Journal club: Surviving flooding

Like human beings, plants need to control water uptake to survive. Unlike humans, they cannot simply move to a dryer place when water levels rise, or go to a water source when they are in danger of dehydration. Instead, they need to cope while standing still. Plants take up water mostly via transporters in their roots. These transporters are called aquaporins (aqua = water, porin = protein) and only let water pass through. Aquaporins are located in the membranes surrounding the root cells and thus allow water to pass through the cell layers to the interior of the root. When the water reaches the central cylinder it starts its travel upwards to the leaves.

The transporters in the root can be opened, closed or removed from the cell membrane depending on the amount of water in the environment. When there is very little water available, the plant needs a lot of water transporters. In case of flooding the opposite, as few transporters as possible, is not always advantageous. When the aboveground parts of the plant are also under water, little water uptake is advantageous, so the plant will indeed want to restrict root water permeability. However, when the aboveground parts of the plant are not under water, water uptake is still required, since water is lost to evaporation. Thus, the aboveground environment determines the root water permeability that leads to greatest fitness. It is therefore reasonable to suppose that plants in locations with different kinds of recurrent floods have adapted by different responses to root flooding.

In their recent paper, Shahzad and co-authors describe their search for genetic factors that are involved in the regulation of root water permeability. In other words, they wanted to find parts of the genome, the heritable ‘code’ that each organism contains, that regulate this process. To find these parts, they performed a method called ‘QTL mapping’ in the model plant Arabidopsis thaliana (thale cress). First, the researchers took two populations of thale cress that differed in root water permeability. They then crossed these populations, resulting in offspring with pieces of the genome from each of the parents. The root water permeability of this offspring can be intermediate between the two parents or something more extreme, that is, close to that of either of the parents. Next, the genetic code of all the offspring with an extreme phenotype is checked. This offspring will have either parent’s DNA at random at most sites of the genome. However, the piece of the genome that is correlated with root water permeability will come from the parent whose root water permeability was inherited. In this way, Shahzad and co-authors found a region in the genome that explained 15% of the observed differences in root water permeability. This region contained the code of several genes. They then changed the code of each these genes one by one to check which gene contributed to root water permeability. This led to the discovery of a gene that negatively affects root hydraulics, which they named Hydraulic Conductivity of Root 1 (HCR1). The activity of this gene is influenced by potassium and oxygen levels, thus integrating diverse signals in the soil.

This brings us back to the strategy decision of plants with flooded roots. To study the effect of HCR1 on a plant’s response to flooding, the researchers studied a wild-type cultivar of thale cress and plants from the same cultivar with a mutated, that is, nonfunctional, HCR1 gene. When only the roots of these plants are flooded, the mutant grows more and has a higher water content in the aboveground parts of the plant than the wild-type plant. This confirms their hypothesis that a decrease in root water permeability is not always advantageous when roots are flooded. Apparently, in the wild-type plants the decrease in root water permeability by HCR1 results in less water uptake while the aboveground parts of the plant loose water by evaporation, resulting in a dehydrated plant. In contrast, in plants recovering from submergence the wild-type plants outperform the mutants. This shows that HCR1 increases plant growth and shoot water content in plants recovering from submergence.

Thus, the researchers discovered a gene involved in root water permeability regulation: HCR1. In further experiments they show that this gene differentially affects a plant’s fitness in different flooding conditions in one specific cultivar. The researchers subsequently discover that cultivars of thale cress from different locations across the world differ in their code of HCR1. These populations also differ in root water permeability, suggesting that changes in the code of HCR1 are a way in which plants have adapted to different flooding conditions. Future work will have to show whether the correlation between differences in HCR1 and root water permeability in the different cultivars is indeed causal. In addition, it remains to be elucidated how HCR1 decreases root water permeability in the first place.

Shahzad, Z. et al. (2016) A Potassium-Dependent Oxygen Sensing Pathway Regulates Plant Root Hydraulics. Cell 167, 87–98.e14. DOI:

Disclaimer: blog posts in the category ‘journal club’ are not intended to cover the whole paper discussed. Instead, I discuss the parts that I think are most interesting for a general public. I try my utmost to prevent any mistakes in these blogs, I apologize in advance for any mistakes that I make anyway.

PhD life: improving my scientific writing skills

Doing a PhD is not only about doing research, is it also about growing as a researcher and learning new skills.

To learn those skills, I go to conferences, talk with coworkers and follow courses. At the moment I am following the course ‘The Art of Scientific Writing’. While I have the classes on the campus of Utrecht University, it is offered by the company Artesc. A few months ago I already followed their course ‘The Art of Presenting Science’ and it was a real eye-opener. Seemingly vague terms as ‘voice direction’, ‘attention with yourself’ and ‘letting go’ led to huge presenting improvements in all of the participants.

The writing course is not as mind blowing as the presenting course, but it is a useful and fun course nonetheless. The course consists of three full-day meetings, once every two weeks. As preparation for each course day we write (parts of) articles about our research. During the course days, we get taught some theory about writing, but mostly spend the time sharing our writing experiences and giving feedback on each other’s work.

Apart from me, there are seven other PhD students following this course, only one of whom also works with plants. Although we do not get clear tips and tricks, talking about our work with such a diverse group of people is very helpful. It is good to hear how other people go about writing and what kind of help they get from their supervisors. Also, getting feedback on my work from scientists outside of my field in itself already makes the course worth going to. It is good to hear what is clear and interesting to people not into my topic and what is confusing. After all, as the teacher said, further employers or grant agencies might very well not be in my exact field either, but they will read my papers to judge my work.