Arenicola marina (lugworms) are intertidal marine polychaete worms. Ecologically lugworms are responsible for increasing the permeability of the sand, sediment oxygenation and speeding up carbon cycling via the breakdown of buried organic matter. The worms themselves contain polyunsaturated fatty acids that are commercially important in the aquaculture of fin and shellfish. There is, however, some debate over the principal carbon source for the worms themselves. The aim was to investigate the bacterial dynamics in a polychaete worm growth mesocosm and determine the potential contribution of polyunsaturated fatty acid biosynthesis by bacteria to the nutrition of Arenicola marina.

Two full length AQP genes (<i>LrAQP-A</i> and <i>LrAQP-G</i>) were isolated from the earthworm <i>Lumbricus rubellus</i> by RACE-PCR.  Sequence analysis revealed a number of unusual residues in the critical aqueous pore region in both AQPs, including a substitution in the first canonical NPA box from an alanine residue to a glycine in LrAQP-G. This unusual NPG motif was also identified in AQP genes isolated from a further 6 annelids studied suggesting that although the NPG motif is unique amongst Animalia studied to date, it is common within the annelids.  In addition to this substitution, LrAQP-G contains an insertion of 10 amino acids in its first extracellular loop and putative phosphorylation sites in the intracellular C terminus.  LrAQP-A also contained unusual pore substitutions and putative phosphorylation sites at the C terminus.  Phylogenetic analysis suggests LrAQP-A is more closely related to other invertebrate AQPs whereas LrAQP-G clusters on a branch of its own. Both AQPs were present in all tissues examined, including the major osmoregulatory tissues; integument, nephridia and gut.  qPCR revealed that <i>LrAQP-A</i> transcripts are more abundant than <i>LrAQP-G </i>in the integument, reproductive organs, calciferous glands and nephridia.  <i>In situ</i> hybridisation revealed both transcripts to be largely co-localised in discrete cell types in the outer epidermal cells of the bodywall, the coleomic surface of the gut and in the endothelia of the nephridia. Functional characterisation in oocyte swelling assays revealed that LrAQP-A facilitates the mercury-sensitive transport of water at similar rates to human AQP-5.  The rate of water transport was increased significantly by lowering the pH of bathing media.  LrAQP-G also facilitated water transport but at rates ~50% less than LrAQP-A and was mercury and pH insensitive.  Neither AQP transported glycerol or urea but interestingly LrAQP-A is permeable to NH₃ in a pH-dependent manner. Both LrAQP-A and LrAQP-G showed partial loss of function after PKC-mediated phosphorylation. In environmental stress experiments the expression of both genes was modulated significantly.  In worms exposed to wet soil both the integument and nephridia gene expression of LrAQP-A was reduced.  In hyposmotic saline, LrAQP-G was downregulated in the integument.  In hyperosmotic saline LrAQP-G was again downregulated in the integument but was upregulated in the gut. LrAQP-A and LrAQP-G are intimately involved with water transport in <i>L. rubellus</i>.  In addition they seem to be modulated in the short and long term dependent on osmotic conditions.

This thesis is a study of the swimming locomotion of the polychaete worm, Nereis diversicolor. Previous research has shown that there are two distinct jet-like flow regions in the wake of a swimming polychaete worm (Hesselberg 2006). In the first section of this thesis, this flow pattern is studied in greater detail using a high resolution particle image velocimetry (PIV) technique. A small region close to the wave crest of the undulating worm is recorded and the fluid velocity vector fields are plotted. The close-up PIV results show how the jet-like fluid pattern is formed due to the action both of a single sweeping parapodium and to the interaction between adjacent parapodia, proving for the first time that Gray’s (1939) explanation of the propulsion mechanics is in fact correct. The second part of this thesis is focused on the pumping action of the polychaete worm, a behaviour adopted by the worms to create a flow of nutrients through their burrows. Particle image velocimetry (PIV) experiments were performed on tethered polychaete worms, Nereis diversicolor. The tethered worms moved in a gait which was different from that of freely swimming ones. They used a much smaller body wave amplitude, pumping liquid with very high efficiency by cooperative movement of their body and parapodia. In the third part of the thesis, a mechanical model was designed and built. The model consisted of a series of paddle units. Each paddle was driven by a servo motor. Breugem (2008) did a CFD simulation of the paddle model. Similar fluid patterns were generated by the physical model. Reversed flow was found at low Reynolds number (Re) and higher Re situations. The flow direction could be controlled by simply adjusting the beating frequency of paddles. The mechanical model is not sufficient to mimic the pumping locomotion of the worms due to absence of an undulatory movement. The pumping efficiency is low compared to pumping worms.

Les lombriciens remplissent, dans les agrosystèmes, de nombreux services, importants pour la production et le bon fonctionnement du sol. Cependant, on manque de connaissances sur la manière dont les facteurs jouent, au champ, sur la densité et la diversité spécifique. Cela rend difficile la prévision des effets des pratiques sur la macrofaune du sol et la mise au point de systèmes de culture en Agriculture Biologique, favorables aux populations de vers endogés.L'objectif de cette thèse était d'analyser, au champ, les variations au cours de l'année de l'abondance des lombriciens dans le contexte de l'Agriculture Biologique du Bassin Parisien. Nous nous sommes tout particulièrement interessés au cas des espèces endogées dont nous avons suivi les abondances dans 5 parcelles pendant 2 ans (2009 et 2010). L'analyse de ces données (et de la littérature scientifique) nous a amené à proposer un modèle simulant la dynamique des populations de vers de l'espèce la plus fréquemment rencontrée sur ces parcelles, A. Caliginosa. Ce modèle est basé sur celui de C. Pelosi (Pelosi et al., 2008).L'analyse des données de suivi des populations a montré qu'il existait un schéma général décrivant l'évolution annuelle de l'abondance (i.e. la densité de vers endogés actifs dans la couche 0-30 cm) de ces parcelles labourées et cultivées en céréales. Ce schéma général est caractérisé par une première phase de décroissance (ou de stabilité) en fin de printemps, suivie d'une période estivale pendant laquelle la population est stable, avant d'augmenter à nouveau à l'automne, pour atteindre un niveau maximal supérieur à celui de l'entrée de l'été. Enfin, l'hiver, l'abondance chute à nouveau. Ce travail, qui confirme les données générales de la littérature sur les endogés, a cependant montré que par rapport à ce schéma il existait d'importantes variations d'une année sur l'autre, entre A. caliginosa et A. rosea et en fonction des parcelles. Les causes de ces variations, complexes, sont discutées dans cette thèse.Parmi ces causes, le travail du sol, et tout particulièrement le labour, joue un rôle important. Cela nous a amené à mettre en place un essai, sur deux des parcelles du suivi, pour étudier les effets de cette opération sur la dynamique des populations des deux espèces endogées citées ci-dessus. Les résultats obtenus suggèrent que les effets du labour sont variables en fonction de l'espèce considérée. A. caliginosa s'est révélée plus sensible qu'A. rosea, dont les abondances n'ont pas été systématiquement affectées. Celles d'A. caliginosa ont été réduites, juste après le labour en 2009, avec un certain retard (deux mois environ) après cette opération. Ces résultats soulignent ainsi la nécessité d'étudier l'effet des techniques culturales à travers leur impact sur la dynamique des populations (et non sur le niveau d'abondance moyen).La troisième partie de notre travail a été consacrée à l'amélioration du modèle Wormdyn. Nous l'avons tout d'abord adapté au cas de l'espèce A. caliginosa en nous basant sur une étude bibliographique approfondie pour fixer la valeur des paramètres du cycle de vie. Nous avons ensuite introduit une fonction décrivant l'effet de la densité dépendance sur l'abondance. Le modèle a correctement simulé le niveau moyen des abondances mesurées dans les parcelles suivies, malgré une tendance générale à la surestimation des effectifs lorsque les conditions du milieu sont favorables. L'ajout de la densité dépendance a corrigé partiellement ce biais et ouvre à la prise en compte d'autres facteurs de variation des populations, au premier rang desquels la qualité et la quantité des ressources trophiques. / The earthworms fulfil, in the agroecosystems, many services, crucial for the production and proper functioning of the soil. Therefore, it is necessary to deepen our understanding of the drivers of the changes with time of the density and the specific diversity of earthworms communities. Indeed such a knowledge is necessary to predict the effects of the agricultural practices on soil macrofauna and to design cropping systems in organic farming, beneficial to the earthworm abundance. The purpose of this PhD thesis was to analyse, in agricultural fields, the annual variations of the earthworm abundances in the organic farming context of Northern France. We focused on endogeics species, whose abundance was measured during two years (2009 and 2010) in five cropped fields. A model, simulating the earthworm population dynamics of the most abundant species in our cropped fields, A. caliginosa was parametrised with the data collected in thosse fields (and the bibliography). It was also inspired by Pelosi's model (Pelosi et al., 2008). The analysis of the populations dynamics showed a general scheme describing the annual evolution of the abundance (i.e. active endogeic earthworms in the 0-30 cm layer) of these ploughed fields, cropped with cereals. This scheme is characterized by a four-step evolution. a decrease in the abundance (or a stability) at the end of the spring, followed by a summer period with a stability of the population, before an increase at fall, where the abundance reached a higher level compared to the end of spring. Lastly, in winter, the abundance decreases again. This study, which confirmed the general data given by the literature, revealed also significant variations from one year to the other, between A. caliginosa and A. rosea, and also as a function of the crop field. The causes of these variations are discussed in this PhD thesis. Among the possible causes of these variations, soil tillage, especially ploughing, played an important role. This led us to carry out an experiment to study the effects of this practice on the population dynamics of the two endogeic species mentionned above. The results obtained suggested that the effects of the ploughing was species dependent. A. caliginosa was more sensitive than A. rosea, whose abundances were not systematically affected by the ploughing. Those of A. caliginosa were reduced immediately after ploughing in 2009, with some delay (about two months) after this operation. These results emphasize the necessity to study the effect of the agricultural practices through their impact on population dynamics (and not only through the average level of abundance). The third part of our work was devoted to the improvement of the model Wormdyn. We first adapted the model to the species A. caliginosa based on a literature review to determine the the life cycle parameter values for this species. A function describing the effect of density dependence on the abundance was also introduced in the model. The model correctly simulated the average abundances measured in the cropped fields, despite a general tendency to overestimate the abundances, when environmental conditions are favorable. This was only partially corrected by the addition of the density dependence function. The model has to be improved by the introduction of the effect of other factors, first and foremost the quality and quantity of trophic resources.