Concentration area

Agricultural Microbiology: Comprises the study of microorganisms associated with water, soil, plants and animals. The Program’s research activities focus on aspects of genetics, physiology, ecology and diversity of microorganisms, in addition to their applications in biotechnology and food production, antimicrobials, biofuels and metabolites of interest applied in agriculture and livestock.

Research Lines

Line 1: genetics, physiology and ecology of microorganisms.

Regulation of gene expression and global regulatory mechanisms. Pathogenicity and virulence factors. Analysis of microbial genomes. Microbial growth and fermentation processes. Metabolic flux and metabolomics. Development and structure of microbial communities associated with water, soil, plants and animals. Biodiversity in aquatic and terrestrial environments. Interactions between populations of microorganisms. Nutrient cycling and biogeochemical cycles. Antimicrobial agents. Biological associations of microorganisms in plants and animals.

Line 2: Processes and microbiological products.

Isolation, selection and breeding of mycelial fungi, yeasts, bacteria and viruses and processes development for the production of cells, enzymes, proteins and metabolites of interest for the agricultural and environmental industry. Development of methods for detection and control of pathogenic microorganisms, spoilage of food and resistant to antibiotics.

Research Groups

The emphasis is on research for scientific and technological development aimed at optimizing processes that use microorganisms in biological associations. Biological associations have been a model for understanding phenomena involving the biology of organisms, including studies of physiology, occupation and distribution in ecosystems, regulation of gene expression and study of genetically modified ones. Studies on biodiversity, taxonomy and identification of the microorganisms involved are also carried out.

Research lines:

Biological Nitrogen Fixation

Objectives: Physiology, biochemistry, genetics and ecology of rhizobia; Symbiosis physiology; Agronomic aspects of symbiosis in alfalfa, bean and soybean crops; Microbiology and inoculant production technology.


Objectives: Biology, physiology, ecology and molecular genetics of ectomycorrhizal fungi and the ectomycorrhizal association, with an emphasis on plant species of Pinus and Eucalyptus; Biology, physiology and ecology of arbuscular mycorrhizal fungi and their association with plants of agronomic and forestry interest; Biology Ecology and taxonomy of orchid mycorrhizal fungi for in vitro propagation; Microbiology and inoculant production technology.

Endophytic Microorganisms

Objectives: Isolation of endophytic microorganisms; Study of the distribution in the internal structures in stages of maturation of coffee fruits; Study of the colonization mechanisms of bacteria and endophytic yeasts; Characterization of pectinases of endophytic microorganisms and compounds related to the quality of the coffee drink.

The group aims to consolidate and scientific competence in the knowledge of physiology, molecular biology, genetics and taxonomy of mushroom-forming fungi with economic potential and of food and medicinal interest. The study, selection and improvement of these fungi may contribute to the development of alternatives for agribusiness. In addition, the adaptation of mushroom cultivation techniques to Brazilian conditions will allow the dissemination of the production practice that may result in the use of agro-industrial waste as substrates in the production of seeds or compounds. The development of processing and storage techniques aims to guarantee the conservation of the product with quality and microbiological safety standards. The market aspects covered will provide guidelines for the productive sector to meet internal and external demand.

Research lines:

Production, processing, biotechnological and market aspects of mushrooms

Objectives: Biology, physiology, ecology and molecular genetics of edible and medicinal mushrooms; Production and processing of mushrooms; Biotechnological and marketing aspects.

Due to the importance of living organisms, including microorganisms, in maintaining the ecological balance, this group aims at consolidating and scientific competence in the area of ​​knowledge of physiology, molecular biology, genetics and taxonomy of microorganisms involved with bioremediation processes, production of biosurfactants and advanced oil recovery. With a view to preventing the rapid destruction of the environment as well as the rapid destruction of non-renewable natural resources, isolating and characterizing the various microorganisms involved in the process, as well as understanding the microbial activity in nature, it is crucial for the balance of nature and also to increase productivity in a sustainable way. The development of methodologies and the understanding of the structure and function of microorganisms in ecosystems are also among the objectives of this group.

Research lines:

Bioremediation, biodiversity and bioindicators of environmental quality

Objectives: Isolate microorganisms capable of degrading recalcitrant components; Constitute a consortium of microorganisms for use in bioremediation processes; Monitor the bioremediation process using microbiological and biochemical indicators; Determine the G + C content of the microbial community in contaminated environments; Adapt and validate the procedure for monitoring the progress of environmental decontamination.

Isolation of bacteria, yeasts and filamentous fungi that produce enzymes of agro-industrial interest, or co-participants in fermentation processes; Culture media were developed for the production of pectinolytic and xylanolitic enzymes for use in the food, textile and paper and cellulose industries; Development of yeast beta-galactosidase immobilization techniques, aiming at the industrial hydrolysis of lactose for the production of lactose-free milk, for individuals intolerant to it; Problem solving, in the basic area, of these fermentative processes; Training of human resources for teaching and research in public and private institutions.

Research lines:

Yeast Physiology and Biotechnology

Objectives: Expression and secretion of recombinant proteins in yeasts; construction of an expression system in Kluyveromyces lactis; Physiology of Kluyveromyces lactis under nutritional stress; Oxidreductive metabolism of Kluyveromyces sp; Production of proteins and metabolites of industrial interest.

Fungi Producing Enzymes of Industrial Interest

Objectives: Isolation and selection;
microbial growth and regulation of enzyme synthesis;
methods of immobilizing enzymes and cells;
genetic improvement by mutation, recombination (transformation, fusion of protoplasts and parasyxal cycle).

Carbohydrate Metabolism in Microorganisms

Objectives: Regulation of energy reserve carbohydrate and hexose monophosphate biosynthesis pathways.

Microbiology of Fermentation Processes and Agro-Industrial Products

Objectives: Isolation, characterization and selection of microorganisms involved in fermentations with an emphasis on coffee, milk and derivatives, among others .; quality improvement of agro-industrial products.

The research carried out by the group involves the study of enzyme-producing fungi and phytopathogenic fungi through classical and molecular genetics. Enzyme-producing fungi belong to the genus Penicillium, where special emphasis is placed on improving the production of pectinases and xylanases. The improved lines will be used in the textile industry (degumming of natural fibers), cellulose (pulp bleaching) and food (clarification of juices and wines). Phytopathogenic fungi Crinipellis perniciosa, Fusarium oxysporum f. sp. phaseoli, Fusarium solani and Colletotrichum lindemuthianum are being investigated in order to identify the genes involved in the host-pathogen interaction in order to develop strategies to control these pathogens in the future.

Research lines:

Genetics of Phytopathogenic Fungi

Objectives: To isolate mutants for the pathogenicity of Crinipellis perniciosa, Colletotrichum lindemuthianum, Fusarium spp by means of traditional mutagenesis and insertional mutagenesis using the REMI process (integration mediated by restriction enzymes) and transposons; Study the regulation of genes by inactivation; isolate transposable elements and elucidate the mechanisms of transposition and the role of these elements as generators of genetic variability.

Molecular Genetics of Fungi Producers of Industrial Interest Enzymes

Objectives: Isolate and select microorganisms (microbial growth and regulation of enzyme synthesis); genetically improve strains by mutagenesis, recombination (transformation, fusion of protoplasts and parassexual cycle);
Isolate and characterize genes;
Elucidate the structure and gene organization and regulation of gene expression.

The studies of the biochemical and genetic mechanisms of the interaction between plants and mutualistic microorganisms aiming at the manipulation of associations in forest production systems, have addressed the chemical communication events involved in the establishment and function of symbiosis. The processes related to the symbiotic life cycles and the formation of the characteristic structures of associative life have also been investigated. Currently, symbiotic interactions are being addressed from the point of view of quantitative genetics, with an emphasis on ectomycorrhizal basidiomycetes. The team aims, with the knowledge of the interactions between plants and endosymbionts, to manipulate the symbiosis aiming at the higher productivity of the forest cultures in a sustained way.

Research lines:

Eucalyptus-ectomycorrhizal fungus interaction

Objectives: To investigate the chemical determinants that regulate the initial events of the formation of ectomycorrhiza;
Investigate the formation and germination process of ectomycorrhizal fungi spores;
To study the interaction between the host plant and monocariotic and dicariotic strains of Pisolithus.

The biology of the microorganisms relevant to food processing, conservation and deterioration is a fundamental study to guarantee the quality and safety of food products. The microbiological safety of food stocks has social and economic implications, in addition to having a major impact on public health. Technological, ecological, physiological and genetic aspects are covered in the projects of this group and the emphasis is given in three aspects:

(1) pathogenic bacteria carried and propagated by food and its pathogenic factors;
(2) microbiological quality associated with food processing methods and regulations and standards;
(3) physiological and genetic bases of antibiotic resistance in bacteria from foods of animal origin. In addition, the use of microorganisms in food fermentation processes has great potential in the development of new and better products with their own characteristics and that add value to them. The safety aspect of these products is also emphasized.

Research lines:

Microbiology of Milk and Derivatives

Objectives: To define thermobacteriological parameters for new dairy products;
To study the action, growth and destruction of deteriorating and pathogenic psychrotropics in the milk and dairy products production line;
Determine expiration dates, methods and conservation for new products and propose quality standards;
Develop protocols for quality assurance systems (HACCP) in the dairy and dairy industries.

Microbiology of Fermented Meat Products

Objectives: Study of fermentation of fermented meat products;
Isolation and characterization of microorganisms from natural fermentation products;
Safety of fermented meat products.

Foodborne Pathogens

Objectives: Physiology and Genetics of pathogenic and food spoilage bacteria;
Pathogenicity of bacteria associated with emerging food diseases;
Analysis of the genetic diversity of pathogenic bacteria using molecular markers.

Microbiological Quality of Food

Objectives: Study of the microbiological quality of food associated with processing methods in the industry;
Detection and control of pathogenic and food spoilage bacteria;
Methods of detecting food pathogens, including immunochemical methods, methods based on DNA hybridization, polymerase chain reaction (PRC);
Antibiotic resistance in pathogenic bacteria and normal microbiota contaminating food.

Ruminant animals depend on anaerobic microorganisms to carry out the fermentation of food in the rumen. Volatile fatty acids and microbial protein resulting from rumen fermentation are the main source of energy and nitrogen for the ruminant, respectively. However, fermentation also produces undesirable compounds such as methane, decreasing food efficiency and contributing to the greenhouse effect. In addition, excessive protein deamination causes nitrogen loss in the form of urea and causes pollution of subsurface waters. The study of the biochemistry, physiology, genetics and microbial ecology of the ruminal ecosystem has helped to model the rumen microbial communities and their respective activities, with a direct impact on increasing the ruminant’s feed efficiency. Ecological interactions between rumen anaerobes and various pathogens are also the object of study due to the importance of this association in food security, meat exports and the dissemination of antibiotic resistance genes.

Research lines:

Utilization of agro-industrial waste for biotechnological production of food additives for ruminants

Objectives: To isolate and characterize rumen microorganisms capable of producing propionate and succinate from the fermentation of cheese whey lactose, and to evaluate the in vitro and in vivo effects of fermented whey as a food additive in ruminant nutrition.

Study of the activity of propolis and bacteriocins on the growth and antimicrobial resistance of bacteria that cause bovine mastitis

Objectives: To evaluate the antimicrobial effect of green propolis and bacteriocins on bacteria that cause bovine mastitis to prevent and treat intramammary infections.

Use of Bacteriocins for Ruminal Fermentation Manipulation

Objectives: To determine the occurrence of antimicrobial activity among bacteria isolated from bovine rumen, and to select isolates to be used in the manipulation of rumen fermentation products and in the inhibition of pathogenic bacteria of zootechnical and veterinary interest.

Various pathogenic microorganisms can be carried by food, especially by foods of animal origin. The study of responses to stresses from these pathogens is essential to ensure the quality and safety of food. Microbiological safety in food has a social, economic and public health impact. Pathogens in the viable non-cultivable state cannot be detected by traditional techniques, but they can resuscitate and maintain virulence in host organisms, constituting a potential risk for food consumption. Physiological and genetic aspects are covered in the projects of this group and the emphasis is given in four aspects:

1) microbiological quality of products of animal origin;
2) pathogenic bacteria carried by food and its pathogenicity factors;
3) physiological and genetic bases of resistance to stress and viable non-cultivable state and,
4) methods of detecting microorganisms in the VNC state.

Research lines:

Physiology and Genetics of Food-borne Pathogens

Objectives: Physiology and Genetics of food pathogenic bacteria; Stress response of pathogenic bacteria; Pathogenicity of bacteria associated with foodborne diseases; Analysis of the genetic diversity of pathogenic bacteria using molecular markers.

Microbiology of Animal Products

Objectives: To study the action, growth and destruction of psychrotrophic spoilers and pathogens in the food production line of animal origin; Determine expiration dates, methods and conservation for new products and propose quality standards; Develop protocols for quality assurance systems (HACCP) in animal product industries.

Microorganisms in the Viable Non-Cultivable State (VNC)

Objectives: Physiology and genetics of pathogenic and food spoilage bacteria in the viable, non-cultivable state. Development of VNC detection methods, including fluorescence and molecular microscopy techniques

Fermented foods have been part of the human diet since ancient times. different types of fermentation processes are widely used in the production of a wide variety of products such as alcoholic, lactic and acetic fermentation. In this context, the role performed by the microbiota, be it autochthonous (naturally present in the raw material) or intentionally added (such as yeast). Microbial enzymes are an important part of fermentation process, as they act on the substrate catabolizing complex particles into smaller products, especially amylases, proteases and lipases. In addition to features sensors of interest, fermentation also results in the extension of the shelf life of the
food, as organic acids with a biopreservative effect are produced, in addition to bacteriocins with antimicrobial activity, providing greater safety to the final product. The fermentation can also result in nutritional enhancement and provide functionality to the food,
contributing to the improvement of consumer health. Understanding the role of microbiota in the quality of fermented food has been the guiding point of research developed by our work team.

Research lines:

Prospection of fermented food microorganisms for industrial application
Objectives: Isolate and characterize microorganisms from different types of food – such as cheese artisans, kombucha, natural fermentation breads – aiming at obtaining enzymes, compounds of industrial interest or biomaterials, among others.

Influence of microbiota on physicochemical sensory and functional characteristics of fermented food
Objectives: to assess the role of microbiota and population dynamics throughout the process fermentation in the sensory and functional properties of fermented foods of animal origin and vegetable.

Development of playful prototypes for educational purposes on the subject of fermented food 
Objectives: Develop playful prototypes about the benefits of food fermentation for use in school and/or university environments as a teaching-learning strategy.