ZooScan with ZooProcess and Plankton Identifier (PkID) software is an integrated analysis system for acquisition and classification of digital zooplankton images from preserved zooplankton samples. Zooplankton samples are digitized by the ZooScan and processed by ZooProcess and PkID in order to detect, enumerate, measure and classify the digitized objects. Here we present a semi-automatic approach that entails automated classification of images followed by manual validation, which allows rapid and accurate classification of zooplankton and abiotic objects. We demonstrate this approach with a biweekly zooplankton time series from the Bay of Villefranche-sur-mer, France. The classification approach proposed here provides a practical compromise between a fully automatic method with varying degrees of bias and a manual but accurate classification of zooplankton. We also evaluate the appropriate number of images to include in digital learning sets and compare the accuracy of six classification algorithms. We evaluate the accuracy of the ZooScan for automated measurements of body size and present relationships between machine measures of size and C and N content of selected zooplankton taxa. We demonstrate that the ZooScan system can produce useful measures of zooplankton abundance, biomass and size spectra, for a variety of ecological studies.

http://cce.lternet.edu/docs/bibliography/Public/141ccelter.pdf

Digital zooplankton image analysis using the ZooScan integrated system

Implementation of the European Marine Strategy Framework Directive: A methodological approach for the assessment of environmental status, from the Basque Country (Bay of Biscay)

Bacterial metal resistance genes and metal bioavailability in contaminated sediments.

https://hal.archives-ouvertes.fr/hal-00683349/document

Lower trophic levels and detrital biomass control the Bay of Biscay continental shelf food web: Implications for ecosystem management

Atlantic bluefin tuna (Thunnus thynnus) are highly migratory predators whose abundance, distribution, and somatic condition have changed over the past decades. Prey community composition and abundance have also varied in several foraging grounds. To better understand underlying food webs and regional energy sources, we performed stomach content and stable isotope analyses on mainly juvenile (60–150 cm curved fork length) bluefin tuna captured in foraging grounds in the western (Mid-Atlantic Bight) and eastern (Bay of Biscay) Atlantic Ocean. In the Mid-Atlantic Bight, bluefin tuna diet was mainly sand lance (Ammodytes spp., 29% prey weight), consistent with historic findings. In the Bay of Biscay, krill (Meganyctiphanes norvegica) and anchovy (Engraulis encrasicolus) made up 39% prey weight, with relative consumption of each reflecting annual changes in prey abundance. Consumption of anchovies apparently declined after the local collapse of this prey resource. In both regions, stable isotope analysis results showed that juvenile bluefin tuna fed at a lower trophic position than indicated by stomach content analysis. In the Mid-Atlantic Bight, stable isotope analyses suggested that >30% of the diet was prey from lower trophic levels that composed <10% of the prey weights based upon traditional stomach content analyses. Trophic position was similar to juvenile fish sampled in the NW Atlantic but lower than juveniles sampled in the Mediterranean Sea in previous studies. Our findings indicate that juvenile bluefin tuna targeted a relatively small range of prey species and regional foraging patterns remained consistent over time in the Mid-Atlantic Bight but changed in relation to local prey availability in the Bay of Biscay.

/pdf/diet-of-young-atlantic-bluefin-tuna-thunnus-thynnus-in-huzhfjllhz.pdf

Diet of young Atlantic bluefin tuna ( Thunnus thynnus ) in eastern and western Atlantic foraging grounds

The objective of this study was to investigate whether successive recruitment failures in the anchovy fishery in the Bay of Biscay were due to changes in the zooplankton biomass or composition. Image analysis and automatic recognition were used to analyse zooplankton samples collected during diel egg production method spring surveys from 1998 to 2006. We were not able to detect any trend in zooplankton biomass during this period. The zooplankton spatial distribution showed permanent features with large organisms being more abundant over the shelf break and outer areas. Finally, we found a negative correlation between anchovy recruitment and zooplankton biomass which suggests that the 2002‐2006 failures in anchovy recruitment in the Bay of Biscay are not due to a decrease in mesozooplankton biomass.

/pdf/spring-zooplankton-distribution-in-the-bay-of-biscay-from-1x249gm3lc.pdf

Kevin Denis

Papers

Spring zooplankton distribution in the Bay of Biscay from 1998 to 2006 in relation with anchovy recruitment

Links between bacterial communities in marine sediments and trace metal geochemistry as measured by in situ DET/DGT approaches