🌱 TWiB December 13, 2021
Here comes another collection of stories shared by people following @BotanyOne on Twitter. I'm relying in you all to know what's happening in Botany this week and next, as there's a lot of meetings that I have to attend as term comes to a close. The upside of this is that there should be better blogging on Botany One next year.
Speaking of exciting projects, there's a call for papers Plants People Planet has out: Increasing the integration of urban horticulture into cities: Challenges and opportunities. There's an interesting selection of editors that shows they're looking at the people element as well as the plants. I've only just realised that I don't have a Google Scholar alert for Urban Botany, so I've corrected that. I think that's an easily overlooked topic when you think about where you find 'nature'.
Apart from meetings, my plan for this week is working from home avoiding Omicron, If all goes well, then there'll be the final email of the year with you this time next week. Until then, take care.
Alun (webmaster@botany.one)
In Botany One
Computer vision for phenotyping of photomorphogenesis — www.botany.one Can high-resolution imaging and computational processing be used to quantify variation in photomorphogenesis among Arabidopsis seedlings?
Asian squirrels go nuts for nectar — www.botany.one A rare plant found on Thailand's highest mountain courts an unusual pollinator.
How much does a phytolith look like an average phytolith? — www.botany.one The phylogenetic pattern in phytolith shape was successfully revealed by applying geometric morphometrics to 2D phytolith shape outlines, strengthening the potential of phytoliths to track the evolutionary history and paleoecology of grasses.
Botanists take a step back to move forward in understanding grass — www.botany.one A 19th century idea of how grass grows has proven more accurate than later ideas, according to new research.
Virtual conferences are more inclusive. Will that disappear when in-person conferences return? — www.botany.one COVID 19 may have prevented people from attending conferences in person, but the virtual alternatives have opened attendance to many more people.
News & Views
We are professional fire watchers, and we're astounded by the scale of fires in remote Australia right now — theconversation.com While southern Australia experienced a wet winter and a soggy spring, northern Australia has seen the opposite. Extreme fire weather in October and November led to bushfires across 120,000 square kilometres of southern savanna regions.
Why a career in statistical ecology? — oliviergimenez.github.io
"I have been interviewed recently by Lise Viollat who’s preparing a documentary for our national research group in statistical ecology. I have written my two cents answers to her challenging and very relevant questions. Thank you Lise for the interview!"
Creating a Better Leaf — www.newyorker.com Could tinkering with photosynthesis prevent a global food crisis?
#AdventBotany 2021 - Day 7 - Ives has no names — research.reading.ac.uk Joseph Christmas Ives is perhaps best known for his exploration of the Colorado River published as Report upon the Colorado River of the West explored in 1857 and 1858 (Ives & Humphreys, 1861). Born on 25th December 1828, which might go some way to explaining his middle name and the choice of this #AdventBotany topic, he was an engineer, soldier and explorer (Crompton, 1999).
The one thing you need to know about molecular evolution — kamounlab.medium.com The mathematical proof for natural selection is written in DNA in the most striking and beautiful fashion. Let’s find out how.
Women Scientists Described A Culture Of Sexual Misconduct At The Smithsonian’s Tropical Research Institute — www.buzzfeednews.com Many researchers dream of one day working at the Smithsonian’s facility in Panama. But 16 women scientists told BuzzFeed News that their experiences there were nightmares ruled by prominent men who exploited their powers.
Truth or fiction: gardens can save our wildlife — www.discoverwildlife.com Can small isolated patches of habitat really offset the damage we are doing to our environment? Professor of biodiversity and conservation Kevin Gaston provides the answer.
“The dynamics of vegetation grazed by a food-limited population of Soay sheep on St Kilda” — jecologyblog.com This research article provides an unprecedented record of vegetation change in response to and impacts on an unmanaged ungulate population on a temperate island over 35 years.
Scientific Papers
Stomatal closure during water deficit is controlled by belowground hydraulics
Adballa et al. used a novel root pressure chamber to measure, during soil drying, the relation between transpiration rate (E) and leaf xylem water pressure (ψleaf-x) in tomato shoots grafted onto two contrasting rootstocks, a long and a short one. In parallel, they also measured the E(ψleaf-x) relation without pressurization. A soil-plant hydraulic model was used to reproduce the measurements. They hypothesize that: 1) stomata close when the E(ψleaf-x) relation becomes nonlinear; and 2) nonlinearity occurs at higher soil water contents and lower transpiration rates in short-rooted plants.
Widespread homogenization of plant communities in the Anthropocene — www.nature.com
Daru et al. demonstrate widespread and temporal decreases in species and phylogenetic turnover across grain sizes and spatial extents. The extent of homogenization within major biomes is pronounced and is overwhelmingly explained by non-native species naturalizations. Asia and North America are major sources of non-native species; however, the species they export tend to be phylogenetically close to recipient floras. Australia, the Pacific and Europe, in contrast, contribute fewer species to the global pool of non-natives, but represent a disproportionate amount of phylogenetic diversity.
The main oxidative inactivation pathway of the plant hormone auxin
Hayashi et al. show that the predominant natural auxin, indole-3-acetic acid (IAA), is mainly inactivated via the GH3-ILR1-DAO pathway. IAA is first converted to IAA-amino acid conjugates by GH3 IAA-amidosynthetases. The IAA-amino acid conjugates IAA-aspartate (IAA-Asp) and IAA-glutamate (IAA-Glu) are storage forms of IAA and can be converted back to IAA by ILR1/ILL amidohydrolases. They further show that DAO1 dioxygenase irreversibly oxidizes IAA-Asp and IAA-Glu into 2-oxindole-3-acetic acid-aspartate (oxIAA-Asp) and oxIAA-Glu, which are subsequently hydrolyzed by ILR1 to release inactive oxIAA.
Satori et al. assess the level of open-access trait documentation of crop wild relatives of 29 important crops, their resilience, how threatened they are in situ, how well they are preserved ex situ and they provide priorities for their conservation and use in breeding programmes.
A constraint on historic growth in global photosynthesis due to increasing CO2
Kennan et al. quantify the historic effect of CO2 on global photosynthesis by identifying an emergent constraint that combines terrestrial biosphere models with global carbon budget estimates. Their analysis suggests that CO2 fertilization increased global annual photosynthesis by 11.85 ± 1.4%, or 13.98 ± 1.63 petagrams carbon (mean ± 95% confidence interval) between 1981 and 2020. Their results help resolve conflicting estimates of the historic sensitivity of global photosynthesis to CO2, and highlight the large impact anthropogenic emissions have had on ecosystems worldwide.
Tropical tall forests are more sensitive and vulnerable to drought than short forests — onlinelibrary.wiley.com
Liu et al. investigated the impact of drought on the dynamics of forest canopies with different heights using time-series records of remotely sensed Ku-band vegetation optical depth (Ku-VOD), a proxy of top-canopy foliar mass and water content, and separated the signal of Ku-VOD changes into drought-induced reductions and subsequent non-drought gains. Both drought-induced reductions and non-drought increases in Ku-VOD varied significantly with canopy height. Taller tropical forests experienced greater relative Ku-VOD reductions during drought and larger non-drought increases than shorter forests, but the net effect of drought was more negative in the taller forests.
Plant cell polarity as the nexus of tissue mechanics and morphogenesis — www.nature.com
Gorelova et al. review the role of cell polarity at the interface of tissue mechanics and morphogenesis. They also aim to integrate biochemistry-centred insights with concepts derived from physics and physical chemistry. Lastly, they propose a set of questions that will help address the fundamental nature of cell polarization and its mechanistic basis.
ReadCube: https://rdcu.be/cCXrw
Genetic determinants of endophytism in the Arabidopsis root mycobiome
Mesny et al. sequence the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with other 79 plant-associated fungi. Their analyses indicate that root mycobiota members evolved from ancestors with diverse lifestyles and retain large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. They identify a set of 84 gene families associated with endophytism, including genes encoding PCWDEs acting on xylan (family GH10) and cellulose (family AA9).
Careers
Post-Doctoral Research Associate- Ecology Evolutionary Biology We’re seeking a postdoctoral researcher to join our team in investigating a DOE-funded grant examining the consequences of global change on plant and mycorrhizal fungal phenological and biogeochemical processes. The primary work of the postdoctoral researcher will be laboratory-based extraction and amplification of soil microbiomes followed by bioinformatic analysis of microbial diversity and composition
Postdoc - Study how gene regulation drives GxE and adaptation to help breed resilient crops We are hiring a postdoctoral fellow with experience in quantitative genetics, genomics, plant breeding, bioinformatics, statistical genetics, and/or molecular genetics. Researchers in human, animal, and other model organisms and evolution are especially encouraged to apply.
Research Technician - Crop Genomics We are hiring a research technician with experience in molecular biology, genetics, plant biology, and/or fieldwork. Researchers in human, animal, and other model organisms are encouraged to apply.
Assistant Editor, SEB Publications at Society for Experimental Biology
As the Assistant Editor for this journal, the successful candidate will be responsible for: the processing of manuscripts to ensure timely progress through peer review, working with the journal’s publisher to ensure accurate publication of journal content, any administration required to support journal development, imaginatively promoting Conservation Physiology content, as well as content from across the SEB’s journals, providing support for co-located SEB journal The Journal of Experimental Botany and any additional work for the other SEB journals as required.
PhD: Why are there so few C2 grasses? This studentship will seek to identify why there are so few C2 grasses by investigating grass photosynthetic diversity within an ecological and phylogeographical context to understand how C4 photosynthesis emerged in the grasses. To do this, the student will train in plant phenotyping, fieldwork, phylogenetics, and use of public collections while undertaking fieldwork in Argentina and customized training at the University of Bangor and Kew Herbarium.
Identification and analysis of tRNA-like genes in Arabidopsis A Short-term (10 month; ca 1,700 EUR/month) fellowship is available at Wojciech Karlowski’s Laboratory at the Department of Computational Biology, Adam Mickiewicz University in Poznan. The position is founded with a National Science Centre Grant “Identification of tRNA-like sequences in Arabidopsis thaliana”.
PhD: WR DTP fully-funded project: Developing phage therapy to reduce plant pathogen virulence Plant pathogenic bacteria cause considerable losses to food production. This project will develop a novel biocontrol approach to reduce the virulence of plant pathogenic Ralstonia solanacearum bacterium (causative agent of bacterial wilt) using phages – viral parasites of the pathogen. It builds upon previous work (Wang et al. 2019 Nature Biotechnology), where the phage efficacy was found to be based not only on pathogen density reduction but also on evolutionary trade-offs that made phage-resistant mutants less pathogenic. The key aim of this project is to mechanistically understand how phage resistance turns pathogens less virulent.
Improving Nitrogen Use Efficiency in Cereal Crops for Sustainable Food Production The successful applicant should have, or be in the process of obtaining an Honours Degree, or equivalent, in Plant Science, Applied Statistics or a related science subject with a minimum achievement of an upper second class (good 2:1). Applicants with an appropriate Masters degree are particularly encouraged to apply. Those interested in gaining expertise in a wide variety of molecular biology techniques are also strongly encouraged to apply since the project takes diverse disciplines, including genetics, plant hormone signalling, symbiosis, metagenomics and analytical biology.
Editor - Journal of Ecology We are seeking an Editor to strengthen and complement the editorial team and to continue raising the Journal’s profile worldwide. To complement our Editor team, we are looking for an active researcher broad interests in plant ecology. Expertise in community or population ecology is particularly welcomed but nor required.
Temp Bio Sci Research Tech 1 This recruitment will be used to fill 4 full-time Temporary Biological Sciences Research Technician 1 positions for the Department of Forest Ecosystems and Society at Oregon State University (OSU). These positions will assist with field data collection as part of a study on early seral forest biodiversity in the Klamath Mountains ecoregion of southwest Oregon led by the Landscape Fire and Conservation Science Research Group at Oregon State University (OSU)
Professor and Associate professor in plant biology Umeå Plant Science Centre (UPSC) and the Department of Plant Physiology seek a Professor and an Associate Professor/Senior Lecturer for research, and to a minor part also teaching, in plant biology. The positions is permanent on full time, start 1/7 2022 (or later) and excellent research in the area is required.
PhD: The role of intraspecific trait variation in shaping the resilience of natural populations and communities The DPhil student will use state-of-the-art field data collection methods to quantify the functional trait syndromes of three species (Linum catharticum L., Parnassia palustris L. and Saxifraga tridactylites L.) in Fife and internationally across Europe in novel and established communities, raised under mono- and poly-cultures. Data on demographic rates will be collected to then infer which and how functional trait sub-syndromes best predict population dynamics using stage-structured models. These models will be build allowing for intra- and inter-specific competition, and be made environmentally-explicit. This hierarchical approach will allow the student to explore viability of individual species populations, based on their demographic resilience characteristics (e.g. resistance, recovery time) but also predict community assembly outcomes.
PhD: Identifying genetic regulators of reproductive transitions in evolutionarily-divergent trees to facilitate rapid breeding This project will identify candidate genes controlling the age at which these two species first flower (the juvenile-to-adult transition) and candidate genes that control the annual decision to flower in adult trees. This will be achieved by two approaches: 1) an unbiased investigation of all possible genes involved through next-generation sequencing approaches (RNA-seq and transcriptome bioinformatic analysis), and 2) identifying oak and Sitka orthologs of known flowering genes from the annual plant Arabidopsis thaliana and testing whether expression of these genes is associated with tree flowering using quantitative real-time PCR (qPCR).
Assistant Professor for Molecular Plant Breeding and Genomics Job Summary The department of Plant and Soil Sciences in the College of Agriculture, Food and Environment, is seeking an Assistant Professor of Molecular Plant Breeding and Genomics. This is a tenure eligible position with a 12-month appointment and approximately 70% research, 25% teaching, and 5% service responsibilities. The annual DOE will be aligned with this colleague’s strengths and college/department needs.
Biodiversity Co-ordinator & Principal Curator Botany
Amgueddfa Cymru is committed to safeguarding and restoring nature and our environment. We have the largest and most comprehensive collection of Welsh geology, zoology and botany specimens in the world, and this provides a unique record of the natural history of Wales, charting evolutionary and environmental change.
Research Associate - Plant-Microbe Interactions (Fixed Term) Applications are invited for a Post-doctoral Research Associate/Assistant position in the group of Dr Sebastian Schornack (www.schornacklab.net, twitter: @dromius) at the Sainsbury Laboratory (SLCU), Cambridge University, to study plant-microbe colonisation processes. The overall aim of this position is to use biochemical and/or bioinformatic approaches to elucidate how plant processes impact on the colonisation by detrimental or beneficial microbes and how microbes shape plant development.
Horticulturist Responsible for the design, care, maintenance and interpretation of the gardens located on Smithsonian grounds. Designs garden spaces and landscapes that utilize unique, underused, or new plant material to engage and educate visitors. Operates and maintains a variety of equipment to complete assignments. Provides educational programs, presents lectures and leads tours for wide ranging audiences.
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Computer vision for phenotyping of photomorphogenesis — www.botany.one Can high-resolution imaging and computational processing be used to quantify variation in photomorphogenesis among Arabidopsis seedlings?
Virtual conferences are more inclusive. Will that disappear when in-person conferences return? — www.botany.one COVID 19 may have prevented people from attending conferences in person, but the virtual alternatives have opened attendance to many more people.