Genetic properties of soil bacterium with biofertiliser qualities decoded

Soil bacteria can be used in the fight against plant diseases such as blackleg, which affects potatoes.

The soil bacterium Bacillus amyloliquefaciens is normally found living around plant roots and it is already known that it encourages plant growth. The metabolic products that it uses to achieve this, however, have not yet been identified. Nevertheless, the first attempts to use biofertilisers based on this bacterium are already underway. On a long-term basis, they now look to undergo yet further development. Researchers from Berlin and Goettingen have succeeded in decoding the genome of the bacterium in its entirety. As the scientists under Rainer Borriss of Humboldt University in Berlin have reported in the specialised magazine Nature Biotechnology (2007, online, 19 August), the molecular processes that encourage the plant growth have been laid bare in detail. With this, a path has been cleared for the targeted application of the bacterium as a biological fertiliser or pesticide, say the researchers.

Some produce cancer-inhibiting substances, others have the ability to break down crude oil whereas others trigger serious illnesses. Bacteria can be found at almost every point of the globe and possess an incredibly wide range of characteristics. In 2001, In order to shed some light on the genetic structure of bacteria and to exploit these realisations for medicine, agriculture, nutrition and industry, the German Federal Ministry for Education and Research (BMBF) initiated the funding program GenoMik "Genome Research into Microorganisms".

Under the roof of this initiative, which in the meantime is continuing as GenoMikPlus, the scientists are targetedly searching, among other things, for bacteria candidates that possess plant-growth-promoting, plant-growth-inhibiting or pollutant-diminishing abilities. Among the latter category is the sea bacterium Alcanivorax borkumensis, which uses oil as an energy source and whose complete genome was worked out one year ago.

In the framework of the "GenoMik" program, German researchers are specialised in microbial research across three competence centres in Goettingen, Bielefeld and Würzburg. Since 2006, these projects have been known as "GenoMikPlus" and have been supported with 21 million euros by the German Federal Ministry for Education and Research (BMBF). More

The soil bacterium Bacillus amyloliquefaciens has plant-growth-promoting characteristics and is related to the bacterium Bacillus subtilis, one of the most important microorganisms in industrial biotechnology and whose genome has already been sequenced. However, exactly how these Bacillus amyloliquefaciens’ positive effects work on molecular-biological level is far from well understood. Now, scientists working under Rainer Boriss of the Humboldt University Berlin, a Professor at the Institute for Biology, together with colleagues working under Gerhard Gottschalk from the Laboratory for Genome Analysis at the University of Goettingen, have completely decoded the bacterium’s genome and have made initial comparisons with Bacillus subtilis. "With the genetic configuration now understood, we can specifically examine the mechanisms that provide the basis for the growth-promoting effects of the bacterium", stresses Borriss.

Special qualities discovered in the genome

As the scientists recently reported in the specialised magazine Nature Biotechnology (2007, online, 19 August), in the process of decoding the genome they came across a number of genetic special characteristics. For example, in the genome from Bacillus amyloliquefaciens, they found so-called DNA islands. “These regions in the genome strongly deviate in their composition from the usual basic structure”, explains Gerhard Gottschalk, Head of the Göttingen-based Genome Analysis Laboratory. Whereas the rest of the genome strongly resembles the genetic material of other, related soil bacteria, in the ‘islands’, the scientists have discovered genes that are linked to the specific means of existence of the bacterium in the plant root area. The scientists are now assuming that the Bacillus amyloliquefaciens has emerged from a ‘normal’ soil bacterium and that, through the inclusion of foreign DNA, has acquired an ability to positively interact with plant cells. The scientists have already been able to show that the bacterium is able to make use of additional sources of nutrition using genes from inside of these DNA islands.

Possible application as biofertiliser and biopesticide

During the genome analysis, the scientists also uncovered large gene groups that are clearly responsible for the positive effect that the bacterium has on plant health. Through these gene groups, a variety of substances are produced by the bacterium, which counteract other bacteria and fungi that can cause disease in plants. Together with researchers from the TU Berlin and the University of Bonn, the chemical nature of these connections has already been explained. “In the future, it will be possible to use the bacterium as a biopesticide in the containment of pests and thereby limit the use of agrochemicals“, explains Borriss.

Berlin company to take on soil bacteria

Already today, the first attempts are being made to employ the bacterium in agriculture. A product of this kind has been developed from Berlin-based Biotech company ABiTEP GmbH, which is specialised in the utilisation of soil microorganisms of the genus Bacillus for use in agriculture, and in its related biotechnological enhancement. The company was created by Rainer Borris, one of the researchers involved in the genome project, as well as further partners and is mainly based on work carried out by the former Research Centre for Biotechnology (FZB) as well as the FZB Biotechnik GmbH, which emerged from the Centre. In 2005, FZB Biotechnik GmbH was shut down its operations, which saw the plant protection program move over to ABiTEP.