eDNA in the Peruvian Amazon - ACCA & NatureMetrics

eDNA in the Peruvian Amazon

  • Conservación Amazónica (ACCA), a Peruvian non-profit organisation used NatureMetrics aquatic eDNA service to conduct a vertebrate survey at the Los Amigos Research Station in the Peruvian Amazon.

  • This study highlights the power of eDNA to generate powerful data for conservation managers in remote megadiverse regions.


Conservación Amazónica (ACCA) is a Peruvian non-profit organization that works towards the protection of one of the most biodiverse places on the planet: the Andes-Amazon region in Peru.

Their aims were to:

  • Use eDNA to survey biodiversity at the Los Amigos Research concession in the Andean-Amazonian altitudinal gradient, with a particular focus on oxbow lakes.

  • Set the foundation for long-term monitoring that allows comparative studies and monitoring of changes on a wide geographic scale.


At Los Amigos Biological Station, a large amount of monitoring is conducted by researchers using traditional survey methods in terrestrial habitats, but certain groups (especially fish and elusive mammals) are still difficult to survey on a regular basis, and there remains much to be learned about the biological communities of freshwater habitats such as oxbow lakes.


Environmental DNA surveys circumvent the typical challenges of biodiversity surveys, providing a non-invasive, highly efficient data collection method that can be undertaken by non-specialists. These eDNA surveys therefore offer an easy and efficient way for NGOs such as ACCA to unlock crucial biodiversity data in highly diverse tropical ecosystems.

This pilot study used the NatureMetrics aquatic eDNA service with a vertebrate metabarcoding analysis to generate vertebrate biodiversity data in typically understudied waterbodies. The team collected eDNA samples in two oxbow lakes and a blackwater lagoon. These important habitats are often nutrient-rich and provide a fertile environment for nurseries of fish larvae yet remain under-represented in baselining metrics as they can be hard to access.

14 samples were collected across 4 different sites: the oxbow lakes Cocha Lobo & Cocha Gato, the blackwater lagoon Pozo Don Pedro, and in the Los Amigos River.

The primary benefits of using  eDNA included:

  • Easy-to-use kits meant the on-site team could quickly be trained in sample collection, and all the necessary equipment could easily be carried into the field.
  • Data collected on multiple taxonomic groups for the same in-field effort.
  • Generates large amount of data in difficult to access areas, including typically high-effort sampling areas such as the oxbow lakes and palm swamps.
Los Amigos Conservation Concession - ACCA
Image Credit


Across the 14 eDNA samples, eDNA analysis detected a total of 153 vertebrate species. Alongside 98 fish species, we detected 11 amphibians, 10 birds. 5 reptiles, and 29 mammals.

  • 50 vertebrate species were detected in Cocha Lobo, 44 in Pozo Don Pedro and 46 in Cocha Gato

  • 81 vertebrate species were detected in the Los Amigos river, even though the water here was so heavy with sediment that only 0.25L could be filtered for each sample.

  • Species of note included jaguar (Panthera onca), giant river otter (Pteroneura brasiliensis), tapir (Tapirus terrestris), gold piranha (Serrasalmus maculatus), smooth-fronted caiman (Paleosuchus trigonatus), freshwater stingray (Potamotrygon motoro), spider monkey (Ateles belzebuth), hoatzin (Opisthocomus hoazin).

  • Eight bat species from four different families were detected in Pozo don Pedro, which sits amid an aguaje swamp. The bats feed on the pollen from the aguaje palms.

  • Two different eDNA filters were trialled side-by-side in this pilot study, and the detections and relative abundances were strongly correlated between the two filter types (Figure 1). This demonstrates the robustness of the methodology and helps build confidence in the results.

Figure 1. The proportion of the sequencing output allocated to the different orders. S = filter type 1; H = filter type 2; C = both results combined.

Larger Version of Data


  • The team at ACCA plan to build on the initial baseline data collected during this study and hope to integrate eDNA tools as part of large-scale monitoring plans, broadening their focus into other taxonomic groups.

  • The ACCA team are also progressing with their vision to build a small genomics lab at the CICRA research station in the future.


“[The] analysis gives us an insight into the presence of the species living in and around our conservation area. Establishing a baseline of biodiversity is extremely important to us, as we need to understand the ecosystem in order to protect it.”

“The eDNA pilot of NatureMetrics has inspired us to continue the implementation of this easy and fast conservation tool and explore the biodiversity in remote areas with illegal activities (hunting, logging, mining), to set up an aquatic biodiversity baseline and to use eDNA more specifically to identify bat and rodent species, which are hard to name solely based on photographic observations.”

“For us as conservationists, eDNA is an indispensable tool to monitor and subsequently protect wildlife.”

– Dr Judith Westveer, Science Director, ACCA (Asociación para la Conservación de la Cuenca Amazónica)


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