Of apples and oil pumpkins: News from microbiome research

The extent to which the composition of the microbiome of apples and oil pumpkins depends on the geographical location and what insights can be derived from this for breeding, health and shelf life of the fruits is shown in two recent publications by researchers at TU Graz.

We refer to the microbiome as the community of microorganisms that exist in or on all organisms, including bacteria and fungi. A team from the Institute of Environmental Biotechnology at Graz University of Technology (TU Graz) led by Institute head Gabriele Berg has now investigated the microbiomes of apples and oil pumpkins in two independent studies. The researchers have found that bacteria useful to plants are largely "inherited," i.e., passed on to the next generation, while the community of fungi in the microbiome is highly dependent on the particular soil microbiome and thus on the locality.

Microbiome-guided breeding of oil pumpkins

The breeding of the Styrian oil pumpkin is relatively recent—it started about 150 years ago and is well documented. Through selective breeding of resistant, increasingly tasty and high-yielding pumpkins, the seed microbiome of the oil pumpkin has changed over the generations. Using a well-documented breeding line, the environmental biotechnologists at TU Graz were able to demonstrate for the first time that the microorganisms on the seeds of the pumpkin are inherited and probably crucial for certain plant traits. Peter Kusstatscher, one of the study authors, explains: "We studied bacteria and fungi on oil pumpkin seeds and found that the plant passes on much of its bacteria on the seed—up to 60 percent, in fact—to the next generation, while fungal diversity on the seed depends largely on the local soil microbiome." Kusstatscher continues, "It's mainly microorganisms that are useful for the plants that are inherited. In this respect, the plant behaves in a similar way to humans: babies also get their microbiome from their mothers."

The results published in Frontiers in Plant Science pave the way towards a microbiome-controlled breeding of oil pumpkins. Selective breeding of a beneficial seed microbiome results in plant traits that have a positive impact on yield, health and storability of oil pumpkins.

On the tracks of the universal apple microbiome

Apples are among the most popular and widely consumed fruits in the world. Fruit quality, yield, and storability are important factors for fruit growers, fruit trade, and consumers. In a worldwide study, the apple of the variety "Royal Gala" was examined for the first time with regard to the composition and possible local differences of its microbiome. An international team was able to show that the nature and structure of the fungal and bacterial communities of the apple at the time of harvest vary from region to region, i.e. they are strongly dependent on the geographical location and thus on the prevailing climatic conditions and management practices. In particular, the fungal diversity of the fruit is significantly dependent on the locality and suggests a relationship to the type and frequency of post-harvest diseases. On the other hand, a continental pattern can be drawn especially for the bacterial community which indicates adaptation of the apple microbiome to local environments.

Ahmed Abdelfattah, Marie Curie post-doctoral fellow at the Institute of Environmental Biotechnology at TU Graz and lead author of the study explains: "Despite the variations we observed in the apple microbiome, we were still able to identify a so-called 'core' microbiome i.e. members of the microbiome that are shared globally among the apples. This global 'core' microbiome is represented by several beneficial microbial indicators and makes up a large portion of the fruit's microbial community."

Similar to the study results on oil pumpkin, this study lays another foundation for new approaches to improving fruit quality and health, in this case of apples. Furthermore, the results form the basis for investigations of complex microbial interactions on the surface of apple fruits. The study results were published in Environmental Microbiology.

Both studies highlight the importance of the microbiome for health issues from the crop in the agro-ecosystem to humans who consume the food. At the same time, new avenues for microbiome management are opening up for environmentally friendly pest control.