A synthetic dataset of atmospheric deposition and stomatal uptake

SynFlux: a synthetic dataset of atmospheric deposition and stomatal uptake at flux tower sites

Holmes C. D., Ducker J. A. (2018) –

Holmes Christopher D., Ducker Jason A.,


Zenodo [data set] – https://doi.org/10.5281/zenodo.1402054


SynFlux quantifies atmosphere-biosphere fluxes of ozone at flux tower sites. It combines micrometeorological measurements at eddy covariance flux towers with air pollution monitoring networks. Reported quantities include deposition velocity, stomatal conductance, deposition flux, and stomatal uptake flux.

The method and its performance are documented in

Ducker, J. A., Holmes, C. D., Keenan, T. F., Fares, S., Goldstein, A. H., Mammarella, I., Munger, J. W., and Schnell, J. (2018) – Synthetic ozone deposition and stomatal uptake at flux tower sites – Biogeosciences Discuss – https://doi.org/10.5194/bg-2018-172

The equivalence of two algorithms found in the literature to derive ozone stomatal fluxes and both based on the similarity between ozone stomatal fluxes and water vapour stomatal fluxes

Comparison of different algorithms for stomatal ozone flux determination from micrometeorological measurements

Gerosa G., Derghi F., Cieslik S. (2007)

Giacomo GerosaFederico DerghiStanislaw Cieslik,


Water Air Soil Poll. 179: 309–321 – https://doi.org/10.1007/s11270-006-9234-7



The determination of stomatal ozone fluxes is essential to assess the potential damage to plants due to ozone uptake. This parameter is not accessible directly with measurements, but can be deduced through algorithms using observational data. Total ozone fluxes and water vapour fluxes are generally used. Water vapour fluxes give an indication on stomatal aperture, which is the controlling factor of ozone uptake by vegetation. In this work, a series of observations made during the growing season over an onion field are used to show the equivalence of two algorithms found in the literature to derive ozone stomatal fluxes and both based on the similarity between ozone stomatal fluxes and water vapour stomatal fluxes. One of these algorithms uses the Penman-Monteith approach, where the water vapour pressure deficit is calculated using air temperatures; the second calculates, with another formulation, the water vapour deficit from the leaf temperature. The two approaches lead to the same results if applied properly, as shown in this work, both theoretically and numerically.

Comparison of different stomatal conductance algorithms for ozone flux modelling

Comparison of different stomatal conductance algorithms for ozone flux modelling

Büker P., Emberson L. D., Ashmore M. R., Cambridge H. M., Jacobs C. M. J., Massman W. J., Müller J., Nikolov N., Novak K., Oksanen E., Schaub M., de la Torre D. (2007)

P. Bükera, L. D. Embersona, M. R. Ashmorea, H. M. Cambridgea, C. M. J. Jacobsb, W. J. Massmanc, J. Müllerd, N. Nikolove, K. Novakf, E. Oksaneng, M. Schaubf, D. de la Torreh,

a Stockholm Environment Institute, University of York, York, North Yorkshire YO 10 5DD, UK

b Alterra, Droevendaalsesteeg 3, 6708 PB Wageningen, The Netherlands

c USDA Forest Service, Rocky Mountain Research Station, Fort Collins, CO, USA

d Institute of Agronomy and Crop Science, Martin-Luther-University Halle-Wittenberg, Ludwig-Wucherer-Straß 2, D-06099 Halle, Germany

e N & T Services, 6736 Flagler Road, Fort Collins, CO 80525, USA

f Forest Ecosystems and Ecological Risk, Swiss Federal Research Institute WSL, Zuercherstraß 111, 8903 Birmensdorf ZH, Switzerland

g Department of Biology, University of Joensuu, P.O. Box 111, 80101 Joensuu, Finland

h Institute for Energetics, Environment and Technological Research (CIEMAT), Avda. Complutense, 22, 28040, Madrid, Spain


Environ. Pollut. 146: 726–735 – https://doi.org/10.1016/j.envpol.2006.04.007



A multiplicative and a semi-mechanistic, BWB-type [Ball, J.T., Woodrow, I.E., Berry, J.A., 1987. A model predicting stomatal conductance and its contribution to the control of photosynthesis under different environmental conditions. In: Biggens, J. (Ed.), Progress in Photosynthesis Research, vol. IV. Martinus Nijhoff, Dordrecht, pp. 221–224.] algorithm for calculating stomatal conductance (gs) at the leaf level have been parameterised for two crop and two tree species to test their use in regional scale ozone deposition modelling. The algorithms were tested against measured, site-specific data for durum wheat, grapevine, beech and birch of different European provenances. A direct comparison of both algorithms showed a similar performance in predicting hourly means and daily time-courses of gs, whereas the multiplicative algorithm outperformed the BWB-type algorithm in modelling seasonal time-courses due to the inclusion of a phenology function. The re-parameterisation of the algorithms for local conditions in order to validate ozone deposition modelling on a European scale reveals the higher input requirements of the BWB-type algorithm as compared to the multiplicative algorithm because of the need of the former to model net photosynthesis (An).

The importance of using photosynthesis-based representation of stomatal resistance in dry deposition schemes under a changing climate and rising CO2 concentration

Influence of plant ecophysiology on ozone dry deposition: comparing between multiplicative and photosynthesis-based dry deposition schemes and their responses to rising CO2 level

Sun S., Tai A. P. K., Yung D. H. Y., Wong A. Y. H., Ducker J. A., Holmes C. D. (2022)

Shihan Sun1, Amos P. K. Tai1-2, David H. Y. Yung1, Anthony Y. H. Wong1-3, Jason A. Ducker4, Christopher D. Holmes4,

  • 1 Earth System Science Programme and Graduate Division of Earth and Atmospheric Sciences, Faculty of Science, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
  • 2 State Key Laboratory of Agrobiotechnology and Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
  • 3 Department of Earth and Environmental, Boston University, Boston, USA
  • 4 Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, Florida, USA


Biogeosciences 19: 1753–1776 – https://doi.org/10.5194/bg-19-1753-2022



Dry deposition is a key process for surface ozone (O3) removal. Stomatal uptake is a major component of O3 dry deposition, which is parameterized differently in current land surface models and chemical transport models. We developed and used a standalone terrestrial biosphere model, driven by a unified set of prescribed meteorology, to evaluate two widely used dry deposition modeling frameworks, Wesely (1989) and Zhang et al. (2003), with different configurations of stomatal resistance: (1) the default multiplicative method in the Wesely scheme (W89) and Zhang et al. (2003) scheme (Z03), (2) the traditional photosynthesis-based Farquhar–Ball–Berry (FBB) stomatal algorithm, and (3) the Medlyn stomatal algorithm (MED) based on optimization theory. We found that using the FBB stomatal approach that captures ecophysiological responses to environmental factors, especially to water stress, can generally improve the simulated dry deposition velocities compared with multiplicative schemes. The MED stomatal approach produces higher stomatal conductance than FBB and is likely to overestimate dry deposition velocities for major vegetation types, but its performance is greatly improved when spatially varying slope parameters based on annual mean precipitation are used. Large discrepancies were also found in stomatal responses to rising CO2 levels from 390 to 550 ppm: the multiplicative stomatal method with an empirical CO2 response function produces reduction (−35 %) in global stomatal conductance on average much larger than that with the photosynthesis-based stomatal method (−14 %–19 %). Our results show the potential biases in O3 sink caused by errors in model structure especially in the Wesely dry deposition scheme and the importance of using photosynthesis-based representation of stomatal resistance in dry deposition schemes under a changing climate and rising CO2 concentration.

The first land plants had the genetic tools to build stomata, a key adaptation for life on land

How ancient plants ‘learnt’ to use water when they moved on to land – new research

Bowles A. (2022)

Alexander Bowles, University of Bristol


“Plants, whether they are enormous, or microscopic, are the basis of all life including ourselves.” This was David Attenborough’s introduction to The Green Planet, the latest BBC natural history series.

Over the last 500 million years, plants have become interwoven into every aspect of our lives. Plants support all other life on Earth today. They provide the oxygen people breathe, as well as cleaning the air and cooling the Earth’s temperature. But without water, plants would not survive. Originally found in aquatic environments, there are estimated to be around 500,000 land plant species that emerged from a single ancestor that floated through the water.

In our recent paper, published in New Phytologist, we investigate, at the genetic level, how plants have learnt to use and manipulate water – from the first tiny moss-like plants to live on land in the Cambrian period (around 500 million years ago) through to the giant trees forming complex forest ecosystems of today.

How plants evolved

By comparing more than 500 genomes (an organism’s DNA), our results show that different parts of plant anatomies involved in the transport of water – pores (stomata), vascular tissue, roots – were linked to different methods of gene evolution. This is important because it tells us how and why plants have evolved at distinct moments in their history.

Plants’ relationship with water has changed dramatically over the last 500 million years. Ancestors of land plants had a very limited ability to regulate water but descendants of land plants have adapted to live in drier environments. When plants first colonised land, they needed a new way to access nutrients and water without being immersed in it. The next challenge was to increase in size and stature. Eventually, plants evolved to live in arid environments such as deserts. The evolution of these genes was crucial for enabling plants to survive, but how did they help plants first adapt and then thrive on land?

Read more: Ferns: the houseplants that reveal how tropical rainforests are responding to climate change

Stomata, the minute pores in the surface of leaves and stems, open to allow the uptake of carbon dioxide and close to minimise water loss. Our study found that the genes involved in the development of stomata were in the first land plants. This indicates that the first land plants had the genetic tools to build stomata, a key adaptation for life on land.

The speed in which stomata respond varies between species. For example, the stomata of a daisy close more quickly than those of a fern. Our study suggests that the stomata of the first land plants did close but this ability speeded up over time thanks to gene duplication as species reproduced. Gene duplication leads to two copies of a gene, allowing one of these to carry out its original function and the other to evolve a new function. With these new genes, the stomata of plants that grow from seeds (rather reproducing via spores) were able to close and open faster, enabling them to be more adaptable to environmental conditions.

Images of a plant's stomata, open and closed.

Old genes and new tricks

Vascular tissue is a plant’s plumbing system, enabling it to transport water internally and grow in size and stature. If you have ever seen the rings of a chopped tree, this is the remnants of the growth of vascular tissue.

We found that rather than evolving by new genes, vascular tissue emerged through a process of genetic tinkering. Here, old genes were repurposed to gain new functions. This shows that evolution does not always occur with new genes but that old genes can learn new tricks.

Before the move to land, plants were found in freshwater and marine habitats, such as the algal group Spirogyra. They floated and absorbed the water around them. The evolution of roots enabled plants to access water from deeper in the soil as well as providing anchorage. We found that a few key new genes emerged in the ancestor of plants that live on land and plants with seeds, corresponding to the development of root hairs and roots. This shows the importance of a complex rooting system, allowing ancient plants to access previously unavailable water.

A dam floor cracked by lack of water.
Hot weather and climate changes left this Bulgarian dam almost empty in 2021. Minko Peev/Shutterstock

The development of these features at every major step in the history of plants highlights the importance of water as a driver of plant evolution. Our analyses shed new light on the genetic basis of the greening of the planet, highlighting the different methods of gene evolution in the diversification of the plant kingdom.

Planting for the future

As well as helping us make sense of the past, this work is important for the future. By understanding how plants have evolved, we can begin to understand the limiting factors for their growth. If researchers can identify the function of these key genes, they can begin to improve water use and drought resilience in crop species. This has particular importance for food security.

Plants may also hold the key to solving some of the most pressing questions facing humanity, such as reducing our reliance on chemical fertilisers, improving the sustainability of our food and reducing our greenhouse gas emissions.

By identifying the mechanisms controlling plant growth, researchers can begin to develop more resilient, efficient crop species. These crops would require less space, water and nutrients and would be more sustainable and reliable. With nature in decline, it is vital to find ways to live more harmoniously in our green planet.

Photo’s of stomata

Microscopy of Nature

Vossen R. (xxxx)



Stomata are small openings that mainly occur on the underside of leaves. They are surrounded by specialised cells and they regulate the gas exchange between the plant and it’s environment, the plant is ‘breathing’ through them, as it were. Stomata are very recognizable by the two kidney- or bean-shaped guard cells that regulate the size of the opening. The guard cells are specialised epidermal cells which contain vacuoles that change their shape when water is absorbed due to a process called turgor, causing the stomata to open. The stomata are opened by stimuli like high humidity and bright light. Depending on the plant family, guard cells are often surrounded by so-called subsidiary cells.

As for the morphology of stomata, some different shapes can be distinguished:

● anomocytic: without subsidiary cells

● paracytic: with lateral subsidiary cells oriented parallel with the guard cells

● tetracytic: with both lateral and polar subsidiary cells

Stomata are fascinating objects to study, in each plant they look a bit different or are positioned differently. To observe stomata we need to peel off the epidermis from the underside of a leaf. If you tear a leaf apart, often a small piece of the epidermis will come off. Especially with thicker leaves this works quite well. Easy to begin with are the leaves of HostaPrunus laurocerasus (Cherry laurel) and Tradescantia.


Stomata on the move

Guarding and hijacking: stomata on the move

Wang M., Ji Q., Liu P., Liu Y. (2022)

Trends in Plant Science – https://doi.org/10.1016/j.tplants.2022.05.004


Stomata–pathogen interactions are a fascinating part of plant immunity. Stomata perceive pathogens and close; in turn, successful pathogens reopen stomata to enter the apoplast. Recent studies by Hu et al. and Roussin-Léveillée et al. demonstrate that, following entry, Pseudomonas syringae closes stomata and, thus, reduces transpiration in infected leaves, adding another layer of complexity to the stomata–pathogen interaction.

EgSPEECHLESS Responses to Salt Stress by Regulating Stomatal Development in Oil Palm

Figure 2. Salt stress activates stomatal production in oil palm. (a) Abaxial stomata of oil palm in mock and salt stress groups. Oil palm seedlings were treated with either water or NaCl solutions with 100 mM NaCl, 250 mM NaCl, 500 mM NaCl for 14 days respectively. Stomata are green colored. Scale bar = 30 µm. (b) Stomatal index of samples from (a). (c) Stomatal density of samples from (a). Values are mean ± SD; n = 20. One-way ANOVA with post-hoc Tukey HSD; p < 0.01. Samples were treated daily with 150 mL of either water (Mock) or NaCl for 14 days.

EgSPEECHLESS and Its Putative Binding Targets stomatal Development Are Involved in the Salt Response of Oil Palm

Song Z., Wang L., Lai C., Lee M., Yang Z., Yue G. (2022)

Zhuojun Song 1, Le Wang 1, Chongcheong Lai 1, May Lee 1, Zituo Yang 1, Genhua Yue 1-2,

1 Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore

2 Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore


Int. J. Mol. Sci. 23: 4659 – https://doi.org/ 10.3390/ijms23094659


Figure 7. A proposed model of the regulatory networks of EgSPCH in response to different levels of salt stress. In contrast to Arabidopsis, where salt represses the stomatal development to reduce water loss, salt activates the transcription of EgSPCH, which directly increases the stomatal production of oil palm. EgSPCH putatively binds to ~41% of DEGs, including key transcription factors that regulate diverse biological processes. In addition, some GO items, which are involved in the known biological processes in response to salt stress, were found in different concentrations of NaCl.


Oil palm is the most productive oil producing plant. Salt stress leads to growth damage and a decrease in yield of oil palm. However, the physiological responses of oil palm to salt stress and their underlying mechanisms are not clear. RNA-Seq was conducted on control and leaf samples from young palms challenged under three levels of salts (100, 250, and 500 mM NaCl) for 14 days. All three levels of salt stress activated EgSPCH expression and increased stomatal density of oil palm.

Around 41% of differential expressed genes (DEGs) were putative EgSPCH binding target and were involved in multiple bioprocesses related to salt response. Overexpression of EgSPCH in Arabidopsis increased the stomatal production and lowered the salt tolerance.

These data indicate that, in oil palm, salt activates EgSPCH to generate more stomata in response to salt stress, which differs from herbaceous plants. Our results might mirror the difference of salt-induced stomatal development between ligneous and herbaceous crops.

Stomata and CO2

Where Does Carbon Dioxide Enter the Plant?

Timmy (2022)


Plants take in carbon dioxide and release oxygen gas as part of photosynthesis. The process by which they do this is fascinating, and scientists are still working to understand all the intricacies involved.

In this blog post, we will explore where carbon dioxide enters the plant and how it is transported throughout the organism. We will also discuss what happens to the carbon dioxide once it is inside the plant. Stay tuned for an interesting look at one of nature’s most important processes!


Species with a high number and density of stomata and a large size are much more likely to adsorb pollutants such as carbon monoxide

Foliar stomata characteristics of tree species in a university green open space

Susilowati A., Novriyanti E., Rachmat H. H., Rangkuti A.B., Harahap M. M., Ginting I. M., Kaban N. S., Iswanto A. H. (2022)

ARIDA SUSILOWATI : Faculty of Forestry, Universitas Sumatera Utara. Jl. Tri Dharma Ujung No. 1, Kampus USU, Medan 20155, North Sumatra, Indonesia

EKA NOVRIYANTI : Research and Development Institute of Forest Fiber Technology, Ministry of Environment and Forestry. Jl. Raya Bangkinang-Kuok Km 9, Kampar, Riau, Indonesia

HENTI HENDALASTUTI RACHMAT : Forest Research, Development and Innovation Agency, Ministry of Environment and Forestry. Jl. Raya Gunung Batu, Bogor, West Java, Indonesia

AHMAD BAIQUNI RANGKUTI & MOEHAR MARAGHIY HARAHAP & IDA MALLIA GINTING & NARA SISILIA KABAN & APRI HERI ISWANTO : Faculty of Forestry, Universitas Sumatera Utara. Jl. Tri Dharma Ujung No. 1, Kampus USU, Medan 20155, North Sumatra, Indonesia


Biodiversitas 23: 1482-1489 –

https://smujo.id/biodiv/article/view/10000 articlesBySameAuthorPage=3


Stomata, a gas regulatory system of leaves, provide a great chance to investigate the interaction between plants and their environment. Stomata consist of surrounded by two guard cells. Stomata are found in all parts of the plant that are exposed to the air, especially the leaves. In identifying a plant species, it is necessary to have epidermal characteristics such as stomata to complete the taxonomic data. Several studies have been conducted on the type of stomata on the leaves of some dicotyledonous and monocot plants, but not many have reported similar studies on green space. Universitas Sumatera Utara (USU) campus also plays an important function as green space (GS) in Medan City due to its richness in tree collection number and species. In line with the effort in o maximizing the role of trees as the core element of green space, exploring the characteristics of stomata is important to conduct. Therefore, this study aimed to analyze the leaf stomata characteristics of several tree species in the green open space of the USU campus. A total of 83 tree species were taken for their leaves to investigate the stomata characters. Three healthy mature leaves on the lower part of newly grown branches were collected from each plant. The replica and the nail polish method were employed for stomata slice making. The stomata type, length, wide, density and distribution were observed. The result showed that 83 tree species in the USU campus have varied stomata types, with the percentage were highest characteristic found in paracytic (91.46%), followed by anomocytic (6.02%), anisocytic (1.20%), and diacytic (1.20%). The longest stomata were observed in Antidesma bunius (32.04 ????????). The widest stomata were noticed in Garcinia mangostana (37.62 ????????). Meanwhile, the shortest and narrowest stomata were found in Shorea laevis, which were 5.43 ???????? and 3.72 ????????, respectively. The species with the highest stomatal density was Schleichera oleosa (4294 mm-2). According to the study, the tree species at USU generally have high stomata density, length, and width, making them more suitable for green space. Species with a high number and density of stomata and a large size are much more likely to adsorb pollutants such as carbon monoxide.