#GenomicLab

Pantanal


The Pantanal is considered the largest continuous wetland on the planet, with approximately 179,300 km² (area larger than Portugal and Austria combined) and supplied by the Paraguay River Hydrographic Region, is a biome predominantly Brazilian, 78% of which are located in Brazil, 18% in Bolivia and 4% in Paraguay.

Watershed


The Pantanal has a periodic flooding system, in which part of the year is flooded and part of the year is dry, making it a hostile environment for many species. The species that remain there have a high degree of resistance to the natural transformations of the biome, and resilience, which demonstrates the ability of organisms to recover after drastic environmental changes.


Hydrographic basin where the Pantanal is located, covering the states of Mato Grosso and Mato Grosso do Sul
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Pantanal of the Nhecolândia sub-region (Mato Grosso do Sul) in full season


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Pantanal in the Cáceres sub-region (Mato Grosso) in full season


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Pantanal of the Cáceres sub-region (Mato Grosso) in the dry season



Another interesting feature of the Pantanal is that many endangered species in other locations in Brazil they persist in large populations in the region. The Pantanal is an immense reserve (or bank) where many species of animals can re-colonize (breed and spread) adjacent biomes that have their populations threatened or affected, like the Cerrado and the Atlantic Forest.


The genetic heritage of the Pantanal's biodiversity

To understand whether this potential is viable, we need to study the genetic heritage of the Biome. The Brazilian Pantanal is home to about 263 species of fish, 41 of amphibians, 113 of reptiles, 463 birds and 132 mammals, two of which are native to the region itself. Almost 2 thousand plant species have already been identified and classified according to their potential, some of them with medicinal potential, being an important source of natural products. The fires recent years destroyed 30% of the Brazilian Pantanal area, equivalent to 30 times the size of the city ​​of São Paulo or an area larger than the whole of Denmark(LASA, 2020). Many species have been heavily affected and some populations may have been lost.



Burned


It is essential to carry out a genetic survey of the biodiversity of the Pantanal as As soon. Mapping the Pantanal's genetic heritage will provide information valuable and comprehensive information on the diversity, distribution and characteristics of the species inhabit this Biome, otherwise, we will never know what is being lost.




Multisectoral consortium for the Pantanal: sequence to preserve

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O #GenomicLab (genomiclab.org) is part of the multisectoral consortium that has academics, NGOs and private companies, to carry out a citizen science project based on genomic data to map the Pantanal's biodiversity. The partnership will use tools that make use of DNA sequencing, such as barcoding DNA bars), meta-barcoding and environmental DNA (eDNA).








Barcoding: (i) small samples of individuals (fauna / flora) are collected, (ii) the DNA of these samples is extracted, (iii) 1 or 2 genes (also called molecular markers) from each of the DNA’s is amplified by the PCR technique, (iv) the genes amplified by the PCR are sequenced and the sequences generated analyzed in order to identify which species corresponds to this DNA.

These methods allow obtaining evidence about the route of animals in certain areas without the need to observe them closely. The marks and clues they leave in the environment (excretions, hair, scales, skin, etc.) carry their DNA (eDNA) and with these methods and modern technologies we can determine "who passed through there".


Costs, Time, Human resources

These methodologies have advantages, since they do not depend on the luck of finding the right animal, nor all the necessary logistics to go to the field, equipment and hours of observation, but use the DNA left in the environment (eDNA), which will be used to determine if it is or passed in that area. The data obtained (DNA barcodes, GPS coordinates, photographs taken by tourists and local residents, physical-chemical characteristics of water and soil) will be used to: (i) create prediction models for species distribution, with the objective of better understanding where each species is located or what areas it traverses, (ii) helping to make better conservation decisions and (iii) assessing the impact of human activity on the distribution of biodiversity: the richness and distribution of species in the unburned areas compared to the areas burned?

The DNA footprints in the Pantanal

Comparison of biodiversity between burnt and unburnt areas:

Based on laboratory results (meta-barcoding) we will have a profile of which animals are using the areas that burned as well as those that didn't. From mathematical models and data obtained by satellite images we can extrapolate the results obtained in the areas that did not burn for the areas that burned, so you can get an idea of ​​how many and which animals should occur there. When we compare the results of this model in results of our collections in burnt areas, we will have an excellent estimate of how many animals and which groups were lost due to the burning of the year 2020. With this information, it will be possible to design more specific conservation actions and evaluate the possibility of restocking in these areas.

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Citizen participation4>

Citizen participation:

In parallel with eDNA extraction and sequencing, our methodologies will be validated based on the observation of fauna made by society. validate these methodologies with observations of fauna. For this, in addition to the researchers, we will count on the participation of tourists and local residents, sharing the photos of animals in the Pantanal with the location from which they were taken (and possible coordinates of GPS). The photos will allow us to validate our model. The project will offer a list of suggestions and record books so that the observation made by tourists, residents etc., even without the coordinated, can be incorporated into our assessments, provided that with some geographic accuracy. Tour guides will contribute to this accuracy. Participation of high school teachers and students in the collections, DNA extraction and sequencing of the barcoding of Pantanal species.

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Results:

Results:

Engagement in environmental protection, training of human resources, initiation promotion of interest in science. The data obtained will also serve to assist in the classification of the degree of rarity of each species (in this case the least abundant) to prioritize complete genome sequencing most threatened, serving as a basis for prioritizing all actions and efforts de-extinction. The project will be completed in 12 months. In this short space your contributions will have a long-term impact: (i) the biodiversity data obtained will serve as a basis for comparative studies over time, aiming to follow the changes caused by the burned over the years, (ii) awareness of the importance of biodiversity for conservation, (iii) expanding citizen participation in conservation campaigns and actions and (iv) the training of teachers and students of the School in the use of DNA sequencing tools, which translates into the availability of citizens trained in the use of DNA technologies for various conservation actions.



Schedule

Activity / Month 1 2 3 4 5 6 7 8 9 10 11 12
Acquisition of equipment and reagents x x x
Teacher training (collection, DNA extraction and sequencing) x x x
Collections in the Pantanal (soil and water) x x x x x x
DNA extraction and sample sequencing characterized biological (barcoding), with teachers and high school students x x x x x
Sequencing of environmental DNA (meta-barcoding) x x x x x
Database Pantanal biodiversity publicly available and progressively updated x x x x x
Photo organization and analysis of the Pantanal fauna obtained by tourists and locals x x x x x x x x x x x x
Organization and analysis of Pantanal fauna photos obtained x x x x x x x x
Genome sequencing full of less abundant or rare species x x x x x x

Goals

1- Preliminary mapping of Pantanal biodiversity, comparing areas burned and not burned.
2 - Predictive modeling of species distribution


Samples to be collected:

Pond water (banks of aquatic macrophytes) and soil (surface and 15cm deep) of burnt and unburnt areas. All samples collected will be transported in a refrigerated environment to the place where the extracted DNA, and will be characterized by physical-chemical analysis.


Field stations: 2 field stations in the South Pantanal (Corumbá and Aquidauana in the Mato Grosso do Sul) and 2 field stations in the North Pantanal (Cáceres and Cuiabá in the state of Mato Grosso). Each equipped with BentoLab ® (for DNA extraction) and MinION ® (ONT) for barcoding. Meta-barcoding using eDNA will be done using different sequencing technologies.

Training: collection, DNA extraction and sequencing for teachers / researchers Higher Education, High School Biology teachers. Activities may be carried out in secondary and elementary schools aiming at the dissemination of information about the diversity found and its importance for this Biome. For this, the partnership will be made with the schools of the state and municipal education network and will count on the participation of undergraduate students of the biological sciences course in the various municipalities involved in the study.




APOIO NECESSÁRIO

Oligos (barcoding / meta-barcoding)
Falcon tubes (15ml, 50ml)
Eppendorf tubes
Pipetters and tips (P10, P200, P1000)
DNA extraction kits (for example: DNA PowerWater, DNA PowerSoil)
MinION (ONT)
BentoLab
Genomic DNA library and sequencing reagents (MinION-ONT, Illumina, Ion Torrent and PacBio)
Field work fuel
PCR Kits (Taq High Fidelity Polymerase)
Thermal bag (temporary sample storage in the field)
Media editing services (book, posters, posters and videos)

Support


Pesquisadores
Alberto Dávila - #GenomicLab (Rio de Janeiro, RJ)
Alexsandra Favacho - FIOCRUZ-Mato Grosso do Sul (Campo Grande, MS)
Andre Luiz Julien Ferraz - UEMS (Aquidauana-MS)
Camila Mazzoni - BeGenDiv (Berlim, Alemanha)
Diego José Santana Silva - UFMS (Campo Grande, MS)
Edvagner de Oliveira - E.E. Onze de Março, Seduc-MT (Cáceres, MT)
Ernandes Sobreira Oliveira Junior - UNEMAT (Cáceres, MT)
Gecele Matos Paggi (UFMS) (Campo Grande, MS)
Janaína Guernica Silva - UFMS (Corumbá, MS)
Jeronimo Alencar - IOC/FIOCRUZ (Rio de Janeiro, RJ)
Luanne Lima - ICMBio/CENAP (Atibaia, SP)
Lucí Helena Zanata - UFMS (Corumbá, MS)
Maria Luiza Machado Campos - UFRJ (Rio de Janeiro, RJ)
Marivaine da Silva Brasil - UFMS (Corumbá, MS)
Nelson Peixoto - IOC/FIOCRUZ (Rio de Janeiro, RJ)
Ricardo Henrique Gentil Pereira - UFMS (Aquidauana, MS)
Roberta Azeredo Murta da Fonseca - UFMS (Corumbá, MS)
Rodrigo Jardim - #GenomicLab (Rio de Janeiro, RJ)
Sérgio Serra - UFRRJ (Seropédica, RJ)

Simone Chinicz Cohen - IOC/FIOCRUZ (Rio de Janeiro, RJ)
Walfrido Tomas - Embrapa-Pantanal (Corumbá, MS)
William Marcos da Silva - UFMS (Corumbá, MS)
Wilkinson Lopes Lázaro - UNEMAT (Cáceres, MT)
Zoraida Fernandez - FIOCRUZ-Mato Grosso do Sul (Campo Grande, MS)





Developed by PET-SI/UFRRJ 2020