Microbiome Archives - apple-biome

The study of the microbiome enables new strategies for…

November 27, 2021November 27, 2021
by Ahmed Abdelfattah

Agriculture is facing enormous challenges worldwide due to global changes caused by human activities. Drought, severe weather events, record temperatures and emerging pathogens threaten the world’s food supply. For this reason we need to make our crops more robust without further polluting the environment. Microbiome research and management offer great potential to achieve these goals. A new study by an international research group led by Graz University of Technology (TU Graz), published in the scientific journal New Phytologist, opens up new perspectives here.

The importance of the microbiome for living organisms

Microbiome research is only a few decades old, but it has already produced some groundbreaking findings. One is that humans, animals and plants have very specifically adapted microbiomes that have taken over essential functions. Both organism and microbiome have evolved in co-evolution, i.e. in mutual influence. This was confirmed by the present study. Today, we consider all organisms to be “holobionts”—jointly functioning units with numerous specialized microorganisms. The latter are always numerically superior; humans, for example, have ten times more microorganisms than their own cells. The microbiome is thus classified as an important target for new health therapies and prophylaxis. This is equally true for cultivated plants, but the potential here has so far been little known or exploited.

Confirmation of the coevolution theory

The interdisciplinary group of researchers compared the microbiome of modern domesticated apple crops—i.e. specifically bred and cultivated varieties—with the microbiome of their wild ancestors as well as with the microbiome of closely related species. With the help of molecular analyses and bioinformatic methods, the group was able to determine for the first time that the microbiome is inherited to the same extent as the genes. Apples that are genetically similar thus also harbor a similar microbiome. And surprisingly, our modern apple varieties still contain some of the microbiome of their wild ancestors.

The study shows that the microbiome is also “bred” and has greatly changed over time. Until now, this has happened unintentionally and many microorganisms have been lost in the process. These lost microorganisms could now help us to make our crops fit for climate change again. This is because the focus of breeding now is no longer on the size and sweetness of the apples, but on their resilience and health. The research group is convinced that the microbiome of the wild ancestors originating from the inner-Asian Tien Shan mountain range contains valuable microorganisms for this purpose.

Useful research results for agriculture

For the first author in the study, Ahmed Abdelfattah from the Institute of Environmental Biotechnology, “the results clarify a long scientific debate and lay the groundwork for new ecological strategies in plant breeding.”

It would be conceivable, for example, to change the plant microbiome through the targeted introduction of microorganisms in order to increase the resistance of the plants. This is what the Institute of Environmental Biotechnology at TU Graz specializes in, and Marie Curie Fellow Ahmed Abdelfattah specifically chose it as a research location due to its expertise in the field of microbiome biotechnology. “My apple microbiome journey started during my visit, as Ph.D. student, to Dr. Michael Wisniewski’s lab in 2015”, Abdelfattah says. Wisniewski, the last author of the article and on whose the research the original experiment was designed, is a professor at Virginia Tech with a long-established scientific contribution to fruit research.

In Graz again, the vision of Institute head Gabriele Berg and her team is to use this new knowledge for plant health as well as for that of humans and our planet. The apple is thus only a symbol, as it has been many times in human history.

More information: Ahmed Abdelfattah et al, Evidence for host–microbiome co‐evolution in apple, New Phytologist (2021). DOI: 10.1111/nph.17820

Seeds transfer their microbes to the next generation

January 15, 2021November 27, 2021
by Ahmed Abdelfattah

Scientists have been pondering if the microbiome of plants is due to nature or nurture. Research at Stockholm University, published in Environmental Microbiology, showed that oak acorns contain a large diversity of microbes, and that oak seedlings inherit their microbiome from these acorns.

Oak seedling grown in Microcosm at Stockholm University . Environmental Microbiology, “Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root”: https://doi.org/10.1111/1462-2920.15392

“The idea that seeds can be the link between the microbes in the mother tree and its offspring has frequently been discussed, but this is the first time someone proves the transmission route from the seed to the leaves and roots of emerging plants,” says Ahmed Abdelfattah, researcher at the Department of Ecology Environment and Plant Sciences (DEEP) at Stockholm University.

The microorganisms found on the seed are often valuable for the plant, promoting its growth and protecting it against certain diseases. Each plant species harbors a distinct microbial community, with some of the microbes living on its surface and others inside the plant’s tissues.

The finding also means that since the microorganisms from the seed are there first, they can constitute a barrier which influences subsequent colonization by other microbes from the environment. The experiment was done in oaks, since it’s one of the most abundant tree species in the Swedish and European forests.

“The microorganisms from the seed are also expected to be very important for plant health and functioning,” says Ahmed Abdelfattah.

Discription of the Microcosm design used in Environmental Microbiology, “Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root”: https://doi.org/10.1111/1462-2920.15392 Drawing by Ahmed Abdelfattah

The fossil record indicates that plants have been associated with fungi and bacteria—constituting the microbiome—for more than 400 million years. Several species the scientists found on the oak seeds are already shown by other studies to be involved in the protection against several plant pathogens, growth-promotion, nitrogen-fixing, and the detoxification or biodegradation of toxic environmental pollutants.

Demonstrating inheritance under natural conditions is challenging since seeds are exposed to and dependent on their surrounding environment when they sprout, especially the soil, which is a microbially rich environment. Therefore, it’s nearly impossible to differentiate between which microorganism actually come from the seed or from the soil. The research team therefore used a novel culturing device, to grow oak seedlings in a microbe-free condition and keep the leaves separated from the roots. This allowed them to be certain that the microorganisms came from the seed, and that they could demonstrate that some seed microorganisms migrate to the roots, and some others to the leaves.

“Plant leaves and roots are already known to harbor distinct microbial communities, as shown by several recent studies. In this study however, we were surprised to see that it is also true at an early stage of the plant development, and that the seed could, at least partially, be responsible for these differences,” says Ahmed Abdelfattah

“Several breeding companies are taking into consideration the seed microbiome in their programs hoping to have super plants with better genes and better microbes. One technique used, is to treat seeds with beneficial microorganism with the aim that those microbes will eventually colonize the plant and exert their effects throughout the plant’s life,” says Ahmed Abdelfattah.

The next step for the research team is now to discern which is the major source of the of the microbiome—the environment or the seed.

Publication:
Find the article in Environmental Microbiology, “Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root”: https://doi.org/10.1111/1462-2920.15392

Photos by: Ahmed Abdelfattah

Contact details:

Ahmed Abdelfattah
E-mail: ahmed.abdelfattah@tugraz.at
Phone: +39 3894935346

Ayco Tack
E-mail: ayco.tack@su.se
Phone: +46704942557

The Press Office at Stockholm University
press@su.se
Phone: +46 (0)8-16 40 90