Research discovers bacteria capable of killing disease-causing fungus that reduces sugarcane productivity

A study developed at the National Center for Research in Energy and Materials (CNPEM) discovered three strains of bacteria of the genus Pseudomonas capable of inhibiting the growth and even causing the death of the fungus responsible for the disease called pineapple rot, which attacks sugarcane fields mainly during the planting period.

The results of the work, published in the scientific journal Environmental Microbiology,  Society for Applied Microbiology, enable the development of biological fungicides as an alternative to the pesticides currently used against the pest.

The three strains of bacteria were able to inhibit, vitro, up to 80% of the mycelial growth of the fungus Thielaviopsis ethacetica, present in the soil and which takes advantage of cuts or injuries in sugarcane billets to enter the plant and reduce sprouting by up to 50%, reducing productivity. The mycelia form the branching mass, composed of a set of tangled filaments (hyphae), which carry essential nutrients for the survival of the fungus.

The research showed that these bacteria produced 62 different volatile organic compounds (VOCs), which negatively regulated genes related to carbohydrate metabolism, essential for the growth of the fungus. VOCs are products resulting from the metabolism of bacteria and can be obtained in the form of liquids and gases, which evaporate easily at room temperature. One of the advantages is that they can reach long distances when applied to crops.

“For the first time, we saw that the molecule acts directly or indirectly on the pathogen’s DNA, causing damage. It is a compound that breaks down DNA. This type of molecule is little explored in Brazil. Our objective is to become strong in this line of research, being a reference in the study of these molecules in our country”, he told Agência FAPESP Juliana Velasco de Castro Oliveira, researcher at the Brazilian National Biorenewable Laboratory (LNBR), CNPEM, and coordinator of the work.

The study received support from FAPESP through the Bioenergy Research programs (BIOEN) and Research in Partnership for Technological Innovation (PIES).

During transcriptomic analyzes of the fungus' response to VOCs (used to identify and quantify the expression of new or previously known genes) and electron microscopy, scientists detected changes in the expression of important genes as well as critical morphological changes in mycelia treated with VOCs. , proving its lower growth and even cell death.

“We managed to find strains of bacteria that are efficient in controlling the pathogen that causes significant damage to sugarcane crops. We also identified molecules that had not been described as having the capacity to kill these fungi and proved that these molecules can cause damage to DNA, which is little documented in the literature”, summarizes Oliveira.

Pineapple rot is a disease that affects several tropical crops, but in Brazil it has an impact especially on the productivity of the sugar-energy sector. The fungus can prevent seedlings from germinating or delay their development, leaving the affected areas with major flaws.

As the fungus reproduces inside the plant, the stem fibers have a reddish color, which gradually becomes darker and covered with spores. The fermentation caused by the pathogen releases an odor similar to pineapple, hence the name of the disease.

With the increase in incidence in recent years, the disease is among the most common in sugarcane fields. Brazil is the world's largest producer of sugar cane. In harvest 2020/21, was responsible for the production of 654,5 million tons, destined for the production of 41,2 million tons of sugar and 29,7 billion liters of ethanol.

Some management techniques at planting time, such as seedling selection and soil preparation, help prevent pineapple rot. However, to control the infection, it is necessary to use pesticides, which can pose risks to the environment and human health if they are not applied in the appropriate manner and quantity.

“Brazil is an agricultural powerhouse. We know that it is not yet possible to completely replace chemical pesticides with biological alternatives. With new studies, like ours, this offer can grow in the market, being a sustainable alternative that can help reduce the country's dependence on importing products”, said the researcher.

In total, Brazil imports more than 330 thousand tons of insecticides, herbicides and fungicides per year, according to data from the Ministry of Economy. Furthermore, between 2019 and 2021, at least 1.500 new pesticides were authorized for use.

New technologies

The researchers began the work using the LNBR's microorganism bank, which has a collection of around 7 bacteria from different types of soil and roots. They selected 70 microorganisms from different genera and locations, such as Tocantins, Mato Grosso and São Paulo. This sample was subjected to tests vitro to evaluate the ability to inhibit the growth of the fungus, reaching the three strains of the genus Pseudomonas, which were confirmed through genetic sequencing.

Now scientists have begun a new phase to discover the species of these strains. “We know they are different, but we are not yet sure what they are. To do this, we will need to fully sequence these bacteria. We even saw that one of them is from a species that has not yet been described. In partnership with Unicamp [Universidade Estadual de Campinas], we will try to describe it soon”, stated Oliveira.

Scientists from the Postgraduate Program in Genetics and Molecular Biology at Unicamp and the Federal University of Lavras (MG) participate in the research group. “Nowadays it is not possible to do research alone, especially when you are exploring a new area. Therefore, the importance of grouping expertise”, he added.

At the National Synchrotron Light Laboratory (LNLS), responsible for operating Sirius (fourth generation particle accelerator), spectroscopy analyzes confirmed the ability of biomolecules to produce damage to the pathogen's DNA. To reveal this kind of “fingerprint” of biomolecules, high-sensitivity research techniques using infrared were used.

Furthermore, at the National Nanotechnology Laboratory (LNNano), which is also part of the CNPEM, transmission and scanning microscopy resources were used to show the severe morphological changes in the mycelia.

In 2019, other research coordinated by Oliveira had already highlighted the potential of bacteria to promote the growth of agricultural crops without causing water pollution and harmful changes to the soil itself.

The article Bacterial volatile organic compounds induce adverse ultrastructural changes and DNA damage to the sugarcane pathogenic fungus Thielaviopsis ethacetica can be read at: https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.15876.