A. Hussain, C. R. Black, I. B. Taylor, J. A. Roberts, Soil compaction. A role for ethylene in regulating leaf expansion and shoot growth in tomato? Plant Physiol. 121, 1227–1238 (1999).
This paper described a link between ethylene levels and plant growth in compacted soil. Plants with higher ethylene production have reduced growth in compacted soil when compared to plants with lower ethylene production.
F. An, Q. Zhao, Y. Ji, W. Li, Z. Jiang, X. Yu, C. Zhang, Y. Han, W. He, Y. Liu, S. Zhang, J. R. Ecker, H. Guo, Ethylene-induced stabilization of ETHYLENE INSENSITIVE3 and EIN3-LIKE1 is mediated by proteasomal degradation of EIN3 binding F-box 1 and 2 that requires EIN2 in Arabidopsis. Plant Cell 22, 2384–2401 (2010).
This paper investigates the mechanism underlying the increased protein levels of EIN3 and EIL1 in response to ethylene. Increased abundance of EIN3 or EIL1 is used as a reporter of activated ethylene response in the annotated paper.
B. Ma, S.-J. He, K.-X. Duan, C.-C. Yin, H. Chen, C. Yang, Q. Xiong, Q.-X. Song, X. Lu, H.-W. Chen, W.-K. Zhang, T.-G. Lu, S.-Y. Chen, J.-S. Zhang, Identification of rice ethylene-response mutants and characterization of MHZ7/OsEIN2 in distinct ethylene response and yield trait regulation. Mol. Plant 6, 1830–1848 (2013).
Ma et al. identified and characterized the rice ein2 mutant, which is used frequently as a ethylene-insensitive plant line in the annotated paper.
K. D. Montagu, J. P. Conroy, B. J. Atwell, The position of localized soil compaction determines root and subsequent shoot growth responses. J. Exp. Bot. 52, 2127–2133 (2001).
This paper provides evidence supporting that roots can sense compacted soil and avoid growth in compacted soil.
J. M. Alonso, T. Hirayama, G. Roman, S. Nourizadeh, J. R. Ecker, EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis. Science 284, 2148–2152 (1999).
Alonso et al. characterized the Arabidopsis ein2 mutant, which is defective in ethylene response. This plant line is also used in many experiments done in the annotated paper.
hormone
A hormone is a chemical produced by organisms to regulate activities such as growth, development and resposes to the environment.
T. Fujikawa, T. Miyazaki, Effects of bulk density and soil type on the gas diffusion coefficient in repacked and undisturbed soils. Soil Sci. 170, 892–901 (2005).
This paper investigates factors that affect gas diffusion in soil. It notes that air-filled porosity and bulk density are important factors.
J. Correa, J. A. Postma, M. Watt, T. Wojciechowski, Soil compaction and the architectural plasticity of root systems. J. Exp. Bot. 70, 6019–6034 (2019).
This paper reviews the effects of soil compaction on soil properties and root traits. It notes that in compacted soil, main effects on roots include decreased root length and increased root diameter.
This result demonstrates that soil compaction (and the associated increase in soil moisture due to decreased porosity) affects ethylene diffusion rates, consistent with our restricted gas diffusion model.
The authors found that ethylene diffused rapidly to the bottom chamber through empty column while diffused more slowly through uncompacted soil. However, ethylene was not able to diffuse through compacted soil even after 20 days of experiment. This suggests that soil compaction indeed affects the diffusion of ethylene.
A 1-cm-thick soil column (connecting two air-filled chambers) was either left empty (control) or filled with uncompacted soil (1.1 g cm–3) or compacted soil (1.6 g cm–3) (Fig. 3I and fig. S25B). Ethylene was injected into the upper chamber (an increase in pressure was avoided) and ethylene concentrations were subsequently measured over time in the lower chamber until an equilibrium was reached between the chambers.
In this experiment, the authors used a vertical equipment consisting of a glass chamber at the top, a glass chamber at the bottom, and a column between the two chambers connecting them. The column is filled with uncompacted or compacted soil, or left empty. Ethylene was injected to the upper chamber to a certain initial concentration, and then was allowed to diffuse through the column to the bottom chamber. Samples were taken from the upper and the bottom chambers for measurement of ethylene concentration.
slower outward ethylene diffusion rates under compacted soil conditions (Fig. 3H and fig. S25) due to the decreased volume of air-filled pores (1) (Fig. 1, A to D, and movies S1 and S2). This will result in a higher ethylene concentration close to roots (Fig. 3, F and G) and therefore in root cells, consistent with soil compaction triggering an ethylene response
The authors' mathematical model predicted that ethylene diffusion was slower in compacted soil when compared to that in uncompacted soil, resulting in a higher concentration of ethylene around roots.
Mathematical modeling
The authors constructed mathematical models to predict the efficiency of ethylene diffusion in uncompacted or compacted soil.
when reporter lines were grown in compacted soil, both ethylene reporters were detected in root elongation zone cells
The authors observed increased intensity of GFP signals in roots grown in compacted soil. This suggests that soil compaction triggers ethylene response.
We used transgenic Arabidopsis and rice expressing either an ethylene biosensor featuring EIN3 (9) or OsEIL1 sequences fused with GFP
In this experiment, the authors grew Arabidopsis or rice roots expressing GFP-based ethylene-responsive reporters, 35S:EIN3-GFP (Arabidopsis) and proOsEIL:OsEIL1-GFP (rice) in uncompacted or compacted soil. They measured ethylene response by visulizing the intensity of green signals released by the reporters.
similar to roots exposed to soil compaction
The authors found that ethylene treatment alone induced increased root width and flattened cap shape, further supporting that ethylene is a critical controller of root growth in response to soil compaction.
ethylene treatment
In this experiment, the authors treated wild-type rice roots with or without ethylene. They measured root width and cap shape.
Soil compaction caused wild-type rice roots to double in width and their root caps to develop a “flattened” shape (compare Fig. 2, H and I). Soil compaction–induced radial growth and root cap shape changes were blocked in osein2 (Fig. 2, J, K, and O). Hence, root tip shape changes induced by soil compaction appear to be controlled primarily by ethylene and not by mechanical impedance.
The authors observed induced radial growth and root cap shape changes in wild-type but not ein2 mutant grown in compacted soil when compared to plants grown in uncompacted soil. This suggests that ethylene but not mechanical impedance plays the primary role controlling root grwoth changes.
we compared their impact on root tip shape
In this experiment, the authors aimed to determine if mechanical imdedance plays a role in affecting root growth in compacted soil, in addition to the effects caused by ethylene. The authors grew wild-type rice and ethylene-insensitive rice ein2 mutant in compacted or uncompacted soil. Supposedly, ein2 mutant should also show some degrees of root growth change if mechanical impedance plays a role. They imaged roots with microscope and measured the area of root cap.
perhaps to avoid growth in compacted soils
Montagu et al. reveal that the position of soil compaction affects root growth. When roots grow through compacted soil into uncompacted soil, total root growth is reduced. However, when roots grow through uncompacted soil into compacted soil, more compensatory root growth happens in the uncompacted soil and total root growth is not changed. This suggests that roots can sense soil compaction and avoid growing in compacted soil.
this growth response also occurred in other classes of roots
In this experiment, the authors grew different Arabidopsis lines in compacted or uncompacted soil. Arabidopsis lines used included wild-type (in which the ethylene response functions normally) and lines defective in ethylene response (etr1). They used microscope to image root tips and measure epidermal cell length and cortical cell diameter.
unlike the wild type (Fig. 2B), both osein2 and oseil1 roots were able to penetrate highly compacted soil (Fig. 2, D and F; quantified in Fig. 2G)
The authors found that wild-type plants had less root growth in compacted soil when compared to uncompacted soil. However, no difference was observed between uncompacted soil and compacted soil for plants defective in ethylene response. This indicates that ethylene is required to inhibit root growth in compacted soil.
computed tomography
Computed tomography is a technique that uses X-ray and computational tools to generate images.
we grew rice lines in columns entirely filled with either uncompacted soil (1.1 g cm–3) or highly compacted soil (1.6 g cm–3, with a 1-cm top layer packed at 1.1 g cm–3 to help establish seedling root growth).
In this experiment, the authors grew different rice lines in compacted or uncompacted soil. Rice lines used included wild-type (in which the ethylene response functions normally) and lines defective in ethylene response (osein2 and oseil1). They used computed tomography to generate images of roots and measured root length.
The first author showed a video demostrating the facility for growing plants and the imaging system: https://www.youtube.com/watch?v=pk5_7cA5qLo
(9)
An and colleagues revealed that loss of EIL1 suppresses response to ethylene in Arabidopsis.
transcription factor
A transcription factor is a protein that facilitates transcription, a process that makes RNA from DNA.
(13)
Alonso and colleagues characterized an ein2 mutant in Arabidopsis and found that ein2 mutant did not respond to ethylene.
(12)
Ma and colleagues identified a rice mutant that cannot respond to ethylene. They found that the mutation happened in a gene encodes a protein that is homologous to the EIN2 protein in Arabidopsis.
oseil1
This is a type of rice plant in which EIL1 (EIN3-like 1) gene is not functional.
osein2
"Os" represents Oryza sativa, which is the name for rice in a scientific naming system.
This is a type of rice plant in which EIN2 (ETHYLENE INSENSITIVE2) gene is not functional.
Similarly, ethylene treatment reduced root length (fig. S8A) while increasing root width
The authors found that roots grown under high levels of ethylene or in compacted soil showed similar characteristics, reduced root length and increased root width, when compared to roots grown under low levels of ethylene or uncompacted soil.
cortical cell
Cortical cell is a layer of cells lying underneath the epidermal cells.
epidermal cell
Epidermal cells are the cells on the surface of plants.
anatomical analysis
Anatomy is a branch of biology focusing on the structure of organisms or a certain part of organisms.
Anatomical analysis is the analysis in such field. Here, the authors focus on the stucture of root cells.
phenocopied
Phenocopy means the plants grown under a certain condition have similar characteristics to the plants grown under a different condition.
Roots exposed to elevated levels of ethylene exhibited growth inhibition
In this experiment, the authors did two sets of experiments. First, they grew plants with or without exposure to high levels of ethylene and measured root length and root diameter. Second, they grew plants in uncompacted or compacted soil and did the same measurements.
Hypoxia reporters were not induced by the gas barrier but were induced by submergence (figs. S4 to S6). We conclude that EIN3-GFP induction results from restricted ethylene diffusion rather than from hypoxic conditions (11).
The authors found that the green signal indicating hypoxia response is not enhaced in roots with gas barrier when compared to roots without gas barrier. This suggests that the enhanced ethylene response is not due to hypoxia.
RAP2.12-GFP
RAP2.12 (RELATED TO AP2 12) is a protein, of which the level increases when plants are under hypoxia condition. RAP2.12-GFP is a protein made by fusing RAP2.12 protein with GFP and is used to indicate whether hypoxia response is triggered in plants.
(10)
This work uses pPCO1:GFP-GUS and pPCO2:GFP-GUS as reporters of hypoxia condition.
pPCO2:GFP-GUS
This is a GFP-based reporter indicating whether hypoxia response is activated in plants. The presence of green signals in roots means hypoxia response is activated.
pPCO1:GFP-GUS
pPCO1 means the promoter region of the gene PCO1 (PLANT CYSTEINE OXIDASE 1), which is required to turn PCO1 on. PCO1 gene is turned on under hypoxia condition, which is a indicator of hypoxia response in plants.
Here, pPCO1 is fused with DNA sequences encodes GFP and GUS. Under hypoxia condition, pPCO1 turns on the production of GFP so scientists can determine if hypoxia response is activated in plants by visualizing GFP.
hypoxia
Hypoxia means a condition with not enough oxygen.
we treated roots expressing
In this experiment, the authors applied the gas barrier to the tips of roots expressing GFP-based hypoxia-responsive reporters, pPCO1:GFP-GUS, pPCO2:GFP-GUS and RAP2.12-GFP. They measured hypoxia response by visulizing the intensity of green signals released by the reporters.
root elongation zone
Root elongation zone is a zone of roots where root cells are expanding.
restricting gas diffusion from root tip tissues triggered a rapid and sustained increase in EIN3-GFP
The authors found enhanced ethylene-responsive green signals in roots with gas barrier when compared to roots without gas barrier. This result suggests that the inhibition of gas diffusion between roots and soil induces accumulation of ethylene and activation of ethylene response.
examined the effect of covering root tips with a gas-impermeable barrier
In this experiment, the authors applied a type of grease (gas barrier) to root tips to inhibit gas diffusion. They measured ethylene response by visulizing the intensity of green signals released by the ethylene-responsive EIN3-GFP marker.
Arabidopsis ethylene response reporter
An and colleagues reveal that the protein levels of EIN3 increase in response to ethylene. This is the fundment of using EIN3-GFP to measure ethylene response in plants.
EIN3-GFP (green fluorescent protein)
Green fluorescent protein is a protein that emits green light after absorbing light at a different wavelength. EIN3 (Ethylene-insensitive 3) is a protein, of which the level increases when plants' response to ethylene is triggered. EIN3-GFP is a protein made by fusing EIN3 protein with GFP and is used to indicate whether ethylene response is triggered in plants.
Ethylene is produced by root tissues, and its level increases when roots are exposed to compacted soil
Hussain and colleagues find that tomato plants with higher ethylene production have reduced growth in compacted soil when compared to tomato plants with lower ethylene production. This provides a connection between ethylene levels and plant growth in compacted soil.
bulk density (BD)
Bulk density indicates the degree of soil compaction. it is calculated as the dry weight of soil per unit soil volume. The soil volume includes the volume of soil particles and the volume of soil pore space among particles.
rhizosphere
Rhizosphere is defined as the section of of soil surrounding plant roots, which contains chemicals released from plant roots and a population of microorganisms.
restricts diffusion of gases between roots
This work reveals that air-filled porosity, bulk density, soil disturbance, the type of diffusion gases, and soil texture are factors that affects gas diffusion in soil.
severely degrading ~65 million hectares of land globally
Soil compaction also has huge effects on crop yield and economy.
Read more in a publication by World Economic Forum: https://www.weforum.org/agenda/2021/01/crop-yield-agriculture-chemical-breakthrough/
Soil compaction
What causes soil compaction? What are the consequences of soil compaction?
Read more in a publication by University of Minnesota Extension: https://extension.umn.edu/soil-management-and-health/soil-compaction
which would be relevant to research into the breeding of crops resilient to soil compaction
The authors of this paper discussed in a news article that specifically shutting down ethylene response in root tips may be a good way to generate crops resistant to soil compaction.
Read more in The Science Breaker: https://www.thesciencebreaker.org/breaks/plant-biology/how-roots-help-us-fight-against-hard-soils
wild-type
Wild-type refers to individuals of a species that are in the typical form of that species and occur in nature.
Arabidopsis
Arabidopsis (Arabidopsis thaliana) is a plant species that is widely used as a model organism in plant research.
mutant
Mutants refer to individual organisms of a certain species that are considered "abnormal" when compared to normal individuals of the same species that occur in nature. Usually, in a mutant, at least one gene is artificially disrupted and does not function normally. Mutants are powerful tools to study the function of a gene.
ethylene
Ethylene is a gaseous plant hormone that regulates many plant activities such as fruit ripening, leaf development, responses to environmental stresses etc.