Biotechnology applied to agriculture has received great efforts to develop innovative solutions that contribute to the sustainability of the management of economically important crops.
By looking closely at the soil, a microbiological profile of the environment can be traced through the discovery of microorganisms present, under certain conditions and at a certain time. The soil microbiota, as it is called, can be compared to a “photograph”, which is taken from the soil by analyzing it, determining all its biological diversity. Through the combination of advanced genetic and molecular biology techniques, these microorganisms are identified and grouped, many of which would never be identified by classical microbiology techniques, since they cannot be cultivated.
Biotrop, a partner company of 3tentos, developed a platform to generate results that reflect the quality of the agricultural system to the detriment of this microbiota: Agrobiota. Based on metagenomic analyses, a pipeline of data analysis from DNA genetic sequencing was developed, which transforms the results into functional interpretations of the biological activity found in the area, entering the microbiome of these soils.
How the soil microbiome supports agricultural development
Through the DNA of the soils one can access countless information. One of them is the identity of microorganisms, identifying benefits or harms that these species cause to the environment. Or even, through genes, identify enzymes and other molecules capable of modifying the environment around them, such as compounds capable of solubilizing phosphorus. Thus, by extracting DNA from a soil sample and studying it, it is possible to access its biological profile and understand how its health is.
With Agrobiota, it is possible to identify areas that differ in terms of management, and access which practices employed are beneficial to the system and harmful management practices, which reduce the population of beneficial microorganisms, or promote an increase in the frequency of phytopathogenic species, indicating management corrector to the system. This information, derived from soil DNA, is generated through molecular biology, genetics and bioinformatics analyses, defined as soil metagenomics.
Metagenomics as a tool to understand soil biodiversity
Metagenomics arises with the objective of revealing the composition of the microbiological community of a certain environment without the need to cultivate these microorganisms in the laboratory. Through this technique, the genetic diversity of microorganisms in arable soils is analyzed and, thus, their microbiome is defined. The technique begins with the collection and extraction of DNA from the soil. As it is critical for all other stages of the analysis, it must be carried out in a very controlled manner.
Subsequently, the identification of fungi and bacteria is carried out through the analysis of the 16S rRNA and ITS genomic regions, used for identification at the genus and species level, functioning as a fingerprint of each microorganism. After sequencing these genes, the data are analyzed by bioinformatics tools.
Bioinformatics analyzes use databases to identify the species present in the sample, as well as the biological functions they present. Thus, after all these analyses, the team of researchers is able to issue a report with the biological profile of the soil, pointing out which microorganisms are present in the environment from which they were collected and their relevant functions for agriculture.
Based on the principle of soil metagenomics, this tool is capable of delivering a report in which general information on the microbiome of the evaluated area is obtained, calculated through an index, the Genetic Guided Hypothesis (GGH), which provides an overview of the area, reflecting the “health” of the system (Figure 1A).
From the understanding of the general aspects, the data are worked in more depth for each of the “dimensions” of the soil microbiome. In the detailed diagnosis, several functional groups are presented, within Fertility and Biological Agents, where the microorganisms present in the evaluated areas are positioned according to their biological role (Figure 1B). Thus, it is possible to understand which functions are deficient and which are at adequate levels, positioning the management in search of restoring the soil microbiota and the gaps in each functional group.
Together with these data, it is also possible to elucidate the main phytopathogenic genera present in the sample, allowing a prophylactic management to reduce the possibility of the occurrence of diseases associated with the presence of these agents in the soil (Figure 1C). In the example presented, there is a high occurrence of Fusarium, a genus of phytopathogens of great importance for several agricultural crops. For this situation, it is recommended to improve the quality of the microbiota by applying biofungicide microorganisms, including Bacillus velezensis, B. amyloliquefaciens and Trichoderma harzianum.
Finally, the Agrobiota enters the phylogenetic diversity of the studied soils, based on the occurrence and frequency of the observed species (Figure 1C). Thus, when comparing the sample with universal databases, it is possible to indicate the level of biodiversity of the system and allow interpretations that relate the practice of management with the results, bringing conclusions about what is favorable or not to the maintenance of the diversity of the environment. studied.
Thus, it becomes possible to fill gaps not explored by other techniques and analyses, optimize and direct the management of areas to reach the maximum productive potential of crops of agricultural importance. With this tool, it is possible to position products and practices that contribute to the maintenance or increase of biodiversity.
