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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, considering species abundance as well as presence-absence, 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 project will deploy camera trapping and sign and visual encounter surveys—traditional tools whose accuracy and precision for describing animal abundance and richness are well understood—simultaneously with eDNA sampling from soil and water and invertebrate DNA (iDNA) and sampling from insect blood-meals to calibrate the DNA-based methods through comparison with the traditional methods. Such calibration efforts have begun in the temperate zone, but this project will be the first to use multiple methods in a high biodiversity tropical area and use them to test hypotheses about both individual species abundance and species composition.
Through the simultaneous deployment of these methods, the project will describe the species composition of mammal communities associated with Brazil nut (Berhtolletia excelsa) rich forests and address the still-open question of whether Brazil nut harvest and management practices affect vertebrate communities and species abundance. The project will use metabarcoding for broad species detection and community-wide surveys, as well as quantitative PCR (qPCR) to test hypotheses for a subset of mammal species whose abundance is expected to be impacted by harvesting. Regardless of the success of the eDNA methods, the traditional sampling methods will allow the project team to address the question of biodiversity consequences of harvest and make recommendations for improved natural resource management in Brazil nut extraction areas.
The publicly available barcode database compiled by the project will be made available to the academic, public (biodiversity management and protection agencies), and private (consulting companies) sectors for research, monitoring, enforcement, and environmental impact assessments, respectively. Graduate students and postdoctoral associates at the two participating Brazilian universities will be trained in the use of qPCR techniques with broad applicability to biomedical/human health fields, as well as ecological contexts. Importantly, this project will enable new Brazil-U.S. research collaborations through exchanges among the USDA National Genomics Center and the Aguiar and Galetti labs at the University of Brasilia (UNB) and the Federal University of São Carlos (UFSCar).
Summary of Recent Activities:
During the second quarter of 2023, this PEER team focused on advancing their field activities, including training local residents and sample collection. In April, they organized a ten-day field expedition with all researchers from the project, including UFSCar’s team (Pedro M. Galetti Jr., Patrícia D. de Freitas, Carla C. Gestich and Bruno H. Saranholi), UNB’s team (Dayse S.S. Ferreira and Jose M. Fragoso), U.S. Forest Service (USFS) (Kirsten Silvius), and local NGO partner Fundação Vitória Amazônica (FVA) (Francisca Saldanha). The group traveled to the Tapiira community, which is located in the middle of Unini River, where they brought together local residents from all nearby communities along the river. For five days, the researchers taught selected 13 residents on all activities related to the project. Edmilson Fragoso da Silva, the president of the Association of the Residents of the Unini River (AMORU), went through all the ten local communities prior to the team’s arrival, talked with each community president, and selected potential parabiologists for the course. Two to three people from each community attended the training, which encompassed the use of data sheets and guides, protocols for sighting and vestige data collection, use of camera trapping, use of GPS and compass equipment, and fly collection for use in iDNA research. The local residents were oriented about the selection of the best transect starter points and linearity. An overview of the training was published in English and Portuguese in the USFS-Brazil newsletter. At the end of the course, four pairs of parabiologists were selected to be responsible for three transects near their native communities. Thus, the PEER team established 12 transects along the Unini River. As soon as the researchers left the Unini River, the parabiologists started opening the transects, and about one week later they began installing the camera traps (three per transect) and collecting data on sightings and vestiges of vertebrates. They collected data weekly for one month, beginning just after the nut harvest season. They also installed the fly traps (three per transect, totaling 36 samples) to collect insects during three days in the beginning of the period of data collection and in another three days at the end of this period, after one month.
In June, Dayse traveled back to the Unini River to monitor the work carried out by the parabiologists. She gathered the fly samples they had collected and the forms with all data collected on sightings and vestiges, and she changed out the memory cards in the camera traps. Also, in this visit in all the transects, together with the parabiologists, she collected water samples for environmental DNA analysis. They collected 1 liter of water in three different locations along each transect (totaling 33 water samples, since in some transects there were no water bodies along the transect). These samples were filtered by two other parabiologists trained for that function in the team’s first visit. Oyama S. Colares Filho and Rosangela F. da Silva are teachers in the school at the Tapiira community and were responsible for centralizing DNA samples from the parabiologists responsible for the transects. The filters and flies were sent to UFSCar, to be analyzed by Dr. Galetti’s team. The cards from camera traps and forms with data collected will be computed by Dayse and analyzed in the following months. Another collection period is scheduled to happen around September-October 2023, just before nut tree fructification period. For that purpose, another expedition will be carried out to recycle the parabiologists and optimize the data collection.
Also during this most recent quarter, the iDNA and eDNA team finished the DNA extraction, PCRs processing, and sequencing analysis of samples from Terra Ronca State Park. They characterized the mammal community by using water samples (eDNA) and mosquito and fly samples (iDNA). With this pilot study, besides improving collection procedures, the team also suggested some adjustments in laboratory procedures that will be implemented with the Amazonian samples.
As stated in the previous reports, the project has established a collaboration with the researcher Gonzalo Barquero, director-president of the NGO Tropical Sustainability Institute, to support their pilot survey in the Terra Ronca State Park. He collaborated in logistical access to the area, but also shared his previous results from camera traps for comparison with those obtained from eDNA and iDNA samples. The project also formalized a collaboration with the NGO FVA (Fundação Vitória Amazônica), which has been working in Unini and Jaú since their establishment and which supported management plan development for both areas. They have been supporting the PEER researchers in all field expeditions and approximations with local communities. In addition, the team have been connected with the Association of the Residents of the Unini River (AMORU), which is responsible for managing and contracting the community parabiologists who will support the project.
USFS has generously granted $104,280 to project partner FVA to support the increased costs of the PEER project, add an additional research component on soils and soil microbes in the Brazil nut forests, and facilitate uptake of the research results into management and marketing work by this civil society organization. Work with soils is done under the working hypothesis that aboveground animal and tree diversity affects the type of carbon inputs to the soil, and through that the functional traits of the soil microbial community and the relative amount of carbon that is either metabolized or sequestered in the soil. The title of the project is "Biodiversity and Ecosystem Function in Brazil-nut rich forests in the Unini River basin.” Until now, this grant helped the PEER project in the costs of the two expeditions carried out in 2023. For the next expedition, it will be important for soil collection as foreseen in the project of carbon input.
In the last half of 2023, the data and samples collected in this first season of surveying will be analyzed and the first preliminary results will be discussed. Just before the next fruiting season and the reduction of river level (September-October), the researchers will carry out another expedition to work with the parabiologists and collect more samples and data. This expedition will include the sampling of soil to encompass the carbon study being supported by USFS.
Publication
Carvalho, C., Oliveira, M., Rodriguez-Castro, K., Saranholi, B., & Galetti Jr, P. 2021. Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance. Molecular Ecology Resources. DOI:10.1111/1755- 0998.13543
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