A molecular method for the identification of resting eggs of acartiid copepods in the Thau lagoon, France

Acartia and Paracartia species, often known to co-occur, can exhibit complex life cycles, including the production of resting eggs. Studying and understanding their population dynamics is hindered by the inability to identify eggs and early developmental stages using morphological techniques. We have developed a simple molecular technique to distinguish between the three species of the Acartiidae family (Acartia clausi, A. discaudata and Paracartia grani) that co-occur in the Thau lagoon (43�250N; 03�400E) in southern France. Direct amplification of a partial region of the mitochondrial cytochrome oxidase I gene by polymerase chain reaction and subsequent restriction fragment length polymorphism results in a unique restriction profile for each species. The technique is capable of determining the identity of individual eggs, including resting eggs retrieved from sediment samples, illustrating its application in facilitating population dynamic studies of this ubiquitous and important member of the zooplankton community.

Monitoring marine plankton ecosystems: Identification of the most relevant indicators of the state of an ecosystem

The number of variables involved in the monitoring of an ecosystem can be high and often one of the first stages in the analysis is to reduce the number of variables. We describe a method developed for geological purposes, using the information theory, that enables selection of the most relevant variables. This technique also allows the examination of the asymmetrical relationships between variables. Applied to a set of physical and biological variables (plankton assemblages in four areas of the North Sea), the method shows that biological variables are more informative than physical variables although the controlling factors are mainly physical (sea surface temperature in winter and spring). Among biological variables, diversity measures and warm-water species assemblages are informative for the state of the North Sea pelagic ecosystems while among physical variables sea surface temperature in late winter and early spring are highly informative. Although often used in bioclimatology, the utilisation of the North Atlantic Oscillation (NAO) index does not seem to provide a lot of information. The method reveals that only the extreme states of this index has an influence on North Sea pelagic ecosystems. The substantial and persistent changes that were detected in the dynamic regime of the North Sea ecosystems and called regime shift are detected by the method and corresponds to the timing of other shifts described in the literature for some European Systems such as the Baltic and the Mediterranean Sea when both physical and biological variables are considered.

A new approach for objective identification of turns and steps in organism movement data relevant to random walk modelling

1. A first step in the analysis of complex movement data often involves discretisation of the path into a series of step-lengths and turns, for example in the analysis of specialised random walks, such as Lévy flights. However, the identification of turning points, and therefore step-lengths, in a tortuous path is dependent on ad-hoc parameter choices. Consequently, studies testing for movement patterns in these data, such as Lévy flights, have generated debate. However, studies focusing on one-dimensional (1D) data, as in the vertical displacements of marine pelagic predators, where turning points can be identified unambiguously have provided strong support for Lévy flight movement patterns. 2. Here, we investigate how step-length distributions in 3D movement patterns would be interpreted by tags recording in 1D (i.e. depth) and demonstrate the dimensional symmetry previously shown mathematically for Lévy-flight movements. We test the veracity of this symmetry by simulating several measurement errors common in empirical datasets and find Lévy patterns and exponents to be robust to low-quality movement data. 3. We then consider exponential and composite Brownian random walks and show that these also project into 1D with sufficient symmetry to be clearly identifiable as such. 4. By extending the symmetry paradigm, we propose a new methodology for step-length identification in 2D or 3D movement data. The methodology is successfully demonstrated in a re-analysis of wandering albatross Global Positioning System (GPS) location data previously analysed using a complex methodology to determine bird-landing locations as turning points in a Lévy walk. For this high-resolution GPS data, we show that there is strong evidence for albatross foraging patterns approximated by truncated Lévy flights spanning over 3·5 orders of magnitude. 5. Our simple methodology and freely available software can be used with any 2D or 3D movement data at any scale or resolution and are robust to common empirical measurement errors. The method should find wide applicability in the field of movement ecology spanning the study of motile cells to humans.

Application of microarrays (phylochips) for analysis of community diversity by species identification

Abstract Molecular probe-based methods (Fluorescent in-situ hybridisation or FISH, Next Generation Sequencing or NGS) have proved successful in improving both the efficiency and accuracy of the identification of microorganisms, especially those that lack distinct morphological features, such as picoplankton. However, FISH methods have the major drawback that they can only identify one or just a few species at a time because of the reduced number of available fluorochromes that can be added to the probe. Although the length of sequence that can be obtained is continually improving, NGS still requires a great deal of handling time, its analysis time is still months and with a PCR step it will always be sensitive to natural enzyme inhibitors. With the use of DNA microarrays, it is possible to identify large numbers of taxa on a single-glass slide, the so-called phylochip, which can be semi-quantitative. This review details the major steps in probe design, design and production of a phylochip and validation of the array. Finally, major microarray studies in the phytoplankton community are reviewed to demonstrate the scope of the method.

Application of microarrays (phylochips) for analysis of community diversity by species identification

Abstract Molecular probe-based methods (Fluorescent in-situ hybridisation or FISH, Next Generation Sequencing or NGS) have proved successful in improving both the efficiency and accuracy of the identification of microorganisms, especially those that lack distinct morphological features, such as picoplankton. However, FISH methods have the major drawback that they can only identify one or just a few species at a time because of the reduced number of available fluorochromes that can be added to the probe. Although the length of sequence that can be obtained is continually improving, NGS still requires a great deal of handling time, its analysis time is still months and with a PCR step it will always be sensitive to natural enzyme inhibitors. With the use of DNA microarrays, it is possible to identify large numbers of taxa on a single-glass slide, the so-called phylochip, which can be semi-quantitative. This review details the major steps in probe design, design and production of a phylochip and validation of the array. Finally, major microarray studies in the phytoplankton community are reviewed to demonstrate the scope of the method.