Endosphere bacteria as a tool for sustainable agriculture

This abstract was selected by our Scientific Committee to pitch on the programme in the R2B session (PM).

Maize is the third most important staple crop worldwide. Due to its subtropical origin, maize growth in the Northern hemisphere has brought up some challenges. Low temperatures are posing stress on plant growth, resulting in eventual yield losses. Plants are closely intertwined with microbes, both in the roots, defined as the root endosphere, and in the closely surrounding soil of which the physicochemical properties are influenced by the root, defined as the rhizosphere. Several bacteria colonizing the maize roots can improve plant growth by suppressing disease, through nutrient mobilization or by influencing the plant pathways. These so-called plant growth promoting rhizobacteria (PGPR) have been proposed as an ecological additive to boost crop yield. To identify new PGPR strains, we established a microbiome based selection by analyzing the microbiome of root and soil samples and bacterial isolation followed by a screening assay for plant growth promoting abilities. We hypothesized that bacterial endophytes identified by being repeatedly enriched and highly abundant in the root endosphere compared to the soil, are an ideal source to select candidates to screen for strains that enhance juvenile maize growth when grown in cold temperature conditions. Based on 16S rRNA next generation sequencing of the maize root and soil samples, we got more insights in the maize root endosphere microbiome grown in Belgian field soil. Different experiments resulted in a main maize endosphere microbiome containing families that are repeatedly enriched and strongly abundant in the maize root. To test the abundance of seed endophytes in the root microbiome, in vitro grown maize roots were analyzed. Here, we concluded that most bacterial traffic occurs from soil to root and seed endophytes are easily outcompeted in the root community. The maize root microbiome was analyzed a second time, this time under cold stress, from which we can analyze the cold effect on the microbial communities in soil and in endosphere samples. The cold effect on the microbial community is small, however, the effect is much more pronounced in the endosphere compared to the soil, suggesting active recruitment of other microbes in plant root environments upon cold stress. Isolating and screening of bacterial maize root endophytes resulted in two highly promising bacterial strains that consistently increase the total fresh weight of juvenile maize plants grown in cold conditions.


Stien Beirinckx (1,2,3)
Tom Viaene (4)
Annelies Haegeman (3)
Fien Amery (3)
Hilde Nelissen (1,2)
Dirk Inze (1,2)
Jane Debode (3)
Caroline De Tender (3,5)
Sofie Goormachtig (1,2)


Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Gent, Belgium (1)
VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Gent, Belgium (2)
Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium (3)
Aphea.bio, Technologiepark 21, 9052 Gent, Belgium (4)
Ghent University , Department of Applied Mathematics, Computer Sciences and Statistics, Krijgslaan 281 S9, 9000 Ghent, Belgium (5)

Presenting author

Stien Beirinckx, PhD, VIB-Center for Plant Systems Biology
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