Aquatic eDNA samples in French Guiana

Personnel involved in data aquisition (by alphabetic order): Sébastien Brosse, Isabel Cantera, Axel Cerdan, Kévin Cilleros, Jean-Baptiste Decotte, Gaël Grenouillet, Amaia Iribar, Jérôme Murienne, Pierre Taberlet, Pablo Tedesco and Régis Vigouroux.

Collecting trips have been conducted in various locations throughout French Guiana.

This dataset was developed to provide the foundation for a biodiversity monitoring programme based on eDNA but also to better understand the impact of human activities on aquatic biodiversity. Locations were thus selected to maximise the geographic coverage of rivers and streams, taking into account undisturbed sites but also sites under human disturbances (close to villages, close to gold mining sites etc.).

Data for this resource have been obtained with support from Labex CEBA (Center for the Study of Biodiversity in Amazonia), Labex DRIIHM (Dispositif de Recherche Interdisciplinaire sur les Interactions Hommes-Milieux) and Labex TULIP (Towards a Unified theory of biotic interactions: role of environmental perturbations). Labex (Laboratoires d’Excellence) are funded by "Investissement d'Avenir" grants managed by the French National Research Agency (ANR) under references ANR-10-LABX-25-CEBA, ANR-11-LABX-0010-DRIIHM and ANR-10-LABX-0041-TULIP. Additional financial support was also obtained from the DEAL Guyane, Office de l’Eau Guyane (Aquatic Metabarcoding project) and through the ANR DEBIT project (ANR-17-CE02-0007-01). SPYGEN, a private company specialised in eDNA, as well as VigiLife, a non-governmental agency, provided financial and laboratory support. Logistic support was also provided by the Parc Amazonien de Guyane and Hydreco Laboratory (Kourou, Guyane).

Sampling sites were located throughout French Guiana Fig. 1.

Figure 1.  

Localisation of the environmental DNA sampling sites.

We collected eDNA samples from November 2014 to 2019. For sampling, laboratory and bioinformatic protocols, we followed Valentini et al. (2016) from 2014 to 2016 and Pont et al. (2018) since 2016. For each sample, we used a filtration kit made of a sterile, single use filtration cartridge (Enviroteck HV; Pall Corporation, Ann Arbor, MI, USA and VigiDNA 0.45 μm; SPYGEN, le Bourget du Lac, France), a peristaltic pump (Vampir Sampler; Bürkle GmbH, Bad Bellingen, Germany) and sterile, single-use tubing. All the materials were handled with sterile gloves. Initial sampling (2014-2015) was performed using a 1 micrometre filtration cartridge (Enviroteck HV; Pall Corporation, Ann Arbor, MI, USA) but 0.45 micron capsules (VigiDNA 0.45 μm; SPYGEN, le Bourget du Lac, France) have been used as standard since 2016. Most of the samples consisted of 30 minutes water filtration using a portable battery powered peristaltic pump (Vampir sampler, Burkle, Germany), but in a few sites, filtration time was reduced to 15 minutes. A single sample per site was collected during initial sampling (2014-2015). Cantera et al. (2019) collected 10 replicate samples in 6 selected sites and showed that two replicate samples per site provided a realistic species list while limiting sampling costs. Two replicate samples were therefore collected in each site since 2016.

The operator always remained downstream from the filtration area and stayed on the bank (for small streams) or on emergent rocks (for larger streams and rivers). For sites located along the same river course, we sampled downstream to upstream to avoid contamination by eDNA transported by the boat (for rivers) or clothes.

Geographical coordinates were obtained using a GPSmap 64S device (Garmin) or similar. Such devices report coordinates accuracy using the CEP50 (Circular Error Probability), meaning that there is only 50% probability that a reported position would be within a distance of X metres to the real position. Considering other sources of GPS errors (such as ionosphere delay and signal multi-path), we estimate the accuracy of the coordinates to be around 30 metres at a 95% confidence level under dense forest cover.

At each site, we placed the input part of the tubing in a high-flow part of the watercourse. Sampling was achieved in rapid hydromorphological units to ensure an optimal homogenisation of the water throughout the water column. Water was pumped ca. 20 cm below the surface and each filtration lasted 30 min (except for a few sites where filtration time was 15 minutes). Each sample results from the filtration of ~34 l of water (~17 litres when filtration time was 15 minutes). At the end of the filtration, we emptied the filtration capsule of water, filled it with 150 ml of preservation buffer (Tris–HCl 0.1 M, EDTA 0.1 M, NaCl 0.01 M and N-lauroyl sarcosine 1%, pH 7.5–8) and stored it in the dark in individual sterile plastic bags. Samples were then stored at room temperature before DNA extraction. Preliminary tests demonstrated that the preservation buffer was suitable for room temperature storage up to a month. Information on DNA extraction, amplification and sequencing, as well as subsequent bioinformatic pipelines, can be found in Cilleros et al. (2019) and Cantera et al. (2019).

Site scale variables were measured directly in the field at the sampling location. Width was measured using a decameter for small streams (less than 15 metres width and 1 metre depth) and using an electronic telemeter (Bushnell Sport 850) for larger rivers. Water depth was measured using a graduated stick in small streams and a depth sounder (Plastimo echotest II) in larger rivers. Turbidity was measured using a Eutech Instrument Turbimeter (TN-100). Temperature, O₂ saturation, O₂ and pH were measured using a WTW 3420 field multimeter. Geographical coordinates were obtained using a GPSmap 64S device (Garmin) or similar. Elevation was derived for the geographic coordinates using the SRTM30 dataset.

The sampling area is delimited by the current administrative boundaries of the French Guiana territory. To the East, the Oyapock river delimits the frontier with Brazil. To the West, the Maroni river delimits the frontier with Suriname. This is an important detail as the delimitation of the territory has not been constant throughout history and a large portion of northern Brazil was disputed between France and Brazil during the 19th century. Even though French Guiana is an overseas territory of France, all occurrences are considered as belonging to the French Guiana "country" to comply with the ISO 3166-1 standard.

2.00000 and 6.00000 Latitude; -51.5000 and -54.5000 Longitude.

The dataset provides information on eDNA sampling sites and fishes presence/absence as inferred from metabarcoding analyses (Cilleros et al. 2019). DNA extracted from the sampling cartridge could, in theory, be used for amplifying any taxonomic group, depending on the downstream molecular biology protocols. Local metabarcoding reference databases for French Guiana biodiversity are currently available for mammals (Kocher et al. 2017b, Kocher et al. 2017a) and insects (Talaga et al. 2017, Kocher et al. 2016), but additional databases are under active development for other groups as well.

Users of this resource should comply with the CEBA data sharing agreement available here: www.labex-ceba.fr/assets/CEBA_Data_Sharing_Agreement_nov2013.pdf