TGAC help improve harvests by completing genome sequence of soil bacterium

19th Aug 2014

TGAC, together with the Universidad Nacional de Rio Cuarto (UNRC), Instituto de Agrobiotecnologica Rosario (INDEAR), and other European partners, have completed the genome sequence of a model strain of the soil bacterium Azospirillum brasilense to help improve farming productivity.

The soil bacterium, isolated from wheat roots in the central region of Argentina, has been used as a bio-fertiliser in agriculture during the last four decades. One of the main characteristics of the Azospirillum bacterium that aids plant health is its ability to be able to produce plant-growth regulators. By sequencing the genome of the bacterium's model strain, Azospirillum brasilense (Az39), the potential mechanisms responsible for growth improvement can be unravelled.

As the most-studied soil bacterium that encourages plant growth, Azospirillum brasilense is responsible for the major improvement of more than a hundred plant species' growth and yield productivity.

To sequence the genome, TGAC performed the optical mapping analysis with an OpGen Argus whole genome mapper to validate the final genome assembly. Bernardo Clavijo, Project Leader of the Bioinformatics Algorithms Development Group at TGAC, explains the analytic process: "Optical mapping is a technology that produces a restriction map of a genome, which is essentially a list of distances at which a known sequence occurs within the DNA. Knowing where this tag lies allow you to anchor shorter assembled sequences from a sequencing experiment and confirm their validity, pretty much like how a few small clouds and their position on an image guide would give you the necessary hints to assemble an otherwise elusive blue sky in a jigsaw puzzle."

David Baker, Platforms and Pipelines Team Leader at TGAC, said: "Whole Genome Mapping is a powerful tool in validating sequencing of small genomes. We are privileged here at TGAC to have the equipment and expertise to run these types of samples. From receipt of sample material to alignment of the optical maps takes just several days' work."

Azospirillum brasilense is a bacterium that is found in the rhizopheres of several grasses. Rhizopheres are the narrow regions of soil that is directly influenced by root secretions and associated soil microorganisms. Microbial inoculants, also known as soil inoculants, are used for agricultural enhancements that use valuable endophytes (microbes) to encourage plant health. Many of the microbes involved form mutual-beneficial relationships with the target crops, while microbial inoculants are applied to improve plant nutrition, they can also be used to promote plant growth by stimulating plant hormone production. Research into the benefits of inoculants in agriculture extends beyond their capacity as biofertilizers. Microbial inoculants can encourage resistance of crop species to several common crop diseases.

The paper, titled: "Complete Genome Sequence of the Model Rhizosphere Strain Azospirillum brasilense Az39, Successfully Applied in Agriculture" is published in genome A (PDF), American Society for Microbiology.

TGAC is strategically funded by BBSRC and operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.

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