Soil provides new microbial sources for natural products

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Soil provides new microbial sources for natural products

Gepubliceerd op
11 december 2015

The role of the soil as a treasure trove of new, useful, natural products is again confirmed by the discovery of as yet unknown genes in Lysobacter bacteria. Research conducted by Wageningen UR and NIOO shows that these genes or gene clusters probably code for currently unknown antimicrobial substances.

Lysobacter bacteria are known for their disease-suppressing properties against the soil fungus Rhizoctonia. This fungus causes root rot in many crops, such as potatoes, sugar beets, vegetables and bulbs. Until now, however, little was known about how Lysobacter bacteria function. Researchers from Wageningen UR and the Netherlands Institute of Ecology (NIOO) therefore mapped out the properties and genes of various Lysobacter species. The results of this research not only confirmed the presence of genes for the production of previously known antimicrobial agents but also identified unknown genes or gene clusters that probably code for as yet unknown antimicrobials. This once again demonstrates the role of soil as an important treasure trove of new, useful, natural products.

Disease-suppressing properties

The soil contains huge numbers of different types of micro-organisms with currently unknown properties. Prior research on soils with disease-suppressing properties has identified a large collection of bacteria of the genus Lysobacter that inhibits the growth of the Rhizoctonia fungus.

Four Lysobacter species

For this study, eighteen Lysobacter isolates from four species were used to test their activity and differing ability to inhibit other micro-organisms. It turned out that most of the isolates could inhibit various plant-pathogenic fungi, bacteria and oomycetes. They also produce multiple enzymes, such as chitinases, glucanases and proteases. The degree of inhibition was affected by growing conditions, such as the type of medium, but also by the presence of the pathogenic fungus itself.

Genome mapped

The complete genome of four Lysobacter species was mapped. Comparison of these genome sequences with existing knowledge in data files shows the presence of genes for the production of known antimicrobial agents (such as Lysobactin, phenazine, WAP-8294A2 and dihydromaltophilin). In addition, the Lysobacters contain unknown genes or gene clusters which probably code for as yet unknown antimicrobials. Research into the metabolites profile of these Lysobacters supports the genetic information. Particularly interesting is the presence of a currently unknown metabolite which is only produced in the presence of Rhizoctonia by one of the Lysobacter species.

Variation per isolate

Lysobacter species have about 50% of their DNA sequences in common, while the other 50% are species or isolate specific. The ability to inhibit various micro-organisms also varies per isolate. This is supported by the genetic information for the production of various metabolites by species.

This collaborative project between Wageningen UR and NIOO is being funded by STW and industry.

More information

1 Diversity and Activity of Lysobacter Species from Disease Suppressive Soils (open access), november 2015; Ruth Gómez Expósito, Joeke Postma, Jos M. Raaijmakers en Irene De Bruijn.

2 Comparative genomics and metabolic profiling of the genus Lysobacter (open access), november 2015; Irene de Bruijn, Xu Cheng, Victor de Jager, Ruth Gómez Expósito, Jeramie Watrous, Nrupali Patel, Joeke Postma, Pieter C. Dorrestein, Donald Kobayashi and Jos M. Raaijmakers.