Heterotrophic microorganisms are important for the flow of carbon and nutrients in the sea. Bacteria, nanoflagellates and ciliates are relevant components of the pelagic food web. In order to be able to predict the outcome of e.g. eutrophication or climate change we need to know how the different components of the pelagic food web are regulated. With the focus on the northern Baltic Sea food web, this thesis deals with limitation and control of heterotrophic protists, the effect of resource heterogeneity on food web efficiency and diversity of nanoflagellates. In-situ microcosm experiments showed that the net growth of heterotrophic flagellates were resource limited throughout the year. Field data confirmed that the abundance of flagellates was bottom-up controlled. Furthermore, field data also showed that the annual average biomass of protists, flagellates and ciliates increased with primary productivity. On a smaller seasonal scale temperature and bacterial biomass were able to explain most of the variation in flagellate biovolume. The temporal variation in ciliate biovolume could not be explained by any bottom-up factors like bacterial biomass, flagellate biomass or chlorophyll a. This and an in-situ microcosm experiment implied that the seasonal dynamics of ciliates were more regulated by predators like mesozooplankton. The food web efficiency i.e. how much of production at the resource level is converted to production at the top trophic level, may be affected by specific size or type of resource. Indoor mesocosms revealed that the food web efficiency was 11 times lower when heterotrophic bacteria dominated basal production instead of nano- and micro-sized phytoplankton. This was due to a lengthening of the food web when pico-sized bacteria constituted the main resource. The PCR-DGGE molecular biological method was used to study the diversity of heterotrophic or mixotrophic chrysomonads. The focus was set on chrysomonads due to their relatively large contribution to the nanoflagellate community. Group-specific PCR primers were optimized for the target group. A field survey in the northern Baltic Sea showed that a handful of chrysomonad sequences were present throughout the year. Significantly more chrysomonads were recorded in the basin with higher primary productive and salinity. In total 15-16 different chrysomonad sequences were recorded. Most of them matched uncultured chrysomonad clones.

[Truncated abstract] The role of marine microzooplankton in aquatic food webs has been studied in most regions of the world’s oceans, with the exception of the subtropical/temperate eastern Indian Ocean. This thesis addresses this gap in knowledge by investigating microzooplankton from five stations on a cross continental shelf transect and in two mesoscale features ∼300 km offshore of south west Western Australia. My primary focus was to measure and evaluate microzooplankton community change over space and time and their impact on phytoplankton on a cross shelf transect, sampling five stations from February 2002 December 2004 as part of a large multidisciplinary investigation into the pelagic ecosystem on the shelf (Chapter 2). This transect was named the Two Rocks transect. I also investigated an eddy pair (Chapter 5), which had originated from water in the vicinity of the Two Rocks transect, also undertaken as part of a larger study, investigating biophysical coupling within mesoscale eddies off south west Western Australia . . . The distribution of mixotrophic cells differed across the transect. Those mixotrophs that use photosynthesis as their primarily energy source exploited nutrient limited conditions inshore consuming particles, while mixotrophs that are primarily heterotrophic survived low prey conditions offshore by photosynthesizing. In the eddies, the grazing behaviour of microzooplankton was dependent on the specific phytoplankton assemblage in each eddy. The warm core eddy had a resident population of diatoms that were consumed by heterotrophic dinoflagellates present in high numbers. The cold core eddy had a warm cap which prevented upwelled water reaching the surface, resulting in stratification and a very active microbial food web, particularly in the surface.

Ce travail de thèse focalise sur le fonctionnement du réseau microbien de la lagune de Thau à travers une approche « Réseau » ayant permis l’étude simultanée de l’ensemble des groupes microbiens (21 groupes) des virus au microzooplancton. La croissance et la mortalité des micro-organismes ont été étudiées expérimentalement lors de plusieurs saisons puis d’une étude en mésocosme. Nous avons déterminé les proportions de mortalité dont sont responsables le microzooplancton et les virus au travers de la lyse virale. Un suivi in situ puis en mésocosme dans la lagune de Thau nous a permis d'observer la réponse des composantes du réseau microbien à un forçage typiquement Méditerranéen, la crue.Il apparait que les bactéries hétérotrophes ont les plus fortes croissances allant jusqu’à 2,18 jour-1. La croissance pour divers groupes pico- et nano-phytoplanctoniques était inférieure à 1,5 jour-1. La cause majeure de mortalité des différents groupes de micro-organismes étudiés est la prédation du microzooplancton (> 90% en moyenne), tandis que la lyse virale semble être un processus sporadique et nettement moins important. Le fait que les taux de prédation observés soient très proches des taux de croissance de différents micro-organismes suggère que le réseau microbien étudié présente une forte efficacité de transfert de la biomasse vers les niveaux trophiques supérieurs.Dans ce contexte, la crue provoque à court terme une diminution de la croissance microbienne et du broutage, alors qu’elle déclenche la lyse virale chez certains groupes. Cependant, la réactivité de ce réseau permet un rétablissement rapide indiquant une forte capacité de résilience de ce système. / The aims of this thesis work were to shed new lights on the functioning of the microbial food web (MFW) in the Thau coastal lagoon through a “global approach” that permit us to study simultaneously the entire MFW components (21 groups) from viruses to microzooplankton. Growth and mortality of microorganisms were studied experimentally along seasons and during a mesocosm experiment. We particularly focus on mortality due to microzooplankton (<200µm) grazing and viral lysis. Responses of the different components of the MFW under a typical Mediterranean forcing, flash flood, was also studied during an in situ monitoring and a mesocosm experiment in the Thau Lagoon.In conclusion, it appears that heterotrophic bacteria show the highest growth rates (until 2.18 day-1). Growth rates of pico- and nanophytolankton groups were always lower than 1.5 day-1. The major cause of mortality of the different group studied, reaching on average 90%, was due to the predation by the microzooplankton. Mortality due to viral lysis appeared to be a “sporadic processes”, less important than microzooplankton grazing indeed. In addition, the observed grazing rates or bacterivory were close to growth rates of microorganisms, suggesting an efficient trophic transfer of the microbial biomass towards higher trophic levels.River flash flood; an important forcing in the Mediterranean coastal zone; triggered on a short time scale, a decrease in growth and grazing rates of microorganisms whereas viral lysis was enhanced. However, the important dynamics of this studied MFW allowed the rapid reestablishment of growth and grazing rates, indicating a strong resilience capability of this system.