Root exuded carbon is taken up by bacteria and bacterial DNA turns over faster than fatty acids in soil

In a recent article in Frontiers in Microbiology, Malik and colleagues highlight that rhizosphere microbial cellular components have variable C turnover. The study shows that bacterial C turnover is higher in nucleic acids (19 h for RNA and 30 h for DNA) than in membrane phospholipid fatty acids (42 d). The authors used a pulse-chase ¹³CO₂ plant labeling experiment and traced the ¹³C from plants through roots into the rhizosphere soil microorganisms.

Roots exude labeled carbon molecules, which are taken up by bacteria and incorporated into DNA and fatty acids. Upon the death of the bacteria, DNA and fatty acids are released into the soil and eventually incorporated into soil organic matter (SOM). Figure by RBN.

The results highlight two ecological aspects:

1) Since soil microbial biomass is thought to be important in maintenance of soil organic matter (SOM), the findings that microbial fractions have variable turnover rate suggest that their macromolecular structure and composition is important in determining the degree of microbial contribution to SOM formation. To put it in simple words, what constitutes the microbial cells could influence how much of it remains in soil which acts as a carbon sink.

2) Higher turnover of bacterial nucleic acids than fatty acids suggests that bacterial role in the initial assimilation of plant C could be higher than current estimates. This is because lipid fatty acids which have been widely used to investigate plant-rhizosphere C flow are biased against bacteria particularly the Gram positive ones which have a very complex cell envelope. The authors suggest that future studies relating to C flow consider the inherent turnover rates of microbial biomolecules while choosing the target biomarker. They also highlight the need for more detailed quantitative investigations with nucleic acid biomarkers to reappraise the rhizosphere microbial food web.

--Written text contributed by Ashish Malik as a solicited RhizoView

Root-knot nematodes induce plants to form new vascular structures

Bartlem, et al., recently published "Vascularization and nutrient delivery at root-knot nematode feeding sites in host roots," which reviews the state of knowledge of an important plant-animal interaction and how the animal penetrates the root, attaches itself to vasculature precursor cells, and then feeds off the plant's photosynthates (sugar) until completing its life cycle by forming eggs. The plant vascular system is composed of xylem and phloem vessels, or tubes. Xylem can be thought of as tubes taking soil resources from roots to the shoot of the plant, whereas phloem takes sugar produced in the shoot down to the roots. Study of the changes induced to the vasculature itself by nematodes has lagged behind other aspects of this cycle.

The process of root-knot nematode parasitism, from Bartlem, et al., 2013.

Nematodes look like worms, though they form their own phylum at the same levels as arthropods, chordates, and mollusks, and separate from the phylum of annelids that contains the common earthworm. They may be more closely related to insects than earthworms due to the fact that they moult as they grow. Nematodes include hookworms than can parasitize mammals, like people. Root-knot nematodes live in the soil and hatch from eggs, then navigate to roots. They attach themselves at the base of the plants vascular system near the root tip and give up their mobile lifestyle as they feed off the plant and swell. The cells that the nematode (N) attaches to become giant cells (GC) through a complex process.

The changes to xylum (Xy) and phloem (Ph) are the focus of this article. The vessels form cages around the giant cells to which the nematode is attached. Image from Bartlem, et al., 2013.

The phloem (Ph) and xylem (Xy) form cages around the giant cells with many connections that allow the transfer of nutrients and water into the giant cells. The nematodes, in turn, are connected via their mouth parts to the giant cells so have a ready supply of food and water. Eventually these structures swell and are visible by the naked eye as galls on the roots. The lucky nematode feeds till laying eggs which will continue the life cycle of the respective species.

More AMF colonization leads to more P uptake, bigger milkweeds, and faster growing caterpillars

A recent article in the Journal of Ecology entitled, "Mycorrhizal abundance affects the expression of plant resistance traits and herbivore performance," addressed knowledge gaps in how variation in the amount of arbuscular mycorrhizal fungi (AMF) present in the soil affects colonization of plant roots, nutrient uptake, and subsequent effects on plant performance and trophic interactions with herbivores. In the first experiment, soil abundance of AM fungi was manipulated by changing the amount of inoculum to be from zero to normal soil levels and common milkweed was planted in that soil. More fungi lead to greater root colonization and formation of mycorrhizae that improved phosphorus (P) acquisition and milkweed growth. In the second experiment, a smaller number of AM fungi soil levels were used and caterpillar eggs of the Monarch butterfly were allowed to hatch on growing plants and their biomass accumulation was measured after 5 days of the caterpillars consuming milkweed leaves. Increasing soil abundance of AM fungi inoculum lead to greater plant growth with more nutrient rich leaves and reduced herbivore resistance that benefited the growth of caterpillars. The results are summarized in the following figure.

This article demonstrated that increasing abundance of AM fungi in the soil increased root colonization and formation of mycorrhizae. Increased amounts of mycorrhizae increased milkweed phosphorus (P) uptake. Caterpillars of the Monarch butterfly benefitted from the nutrient rich leaves and grew faster. (figured created by RBN based on data from the cited article)

Plant root consumption of soil bacteria

Research in a recent article in New Phytologist, "How significant to plant N nutrition is the direct consumption of soil microbes by roots?," attempted to demonstrate the uptake of soil microbes by wheat roots by using nitrogen and carbon isotopic labeling. Conventional wisdom was that plants only take up the chemical ion forms of nitrogen found in soil, ammonium and nitrate. Research over the past decade first showed the the direct uptake of amino acids is widespread in plants, and becomes very important in ecosystems where chemical forms of nitrogen are relatively rare compared to organic, such as in the arctic tundra. More recent work has suggested that Arabidopsis and hakeas may receive nitrogen from intact bacteria, suggesting bacteria are taken up by roots.

In this article, Hill, Marsden, and Jones used a system balance approach to gain an understanding of how microbial nitrogen (N) and carbon (C) behave in soil with active wheat roots. They added microbes enriched with isotopes of nitrogen or carbon in separate experiments. The N and C isotopes were measured by mass spectrometry and scintillation counting, respectively. Basically, the presence of these isotopes within the roots showed that their source was the bacteria. The bacteria could have ruptured in the growing media, releasing amino acids that the roots could take up, or they could have been mineralized by other bacteria and so release chemical forms of nitrogen that were taken up. The authors claim the ratios of the N and C isotopes in the roots suggest complete bacteria entered the roots.

This figure summarizes an experiment consistent with wheat roots taking up bacteria. (created by RBN)

These results are consistent with plant roots taking up whole bacteria, but are inconclusive. Perhaps microscopy or genetic techniques could validate the presence of bacteria inside the plant roots. Still, this may not tell whether the roots actively took up the bacteria, or if the bacteria actively entered the roots, either as pathogens or endophytes. Last, whether the nitrogen entering the plant is used will require confirming its presence in plant metabolic processes.

3D simulation modeling of root system architecture is an indispensable tool for understanding root function

A recent review in Plant and Soil, "Modelling root–soil interactions using three–dimensional models of root growth, architecture and function," highlighted the progress being made in 3D models of root system architecture. Root system architecture (RSA) is the what, when, and where of root growth. The structure of a plant root system can be defined by what classes of roots are present, their angles of growth, how often they branch, and their diameters, among many other traits. In RSA functional-structural modelling, this information is used to recreate realistic plant root systems. Here, RBN explores this paper while adding some extra content.

The first architectural root model was published in 1973 by Lungley. By 1988, ROOTMAP was being used for 3D modeling of crop root systems. While RSA modeling became more complex, more powerful computers and visualization software were also developed. Better models and visualization software together give rise to the evolution of root system architecture models in the following figure.

Figures are from their respective creators, cited below each image. Figures compiled by RBN.

The six current major 3D root system architecture models are: RootTyp, SimRoot, ROOTMAP, SPACSYS, R-SWMS, and RootBox. They are being used to study how specific root traits affect the uptake of a variety of soil resources such as nitrogen, phosphorus, and water. The most recent advancements are including plasticity of roots in response to local nutrient patches, soil characteristics (such as hard pans), and to impenetrable objects such as pot walls or rocks.

Limitations of current models also imply the future directions. Though RSA modeling is being used to understand plant uptake of soil resources, there are problems with up-scaling from single roots to the whole system, especially in defining a useful voxel (3D unit of simulated soil) size. Current models do not include rhizosphere processes or soil microorganisms that are known to be important for resource uptake and root growth. However, as these limitations are addressed, combinations of root and shoot models will lead to true virtual plants.

These six root models were compared head-to-head in this review for a variety of their uses and methods. The paper's authors summarized the models' major differences by their focuses:

RootTyp - detailed, dynamic, and can be used to study many species, including trees
SimRoot - resource acquisition as influenced by specific traits and resource utilization
ROOTMAP - root system plasticity and root proliferation in local patches
SPACSYS - crop modeling with predictions of biomass and yield
R-SWMS - root and soil hydrology to study how water uptake is influenced by RSA
RootBox - L-systems model in Matlab and publicly available

Details of their uses and differences can be found in the paper. The authors conclude by stressing the importance of the models taking into account soil microorganisms and internal plant processes such as hormonal signaling. These models are ready to be used more broadly and in collaboration with plant biologists specializing in other fields. Root system architecture and soil modeling is positioned to offer substantial value to basic and applied science through ecosystem design and crop breeding.

Live from the Root Biology Symposium at the University of Missouri

The Interdisciplinary Plant Group of the University of Missouri hosted the Root Biology Symposium May 28-31. This symposium marked the 30th anniversary of the IPG symposium series, with several having focused on root biology.  Dr. Robert Sharp and Dr. Melissa Mitchum introduced Chancellor Emeritus Richard L. Wallace who gave a brief overview of the IPG. The IPG formed in 1981 with 9 UM faculty, and has grown to 57 faculty. The IPG has gained international recognition as a model of intra-university collaboration. A trophy was awarded to Dr. Douglas D. Randall who established the symposium series in 1983.  As Dr. Wallace said, the audience is lucky to be involved with a symposium so rich, so relevant, and so exciting.

Root Biology News brought daily updates during this time.

Sessions from Wednesday, May 29, 2013

The symposium began with a talk from the Chancellor's Distinguished Visitor, Jianhua Zhang, that covered strategies being used for water conservation in China, particularly partial rootzone irrigation. This was followed by Phil Benfey, who was this year's keynote speaker and wowed the crowd with his research on roots from genes to pioneering phenotyping of root crowns. Taken together, the first two talks demonstrated the importance of future studies investigating the interaction of root traits and agronomic practices.

The rest of the day was spent in a session on root development. The progress being made is impressive in understanding the genetic regulation of root development. Malcom Bennett was the session's keynote speaker and did a great job showing how lateral roots form using live cell imaging and genetic mutants. The talks in the development session demonstrated how state of the art science is finally unravelling how root systems grow, with implications for applications such as understanding the utility of variation in root traits.

The abiotic interactions section began with the keynote talk from Ian Dodd on root to shoot signalling in drying soil. This research was instrumental in the execution of new agronomic practices advocated by Jianhua Zhang with partial rootzone irrigation (PRI). Particularly, the hormone ABA reduces leaf size and transpiration in PRI which leads to transpiration savings.

After dinner, John Kirkegaard talked about the health benefits of GSLs and ITCs in the mustard family. Remember, eat your broccoli!

Sessions from Thursday, May 30, 2013

The abiotic interactions section continued on Thursday morning. Water stress was an important theme. Felix Fritschi showed some fascinating new screening methods for deep roots in soybeans, reminiscent of toxicity screenings in Arabidopsis. Andrew Leakey spoke about climate change and science being done in FACE sites that manipulating carbon dioxide, temperature, and water in the field.

The biotic interactions session began with Sharon Long's keynote talk about root nodule development, and showed how bacterial sigma factors lead to the different stages of nodule development. This work has implications for the possibility of putting the ability to fix nitrogen in non-leguminous crop plants. Other talks showed the how plants respond to root grazing through chemical signaling, and how nematodes take advantage of inhibiting plants' immune systems. The session's last talks focused on the formation of the mycorrhizal symbiosis that is so common in land plants.

The day concluded with the poster session, which was a blast, and a student/post-doc/speaker dinner which allowed for unique opportunities to interact with root biology colleagues.

Sessions from Friday, May 31, 2013

Friday's nutrition session was a great conclusion to a wonderful meeting. Yi-Feng Tsay gave the keynote about how the nitrate transporter CHL1 can sense both nitrate concentrations and temporal changes that help plants regulate the uptake of nitrogen from the soil and transport it within the plant. The last talks of the day largely focused on the importance of root system architecture for determining the placement of roots and the uptake of soil resources. Lixing Yuan, Leon Kochian, and Matthias Wissuwa gave insight to the state of the science of root system architecture being phenotyped and utilized in maize and rice. The progress being made is astounding, and gives hope to feeding the future.

Conclusion

Doug Randall concluded the symposium with a call for action for the science crisis in the USA. He urged the audience (paraphrasing):

Please go home, take your story, and tell people. We can not put up with what's happening in Washington. We need to tell the public what science can do.

We need to turn science around in the eyes of the public.

Is the elongation of Arabidopsis roots influenced by the tides and Earth's magnetic field?

A recent article in Annals of Botany, "Arabidopsis thaliana root elongation growth is sensitive to lunisolar tidal acceleration and may also be weakly correlated with geomagnetic variations," found relations between the coincidence of root elongation rates, tides, and Earth's magnetic fields, especially those influenced by magnetic storms. The researchers grew Arabidopsis seedlings in growth chambers at constant lighting and temperature, which would be two other regulators of plant growth. At the same time, they collected information about the strength of tidal forces, or the influence of the moon and Earth's tides on gravitation, along with information about changes in the local magnetic fields, largely due to magnetic storms. The figure at the bottom of the post shows root elongation rate in black, gravimetric tide in blue, and the strongest magnetic data is orange (Polar Cap Index). In some time intervals, root elongation rate does seem to coincide with the tide. However, the paper does not say if the seeds were also germinated in the growth chambers without the influence of daily light regimes that could set a daily rhythm in the plants, which does seem to be the case here as the root elongation rates peak with 24 hour lengths. If roots do oscillate in growth chambers that limit the influence of light and temperature, and these oscillations coincide with gravimetric and magnetic fields, then roots must have previously unknown abilities of perception. The paper documents other research that suggest these abilities are plausible. The research warrants further watch.

Figure from Annals of Botany, cited above.