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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 (ederson.jesus@embrapa.br), Embrapa (Brazilian Corporation of Agricultural Research)
U.S. Partner: James Cole, Michigan State University
Project Dates:  October 2015 - September 2020

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

Dr. Jesus and his colleagues have been carrying out a field experiment since June 2019 as part of this project, regularly collecting soil and animal samples. In March 2020, however, sampling had to be interrupted due to the current coronavirus pandemic. The samples have been frozen and the PI is awaiting signature of an updated agreement within his institution so he can buy test kits and proceed with DNA extraction and molecular analyses. During the first quarter of 2020, prior to the shutdown, activities on the project included periodontal clinical examinations of calves in the field experiment and collection of subgingival biofilm and soil samples. So far, the researchers have performed 18 periodontal clinical examinations, totaling 1,152 periodontal evaluations of incisors, with a 477 animals found to have gingivitis and 37 with necrotizing gingivitis. With support from Dr. Elerson Gaetti Jardim Jr. and Dra. Christiane Schweitzer, the team also completed statistical analysis of clinical data of 344 bovines examined at farms from the Amazon region. Abstracts about oral microbiomes in cattle, sheep, and goats have been submitted and accepted for presentation at the World Congress of Infectious Diseases, which will be held in Italy in November. Some of the soil samples were sent for re-analysis to confirm whether the results of previous analyses are correct, as well as to analyze additional elements. The analyses are still under way as of mid-April 2020. PhD student Fernando Igne, who is currently on a long-term training visit to Iowa State University, has been working on sequence data analysis of the soil samples and is preparing a manuscript to be submitted for publication in the next few months. Due to access restrictions at Iowa State, lab-based activities are currently limited.

Future plans include extracting DNA from the subgingival biofilm samples collected, sequencing the 16S rRNA gene, tabulating data on the prevalence of lesions and sequencing results, and completing statistical and bioinformatics analysis of the results. Dr. Jesus and his colleagues will also work with U.S. co-partner Dr. Adina Howe at Iowa State on quantifying antibiotic resistance genes in soil samples. The PI expects his current internal contracting issue to be resolved by the end of May 2020 so he can proceed with buying materials and supplies and paying for the necessary analytical work.

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