Bacterial protection

A study published in Science magazine with Brazilian participation shows how plants exploit a specific combination of soil bacteria to protect themselves from pathogens. The study identified 33,000 microorganisms

By Fábio de Castro

Agência FAPESP – Disease-suppressive soils are naturally special ecosystems: in this type of soil, even though pathogenic agents persist, they cause very little damage to plants. Nevertheless, the microorganisms and mechanisms responsible for this characteristic are unknown.

A group of international scientists, with Brazilian participation, has identified a series of bacteria and genes involved in the phenomenon utilizing a metagenomic technique.

The study published in Science magazine indicates that when attacked by pathogens, plants can exploit a combination of specific microbes contained in soil to protect against infections.

The first author of article, Rodrigo Mendes, currently a researcher at the Brazilian Agricultural Research Corporation (Embrapa) participated in the study while completing a post doctorate at the Wageningen University in Holland from 2009 to 2010. From 2003 to 2008, Mendes completed his doctorate that Universidade de São Paulo (USP) as a FAPESP fellow.

The study identified 33,000 bacteria, consistently associated with disease suppression.  According to Mendes, the study, which gained a commentary in Nature Biotechnology magazine, concluded that the suppression phenomenon does not depend solely on the activity of isolated bacteria, but also the synergy of a consortium of bacteria. The data indicate this specific combination of microorganisms is activated by a  signaling within the context of the bacterial community.

“One of the study’s strong points is that it has a transverse focus, covering field observation and identification of the community, bacterial groups, gender, species, the specific lineage of microorganisms and their genes and even the metabolites utilized by bacteria to defend the plant from pathogens,” he informed Agência FAPESP.

One of the general objectives of the research was to contribute to the understanding of how plants utilize and depend on the associated microbial community for survival. Mendes explains that similar studies are frequently conducted in mammals.

“We know, for example, that humans depend on microorganisms present in our intestines or on our skin, which help in absorbing nutrients or protecting against disease, for survival. In this vein, because humans live in conjunction with these microorganisms, many strands of literature consider man to be a superorganism that includes not only then human genome, but also millions of associated microorganisms. We applied this same vision to plants, observing them not only as host organisms, but as superorganism in conjunction with its microbiome,” he explains.

The study was focused specifically on microorganisms that are associated with plant roots. As they are infected, the plants exposed to soil pathogens suffer positive pressure to recruit the bacteria needed for protection. The soil is considered disease suppressive when this community of bacteria is so well selected that even in the presence of the pathogen, the plant is not infected.

“One one extreme, there is suppressive soil in which the plant completely resists the presence of the pathogen. On the other extreme is the soil in which the plant dies quickly after exposure to the pathogen. Our strategy was to evaluate six different levels of disease suppression in similar soil. What differentiated these six sections of soil was precisely the structure of the bacterial community present,” explains Mendes.

Indirect biological control

The first step in the research consisted of field observation with a view to identifying the place in which the infection appears. Secondly, the researchers analyzed the bacterial community present in the six different levels of soil protection, identifying which groups performed some role in this protection.

In the next phase, researchers selected and isolated some target groups in a test initially aimed at showing which specific groups were related to protection in the field. “One of the groups that we used to prove this phenomenon is a well-studied group that is sometimes associated with suppressive soils. But this had never been observed in such detail. Our study reveals a much larger set of different bacteria associated with protection than previously imagined,” he affirmed.

According to Mendes, the study could contribute to the future discovery of new molecules and antibiotic compounds that can be used for biological control of plant disease.

“We could even think about indirect biological control, that is, instead of introducing a biological protection component to the soil, the plant’s genes could be manipulated so that it more efficiently selects microorganisms that increase the level of protection,” he notes.

In order for this genetic engineering to be possible, however, Mendes notes that one must first precisely understand how communication between the plant and the bacteria of interest works.

“We demonstrated that the plant utilizes this resource. Now we have to understand how the plant communicates with this microbiome. From that point on, it will be possible to manipulate the plant in order to prime its capacity for microbial selection,” he adds.

The article Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria (DOI: 10.1126/science.1203980), by Rodrigo Mendes et al can be read by subscribers of Science magazine at: www.sciencemag.org/content/332/6033/1097.full.