Manish Tiwari
Post-Doc
Plant-Microbe Symbioses
University of Wisconsin,
Madison, Wisconsin, US

Varvara Dikaya
Doctoral student
Plant Physiology
UPSC, Umeå, Sweden

Below you can find the assignments from this year’s participants, enjoy!u

Reap the fruits: Catch-22 of modern crop breeding

Among the challenges of modern crop breeding are the growing population, the necessity for reasonable land use, climate change, the spread of crop diseases, and the decreasing resilience of cultivated crops to pests.

In this competition against time and natural forces, we must ask- How prepared are we to meet these challenges? It appears as if we already have all the necessary tools in our hands.

Modern breeding is strongly linked to molecular biology, genetics, and computer technologies. It no longer works purely with phenotypic data and tedious by-hand crossings and progeny selection cycles. Still, it is never just a question of having all the required tools and knowledge available.

Along with the development and use of multiple genome engineering methods (Agrobacterium-induced transformation, viral and nanoparticle DNA/RNA delivery, and CRISPR/Cas-based technologies), there is also an ongoing debate around the commercial use of the genetically modified crops produced. It significantly delays the progression of moving from the lab into the fields. Given the challenges faced, should we expect the question of GMO authorization to be unequivocally resolved in favour of GM crops in the coming years? While the scientific community is overall positive about the implementation of genome engineering technologies in farming practices, it cannot outweigh the public opinion that is strongly affected by the cautious attitude of the governmental bodies.

Besides legal issues, there is also a need for a general improvement of the aforementioned methods: some species are more prone to the removal of external genetic material or silencing, while some exhibit lower transformation efficiency. Still, we cannot ignore the potential of modern technologies to significantly simplify and speed up the production of new crop varieties with desired traits.

Another side of modern breeding is a consistent progression towards accumulating vast amounts of information and working with comprehensive profiles of different plant species over long stretches of time. Large amounts of data come from high-throughput sequencing and omics technologies, which have proved reliable over the past years of plant research. Coupled with automated plant phenotyping systems that screen crops for signs of biotic and abiotic stresses, they constitute powerful tools for collecting comprehensive data on various internal and external parameters of plant growth.

On one hand, large volumes of information will aid in a broad understanding of plants, their genes, traits, and metabolites. On the other hand, demand for a general acceleration of crop breeding and explosive growth of the research data necessitates automating many processes such as the search for desired properties, comparison of plant profiles, selection of potential candidates for further study, and so on. Automation has largely occurred in genome assembly, omics data processing, and plant phenotyping. However, further data accumulation and subsequent processing require much more complex systems, raising questions not only about developing new pipelines in compressed time frames but also about energy consumption, data storage, and ethical issues associated with replacing human labour with machines. Furthermore, it’s evident that a well-established interface is needed for communication between machines and humans and to bring together various fields of science.

We have the opportunity and knowledge to face the challenges of modern crop breeding and significantly improve crop production. However, the question remains: Can we keep up with the ethical, technological, and legal issues of this progress?

Text and Illustration by Varvara Dikaya

One DNA to rule them all…

The representation of evolution as a tree with a strictly vertical transfer of genetic information from ancestor to descendant with genetically isolated terminal nodes (aka species) is an outdated and overly simplified model. Since, apart from gene inheritance from the parents, organisms can receive and transfer DNA from and to very distant species in a process called Horizontal Gene Transfer (HGT).

Massive HGT among Prokaryotes is not only an evolutionary strategy to increase genomic variation but also a distinct feature that complicates the definition of a species in the group. In clades with a higher level of organization (e.g. multicellular animals and plants), HGT seems to follow stricter rules with an overall lower frequency and lower success rates; still, significant gene exchange between distant branches of the tree of life is maintained.

As a separate lineage of Eukaryotes, plants display a broad range of HGT events on different levels of organization, pointing to the importance of these events in evolution.

To start with, the plant genome contains transposable elements (TEs). TEs are mobile genetic elements able to move across genomes. They play a role in gene regulation but may also be a source of genetic diversity and take part in speciation and evolution. While having an unclear ancestry, they are mainly presumed to be a type of “selfish genes” aiming to escape elimination from the host genome. TEs resort to an exchange of hosts and show an ability to jump between close and distant species via a still unknown mechanism.

On the level of the plant cell, there is an ongoing DNA exchange between its three genome-possessing organelles: nucleus, mitochondria, and plastids, which originated from two independent endosymbiotic events:

1. The first occurred between two prokaryotic cells, giving rise to the Eukaryotic cell with the mitochondria (derived from the engulfed α-proteobacterium) and nucleus (with the genome of chimeric bacterial and archaeal origin)
2. The second one resulted in the acquisition of plastids derived from the Cyanobacteria engulfed by an ancient Eukaryotic cell.

During their long co-evolution, all three organelles have significantly rearranged their genomic information, including a massive gene transfer from mitochondria and plastids into the nucleus of the host cell.

Endosymbiosis is an example of the extreme proximity that can evolve between interacting species, with HGT as one of the driving forces, over long stretches of time. However, plants interact with hundreds of other organisms on a daily basis without forming the same type of bond. HGT between species presumably happen via grafting, infection, or parasitic interactions with fungi, bacteria, insects, animals, or other plants. For example, two grafted plants may exchange organelles and consequently experience HGT between the foreign and the host organelles. Another example is soil bacteria such as Agrobacterium tumefaciens that infect plant roots by transferring their virulence genes into the nucleus of plant cells.

The history of these intra-species interactions leave traces in the plant genome, making it according to the gene ancestry “less” of a plant and “more” of a fungi/bacteria/etc. HGT clearly demonstrates the core organizational uniformity of terrestrial life. While the current state of the organismal divergency gives the impression that the “border” of a species is settled, HGT shows how dynamic and volatile the genome and, consequently, the concept of a species is.

Text and Illustration by Varvara Dikaya

!Did you know that plants interact with many different soil bacteria?

All plant parts, the leaves, the stems, the roots, but even fruits and seeds, have an associated microbiome. This is a collective term for different microorganisms which are found on or in the organ. What is striking, is that each plant part has a different microbiome.

So what can these microbes do? In the case of beneficial bacteria, some are known to possess certain functions. For example, they can produce antibiotics and thereby reduce the presence of pathogenic bacteria that are susceptible to the antibiotic. This is something which has been seen in some Streptomyces species, which can reduce the presence of scab disease on potato. Other bacteria, such as Pseudomonas species, have the ability to solubilize phosphorous. This means that more phosphor becomes available for the plant roots to take up. The last example is perhaps the most commonly known: nitrogen fixation. Some bacteria such as rhizobia or Frankia have the ability to engage in root nodule symbiosis with legumes or actinorhizal plants. They will provide the plant with nitrogen in exchange for carbon.

It is important to fully understand how these relationships work, but also how we can use them in for instance sustainable agriculture. Focussing on these relationships, and how to promote them, means that they could replace the use of agrichemicals.

Text and Illustration by Fede Berckx

A personal scientific journey: Dr Marisa Otegui’s interview by Manish Tiwari

Many researchers need to move to another country, leaving behind their friends and families to pursue their research and fulfil their dreams. As immigrants to a foreign country, they encounter several challenges requiring adaptation at personal and professional levels. Among these researchers, women in STEM face several adversaries and still leave their mark on society to be followed by future generations. Prof. Marisa Otegui is an eminent scientist who fits into this category. This interview takes us on her personal scientific and life journey to inspire future generations of early career researchers.

Dr Marisa Otegui is a professor at the Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin–Madison, US. She is also a project leader in the Water and Life Interface Institute (WALII) to decipher cellular response during dehydration to solid state.
She did her PhD at the University of La Plata, Argentina. She came as a FullBright Scholar to pursue a Post-Doctoral in Plant cell Biology at the University of Colorado-Boulder, US. Her research focuses on deciphering mechanisms that regulate membrane and protein trafficking and degradation in plants.
She was the winner of the Vilas Associates Competition in 2017. She received the Kellett Mid-Career Award (2020) and the prestigious Fellow of ASPB Award (2021). She also served as a chair of the Women in Plant Biology Committee at ASPB.

Symbiotic Plant Fungal Interactions in a nutshell

Fede Berckx made a great illustration to visualize different aspects of Symbiotic Plant Fungal Interactions.

Plants and various microorganisms, including fungi, have interacted through evolution in a way that shaped diversity. In fact, researchers believe that this interaction aided the transition to land, ca. 450 million years ago; an interesting topic that we at Physiologia Plantarum are exploring via this Special issue.

Today, mycorrhizal symbiosis is rather the rule than the exception: over 80% of plants engage with fungi. We can see different types of mycorrhizal symbiosis taking place. Researchers distinguish the following types: Arbuscular mycorrhizas, Mucoromycotina fine root mycorrhizas, Ectomycorrhizas, Ericoid mycorrhizas, and Orchid mycorrhizas.
Host specificity plays a major role in determining which plant and which fungus can interact. Some are generalists while others are specialists. Orchid and ericoid fungal symbiosis occur only with Orchidaceae or Ericals host plants (respectively). Almost all orchids act as parasites on their fungal partner at some point in their life and rely on the fungus to receive all their nutrients. Ericoid mycorrhizas are believed to be the most recently evolved symbiosis. The fungi can also interact with non-host plants, where they will act as endophytes, meaning they will live inside the plant tissues but not inside the plant cells as seen during true Ericoid symbiosis.
Some plants have been shown to simultaneously engage with arbuscular mycorrhizal fungi (AMF) and Mucoromycotina fine root endophytes (MFRE). What might be the benefit of doing so? Recent work has suggested that it allows for some plasticity of nutrient uptake, where MFRE may play a bigger role in N nutrition and AMF in plant P nutrition. As MFRE have been less studied than AMF, much more is yet to learn about this dual symbiosis!

All the Light that Plants can See

The light perception of plants is built predominantly around the absorption spectrum of photosynthetic pigments. As photosynthesis is the main source of energy for autotrophic plants, development and growth processes are closely linked to any changes in the light properties. Throughout evolution, plants developed a complex system of light receptors that utilize information about the light amount, spectrum, intensity, and direction. The range in which plants perceive light spans from UV-B (280 nm) to far-red (750 nm) with an absorption gap in the green-yellow region (approx. 500 – 600 nm).

The logical circuits of light receptors are interconnected, and their playgrounds are majorly overlapping in order to make a balanced decision about the developmental program: if the plant has to initiate or delay flowering, if the seed should germinate, or if it is time to change the direction of growth.

Since the absorption maxima of chlorophylls lay in the blue and red regions, those are the regions that give the most information about the potential to perform photosynthesis and grow in given conditions. Four groups of receptors cover this range (Phototropins, Cryptochromes, Zeitlupe family in UV-A/blue and Phytochromes in red/far-red regions) and transmit information downstream to fine-tune the developmental program or redirect it completely.

While UV-B light is not used in photosynthesis, it is dangerous for living cells, and the UVB-RESISTANCE 8 receptor regulates sun protection programs.

In the green absorption gap, there is also a gap of knowledge about the role and mode of action of green light in plants. There is evidence that it (1) is partially used for photosynthesis, and (2) plays a role in morphological response in plants, however, no green light receptors have been described in plants until now.

This great illustration and accompanying text were made by Varvara Dikaya.