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Partnerships for enhanced engagement in research (PEER)
Cycle 4 (2015 Deadline)

Monitoring the disturbance of the microbiota in Amazonian soils during conversion of forest to pasture and its consequences on cattle health

PI: Ederson Jesus (, Embrapa (Brazilian Corporation of Agricultural Research)
U.S. Partner: James Cole, Michigan State University
Project Dates:  October 2015 - September 2018

Project Overview

Pandemics of “swollen face,” a bacterial-origin periodontitis disease afflicting ruminant livestock, have been correlated with deforested areas in Brazil (Döbereiner et al., 2000). This disease, which is also known as "lumpy face," was commonly reported in Brazil during the 1960s and 1980s. New cases have recently been observed in sheep and goat flocks in the Amazon, under the same epidemiological conditions and with the same characteristics observed in bovines. In such circumstances, the disease has destroyed herds of livestock, often up to 90% of the animals. Dr. Jesus and his project collaborators hypothesize a link between the “swollen face” disease and shifts in the soil microbial communities as a consequence of deforestation and pasture introduction. This belief is based on previous evidence showing that this disease is triggered by deforestation, which in turn leads to significant changes in the soil communities, favoring specific populations such as actinomycetes. The team’s objective is to characterize correlations between the soil environment, changes in the microbial community due to deforestation, and the occurrence of this disease. Once more specific correlations are identified, they will experimentally test hypotheses (e.g., causation) generated through isolating key microbes and using culture-dependent and independent techniques. Answering these questions is important to advance towards a cure for the disease and design monitoring methods and alternative management to reduce its incidence. Additionally, confirming the link between the occurrence of diseases, deforestation, and changes in biodiversity will contribute to the delineation of policies to hinder deforestation and to promote biodiversity conservation. As part of the effort, the U.S. Government-supported partner, Dr. James Cole, will provide training and support with bioinformatic analysis of the datasets, sharing analytical tools he uses in his own research.

The world’s growing population and their increasing demand for animal protein raises concerns over the pressure for the creation of new pastures to meet this demand, especially in countries like Brazil, which is the world’s leading beef exporter. New pastures are created at the expense of native lands, including the Brazilian Amazon. In fact, pasture introduction is the major driver of deforestation in the region, and alternatives to reduce this pressure are needed. Within this context, this project can contribute with information to support policymakers in their decisions, as well as to create alternatives to the sustainable management of pre-existing pasture lands. The results of this project may also contribute to designing sustainable, innovative management systems, such as the integrated crop-livestock-forest system, which has been recognized by FAO, the Ministry of Agriculture of Brazil, and Embrapa as an alternative to stimulate the use of pre-existing pasture lands, guarantee food and agricultural security, and discourage the deforestation of new areas for agriculture and livestock production.

Summary of Recent Activities

The last quarter of 2017 was a busy period of field and lab work for PI Dr. Ederson Jesus and his colleagues. They analyzed 69 soil samples from Santo Antonio do Matupi, Boca do Acre, and Bujari for pH, element content, and texture. In addition, 98 soil samples and 40 plant samples from the same locations are being processed for DNA extraction, along with 227 biofilm samples and about 100 samples from rumen and feces. In order to reduce costs, all soil and animal DNA will be sequenced at once, and a contract for the work has been signed with Argonne National Laboratory. Meanwhile, veterinarians and sanitary defense agencies in Acre, Amazonas, Mato Grosso, and Pará states and slaughterhouses in Manaus, Manacapuru, Itacoatiara, Santarém, and Santana do Araguaia were contacted in order to identify potential new sites for sample collection.

4-299 MiGA Workshop
Dr. Jesus (left) with U.S. partner Dr. James Cole of Michigan State University and Dr. Kostas Konstantinidis from Georgia Tech, along with a third U.S. partner, Dr. Adina Howe of Iowa State University at the MiGA workshop (photo courtesy of Dr. Jesus).
On the training and capacity building side of the project, the PI and his team organized a workshop October 17-19 to train participants on the analysis of sequencing data, which includes genomes, metagenomes, and amplicons. Twenty people took part, including students and researchers involved in the PEER project, as well as graduate students from various institutions in Brazil. The workshop took place at the Laboratório Nacional de Computação Científica in collaboration with Dr. Maria Tereza and Luciane Prioli, who supported the group with their computational infrastructure. The workshop began with an introduction to programming on the first day and continued on the next two days with examples of data analysis using the MiGA platform. This platform was developed with NSF funding support by U.S. partner Dr. James Cole of Michigan State University and Dr. Kostas Konstantinidis from Georgia Tech, both of whom served as instructors at the workshop along with a third U.S. partner, Dr. Adina Howe of Iowa State University. The PI Dr. Jesus and his students, postdocs, and fellow researchers also took the opportunity of their counterparts’ visit to have some side meetings before and during the workshop. This was especially important to the students and postdocs because they had the opportunity to present their work to the U.S. partners and to discuss technical issues and future exchange opportunities. The group also discussed potential hypotheses and ways to address data analysis on the PEER project when the data become available.

The main current challenges on the study are finding additional sites that are not conducive to the disease and adjusting the soil DNA extraction protocol to reduce some DNA shearing that has been encountered. The team plans to submit DNA samples for sequencing as soon as the shearing issue is solved. In the meantime, analysis of non-DNA soil data from Santo Antônio do Matupi, Boca do Acre, and Bujari will be carried out in the early months of 2018, and analysis of sequencing data will be carried out as soon as data are available from Argonne. The team will also be discussing which of the new sampling areas visited by co-PI Dr. Iveraldo Dutra will be sampled in the next dry season. Since the researchers took samples in the dry season in 2017, they will do the same in 2018 in order ensure that the samples are comparable. Soil classification will be carried out during the dry season (June through September), which is the only time of the year it is possible, as site access and working conditions are severely hampered during the rainy season.

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