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The Week in Botany 180

December 14, 2020

It's definitely dark now, with sunset before 4pm here. The drizzle is also keeping things flat and grey. On the plus side there's still Botany to see from sunnier places on YouTube. I particularly like Crime Pays But Botany Doesn't. It combines strolls in places of botanical interest with robust language that you wouldn't want young children to hear. It reminds me of my experience of fieldwork, which has tended to be going out into the landscape and swearing at large portions of it when I find unexpected thorns or bees.
As the year is drawing to a close, this is the second-to-last email of the year. There'll be one last round-up of the stories shared by people following @botanyone on Twitter, next week. I'll be taking December 28 off, and (probably) January 4. It's a good time to take a break any year, but I think everyone is due a bit of time off after a year like this one.
Until next week, take care.
Alun (

From Botany One

Syrian seed rescue a triumph of international cooperation
More than 80% of the Syrian seed collection was preserved at Svalbard before the facility was lost.

Under pressure: How do plants strike a balance between growth and defense?
A novel modelling approach explores how resource availability, competition pressure and insect herbivore pressure drive selection.

Tracking down the DNA for salt removal in a rice leaf sheath
The ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice.

Belowground responses of grassland plant species to wind intensity
Does wind intensity affect biomass allocation, root morphology and plant-soil interactions of grassland plants?

Crop diversity and semi-natural habitat a boon to yields as well as pollinators
Greater proportions of semi-natural habitat surrounding fields increased bumble bee and honey bee densities.

When is Botany criminal? When it’s forensic!
"Be advised: Murder most florid contains detailed accounts of crime scenes – which we learn are more correctly termed deposition scenes – and the process of examining such sites. It’s therefore maybe just as well that the book is illustration-free."

News and Views

Not to be sneezed at: how 3D printing is supersizing the tiny world of pollen
Project allows students, scientists and even fashion designers to create giant models of pollen grains from around the world
The Guardian

Hervé Cochard, l'homme qui écoute les arbres
Hervé Cochard, directeur de recherche au Laboratoire de physique et physiologie intégratives de l'arbre en environnement fluctuant du Centre INRAE Auvergne-Rhône-Alpes – Clermont-Ferrand, est une sommité des plus appréciées dans le domaine du fonctionnement hydraulique des plantes sous contraintes environnementales.
Hervé Cochard, research director at the Laboratory of Integrative Physics and Physiology of Trees in a Fluctuating Environment of the INRAE Auvergne-Rhône-Alpes - Clermont-Ferrand Center, is one of the most appreciated authorities in the field of the hydraulic functioning of plants under environmental constraints.

A ggplot2 Tutorial for Beautiful Plotting in R
Back in 2016, I had to prepare my PhD introductory talk and I started using {ggplot2} to visualize my data. I never liked the syntax and style of base plots in R, so I was quickly in love with ggplot. Especially useful was its faceting utility. But because I was short on time, I plotted these figures by trial and error and with the help of lots of googling. The resource I came always back to was a blog entry called Beautiful plotting in R: A ggplot2 cheatsheet by Zev Ross, updated last in January 2016. After giving the talk which contained some decent plots thanks to the blog post, I decided to go through this tutorial step-by-step. I learned so much from it and directly started modifying the codes and over the time I added additional code snippets, chart types and resources.
Since the blog entry by Zev Ross was not updated for some years and step by step this became a unique version of a tutorial, I decided to host the updated version on my GitHub. Now it finds its proper place on this homepage!
Cédric Scherer

Japan set to approve 1st genome-edited food for market
A tomato variety developed by a Tokyo-based start-up is likely to become the first genome-edited food on supermarket shelves in Japan.
The Japan News

Sexy beasts: animals with 'charisma' get lion's share of EU conservation funds
Analysis shows invertebrates are overlooked in favour of mammals and birds despite vital role in healthy ecosystems
The Guardian

They’re Among the World’s Oldest Living Things. The Climate Crisis Is Killing Them.
California’s epic wildfires in 2020 took deadly aim at the state’s most beloved trees.
The New York Times

Why a new potato variety could be a game-changer for farmers in East Africa
Imagine being a potato farmer in Ethiopia, Kenya or Nigeria. On a small piece of land, which you depend on for food and income, you have spent months planting, weeding and watering. Up to twice a week, you manually spray your field, sometimes with limited equipment, or hire someone to do it, spending much of your income on fungicides to avoid crop diseases.
And yet within a week of cold and humid weather, your entire field has been destroyed by late blight, a disease that wipes out a third of all potato yields worldwide.
The Conversation

How Non-Native Plants Are Contributing to a Global Insect Decline
The impact of introduced plants on native biodiversity has emerged as a hot-button issue in ecology. But recent research provides new evidence that the displacement of native plant communities is a key cause of a collapse in insect populations and is affecting birds as well.
Yale E360

Saving Corpse Flowers From Being Inbred to Extinction
To preserve corpse flowers and other rare plants, botanic gardens are borrowing studbooks, an approach used by zoos and horse breeders.
The New York Times

Watch roots from different plants compete for prime real estate underground
When it comes to plants, the roots hidden underground are as important—if not more—than what’s visible above ground. Now, researchers have figured out how roots from different plants divide up the space between them.

Scientific Papers

Cortical tension overrides geometrical cues to orient microtubules in confined protoplasts
Colin et al. used microfabricated wells to confine and deform wallless plant cells in a controlled way to analyze the response of microtubules to cell geometry and surface tension. They demonstrate that microtubules align with cell geometry by default, whereas when surface tension increases (e.g. when turgor pressure increases), they align with the direction of maximal tension. Not only does this explain many observations in plant tissues, but it also provides a simple mechanism at the core of plant morphogenesis, in which microtubules can spontaneously align with tension, in a typical self-organized system.

A unifying framework for studying and managing climate-driven rates of ecological change
During the Anthropocene and other eras of rapidly changing climates, rates of change of ecological systems can be described as fast, slow or abrupt. Fast ecological responses closely track climate change, slow responses substantively lag climate forcing, causing disequilibria and reduced fitness, and abrupt responses are characterized by nonlinear, threshold-type responses at rates that are large relative to background variability and forcing. All three kinds of climate-driven ecological dynamics are well documented in contemporary studies, palaeoecology and invasion biology. This fast–slow–abrupt conceptual framework helps unify a bifurcated climate-change literature, which tends to separately consider the ecological risks posed by slow or abrupt ecological dynamics.
Nature Ecology & Evolution

Gene expression data support the hypothesis that Isoetes rootlets are true roots and not modified leaves
Rhizomorphic lycopsids are the land plant group that includes the first giant trees to grow on Earth and extant species in the genus Isoetes. Two mutually exclusive hypotheses account for the evolution of terminal rooting axes called rootlets among the rhizomorphic lycopsids. One hypothesis states that rootlets are true roots, like roots in other lycopsids. The other states that rootlets are modified leaves. Hetherington et al. test predictions of each hypothesis by investigating gene expression in the leaves and rootlets of Isoetes echinospora.
Scientific Reports

Global human-made mass exceeds all living biomass
Humanity has become a dominant force in shaping the face of Earth. An emerging question is how the overall material output of human activities compares to the overall natural biomass. Elhacham et al. quantify the human-made mass, referred to as ‘anthropogenic mass’, and compare it to the overall living biomass on Earth, which currently equals approximately 1.1 teratonnes. They find that Earth is exactly at the crossover point; in the year 2020 (± 6), the anthropogenic mass, which has recently doubled roughly every 20 years, will surpass all global living biomass.

Anthropogenic modification of forests means only 40% of remaining forests have high ecosystem integrity
Many global environmental agendas, including halting biodiversity loss, reversing land degradation, and limiting climate change, depend upon retaining forests with high ecological integrity, yet the scale and degree of forest modification remain poorly quantified and mapped. By integrating data on observed and inferred human pressures and an index of lost connectivity, Grantham et al. generate a globally consistent, continuous index of forest condition as determined by the degree of anthropogenic modification. Globally, only 17.4 million km2 of forest (40.5%) has high landscape-level integrity (mostly found in Canada, Russia, the Amazon, Central Africa, and New Guinea) and only 27% of this area is found in nationally designated protected areas. Of the forest inside protected areas, only 56% has high landscape-level integrity.
Nature Communications

SciSpends: an exploratory survey investigating nonreimbursed expenses in biological sciences
Socio-economic barriers to participation in science are harmful to the enterprise. One barrier is the phenomenon of scientists paying for expenses related to the conduct of research that are not reimbursed. Favaro and Hind-Ozan conducted an online survey that asked self-selecting respondents to report the amount of money they spent on nonreimbursed expenses, including both costs incurred in the past 12 months and one-time startup costs associated with their current position. They received 857 responses that met criteria for inclusion and reported descriptive statistics summarizing nonreimbursed expenses across career stages. They found the median total of nonreimbursed expenses for the past 12 months was $1680 and the median one-time expenses were $2700, and that as a proportion of income these expenses were highest for those earliest in their careers. They found 13% of respondents spent more on unreimbursed expenses than they earned in a year.

Systematic characterization of gene function in a photosynthetic organism
Using a barcoded mutant library of the model eukaryotic alga Chlamydomonas reinhardtii, Vilarrasa-Blasi et al. determined the phenotypes of more than 58,000 mutants under more than 121 different environmental growth conditions and chemical treatments. 78% of genes are represented by at least one mutant that showed a phenotype, providing clues to the functions of thousands of genes. Mutant phenotypic profiles allow them to place known and previously uncharacterized genes into functional pathways such as DNA repair, photosynthesis, the CO2-concentrating mechanism, and ciliogenesis. They illustrate the value of this resource by validating novel phenotypes and gene functions, including the discovery of three novel components of a defense pathway that counteracts actin cytoskeleton inhibitors released by other organisms. The data also inform phenotype discovery in land plants: mutants in Arabidopsis thaliana genes exhibit similar phenotypes to those they observed in their Chlamydomonas homologs.

The exploitative segregation of plant roots
Much of the world's plant biomass exists out of sight underground in the form of roots. Cabal et al. developed a theoretical model and tested it empirically to explain the rules that govern root growth. Plants adjust how and where their roots grow according to how close neighboring—and competing—plants might be. The model extracts some of the rules about how root balls differ when grown close to neighboring plants compared with being grown in the absence of competition.

Root traits as drivers of plant and ecosystem functioning: current understanding, pitfalls and future research needs
Drawing on literature in plant physiology, ecophysiology, ecology, agronomy and soil science, Freschet et al. review 24 aspects of plant and ecosystem functioning and their relationships with a number of traits of root systems, including aspects of architecture, physiology, morphology, anatomy, chemistry, biomechanics and biotic interactions. Based on this assessment, they critically evaluate the current strengths and gaps in our knowledge, and identify future research challenges in the field of root ecology.
New Phytologist

Convergent evolution of distinct immune sensor systems for fungal polygalacturonases in Brassicaceae
Plant pattern recognition receptors (PRRs) facilitate recognition of microbial surface patterns and mediate activation of plant immunity. Arabidopsis thaliana RLP42, a leucine-rich repeat (LRR) receptor protein (LRR-RP), senses fungal endopolygalacturonases (PGs) through a ternary complex comprising RLP42, the adapter kinase SOBIR1, and SERK proteins. Several fungal PGs harbor a conserved 9-amino acid fragment pg9(At), which is sufficient to activate RLP42-dependent plant immunity. Domain swap experiments using RLP42 and paralogous RLP40 sequences revealed a dominant role of the island domain (ID) for ligand binding and PRR complex assembly. Involvement of the ID in plant receptor function is reminiscent of plant phytosulfokine (PSK) perception through the receptor, PSKR, a LRR receptor kinase. Sensitivity to pg9(At), which is restricted to A. thaliana, exhibits notable accession specificity as active RLP42 alleles were found in only 16 of 52 accessions tested. Arabidopsis arenosa and Brassica rapa, two Brassicaceae species closely related to A. thaliana, perceive plant immunogenic PG fragments pg20(Aa) or pg36(Bra), which are distinct from pg9(At).


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