Long-term molluscs and annelids monitoring in the Pertuis-Charentais, France

The monitoring was conducted every year under the responsibility of Pierrick Bocher with constant participation of Philippe Pineau and Nicolas Lachaussée and managers of the National Nature Reserves of Aiguillon Bay and Marennes-Oléron Bay. Additional help in the field was provided by multiple other colleagues and PhD candidates throughout the years.

Sampling was performed on intertidal mudflats located in national nature reserves: RNN Aiguillon Bay and RNN Moëze-Oléron.

Systematic sampling was performed on four regular 250 m grids, composed of 64 stations each (except for the subsite "Oléron" (OL) which contained 67 stations).

The monitoring was funded by the University of La Rochelle and the CNRS via laboratory donations and staff time. Financial support was received from the Région Poitou-Charentes through a thesis grant to Anne Philippe (2013-2016). LIENSs laboratory and the DYFEA team also provided help with field work costs. The Office National de la Chasse et de la Faune Sauvage (ONCFS) and the Ligue pour la Protection des Oiseaux (LPO) supported this monitoring via staff time and nautical resources dedicated to sample collections.

Benthic macrofauna was collected over a predetermined 250 m grid following a proven sampling protocol (Bocher et al. 2007, Kraan et al. 2009, Bijleveld et al. 2012), see (Fig. 1). Each station was located with a handheld GPS device using WGS84 geodetic datum. Out of 259 stations sampled, only a minority (46%) was sampled by foot (during low tide), taking sediment cores covering an area of 1/56 m² down to a depth of 20 to 25 cm. The top fraction (first 4 cm of the sediment) was separated from the bottom fraction to be able to segregate the accessible benthos fraction for the two main shorebirds species: the red knot Calidris canutus and the dunlin Calidris alpina (Fig. 2). We took an additional core (70 mm diameter) covering 1/263 m² to a depth of 4 cm for sampling exclusively the very abundant mudsnail Hydrobia ulvae (Pennant) (Bocher et al. 2007). When the tide covered the mudflats with water (0.4–2.0 m) and for the very soft and inaccessible lower intertidal areas, sampling was done from boats using inflatable zodiacs or other small vessels. From the boats, two mud cores (100 mm diameter) covering a total of 1/56 m² to a depth of 20 to 25 cm were taken. Only one core was taken into account for H. ulvae, and both were taken into account for any other macrobenthic species.

Figure 1.  

Sampling site with the 259 regular station, across four study sites, in the Pertuis Charentais, on the French Atlantic coast.

Figure 2.  

The harvestable fraction corresponding to the mean bill length of the sandpipers, the dunlin Calidris alpina and the red knot Calidris canutus and composed of the accessible fraction of benthos (found in the top 4 cm of the mud core) and of ingestible sizes (not too large and not too small). Ingestible sizes are species specific, and depend on the shape of the mollusc. Sizes available for C. canutus and C. alpina species are reported in Philippe et al. (2016).

The cores were sieved through a 1 mm mesh, except for the mudsnail H. ulvae cores, which were sieved over a 0.5 mm mesh to prevent the loss of individuals smaller than 1mm (from the apex to the aperture). All living molluscs were collected in plastic bags and frozen (-18°C) until laboratory treatment (Fig. 3). Polychaetes were preserved in 70% ethanol. Living specimens were determined using the identifaction key described in Hayward and Ryland (1996).

Figure 3.  

Processing of benthic samples in the laboratory.

Sample processing: In the laboratory, molluscs were identified under the supervision of a benthic taxonomist. Individuals were counted, and their maximum length was measured to the nearest 0.1 mm using Vernier calipers, width was also measured for bivalves. Hydrobiid mudsnails were size-categorised from 0 mm up to 6 mm (e.g. size class 2 consisted of individuals with lengths ranging from 2 to 2.99 mm).

The flesh of every mollusc specimen except H. ulvae was detached from the shell and placed individually in crucibles (pooled by size class when sizes were smaller than 8.0 mm, flesh and shell together). Crucibles containing molluscs were placed in a ventilated oven at 55 to 60°C for three days until constant mass and then weighed (DM ±0.01 mg). Dried specimens were then incinerated at 550°C for 4 h to determine their ash mass and then a proxy of their energy content: the ash free dry mass (AFDM). [H. ulvae flesh biomass (AFDM_flesh) was estimated for each station from the total biomass (AFDM_flesh+shell) with the following linear regression: AFDM_flesh= 0.6876 × AFDM_flesh+shell + 7E-05 (R² = 0.99; N = 60 individuals sampled in July 2014 in Aiguillon Bay). Flesh biomass of bivalves (Scrobicularidae, as well as Macoma balthica individuals) smaller than 8.0 mm was determined from the total biomass (AFDM_flesh+shell) with the following linear regression: AFDM_flesh= 0.7649 × AFDM_flesh+shell − 7E-05 (R² = 0,9656, N = 122 Scrobiculalidae individuals and 51 M. balthica ind. sampled in January 2014 in Aiguillon Bay).

For bivalves larger than 8.0 mm, shells were placed in adequate numbered stalls and dried in a ventilated oven at 55 to 60°C (DM ±0.01 mg) for three days. For H. ulvae individuals, shell was not separated from the flesh, and shell dry mass was estimated from the total biomass using the following regression: DM_shell = 5.5902 × AFDM_flesh+shell – 0.0006 (R² = 0.98; N=60 ind. sampled in July 2014 in Aiguillon Bay). For the same reason, dry mass of the shell (DM_shell) of small bivalves (< 8.0 mm) was extrapolated using the following regression: DM_shell = 8E-05 × Length 2,6523 (R² = 0,8274, N=122 Scrobiculalidae ind. and 51 M. balthica ind. sampled in January 2014 in Aiguillon Bay).

In the present dataset, we removed all epibenthic species (e.g. crustaceans) since they are nearly absent from the feeding regime of shorebirds in our study area (Bocher et al. (2014). Polychaetes were also identified and counted, but their length and AFDM were not determined due to insufficient numbers of entire individuals to build regression equations. Nearly all polychaete species were removed from the database because the precision of sample sorting and determination varied widely between the years depending on the laboratory operator. Only individuals from the Genus Nephtys (more than 90% of which were Nepthys hombergii) and individuals of the Family Nereididae (more than 90% of which were either Alitta succinea or Hediste diversicolor) were kept because they represent more than 80% of polychaetes in our study sites and comprise the biggest annelids and therefore biomass and prey for shorebirds (pers. observation). They are mentioned under the abbreviations "nepsp" (for Nephtys genus) and "neresp" (for Nereididae family) in the database. For these two polychaete taxa, the columns "length", "width", as well as "AFDM", "Biomass_dens" and "NewTBH" are not available, only densities are available.

In winter 2003-2004, an extensive benthos sampling (864 stations) was conducted following a grid over the whole intertidal zone of Aiguillon Bay and Marennes-Oléron Bay (Bocher et al. 2007). In the following years, the grid was reduced for practical reasons to a 259 points grid spread in four subsites covering three different types of mudflats: Aiguillon Bay on the Charente-Maritime side (AIC, bare mudflat), Aiguillon Bay on the Vendée side (AIV, bare mudflat), Moëze intertidal area (MO, bare mudflat with runnels system) and Oléron Island intertidal area (OL, sandy mudflat covered with seagrass). The grids were defined as a square shape when possible to facilitate movements and navigation on the mud and at sea (Fig. 1). Because this sampling effort was designed primarily for the study of shorebird ecology, grids were placed in protected areas (National Nature Reserve of Moëze-Oléron, and National Nature Reserve of Aiguillon Bay) managed by the LPO (Ligue pour la Protection des Oiseaux) and ONCFS (Office nationale de la Chasse et de la Faune Sauvage), matching wetlands international annual shorebird counting areas. Sampling stations are referenced by spatial coordinates using the WGS84 geodetic datum. The four sampled subsites present contrasted characteristics that are described in Degré et al. (2006) and Bocher et al. (2007).

Due to field complexities or bad weather, some stations were not sampled some years. Namely in 2004, stations 2131-2133 and 2136-2140; in 2006, stations 2103 and 1953; in 2005, stations 1860, 1391 and 1395; in 2008, station 1300; in 2010, station 1958; in 2012, station 2137; and in 2014, stations 2137 and 1311. To this list, all the stations from Marennes-Oléron (site 'OL' and 'MO') in years 2010 and 2011 should be added. The value “NA” (i.e. not available) is given in the data set to avoid misinterpreting these cases for true “absence”.

The dataset includes all occurrences of individuals for the taxa listed in Table 2. Annelids were grouped under the Genus Nephtys of the Family Nerididae. Ruditapes sp. was essentially individuals of the species Ruditapes philippinarum. Scientific names and corresponding AphiaID were derived from the World Register of Marine Species (WoRMS). The combination of both scientific name and AphiaID prevents any confusion when names change over time. Indeed, in ten years of collecting data, various operators have used a list of species that was an extract of a taxonomy (with description of phylum, subphylum, class, subclass, infraclass, superorder, order, suborder, infraorder, superfamily, family, genus, species, and authority). However, classification evolves throughout time, and our dataset needed to be backed to an official registry of species linked to the semantic Web. The World Register of Marine Species (WoRMS, World Register of Marine Species 2016b) provides unique AphiaID for identifying marine species, and maintains a historic of changes of naming or classification. Furthermore, it provides semantic export of species description in RDF compatible with Darwin Core or Dublin Core metadata standards. We used this register in order to disambiguate the identification of species found in the dataset. For that, we have written a Python program querying the Web Service (World Register of Marine Species 2016a) provided by the World Register of Marine Species (WoRMS), for searching and resolving AphiaIDs of our species list, using the WSDL interface (World Register of Marine Species 2016c). For each record in our table, the program sends the name of the species in parameter of the querymatchAphiaRecordsByNames and the service finds for us matching taxa; the program asks then for the full AphiaRecord of the taxon (getAphiaRecordByID), parses it and checks it against our own classification. When a AphiaRecord matches our own table record, we retain it, else we log the uncertain case in order to search manually in the web interface. Only few cases (around 20), identified in the logs of our program, have been searched and solved manually using the web interface of WoRMS. The result is that we provide within our dataset the actual taxonomy of our species extracted from WoRMS, and most importantly their corresponding AphiaID in WoRMS.

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The associated dataset can be freely used for non-commercial purpose, provided it is cited. We draw your attention to the fact that you can contact the authors of the "benthos" dataset to prevent any misuse of the data. You can also consult us for reviewing articles based on our dataset.