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Cycle 9 (2020 Deadline)
Biodiversity correlates of sustainable value chain expansion in the Brazilian Amazon: developing combined environmental DNA (eDNA) and camera trapping protocols to assess vertebrate diversity in managed Brazil nut forests
PI: Pedro Galetti, Federal University of São Carlos (pmgaletti@ufscar.br) (original PI Ludmilla Aguiar), with co-PI José Luiz de Andrade Franco, University of Brasilia/Foundation for Scientific and Technological Enterprises
U.S. Partner: Kirsten Silvius, Virginia Polytechnic Institute and State University
Project Dates: May 2021 - April 2024
Project Overview
 | | A project team member sets an invertebrate trap during sample collection training. Photo courtesy of Dr. Aguiar. |
DNA metabarcoding of environmental DNA (eDNA)—simultaneously identifying multiple species using short sections of DNA from soil or water samples— holds great promise for biodiversity research, but these tools have not been fully refined for assessing animal community structure in general and terrestrial vertebrate communities in particular. eDNA work is more advanced for aquatic than terrestrial systems, facilitated by DNA’s more rapid dispersal in water. This PEER project used camera trapping and sign and visual encounter survey, simultaneously with eDNA sampling from soil and water and invertebrate DNA (iDNA) and sampling from insect blood-meals, to describe the species composition of mammal communities associated with Brazil nut (Berhtolletia excelsa) rich forests. This work was designed to address the still-open question of whether Brazil nut harvest and management practices affect vertebrate communities and species abundance.
Wild-harvested Brazil nuts are an internationally traded food commodity and a key source of income for traditional and indigenous peoples. Brazil nuts are Brazil’s single most valuable non-timber forest product. Understanding the impacts on biodiversity and ecosystem function of nut-biomass extraction and other types of anthropogenic disturbance during the harvest is essential to ensure the ecological sustainability of the resource and provide an important marketing tool, assuring consumers that Brazil nuts from the Brazilian Amazon are harvested using ecologically and socially sustainable approaches.
Final Summary of Project Activities
The PEER team began by carrying out a pilot experiment at Terra Ronca State Park, investigating the mammal community from eDNA and iDNA samples with metabarcoding sequencing to reproduce an ongoing experiment with the RT-PCR approach. They collected water samples and bulk samples of mosquitoes and flies from insect traps and used the RT-PCR procedure to determine the presence of Panthera onca. The samples’ row sequences were processed with bioinformatic tools, which showed 33 mammal species. This pilot phase allowed researchers to adjust their methods for their planned field expedition.
The researchers also joined project partner Fundação Vitória Amazônica (FVA) to visit Brazil nut producing communities in Jaú National Park and Unini River Extractive Reserve. They presented their PEER project at eight community meetings of traditional ribeirinho families living on both banks of the Unini River. After each meeting, the team held conversations with individuals identified as among the most active Brazil nut harvesters in each community.
The PEER team organized a ten-day field expedition to the Amazon with all researchers from the project, including U.S. and local NGO partners. At the Tapiira community, local residents from all the visited communities met and researchers trained 13 pre-selected residents on participating in the project as parabiologists, engaging the local community in participating in the research. At the end of the course, four pairs of parabiologists were selected to be responsible for three transects near their home community. The team established 12 transects along the Unini River, where local parabiologists installed camera and fly traps and collected data on sightings and vestiges of vertebrates for a month. To monitor the work carried out by the parabiologists, a member of the PEER team traveled back twice to the area, gathering fly samples and data collected by the parabiologists, as well as collecting water samples for environmental DNA analysis.
In addition, soil collection took place under a complementary project that seeks to expand the amount of environmental data collected at the study sites: “Biodiversity and Ecosystem Function in Brazil-nut rich forests in the Unini River basin”. A total of 125 soil samples were collected and shipped to laboratories at the ESALQ school at the University of São Paulo, where they were analyzed for soil and microbial community structure by project collaborators.
One difficulty with the eDNA and iDNA approaches is the lack of a complete reference database on target species sequences, especially from areas of high diversity, such as Amazonia. Part of the PEER team worked on construction of a library of sequences with two minibarcodes (12S and 16S) used in the metabarcoding approach for mammals, and produced reference sequences for about 60 mammal species, which will be deposited in the NCBI database.
The researchers recorded 74 mammal species throughout all sampling methods. While findings are still preliminary, they have concluded that for short survey periods of less than 3 months, DNA methods are highly complementary to the traditional transect and camera trap methods used to detect medium and large terrestrial vertebrates and will add taxa to any such survey. For longer term surveys (a year or more), the traditional methods would likely be sufficient for the targeted medium-to-large mammal taxa. For small mammals, which are usually detected with physical trapping, DNA methods are highly complementary to transect-and camera-trap based surveys that do not include traditional methods for capturing small mammals.
The team's project partner Fundação Vitória Amazônica received an additional grant of $104,000 to support the PEER Project work, as well as the complementary work on soils and soil microbes. The team presented findings from the pilot experiment at XI Brazilian Congress of Mammalogists in 2022 and further manuscripts on the larger project are forthcoming.
Publications
B.H. Saranholi, F.M. França, A.P. Vogler, J. Barlow, F.Z. Vaz De Mello, M.E. Maldaner, E. Carvalho, C.C. Gestich, B. Howes, C. Banks-Leite, and P.M. Galetti, Jr. 2024. Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics. Molecular Ecology Resources 24(5): e13961. https://doi.org/10.1111/1755-0998.13961
B.H. Saranholi, K.G. Rodriguez-Castro, C.S. Carvalho, S. Chahad-Ehlers, C.C. Gestich, S.C.S. Andrade, P.D. Freitas, and P.M. Galetti, Jr. 2023. Comparing iDNA from mosquitoes and flies to survey mammals in a semi-controlled Neotropical area. Molecular Ecology Resources 23(8): 1790–1799. https://doi.org/10.1111/1755-0998.13851
C.S. Carvalho, M.E. de Oliveira, K.G. Rodriguez-Castro, B.H. Saranholi, and P.M. Galetti, Jr. 2022. Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance. Molecular Ecology Resources 22(4): 1262–1273. https://doi.org/10.1111/1755-0998.13543
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