling, or unwanted biofilm formation, in a 4,000-liter roof-top photobioreactor (PBR) used to cultivate Synechocystis, and correlated this cell-binding phenotype with changes in nutrient status by developing a bench-scale assay for axenic phototrophic biofilm formation. Second, I created a library of mutants that lack cell surface structures, and used this biofilm assay to show that mutants lacking the structures pili or S-layer have a non-biofouling phenotype. Third, I analyzed the transcriptomes of cultures showing aggregation, another cell-binding phenotype, and demonstrated that the cells were undergoing stringent response, a type of conserved stress response. Finally, I used contaminant Consortia and statistical modeling to test whether Synechocystis mutants lacking cell surface structures could reduce contaminant growth in mixed cultures. In summary, I have identified genetic and environmental means of manipulating Synechocystis strains for customized adhesion phenotypes, for more economical biomass harvesting and non-biofouling methods. Additionally, I developed a modified biofilm assay and demonstrated its utility in closing a key gap in the field of microbiology related to axenic phototrophic biofilm formation assays. Also, I demonstrated that statistical modeling of contaminant Consortia predicts contaminant growth across diverse species. Collectively, these findings serve as the basis for immediately lowering the cost barrier of Synechocystis biofuels via a more economical biomass-dewatering step, and provide new research tools for improving Synechocystis strains and culture ecology management for improved biofuel production. / Dissertation/Thesis / Doctoral Dissertation Biological Design 2016

Made available in DSpace on 2014-06-11T19:22:23Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-08-24Bitstream added on 2014-06-13T20:09:27Z : No. of bitstreams: 1 ribeiro_fas_me_jabo.pdf: 425775 bytes, checksum: 843b646bdf66302b2153ff923717d583 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Esse trabalho objetivou comparar o desempenho produtivo de acarás bandeira criados nos sistemas de criação em aquários e em viveiros escavados dentro de estufa plástica com e sem policultivo com camarão-da-amazônia em duas densidade de estocagem, 1,6 e 3,2 peixes/10 L. Utilizou-se um DIC, em esquema fatorial 3x2, com 4 repetições. Os peixes dos tratamentos viveiro em monocultivo e em policultivo apresentaram mais que o dobro de ganho de peso, menor consumo de ração, melhor conversão alimentar, maior comprimento padrão e uniformidade do lote em relação aos peixes mantidos em aquários. A produção em aquários e em monocultivo apresentaram diferença na sobrevivência. O aumento da densidade influenciou negativamente o ganho de peso e o fator de condição. A menor densidade apresentou médias de comprimento padrão maiores. O consumo de ração, a conversão alimentar, a uniformidade do lote e a sobrevivência não foram afetada pela densidade. A biomassa não apresentou diferença entre as densidades nos aquários e aumentou com a densidade nos tratamentos mono e policultivo. O peso médio e a sobrevivência final dos camarões foram 1,66g e 84,4%, respectivamente. A análise de custos mostrou valores semelhantes para os sistemas semi-intensivos e inviabilidade para o sistema intensivo. Conclui-se que a produção em viveiros escavados, com ou sem policultivo, é mais eficiente e mais rentável que a produção em aquários. / The present study aimed to compare three production systems for freshwater angelfish: intensive indoor aquarium, semi-intensive greenhoused earth pond (monoculture) and greenhoused earth pond in polyculture with amazon river prawn. It was tested two stock densities: 1,6 and 3,2 fish/10 L. The experimental design was entirely randomized, in 3x2 factorial scheme, with four replicates. Water parameters were adequate for species development. Fish from monoculture and polyculture ponds showed over twice weight gain, lower food consumption, better food conversion rate, bigger standard length and group uniformity than the fish maintained in aquariums. Differences in survivors were observed only between aquarium and monoculture pond. The stock density increase reduced the weight gain and body condition. The lower density showed better means of standard length. Food consumption, food conversion rate group uniformity and survivor showed no difference between the densities. The interaction analysis for biomass was statistical significance, showing no difference between the densities inside aquarium and increasing with density within mono and polyculture ponds. The mean final weight and survivor of amazon river prawns were 1,66g e 84,4%, respectively. Cost analysis showed similar values for semi-intensive systems and no viability for aquarium system. It’s concluded that the production under earth pond, regardless of mono or polyculture system, is more efficient and profitable than indoor aquariums system.

Orientador: João Batista Kochenborger Fernandes / Banca: Manuel Vazquez Vidal Júnior / Banca: Maria Inez Espagnoli Geraldo Martins / Resumo: Esse trabalho objetivou comparar o desempenho produtivo de acarás bandeira criados nos sistemas de criação em aquários e em viveiros escavados dentro de estufa plástica com e sem policultivo com camarão-da-amazônia em duas densidade de estocagem, 1,6 e 3,2 peixes/10 L. Utilizou-se um DIC, em esquema fatorial 3x2, com 4 repetições. Os peixes dos tratamentos viveiro em monocultivo e em policultivo apresentaram mais que o dobro de ganho de peso, menor consumo de ração, melhor conversão alimentar, maior comprimento padrão e uniformidade do lote em relação aos peixes mantidos em aquários. A produção em aquários e em monocultivo apresentaram diferença na sobrevivência. O aumento da densidade influenciou negativamente o ganho de peso e o fator de condição. A menor densidade apresentou médias de comprimento padrão maiores. O consumo de ração, a conversão alimentar, a uniformidade do lote e a sobrevivência não foram afetada pela densidade. A biomassa não apresentou diferença entre as densidades nos aquários e aumentou com a densidade nos tratamentos mono e policultivo. O peso médio e a sobrevivência final dos camarões foram 1,66g e 84,4%, respectivamente. A análise de custos mostrou valores semelhantes para os sistemas semi-intensivos e inviabilidade para o sistema intensivo. Conclui-se que a produção em viveiros escavados, com ou sem policultivo, é mais eficiente e mais rentável que a produção em aquários. / Abstract: The present study aimed to compare three production systems for freshwater angelfish: intensive indoor aquarium, semi-intensive greenhoused earth pond (monoculture) and greenhoused earth pond in polyculture with amazon river prawn. It was tested two stock densities: 1,6 and 3,2 fish/10 L. The experimental design was entirely randomized, in 3x2 factorial scheme, with four replicates. Water parameters were adequate for species development. Fish from monoculture and polyculture ponds showed over twice weight gain, lower food consumption, better food conversion rate, bigger standard length and group uniformity than the fish maintained in aquariums. Differences in survivors were observed only between aquarium and monoculture pond. The stock density increase reduced the weight gain and body condition. The lower density showed better means of standard length. Food consumption, food conversion rate group uniformity and survivor showed no difference between the densities. The interaction analysis for biomass was statistical significance, showing no difference between the densities inside aquarium and increasing with density within mono and polyculture ponds. The mean final weight and survivor of amazon river prawns were 1,66g e 84,4%, respectively. Cost analysis showed similar values for semi-intensive systems and no viability for aquarium system. It's concluded that the production under earth pond, regardless of mono or polyculture system, is more efficient and profitable than indoor aquariums system. / Mestre