The microbes of forests

According to a FAPESP's Thematic Project, the substitution of a forest area for an area of cultivated plants could reduce the diversity of the bacteria associated with the surface of leaves by more than 99%

By Fábio de Castro

Agência FAPESP – In 2006, an article published in Science magazine by scientists connected to a BIOTA-FAPESP Thematic Project demonstrated that the plants of  the Mata Atlântica (Atlantic Rainforest) had an impressive diversity of associated bacteria: each tree species has its own distinct and unique community of hundreds of species of bacteria.  

The discovery suggests that the function of these microorganisms in the forest’s normal dynamics could be much more important than originally thought. Now, another Thematic Project initiated in 2009 is expanding that research with a view of better understanding the forest’s microbiological diversity.

One of the most important findings so far in the new project indicates that the substitution of a forest area for an area of cultivated plants could reduce the diversity of the bacteria associated with the surface of leaves by more than 99%. The consequences of such of a move are still being evaluated.

According to the coordinator of the Thematic Project, Marcio Rodrigues Lambais, professor of the Department of Soil Sciences at the Universidade de São Paulo’s Luiz de Queiroz Agriculture School (Esalq), the study is based on the 2006 discovery, which showed that each plant had its own community of bacteria.
 
“Now we are trying to expand the studies to know if the bacterial community varies not only in relation the various species of plants, but also based on the location of plants in different environments, taking into consideration, for example, the position of trees within a given park or comparison of the same plant species in parks that are distant from each other,” explains to Agência FAPESP.

The surfaces of tree leaves, trunks and roots contain complex biofilms comprised of diverse microorganisms that interact amongst themselves, with the plant, with animals and the atmosphere. According to Lambais, these microorganisms associated with the plants – the function of which is still unknown – are being studied through utilization of metagenomic tools.

“The studies show that each plant species has a unique set of bacteria associated with it. And each part of the plant has a different community. On the leaf, bark or root, the same bacterial species are not repeated,” says Lambais. On leaves alone, from 30 to 600 different species were found, depending on the vegetal species.

“If we compute the totality of this diversity, we will conclude that each plant species could have more than 2,000 associated species of bacteria. A massive diversity about which we know practically nothing,” he highlights.

The greater part of the study is being conducted in the land areas utilized in the Thematic Project which generated the studies concluded in 2006, known as Permanent Plots, and is coordinated by professor Ricardo Ribeiro Rodrigues, also from Esalq. The most recent study was conducted on a 10 hectare plot located in Parque Carlos Botelho, where there are 217 tree species.

“The Permanent Plot project had already mapped the characteristics of that entire area and conducted a census of the vegetal species. We already had this data, in addition to other information related to the chemical and physical characteristics of the soil, and we utilized it to aggregate microbiological information. In the study, we managed to demonstrate the relationship between the structure of the community of bacteria and the phylogeny of the plants,” says Lambais.

Differences in cultivated areas

Based on information obtained using molecular technology, the researchers believed that cultivated plants would probably have a much lower quantity and different type of associated bacteria than those found on forest species.

“We had this curiosity and we made this comparison utilizing soybean, sugarcane and eucalyptus. To our surprise, the cultivated plants and forest trees are statistically very similar in terms of the estimated diversity and wealth of bacterial species. Nevertheless, the types of bacteria that live on the leaves of cultivated plants are very different from those that live on plants in the forest,” he says.

While gammaproteobacteria predominate on plants in forest areas, on cultivated plants it is alphaproteobacteria that predominate. “Normally, these alphaproteobacteria are microorganisms that grow rapidly, and, for this reason are well adapted to the short cycle of agriculture crops,” explains Lambais.

A soybean crop, for example, has only a three month cycle before harvest. The community of bacteria present in these crops is adapted to this situation and grows very rapidly.

“In arboreal species the situation is much more stable. The bacterial biofilm on leaves can be developed for a much longer period of time. Undoubtedly, this type of bacterial community has very different functions. Therefore, if we alter the land use, we also change all the processes that depend on this associated microbial community,” he notes.

The study found that substituting a forest area for an identical area of cultivated plants could drastically reduce bacterial diversity. Lambais explains that the calculation was based on a 10 hectare area in the Carlos Botelho forest reserve, which has more than 200 species of trees.  

“Considering that there are 200 vegetal species and each has more than 50 species of bacteria associated to the phyllospere, we have at least 10,000 different species of bacteria per hectare. If we substitute 10 hectares of forest for 10 hectares of sugarcane crop, for example, we will have just 50 bacteria associated to the sugarcane leaf. That means just 50 types of bacteria, instead of 10,000.  Just in this one area, we will have a reduction of more than 99%,” he explains.
On plantations, large areas are dominated by one vegetal species. This impacts the variability of bacterial species, creating an area in which only one group is dominant. Maintaining vegetal diversity is, therefore, also important to maintaining microbiological diversity.

“What we don’t know yet is precisely what the importance of maintaining this diversity of bacteria is. For this reason, we are trying to understand the functional roles of these bacteria in the forest, defining what they do,” says Lambais.

The function of bacteria

 One example of the function of these bacteria was discovered in another area of the Biota program: the Santa Virgínia Center in Serra do Mar State Park. At that site, professor Lambais’ team detected that some plant species have high nitrogen fixing activity on the surface of leaves.

“Nitrogen is an essential element for plant growth and is not found in the forest soil. In order to maintain the forest, the nitrogen must come from the environment. Nitrogen is captured from the air by microorganisms that live on tree leaves and bark,” explains Lambais.

According to the Easlq professor, the Juçara palm tree, a dominant plant in these areas of the Mata Atlântica (Atlantic Rainforest), was identified as one of the plants that have high nitrogen-fixing on leaves. “We have a hypothesis that we are still testing with the palm tree: we believe that predominance of some plant species in the forest is associated with their capacity to associate with nitrogen-fixing bacteria,” he affirms.

Nitrogen-fixing, nevertheless, is only one of the innumerous examples of the functional importance of bacteria in the forest. Some of these bacteria have a high production capacity for antibiotic compositions.

“Why do plants in the forest rarely get sick? Probably because they have the natural protection of the microorganisms that are living there. When a plant is domesticated and grown in large monocultures, it rapidly loses the capacity to inhibit growth of pathogenic microorganisms, and with this, the results are outbreaks of disease on plantations. Protecting the plant could be one of the other functions that other bacteria have,” he notes.

According to Lambais, although the study is still in its first year, the Thematic Project has already had promising results and several publications are in preparation. “We have a large group involved with the project and we have the support of several other people interested in the microbiological issue,” he affirms.