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The Week in Botany 159

July 20, 2020

This week, the Branch Out podcast is back. If you wonder why there isn't a Botany One podcast, then Branch Out, and the excellent In Defense of Plants, are two reasons. They're both clearly the products of a lot of work.
Looking ahead, I see next week we'll have post up on daily rhythms in flower scent, and also something on phylogenetic fuses, which is a return to the problem of angiosperm evolution. I also see that Botany 2020 and Plant Biology 2020 start next Monday - so if you're participating in either of those, I hope you find it useful.
I'll be back with another newsletter next week, with the usual caveats of not getting ill. A plumber fixed my shower this week, so my isolation hasn't been total. But on the plus side I'm very clean. Take care,
Alun (

From Botany One

Wounds divert auxin flow like “rocks in a stream”
The hormone auxin confers stem cell identity on cells surrounding the wound to enable healing.

Hurricanes help mangroves move northward in a changing climate
Storm surges overcome the species’ naturally slow migration.

Topography Leaves Its Mark in Goldenrod Genetics
The variation of montane environments means that the genetics of alpine goldenrods populations differ more than their lowland cousins.

Let’s study weeds and question fundamental theories!
A new review in the Trends in Plant Sciences journal argue the importance of researching weeds.

Modelling rice roots reveals how to pick up phosphorus
Combining experimentally measured single root phene datasets with a 3D continuum multiscale soilroot model enhances the mechanistic insights in soil-root processes that are important for water and P uptake.

Plant community assembly on restrictive gypsum soils
Do environmental factors influence plant community assembly on restrictive gypsum soils?

Modelling practices that support crop improvement
Credibility and transdisciplinarity play crucial roles in modelling to advance crop adaptation and plant improvement.

Restoring “No Man’s Land” with native mycorrhizal fungi and plant seed mixtures
A new study in the Journal of Applied Ecology reveals the importance of introducing symbiotic fungi with native plant species for restoring post-mining ecosystems.

Seaweeds, lichens and phytoplankton, what’s not to like..?
Nigel Chaffey reviews Rocky Shores, by John Archer–Thompson and Julian Cremona 2019

H202 scavenging releases axillary bud outgrowth in rosebush
High levels of H2O2 in a quiescent state prevents bud outgrowth.

News and Views

Adaptive alleles stick together
The ecological drivers of local adaptation in plants are often easy to understand: evolve salt-tolerance to grown next to the sea, change flower colour to attract different pollinators, and so on. However, how that is achieved at the genetic level remains, most of the times, a mystery.
Nature Research Ecology & Evolution Community

Scientists Revive 32,000-Year-Old Plant Right Out of the Pleistocene
The oldest plant ever to be “resurrected” has been grown from 32,000-year-old seeds, beating the previous record holder by some 30,000 years.
Earthly Mission

Summer bushfires: how are the plant and animal survivors 6 months on? We mapped their recovery
Australia roared into 2020 as a land on fire. The human and property loss was staggering, but the damage to nature was equally hard to fathom. By the end of the fire season 18.6 million hectares of land was destroyed.
So what’s become of animal and plant survivors in the months since?
The Conversation

The State of Food Security and Nutrition in the World 2020
"690 million people suffer from chronic hunger. As more people go hungry & malnutrition persists around the Earth globe, achieving #ZeroHunger by 2030 is in doubt."
Food and Agriculture Organization of the United Nations

Bushfire impacts, recovery & outlook
Australia is a no doubt a sunburnt country and our unique landscape shares a long and important relationship with fire. But even our most fire-adapted plants were devastated by the intense summer bushfires. While new growth is emerging and cutting-edge science is saving species - there's still a long road to recovery for our flora that went up in flames. 
Branch Out

Why allotments offer urban oases for bees and butterflies
Half of the world’s people already live in urban areas, and that number will only grow in the future. Is this bad news for biodiversity? Not necessarily. Towns and cities can be home to a surprising amount of wildlife – if they’re managed appropriately.
The Conversation

Climate change: Siberian heatwave 'clear evidence' of warming
A record-breaking heatwave in Siberia would have been almost impossible without human-caused climate change, a study has found.
BBC News

A Plant That Grows a Perch
For flowering plants, entering into an evolutionary relationship with birds as pollinators can be a costly endeavor. It can take a lot of energy to coax birds to their blossoms. On the whole, bird pollinated flowers are generally larger, sturdier, and produce more nectar. They tend to invest heavily in pigmentation. The plants themselves are often more robust as well. Unlike hummingbirds, which usually hover as they feed, other nectar-feeding birds require a perch. Often this is simply a stout branch or a stem, however, a plant endemic to South Africa takes bird perches to a whole new level - it grows one. 
In Defense of Plants

Figures: the Art of Science
How to prepare figures to make an impression on editors, reviewers, and readers
Journal of Biogeography

A window into the seeds of early angiosperms
The discovery of assemblages of small, well-preserved plant fossils from the Early Cretaceous age has provided researchers with a wealth of new insights into the early history of angiosperms. The fossils were found in loosely compacted sedimentary rocks from Portugal and eastern North America and include flowers, fruits and seeds, often so well preserved that it is possible to compare their anatomy with those of living plants on a cellular level.
New Phyt blog


Biodiversity Genomics Postdoctoral Fellowship
The Smithsonian Institution Data Science Lab (, housed within the Office of the Chief Information Officer, is looking to fill a postdoctoral fellowship in the area of biodiversity genomics.
Due to COVID-19 restrictions, the Data Science Lab is working remotely for the foreseeable future. Applicants are not required to relocate to the Washington, DC area.

Postdoctoral and PhD student positions available to study soil-plant-microbe interactions
We are looking for highly motivated postdoctoral researcher and PhD student to work on an exciting interdisciplinary project investigating the effects of drought on rhizosphere microbial communities, the molecular composition of root exudates, and explore interactions between root exudates and microbiome recruitment in the rhizosphere.
Texas, USA.

Scientific Papers

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, Větrovský et al. collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at
Scientific Data

The key role of terminators on the expression and post‐transcriptional gene silencing of transgenes
Fenselau de Felippes et al. present the results of a mutagenesis screening conceived to identify features involved in the protection of endogenes against becoming template for the production of sRNAs. Interestingly, all of the recovered mutants had alterations in genes with proposed function in transcription termination, suggesting a central role of terminators in this process. Using a GFP reporter system, they show that among different genetic elements tested, the terminator sequence had the greatest effect on transgene‐derived sRNA accumulation and that a well‐defined poly(A) site might be especially important. Finally, they describe an unexpected mechanism, where transgenes containing certain intron/terminator combinations lead to an increase in the production of sRNAs, which seems to interfere with splicing.
The Plant Journal

Friendly regulates membrane depolarization induced mitophagy in Arabidopsis
Using time-lapse imaging, electron tomography and biochemical assays, Ma et al. show that uncoupler treatments cause loss of mitochondrial membrane potential and induce autophagy in Arabidopsis. The damaged mitochondria are selectively engulfed by autophagosomes that are ATG5 dependent and labelled by ATG8 proteins. Friendly, a member of the Clustered Mitochondria protein family, is recruited to the damaged mitochondria to mediate mitophagy. In addition to stress, mitophagy is also induced during de-etiolation, a major cellular transformation during photomorphogenesis that involves chloroplast biogenesis. De-etiolation triggered mitophagy regulates cotyledon greening, pointing towards an inter-organellar cross-talk mechanism.

Expanding tropical forest monitoring into Dry Forests: The DRYFLOR protocol for permanent plots
Despite increasing appreciation of their threatened status, biodiversity, and importance to the global carbon cycle, monitoring in tropical dry forests is still in its infancy. Moonlight et al. provide a protocol for permanent monitoring plots in tropical dry forests. Expanding monitoring into dry biomes is critical for overcoming the linked challenges of climate change, land use change, and the biodiversity crisis.
Plants People Planet

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules
The soil microbiome represents one of the most complex microbial communities on the planet, encompassing thousands of taxa and metabolic pathways, rendering holistic analyses computationally intensive and difficult. Naylor et al. developed an alternative approach in which the complex soil microbiome was broken into components (“functional modules”), based on metabolic capacities, for individual characterization. They hypothesized that reproducible, low-complexity communities that represent functional modules could be obtained through targeted enrichments and that, in combination, they would encompass a large extent of the soil microbiome diversity. Enrichments were performed on a starting soil inoculum with defined media based on specific carbon substrates, antibiotics, alternative electron acceptors under anaerobic conditions, or alternative growing conditions reflective of common field stresses. The resultant communities were evaluated through 16S rRNA amplicon sequencing.

Temperature-dependent growth contributes to long-term cold sensing
The slow, winter-long upregulation of VERNALIZATION INSENSITIVE 3 (VIN3) a PHD protein that functions with Polycomb repressive complex 2 to epigenetically silence FLOWERING LOCUS C (FLC) during vernalization, is central to plants interpreting winter progression. Here, by a forward genetic screen, Zhao et al. identify two dominant mutations of the transcription factor NTL8 that constitutively activate VIN3 expression and alter the slow VIN3 cold induction profile. In the wild type, the NTL8 protein accumulates slowly in the cold, and directly upregulates VIN3 transcription. Through combining computational simulation and experimental validation, they show that a major contributor to this slow accumulation is reduced NTL8 dilution due to slow growth at low temperatures.

Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history
As a model for genetic studies, Arabidopsis thaliana (Arabidopsis) offers great potential to unravel plant genome-related mechanisms that shape the root microbiome. However, the fugitive life history of this species might have evolved at the expense of investing in capacity to steer an extensive rhizosphere effect. To determine whether the rhizosphere effect of Arabidopsis is different from other plant species that have a less fugitive life history, Schneijderberg et al. compared the root microbiome of Arabidopsis to eight other, later succession plant species from the same habitat.
The ISME Journal

Enhancing road verges to aid pollinator conservation: A review
Phillips et al. used a formal, global literature review to assess evidence for the benefits of road verges for pollinators (as habitats and corridors), the potential negative impacts of roads on pollinators (vehicle-pollinator collisions, pollution, barriers to movement) and how to enhance road verges for pollinators through management.
Biological Conservation

Two glutamate- and pH-regulated Ca2+ channels are required for systemic wound signaling in Arabidopsis
Upon wounding, plants generate systemic Ca2+ waves and electrical signals that propagate from the wound site to distal tissues. The glutamate receptor–like proteins GLR3.3 and GLR3.6 are required for leaf-to-leaf systemic wound signals in Arabidopsis thaliana. Shao et al. found that wounding or the application of glutamate induced root-to-shoot Ca2+ and electrical signaling in Arabidopsis, which required GLR3.3, GLR3.6, and inhibition of the proton pump AHA1. In cultured mammalian cells, GLR3.3 and GLR3.6 functioned as pH-sensitive, glutamate-gated Ca2+ channels. These findings suggest that wounding induces both the leakage of glutamate from the phloem into the apoplastic space and an increase in the apoplastic pH, leading to the activation of GLRs and the generation of systemic Ca2+ waves and electrical signals.
Science Signaling

Towards genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles
Kranse et al. develop some of the foundational biology required to deliver a functional genetic tool kit in plant-parasitic nematodes. They characterise the gonads of male Heterodera schachtii and Meloidogyne hapla in the context of spermatogenesis. They test and optimise various methods for the delivery, expression, and/or detection of exogenous nucleic acids in plant-parasitic nematodes. They demonstrate that delivery of macromolecules to cyst and root knot nematode male germlines is difficult, but possible.

High plant diversity and slow assembly of old-growth grasslands
The idea that grasslands can be ancient, particularly in climates that also support forests, is not widely recognized. Consequently, scientists and conservation planners often misinterpret old-growth grasslands to be low-diversity, successional vegetation, from which little is lost through conversion to tillage agriculture or tree plantations. Nerlekar and Veldman used a global analysis of herbaceous plant communities to show that after old-growth grasslands are destroyed, the recovery of plant diversity requires hundreds to thousands of years.

Implementing team-based learning in the life sciences: A case study in an online introductory level evolution and biodiversity course
Team-Based Learning (TBL) is a pedagogical tool that has great potential to develop student engagement, accountability, and equity in the online classroom. TBL is rooted in evidence-based educational theories and practices that underlie many active learning approaches such as self-testing, team discussion, and application of knowledge. The use of these approaches is associated with better student performance, retention, and sense of belonging in the classroom, aspects that are often reported to be especially lacking in online courses. Hernandez et al. describe how they implemented TBL in a face-to-face and an online introductory level evolution and biodiversity course.


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