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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 2021

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 first few months of 2021, PhD student Fernando Igne Rocha worked on qPCR analysis of antibiotic resistance and 16S rRNA genes to complement the analyses that he carried out during his internship in Dr. Adina Howe’s laboratory at Iowa State University. In addition, using the outputs from the targeted 16S rRNA through Next Generation Sequencing, the PI Dr. Jesus and his team are seeking assemblies of bacteria potentially involved in the infection or protection cycle of the disease. During the first quarter of 2021 they have also worked on detailed statistical analyses of soil chemical and physical attributes. Dr. Aline Pacobahyba de Oliveira and colleagues have also been revising the soil classification according to the Brazilian Soil Classification System. They decided to carry out new analysis to clarify some unusual patterns that they observed in the data. Thus, the samples of some profiles were under analysis during the reporting period. The profiles were deposited in the Brazilian Soil Information System, which is available to the public for consultation at the link https://www.sisolos.cnptia.embrapa.br/. The PI reports that he acquired the necessary kits for DNA extraction of dental biofilm samples from the second phase of the project, and co-PI Dr. Iveraldo Dutra and his group will start working on DNA extractions for sequencing in the next months.

Meanwhile, after a refined period of revisions, the team’s first paper titled “Land-use system and forest floor explain prokaryotic metacommunity structuring and spatial turnover in Amazonian forest-to-pasture conversion areas” has been accepted for publication in the journal Frontiers in Microbiology (doi: 10.3389/fmicb.2021.657508). As of mid-April 2021, they were awaiting the final proof corrections. In this manuscript, the researchers address the importance of considering the forest floor (association of litter, root layer, and bulk soil microbiota) in measuring regional scales of diversity, shedding light on a prokaryotic metacommunity hitherto underestimated in tropical forests at risk of advancing land use change. Also, Dr. Iveraldo’s team worked on the revision of two papers that are still under review. Finally, the researchers are preparing the first draft of another paper that discusses the effects of forest-to-pasture conversion.

The main challenges this past quarter, as in the past year, came from the effects of the Coronavirus pandemic. The universities and their laboratories remain closed, which has made it impossible for the researchers to extract DNA from their dental biofilm samples and to send them away for sequencing. They have been able to use the laboratories at Embrapa, albeit with restrictions, which has allowed them to continue with some laboratory analyses. Still, some of the analyses needed to revise the soil classifications are delayed, as the laboratories are not operating at full capacity. Plans for the coming three to six months include extracting DNA from the dental biofilm samples, processing data from clinical examinations of animals from the second phase of the project, and sending the samples for sequencing. DNA will also be extracted from soil samples for sequencing and community analysis. The PEER team will work on the analysis linking data on soil type and management, pasture age, forage chemical composition, and bovine periodontitis to encompass the complexity of factors included in this research project. They expect to generate more robust results about the structural process in the coming months. Finally, they will present an accepted abstract at the Global Symposium on Soil Biodiversity (FAO, Rome, Italy) on April 20.

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