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Microbial applications in agriculture

Microbial applications in agriculture

Microbiome analysis

AIT scientists study the diversity and composition of microbial communities colonizing the surfaces and interior spaces (endophytes) of plants and food and unravel their metabolic/functional potential for applications in sustainable agriculture and food systems. The Bioresources Unit has many years of experience in studying plant associated microbial assemblages and was among the first to describe endophyte communities and the factors shaping the structure of these communities on a cultivation-independent basis.

Our offer

  • Microbiome analysis based on variable regions of the 16S rRNA genes for bacteria and the ITS region for fungi including study design, bioinformatic and statistical data analysis.
  • (Meta)genomics and transcriptomics approaches to study the biological function of the plant microbiota and the molecular mechanisms of plant-endophyte communication and interactions.

Strain licensing for biocontrol and plant growth promotion

At AIT more than 5,000 bacterial strains and several hundred fungal strains have been isolated from various environments and plant species, ranging from woody tree species to agricultural crops and wild flowers. Strains are identified using different phylogenetic markers and are organized in our strain collection complying with all requirements of the Nagoya Protocol. Functional screenings, in vitro and in planta experiments provide valuable information on their biotechnological and agronomic potential.

Our offer

  • Screening of microbial strains for specific agronomic traits such as higher yield, biocontrol or improved stress tolerance in our greenhouse facilities or climate chambers.
  • Selection of microbes based on genomic and mechanistic characteristics such as plant hormone production, ACC deaminase activity or other characteristics.
  • Strain licensing: After reaching licensing agreements we provide our strains for commercial application.

Strain identification, characterization & genome analysis

At Bioresources Unit at AIT we offer a detailed portfolio of research services addressing needs during product development and registration of microbe-based applications for agriculture. We offer detailed analysis of genomes, transcriptomes and functions of individual bacterial and fungal strains. Furthermore, scientist at Bioresources Unit provide long lasting experience in the understanding of mechanisms and elucidating the mode of action of biocontrol solutions.

Our offer

  • Phylogenetic and genomic analysis for strain identification.
  • Genome and transcriptome analysis to characterize microorganisms for their metabolic activities such as ACC deaminase activity, production of plant hormones, toxins and secondary metabolites or P-solubilization including risk management.
  • Mode of action studies.

Analysis of plant colonization of associated microbes

Many biocontrol agents and biostimulants are based on beneficial bacteria or fungi. To assure their functionality in planta, the applied microbes should efficiently colonize the rhizosphere, plant surfaces, or the inner plant tissues. At AIT Bioresources we monitor microbial plant colonization by tracking microbes, visualizing their position in plants and monitoring their translocation. Being able to show data to your customers describing the route of microbial colonization and establishment within plants is a valuable tool for commercialization and dissemination of your microbial products.

Our offer

  • Labelling of bacteria and fungi with state of the art in situ techniques such as DOPE-FISH and GFP labelling
  • Visualization of labelled microorganisms within or on the surface of plant tissues using confocal laser scanning microscopy.
  • Development of unique qPCR assays based on specific traceability markers for the identification and tracking of specific strains and for colonization assessment in the field.

Formulation Development

A crucial aspect of microbial products in agriculture is to assure their bioactivity when applied on the field. Therefore, delivery technologies and tailor-made formulation development are key to success. Bioresources Unit offers research services and consulting in formulation development such as encapsulation techniques, seed coatings and foliar sprays.

Our offer

  • Labscale formulation development (capsules, seed coatings, foliar spray)
  • Full biological (viability, germination, shelf life) and physical (abrasion, flowability, morphology, roll-off angle, wettability) characterization of formulated microbes
  • In planta efficacy evaluation of formulated products (greenhouse or field trials)

For more on formulation development, see: Formulations and coating


AIT’s Bioresources Unit offers a portfolio of state of-the-art bioinformatics services in the field of microbiology and plant genomics. Bioinformatics experts at AIT have developed pipelines to efficiently analyze and assemble conventional sequencing and NGS data. Robust statistic tools are applied to interpret your data and to provide purpose-ready reports. Individual service packages are offered ranging from study design and data handling, to NGS analysis, statistical analysis and data interpretation.

Our offer

  • Illumina based 16S rRNA or ITS community analysis
  • Multi locus sequence analysis (MLSA)
  • Whole genome analysis
  • Development of strain specific qPCR systems
  • Genome wide association studies (GWAS )
  • Consulting – from study design to data analysis