November 1, 2021

🌱TWiB November 1, 2021

I've finally managed to change up the monitoring system this week, and I think a few more papers are surfacing that would have been missed otherwise, so I'm happy.

I'm writing this on the 31st. Today is the day that wicked and deceitful forces are said to fly through the air. I'm sure that «insert name of leader» will have a very warm welcome at Glasgow Airport for COP26.

I'll be back next week with another collection of news and research. I'm hoping that the joke above will have aged very badly and some of the stories will be about the progress made on solving some of the world's ecological problems. Whatever there is, it'll be with you at the same time next week.

Take care,

Alun (webmaster@botany.one)

In Botany One

Reconstructing trees from terrestrial laser scans — www.botany.one A new algorithm supports the detailed reconstruction of a variety of trees from a small amount of input data.

Welcome to the wonderful world of … weeds(!) — www.botany.one Plants despised today still have value, and this book explores their contribution to the British ecosystem.

Most Australian shrubs have “sleepy seeds” and seed dormancy types might be driven by rainfall seasonality — www.botany.one Have you ever found it tricky to get some seeds to germinate? You might have wondered if it was the water, or the temperature, or the soil, or perhaps the seeds themselves that are the problem?

Impacts of herbivory on perennial grass species of the Northern Great Basin — www.botany.one How does herbivory impact the survival and growth of three perennial grass species commonly used to revegetate dryland ecosystems?

Trees alone will not save us — www.botany.one

There's more recognition that ecological restoration can be an essential tool in fighting climate change, and there are many projects aimed at restoring degraded forests to capture carbon. Still, the focus on forests ignores much of the land in the tropics that would not naturally be forested. A team of scientists is arguing that people need to become aware of other habitats and their value.

This is about the paper Biome Awareness Disparity is BAD for tropical ecosystem conservation and restoration, but see also ​​10 golden rules of ecological restoration and Urgent need for updating the slogan of global climate actions from ‘tree planting’ to ‘restore native vegetation’.

News & Views

Great scientists are made, not born — holdenfg.org We’ve all heard the story; a famous scientist is asked how they got interested in their subject area and they say something like “I’ve always loved sea otters and wanted to be a marine biologist ever since I was a little boy”. This common storyline is part of why scientific skills are viewed as inherent, people either ARE scientists, or they ARE NOT.

Plants evolved complexity in two bursts – with a 250-million-year hiatus — globalplantcouncil.org A Stanford-led study reveals that rather than evolving gradually over hundreds of millions of years, land plants underwent major diversification in two dramatic bursts, 250 million years apart. The first occurred early in plant history, giving rise to the development of seeds, and the second took place during the diversification of flowering plants. 

GOHREP and PLESI: guides to navigate through your research projects Students can struggle to articulate the goals and rationale behind their research projects and navigate through the day to day challenges of laboratory research. GOHREP and PLESI can be helpful guides.

Rare ‘Penis Plant’ Blooms for the First Time in 25 Years — www.vice.com Experts believe that this is only the third time the aptly named Amorphophallus decus-silvae has bloomed in Europe.

How did Japanese plants get into British gardens? — www.kew.org From botanical smugglers to coded telegrams, Library Graduate Trainee Cecily Nowell-Smith reveals how plants from 6000 miles away made it to our gardens.

This lab asked depressed Ph.D. students what’s hardest—and what parts of grad school help them cope — www.science.org When a 2018 study revealed that Ph.D. students suffer from depression at rates far higher than the general population, it sparked a landslide of concern about graduate student mental health, with some calling it a mental health crisis.

Bell Bowl Prairie Reprieve, Rockford Airport Temporarily Pauses Construction In a dramatic 11th-hour development, an agreement has been reached to temporarily halt construction activity that would destroy the 8,000-year-old Bell Bowl Prairie remnant, located on Rockford Airport property and targeted for demolition as part of a $50 million expansion of the airfield’s cargo operations.

Grave of Antoine-Augustin Parmentier – Paris, France — www.atlasobscura.com The tomb of history's greatest potato promoter is surrounded by tubers.

Why Strawberries Turn a Ghostly Shade of White — www.nytimes.com Researchers unlocked some of the genetic secrets that helped the colorful fruit evolve into so many varieties around the world.

Speak Up to Save 1,000-Year-Old Redwoods A majestic grove of 1,000-year-old redwoods in Northern California is facing an imminent threat — and it needs your help. 

Scientific Papers

A photoregulatory mechanism of the circadian clock in Arabidopsis — www.nature.com

Wang et al. show that cryptochromes (CRYs) mediate blue-light regulation of N6-methyladenosine (m6A) modification of more than 10% of messenger RNAs in the Arabidopsis transcriptome, especially those regulated by the circadian clock. CRY2 interacts with three subunits of the METTL3/14-type N6-methyladenosine RNA methyltransferase (m6A writer): MTA, MTB and FIP37. Photo-excited CRY2 undergoes liquid–liquid phase separation (LLPS) to co-condense m6A writer proteins in vivo, without obviously altering the affinity between CRY2 and the writer proteins. mta and cry1cry2 mutants share common defects of a lengthened circadian period, reduced m6A RNA methylation and accelerated degradation of mRNA encoding the core component of the molecular oscillator circadian clock associated 1 (CCA1). These results argue for a photoregulatory mechanism by which light-induced phase separation of CRYs modulates m6A writer activity, mRNA methylation and abundance, and the circadian rhythms in plants.

ReadCube: rdcu.be/cz3sT

BotanizeR: A flexible R package with Shiny app to practice plant identification for online teaching and beyond — nph.onlinelibrary.wiley.com

Weigelt et al. present BotanizeR, a flexible online tool to make the wealth of digitally available but scattered information on plant characteristics accessible and allow users to practice plant identification. BotanizeR can assist in teaching plant knowledge in a playful way during times of online teaching and beyond and may help to increase the fascination of biology students and laypeople alike for plant diversity.

Eating the messenger (RNA): autophagy shapes the cellular RNA landscape Cellular degradation pathways are instrumental for maintenance of homeostasis, especially under stress. Autophagy, the collection of pathways that shuttle cytoplasmic material to the vacuole for degradation and recycling, is known for shaping the cell’s proteome, lipidome, metabolome, and organelle content in response to environmental and developmental cues. However, until recently, little was known regarding its role in shaping cellular RNA quantity and diversity (RNAome).

Mapping global forest age from forest inventories, biomass and climate data — essd.copernicus.org Forest age can determine the capacity of a forest to uptake carbon from the atmosphere. However, a lack of global diagnostics that reflect the forest stage and associated disturbance regimes hampers the quantification of age-related differences in forest carbon dynamics. This study provides a new global distribution of forest age circa 2010, estimated using a machine learning approach trained with more than 40 000 plots using forest inventory, biomass and climate data.

Single-Cell Transcriptomics Sheds Light on the Identity and Metabolism of Developing Leaf Cells

As the main photosynthetic instruments of vascular plants, leaves are crucial and complex plant organs. A strict organization of leaf mesophyll and epidermal cell layers orchestrates photosynthesis and gas exchange. In addition, water and nutrients for leaf growth are transported through the vascular tissue. To establish the single-cell transcriptomic landscape of these different leaf tissues, Berrío et al. performed high-throughput transcriptome sequencing of individual cells isolated from young leaves of Arabidopsis (Arabidopsis thaliana) seedlings grown in two different environmental conditions. The detection of ∼19,000 different transcripts in over 1,800 high-quality leaf cells revealed 14 cell populations composing the young, differentiating leaf. Besides the cell populations comprising the core leaf tissues, they identified subpopulations with distinct identity or metabolic activity

A designer rice NLR immune receptor confers resistance to the rice blast fungus carrying noncorresponding avirulence effectors — www.pnas.org

Liu et al. generated a mutant of the rice nucleotide-binding and leucine-rich repeat (NLR) immunity receptor RGA5 by engineering its heavy metal–associated domain that recognizes the noncorresponding Magnaporthe oryzae Avrs- and ToxB-like effector AvrPib and confers resistance in transgenic rice to the blast fungus isolates with AvrPib, which is known to trigger blast resistance in rice cultivars carrying the R gene Pib, albeit by unknown mechanisms. Thus, this work demonstrates that integrated domain-containing plant NLR receptors can be engineered to confer resistance to pathogens carrying avirulence effectors that trigger plant immunity by unknown mechanisms, thereby providing a practical approach for developing multilines and cultivars with broad race spectrum resistance.

Ten simple rules for training yourself in an emerging field — journals.plos.org

Woelmer et al. describe 10 simple rules to successfully train yourself in an emerging field, based on their experience as students in the emerging field of ecological forecasting. Their advice begins with setting and revisiting specific goals to achieve your academic and career objectives and includes several useful rules for engaging with and contributing to an emerging field.

From crops to shops: how agriculture can use circadian clocks

Hotta shows evidence of why circadian biology can be helpful in agriculture. However, as evidence is scattered among many areas, they frequently lack field testing, integrate poorly with other rhythms, or suffer inconsistent results. These problems can be mitigated if researchers of different areas start collaborating under a new study area—circadian agriculture.

Misregulation of MYB16 expression causes stomatal cluster formation by disrupting polarity during asymmetric cell divisions

Yang et al. show that the downregulation of MYB16 in meristemoids is directly mediated by the stomatal master transcription factor SPEECHLESS (SPCH) in Arabidopsis thaliana. The suppression of MYB16 before an asymmetric division is crucial for stomatal patterning, as its overexpression or ectopic expression in meristemoids increased stomatal density and resulted in the formation of stomatal clusters, as well as affecting the outer cell wall structure. Expressing a cutinase gene in plants ectopically expressing MYB16 reduced stomatal clustering, suggesting that cutin affects stomatal signaling or the polarity setup in asymmetrically dividing cells.

TLSLeAF: automatic leaf angle estimates from single‐scan terrestrial laser scanning

Leaf angle distribution (LAD) in forest canopies affects estimates of leaf area, light interception, and global-scale photosynthesis, but is often simplified to a single theoretical value. Stovall et al. present TLSLeAF (Terrestrial Laser Scanning Leaf Angle Function), an automated open-source method of deriving LADs from terrestrial laser scanning.

Fairy lanterns in focus — nph.onlinelibrary.wiley.com

So-called fairy lanterns (Thismia) are among the most extraordinary flowering plants, yet little is known about their ecology. There has been a spate of recent species discoveries revealing a bewildering diversity of flower forms. But why these peculiar flowers are so diverse remains a mystery. Thorogood and Yunoh review recent discoveries, placing focus on Southeast Asia as a center of diversity of fairy lanterns.

Careers

PhD position "Multi-Omics Network Reconstruction during plant development - EPSO

The candidate is expected to hold a MSc degree in Statistics, Data Science or a related discipline.

Post-Doctoral Associate This is a one year renewable appointment up to a maximum of 5 years within the Plant Pathology and Plant Microbe Biology Section of the School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456.  The position is currently available with a start date as soon as possible.

Geneticist (Plants)/ Horticulturist/ Molecular Biologist The incumbent serves as the curator of hemp involving preserving, regenerating and producing high quality germplasm and conducting research on the maintenance, genetic diversity, taxonomy, systematics, characterization, enhancement, and evaluation of germplasm.

Research Associate (Fixed Term) We wish to recruit a post-doctoral researcher to investigate The role of circadian oscillators in temperature responses of wheat funded by BBSRC grant BB/W001209/1. This research is a collaboration between the Professors Alex Webb and Ian Henderson in the Department of Plant Sciences and Dr James Locke at the Sainsbury Laboratory Cambridge University.

Assistant Professor We are searching for a tenure-track assistant professor position in Ecology and Evolution of Infectious Plant Diseases in the Department of Botany & Plant Pathology. The successful candidate will be expected to establish a robust and extramurally funded research program that will address ecological and evolutionary processes that drive the dynamics of infectious plant diseases. The focus of the program can be on existing and/or emerging plant infectious diseases that are important to the sustainability of agricultural systems in Oregon and the Pacific Northwest. All research topics within the area of ecology and evolution of infectious plant diseases will be considered.

Assistant Professor The Department of Ecology and Evolutionary Biology at the University of Connecticut (UConn) is pleased to invite applications for a tenure-track faculty position in Quantitative Ecology at the Assistant Professor level. The Department seeks a research scientist who applies and develops innovative quantitative approaches to advance the empirical or theoretical understanding of fundamental ecological questions. We are interested in candidates who understand and predict ecological dynamics and patterns by applying and developing cutting-edge statistics or metrics, writing statistical software, deriving and testing mathematical theory, applying analytical, numerical, or simulation approaches, or addressing the challenges of working with “Big Data”. We are particularly interested in researchers who can address questions that operate across multiple spatial or temporal hierarchical scales and who apply both mechanistic and statistical approaches to their science.

Project Manager We are looking for a colleague (entry to mid-level) who is passionate about ecological restoration, has strong communication and networking skills, and experienced in ecology, wildlife and communication in the Indian context. The candidate will work as a Project Manager to coordinate activities, develop curated materials and online resources for the ERA-India website, manage related social media accounts, and work with Alliance partners to foster responsible ecological restoration.

PhD Position (m/f/d) on “Bacterial genetic determinants preventing fungal dysbiosis in Arabidopsis roots” The Max Planck Institute for Plant Breeding Research (MPIPZ, (http://www.mpipz.mpg.de) in Cologne, Germany, invites applications for a PhD position in the field of molecular microbiology, plant-microbiome interactions, and functional genomics . The position is available in the Multitrophic Plant-Microbe Interactions group headed by Dr. Stéphane Hacquard (https://www.mpipz.mpg.de/hacquard) for a period of three years .

PhD position

"​I am looking for a graduate student to start in Fall 2022 and work on pitcher plant microbial diversity and function. Contact me ASAP for more information!"

Postdoctoral Researcher: Biodiversity Genomics - Careers | Kew Gardens This exciting new position will contribute to RBG Kew’s mission to understand and protect plants and fungi for the benefit of people and the future of all life on Earth, through postdoctoral research on biodiversity genomics of neglected plant crops.

Assistant Professor of Environmental Justice The Department of Environmental Sciences at the University of Virginia seeks a tenure-track assistant professor to begin August 2022. We invite applications from rising scholars in any field in the environmental sciences or a related field in the natural sciences or engineering. The successful candidate will be expected to develop a nationally recognized research program focused on environmental justice and/or climate equity as related to any aspect of the Earth system and to develop courses along those lines.

Director of the Westerdijk Fungal Biodiversity Institute For the Westerdijk Fungal Biodiversity Institute, the Royal Netherlands Academy of Arts and Sciences (KNAW) is seeking an authoritative scientist in mycology with an affinity for biodiversity and taxonomy, a large national and international network, a broad outlook on science and strong management skills.

PhD: Understanding the role of nitrogen speciation in controlling the biodiversity of freshwater algal communities at UK Centre for Ecology and Hydrology - Lancaster on FindAPhD.com You will join a multi-disciplinary team across the UK Centre for Ecology and Hydrology (UKCEH) and Lancaster Environment Centre, one of the largest groupings focused on environment-orientated research in Europe. Your research will be based within the UNESCO World Heritage Site of the English Lake District, with access to leading analytical and experimental facilities in both UKCEH and Lancaster University. You will be trained and become expert in a wide range of ecological and biogeochemical research techniques, including taxonomic identification of algae and stable nitrogen isotope analysis.

Assistant Professor of Arid-Land Ecosystems The School of Natural Resources and the Environment (SNRE) at the University of Arizona (UA) seeks outstanding applicants for a tenure-track position focused on the ecology and management of the vegetation of working grassland-savanna-shrubland-woodland ecosystems of arid and semi-arid regions.

PhD: Deciphering the role of translation in temperature-controlled development In our Ribo-seq data, we identified multiple Arabidopsis uORFs whose translation changes in a temperature-dependent manner. This project will employ genetic and molecular biology approaches to reveal the functions of several candidate uORFs in plant development and abiotic stress responses, with a particular emphasis on temperature-sensitive processes. It will also tackle the question whether and how these uORFs affect gene function, using in vitro and in vivo biochemical assays. These candidate gene-focused approaches will be complemented by transcriptome-wide analysis of translation initiation, aiming to reveal precise dynamics of uORF translation across a range of ambient temperatures.

PhD: How do circadian rhythms shape the responses of plants to climate change? This pioneering PhD project will contribute to these major questions by investigating how future climate scenarios affect plant physiology and development through their effects upon circadian regulation. It will provide training in laboratory-based molecular genetics research with the model plant Arabidopsis thaliana, in quantitative analysis of circadian time-series data using new approaches and computational tools, and offers the possibility of field-based studies of circadian rhythms. The novel biological insights from the PhD will help to better understand how plants respond and adapt to changes in temperature, and contribute to the future development of crops that are more resilient to climate change

PhD: Understanding Host Compatibility in the Marchantia-Phytophthora System The goal of this project is to explore the delicate balance between disease resistance and susceptibility to filamentous pahogens in M. polymorpha. Using comparative macroevolutionary analyses, molecular genetics, and multi-omics approaches, the candidate will investigate widely-conserved and lineage-specific aspects of liverwort immunity in addition to the virulence mechanisms employed by broad host Phytophthora species to promote infection across distantly related host plants. This multidisciplinary project is based in the laboratory of Dr. Phil Carella, located in the Department of Cell and Developmental Biology at the John Innes Centre. It provides an exciting opportunity to explore disease resistance in the emerging model liverwort M. polymorpha and to develop skills across plant pathology, land plant evolution, microbial virulence, and bioinformatics.

PhD: Planting for silence: the role of hedging in mitigating noise pollution This is an exciting PhD opportunity to work on an interdisciplinary project drawing on the world-leading expertise at the RHS (Royal Horticultural Society) and the Acoustics Research Centre, University of Salford. Studies show that hedges reduce noise, and that different species and how they are arranged alter the attenuation. But no work has evaluated noise reduction at the cultivar level or studied the impact of hedge pruning and management. New knowledge from this study will inform the selection and management of hedging to reduce the impact of noise pollution.

Postdoctoral researcher in tropical forest dynamics I am seeking a postdoctoral researcher to join our group at the program for Plant Ecology and Evolution at Uppsala University, Sweden. Funding is available for two (2) years with the potential for some extension. The specific research project is somewhat flexible and will be developed collaboratively but will generally contribute to our overall research program, which focuses on the consequences of environmental heterogeneity on biodiversity, at various spatial and temporal scales

Research Assistant I The Haus Lab in the Department of Horticulture is hiring a Research Assistant I who will provide expert support and assist in overseeing and coordinating root biology research. Major responsibilities include maintaining and enforcing lab safety guidelines, performing routine lab work to support research projects (including ordering, equipment calibration/maintenance, etc.), assisting in planning and designing experiments, running small-scale pilot experiments collecting root data on various plant species, and writing short reports on the analysis of these experiments. The ideal candidate must have a strong expertise in growing diverse plant species in a greenhouse and growth chamber with special interest for candidates who have also worked in a field setting.

Research Associate-Fixed Term The Haus Lab in the Department of Horticulture at Michigan State University is hiring a research associate (postdoctoral position) to lead ongoing root biology research identifying root developmental traits associated with the multiple origins of dry bean and investigating legume root responses to abiotic stressors. Dry beans are an important source of plant-based iron and protein, but production is limited by a number of environmental stressors. Our projects aim to mitigate production losses using inherent, but poorly understood root traits. The successful candidate will lead research projects using developmental, quantitative genetics, and bioinformatic-based approaches. Expertise in plant development or bioinformatics (e.g. genetic mapping and transcriptomics) is preferred. The successful applicant should also have strong writing and communication skills and be able to work independently and as part of an interdisciplinary research team. Completion of a PhD degree program in Plant Science, Horticulture, or other closely related field; related work experience performing basic research techniques specific to the area of research employment such as: greenhouse and growth chamber research, field research, microscopy, or image analysis

Postdoctoral Researcher (Feng Group) We’re looking for a Postdoctoral Researcher to join the Feng Group, working on cutting-edge science in the field of epigenetic reprogramming in plant germlines. The Feng laboratory uses the Arabidopsis male germline as a model system to study the mechanisms underlying germline epigenetic reprogramming.

Research Assistant Phytopathology Dümmen Orange is an international leading breeding company focused on cut flowers, bulbs, tropical plants, pot plants, bedding plants and perennials. To strengthen our multidisciplinary research team we are looking for a Research Assistant Phytopathology. 

PhD: ARC Training Centre for Future Crops Development The ARC Training Centre for Future Crops Development has been established to train a new generation of researchers and leaders to build new capabilities for agriculture. Commencing in 2022, the Centre will train PhD students and early-career researchers in new Agri-technologies and in analysing socio-economic opportunities. Students will have opportunities to engage with industry partners and communities on projects to improve the yield and nutritional value of the crops that underpin the energy and protein content of the human diet.

PhD: Plant communities and climbers in degraded and regenerating forest landscapes of Borneo at UK Centre for Ecology and Hydrology Lianas compete with trees for key resources (light, water, nutrients), increasing mortality of juvenile trees and altering reproductive processes within the canopy, which together influences the capacity for forest regeneration. Climber-cutting is frequently considered in restoration interventions but we need to understand more about the role of lianas in regeneration and the efficacy of such interventions. This innovative project explores the interactions between liana infestation, phenology and native tree regeneration in the fragmented forest landscape across Sabah, Borneo.

Tenure-track Assistant professor in Plant Diversity and Ecology The Department of Plant and Environmental Science (PLEN), University of Copenhagen invites applications for a Tenure-track Assistant Professor within the field of Plant Diversity and Ecology with start 1 May 2022, or as soon as possible thereafter. The position is in the Section for Organismal Biology (SOBI),

Assistant Professor The Department of Biological Sciences at Louisiana State University invites applications for a tenure-track position in Ecology at the level of Assistant Professor. We seek a broadly trained ecologist who addresses questions in any of a variety of sub-disciplines of ecology including but not limited to animal behavior, population demography and regulation, community structure and interactions, or the maintenance and function of biodiversity.

Assistant Professor, Biology The Department of Natural Sciences at the University of Houston-Downtown (UHD) invites applicants for a tenure-track position in Biology with a focus on plant or fungal ecology at the assistant professor level with an anticipated starting date of August 15, 2022.

Postdoctoral Researcher Position The Community Ecology & Restoration Lab of Nick Barber at San Diego State University has an opening for a postdoctoral researcher starting as soon as January 2022.

Lecturer Level B in Molecular Plant Biology (x2) The position is primarily based within the Discipline of Biology (School of Environmental & Life Sciences), at the University of Newcastle’s Callaghan Campus. The position will contribute to undergraduate teaching in key areas such as agricultural and environmental biotechnology, as well as first year courses in general biology.

Postdoctoral Research Fellow in Plant Functional Ecology We are seeking a talented, dedicated and field-experienced Postdoctoral Research Fellow – with proven capacity to lead peer-reviewed publications on plant science – to join the Western Sydney University (WSU) node of the new ARC Centre for Plant Success in Nature & Agriculture. You will be based in Distinguished Professor Ian Wright’s new research team at the Hawkesbury Institute of Environment (HIE). Wright is a global leader in plant functional ecology, best known for work on the leaf economic spectrum, global analysis of plant traits, and optimality theory for plant function

Privacy Policy

We store your email in order to know who to send the emails to. We have to share that list with Revue because they’re the company that actually sends the emails out. We get information about how many emails open, so it might be 50% one week, but we wouldn’t be able to tell if you were in the half that opens the email or the half that didn’t. Revue have their own longer privacy policy.

The email is funded by the Annals of Botany Company.