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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 2019

Project Overview

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).
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

During the second quarter of 2018, Dr. Jesus and his colleagues made an 11-day field visit to Boca do Acre (AM) and Bujari (AC), where they revised the same farms they had sampled in 2017. During this visit, they classified soils and took more soil samples for microbiological analysis. Dr. Aline Oliveira and her group opened trenches in each of the pastures and forests studied. Observations were made in the field and samples were taken from each horizon for chemical, physical, and hydrological analysis back in the lab. The team has found a more complex environment in the forest than expected, so they sampled different strata of the forest and pasture floors in order to account for the complexity and test new hypotheses linked to the distribution of microbes in the forest floor. Regarding this last topic, the researchers also traveled to Pará for a week in order to train students and get some soil samples to test their hypotheses. In other recent fieldwork, postdoc Dr. Ana Carolina Borsanelli examined more animals in Boca do Acre and Bujari to complement the characterization of the disease incidence made last year. She and project co-PI Dr. Iveraldo Dutra also visited other locations in the states of Acre, Amazonas, Pará, and Mato Grosso to examine animals and obtain samples.

On the capacity building side, two project team members, student Thiago Ribeiro and researcher Dr. Mária Coelho participated in the Explorations in Data Analyses for Metagenomic Advances in Microbial Ecology (EDAMAME) Workshop at the Kellogg Biological Station, Michigan State University, in June 2018. This week-long training course provides hands-on training in microbial metagenome analyses, including how to analyze various types of sequences and access useful resources available in public databases and cloud platforms.

Samples collected earlier this year were sent to the Argonne National Lab for sequencing in June 2018, with the results expected by the end of August, at which point the team will begin analyzing the data. Their next visit to the field sites is scheduled for late September. During this visit, the researchers will classify the soils of the remaining farms and take more samples for microbiological analysis. The PI and his team are also planning the second phase of the project, which involves experimentation.

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