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The Week in Botany 157

July 6, 2020

July in Welsh is mis Gorffennaf, which translates as the 'end of summer' as people prepare for the onset of autumn and winter. For some people in Leicester, where the Annals of Botany office is based, today might feel more like March 128th, due to the return of strict lockdown. For botanists following @botanyone on Twitter, it seems a time to look forwards more than back, and there are a lot of jobs getting shared.
Also looking forward, today is the start of #BlackBotanistsWeek. If it's like #BlackInNature, or #BlackBirdersWeek, then we're in for a week of people sharing their enthusiasm about some amazing activities. As long as I'm not struck by COVID, then I hope there'll be plenty to share in an email next week. Until then, stay safe.
Alun (webmaster@botany.one)

From Botany One

New genus and species of probable arbuscular mycorrhizal fungi uncovered in the Rhynie chert
The new species bears a strong similarity to modern-day Archaeospora.

Should we be looking to parasitic plants to help control invasive species?
Biologists have been looking at biological controls like herbivores to control invasive plants. New research suggests we should also look at what parasitic plants can do.

New research shows that Bioenergy plants need to be in the right location to deliver benefits
Finding the win-wins for Bioenergy with Carbon Capture and Storage (BECCS) as we move to net zero – for the UK at least, size matters.

Metalheads! Patterns of extreme mineral accumulation in plants
Examining patterns of mineral accumulation in plants gives clues as to how some plants can accumulate extreme amounts of some minerals.

Running rings around world history
Nigel Chaffey reviews 'Tree story: The history of the world written in rings', by Valerie Trouet. 

Thicker roots: to grow or not to grow? Investigating the dynamics of secondary root growth
Secondary growth of the roots of annual dicots has functional significance with regards to soil resource acquisition and transport, interactions with soil organisms and carbon sequestration.

Unravelling how a mysterious substance may boost plant growth
Capstaff and colleagues investigate how soil-derived fulvic acid may boost growth of alfalfa.

Where did greater yams come from? A global effort to track the ‘yummy’ dispersal history of a polyploid plant
Dr Hana Chaïr and colleagues from France, Austria, Sweden, Vietnam, Vanuatu, Madagascar, Sri Lanka, Papua New Guinea, Nigeria and Japan sequenced 643 greater yam accessions to investigate the dispersal history of yams. 

Convergent nitrogen–phosphorus scaling relationships in different plant organs
Does a general relationship exist to describe N and P partitioning within and among plant organs?

What happens to nutrients, after a carnivorous plant has digested its prey?
While carnivorous plants eat insects, they get most of their energy from photosynthesis, like other plants. New research investigates how carnivory affects photosynthesis.

How does barley make vitamin E?
Vitamin E is increasingly understood to be important for human health. An international team has been editing the barley genome to understand the genetic controls for the vitamin’s creation by the cereal.



News and Views

Amazonian fungi: The ‘dark matter’ of biodiversity
A new study published this week used DNA sequences in soil to estimate the biodiversity of different regions across the Amazonian rainforest.
Kew

Who Pollinates the Flame Azalea?
Despite being visited by a wide array of insect species, only large butterflies seem capable to pollinating the flame azaleas stunning blooms.
In Defense of Plants

Is Plant 'Intelligence' Just a Human Fantasy?
Although plants make up over 80% of the biomass on Earth, for centuries they have been thought of as inanimate and passive things. Researchers even coined the term “plant blindness” to refer to a cognitive bias that literally makes our brains zone out plants in our view and underestimate their importance.
Gizmodo

The biodiversity leader who is fighting for nature amid a pandemic
Elizabeth Mrema has a mighty task ahead of her, leading countries as they negotiate new biodiversity targets.
Nature

Second Brazilian museum fire in two years reignites calls for reform
A recent fire at a natural history museum in Minas Gerais is forcing some researchers to relive the pain of losing priceless specimens and artefacts.
Nature

Dry tropical forests may be more at risk than wet rainforests, study says
Areas with a drier climate have seen greater loss of biodiversity from global warming
The Guardian

#BlackBotanistsWeek
A week celebrating Black, Indigenous and People of Colour who practice botany.
#BlackBotanistsWeek

BIO SCI 9K LEC A: GLOBAL CHNG BIOLOGY (05043)
Dr Treseder invites you to take her online UCI course on Global Change Biology.
UC Irvine

Irish Grasslands Project
"We’re launching a brand new project to increase awareness of Ireland's semi-natural grasslands and help to improve the identification skills needed to record them, whether you're a beginner or a more experienced botanist."
BSBI

Stop making sense: why it's time to get emotional about climate change
The science has been settled to the highest degree, so now the key to progress is understanding our psychological reactions.
The Guardian

Review. The plant microbiome: From ecology to reductionism and beyond (Annu. Rev. Microbiol.)
The last two decades have witnessed tremendous progress in our understanding of plant microbiota. Fitzpatrick, Salas-González et al. highlight recent discoveries from culture-dependent and culture-independent approaches and discuss the future path towards integrating these approaches.
Plantae



Jobs

2 × postdoctoral research associate positions
Professors Jim Elser and Matt Church at the University of Montana and the Flathead Lake Biological Station seek to fill two postdoctoral research associate positions to work on a newly-funded NSF Rules of Life project entitled “The Rules of Life were made to be broken - Connecting Physiology, Evolutionary Ecology, and Mathematics to Identify a Growth Rate Rule”.  These postdoctoral researchers will perform studies of the genomic, physiological, ecological, and evolutionary responses of Pseudomonas and Chlamydomonas in chemostat cultures.
Montana, US

Research Assistant (Carella Group)
Working as part of a team led by Dr Philip Carella, you will manage and support critical lab business. You will lead and assist with long-term experiments in addition to providing horticulture and plant/microbial transformation support
John Innes Centre, UK

PhD Student: Coordination of Physiological Responses to Multiple Stresses by Abscisic Acid in Barley: A Field Focused Study 
The aim of this PhD project is to understand the role of the hormone abscisic acid (ABA) in coordinating plant physiology and growth in response to multiple stresses and climatic fluctuations in barley. The student will conduct experiments in both outdoor and greenhouse conditions to analyse the growth and synthesis of metabolites involved in stress acclimation of a mutant line deficient for ABA under drought alone and in combinations with other stresses (soil compaction and herbivore interaction).
Plymouth, UK

Forest Manager
Tilhill has an exciting opportunity for you to be a key member of our Forestry Team in the role of Forest Manager.
Tilhill Forestry, UK

Postdoctoral Researcher in Trans-generational stress responses
in an integrative project to address the role of trans-generational effects in stress tolerance for a fixed term of two and a half years. There will be a trial period of six months in the beginning. The starting date is 1.10.2020, but a later starting date can be negotiated.
Helsinki, FI

PhD Student
You will analyze existing biodiversity data and current and historical land use to determine to what extent biodiversity depends on current management or on land use history. You will set up a field experiment to evaluate whether biodiversity-targeted management of road verges benefits pollinating insects, or if there is a risk that flower-rich road verges become an ecological trap. Finally, you will quantify if species-rich road verges contribute to pollination services in the surrounding landscape.
Swedish University of Agricultural Sciences, SE

Looking for two PhD students to join iDiv!
1. Macroecology and macroevolution of plant – frugivore trait matching in the tropics
2. Adaptive evolution of plant-frugivore interactions on Madagascar
Leipzig, DE

Wissenschaftliche Mitarbeiterin/wissenschaftlicher Mitarbeiter (m/w/d)
In the frame of a JKI-internal research project (BioSam) you will register and characterize anthropoid and plant pathogenic microorganisms and viruses of the JKI collections with respect to invasive species of cultured plants under climate change condition. You will record and characterize the existing collections of microorganisms and viruses with suitable molecular and microscopic techniques.
The Julius Kühn Institute, DE

Full Professor (W3) of Molecular Genetics
The applicant should be willing to cooperate on interdisciplinary projects and have conducted internationally renowned research in a current field of molecular genetics, for example regulating complex gene networks in reaction to environmental stimuli, growth signals, cell stress, or noxious agents.
Hohenheim, DE

PhD position
A PhD position (co-funded by the Labex ARBRE and the 'Région Grand Est') is available in the Tree-Microbe Interaction Department (Unité Mixte de Recherche Université de Lorraine/INRAEInteractions Arbres-Microorganismes-UMR IAM) in Nancy, France. We seek a motivated individual with an MSc degree, an outstanding academic record, abilities in molecular biology, protein biochemistry, microbiology,and/or plant molecular physiology, as well as strong communication, organisational, and interpersonal skills.
Université de Lorraine, FR

Postdoctoral Researcher in Community Ecology
The Helsinki Institute of Life Sciences invites applications for a POSTDOCTORAL RESEARCHER in community ecology for a fixed term of two years. There will be a trial period of six months in the beginning. The starting date is 1.1.2021, but a later starting date can be negotiated.
Helsinki, FI

Postdoctoral Researcher in Statistics and Machine Learning
The Organismal and Evolutionary Research Programme invites applications for a POSTDOCTORAL RESEARCHER in statistics and machine learning for a fixed term of two years. There will be a trial period of four months in the beginning.
Helsinki, FI

Postdoctoral Researcher in the Monitoring of Species Communities
The Organismal and Evolutionary Research Programme invites applications for a POSTDOCTORAL RESEARCHER in the monitoring of species communities for a fixed term of two years.
Helsinki, FI

University Professor of Systematic and Evolutionary Botany
Applicants have a strong record in studying processes and mechanisms of plant evolution and systematics with emphasis on genetic, genomic, biogeographic or ecological aspects of diversification at the species level (speciation) and beyond (macroevolution).
Vienna, AT

Postdoctoral teaching and research fellow
We seek a full-time postdoctoral teaching and research fellow to join the Living Data Project at McGill University and the Université de Montréal.
The Poisot Lab, CA


Scientific Papers

Biased-corrected richness estimates for the Amazonian tree flora
te Steege et al. show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, they confirm that over 15,000 tree species are expected to occur in Amazonia. They also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come.
Scientific Reports

Pan-Genome of Wild and Cultivated Soybeans
In this study, Liu et al. performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, they constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome.
Cell

GDSL-domain containing proteins mediate suberin biosynthesis and degradation, enabling developmental plasticity of the endodermis during lateral root emergence
Ursache et al. show that differentiated endodermal cells have a distinct auxin-mediated transcriptional response that regulates cell wall remodelling. Based on this data set they identify a set of GDSL-lipases that are essential for suberin formation. Moreover, they find that another set of GDSL-lipases mediates suberin degradation, which enables the developmental plasticity of the endodermis required for normal lateral root emergence.
bioRxiv

An inducible genome editing system for plants
Wang et al. present a new tool with which target genes can efficiently and conditionally be knocked out by genome editing at any developmental stage. Target genes can also be knocked out in a cell-type-specific manner. They state their tool is easy to construct and will be particularly useful for studying genes having null alleles that are non-viable or show pleiotropic developmental defects.
Nature Plants

Highly efficient DNA-free plant genome editing using virally delivered CRISPR–Cas9
Ma et al. report the engineering of a plant negative-strand RNA virus-based vector for DNA-free in planta delivery of the entire CRISPR–Cas9 cassette to achieve single, multiplex mutagenesis and chromosome deletions at high frequency in a model allotetraploid tobacco host. Over 90% of plants regenerated from virus-infected tissues without selection contained targeted mutations, among which up to 57% carried tetra-allelic, inheritable mutations. The viral vector remained stable even after mechanical transmission, and can readily be eliminated from mutated plants during regeneration or after seed setting.
Nature Plants

Rocks in the auxin stream: Wound-induced auxin accumulation and ERF115 expression synergistically drive stem cell regeneration
Canger et al. show that stem cell death diverges the auxin flow, much like rocks in a stream, resulting in an auxin accumulation in the tissues surrounding the wound. They demonstrate that within these tissues, wound-induced expression of the plant-specific transcription factor ERF115 works synergistically with the change in auxin accumulation, thereby specifying stem cell identity in the cells surrounding the damaged stem cells. This gain of stem cell identity drives formative divisions, allowing replacement of the lost stem cells and thus successful regeneration.
PNAS

Wild bee declines linked to plant‐pollinator network changes and plant species introductions
This study characterises the changes in a northern New England wild bee plant‐pollinator network over the past 125 years and reveals a striking increase in exotic bee and plant taxa over time. Mathiasson and Rehan document that declining wild bee species have historic ties to threatened and endangered plant species. These data provide a rare insight into the fragile nature of plant‐pollinator networks.
Insect Conservation and Diversity

Root architecture and hydraulics converge for acclimation to changing water availability
While the mechanisms that directly underlie root growth and development as well as tissue hydraulics are being uncovered, the signalling mechanisms that govern their local and systemic adjustments as a function of water availability remain largely unknown. A comprehensive understanding of root architecture and hydraulics as a whole (in other terms, root hydraulic architecture) is needed to apprehend the strategies used by plants to optimize water uptake and possibly improve crops regarding this crucial trait.
Nature Plants

Measuring Rubisco activity: challenges and opportunities of NADH-linked microtiter plate-based and 14C-based assays
Rubisco is central to carbon assimilation and efforts to improve the efficiency and sustainability of crop production have spurred interest in phenotyping Rubisco activity. Sales et al. tested the hypothesis that microtiter plate-based methods provide comparable results to those obtained with the radiometric assay that measures the incorporation of 14CO2 into 3-phosphoglycerate (3-PGA).
Journal of Experimental Botany

Plants meet machines: Prospects in machine learning for plant biology
Multiple types of machine learning have been developed, each with its own techniques, strengths, and weaknesses, making certain approaches better matches for certain problems than others.
Applications in Plant Sciences

Inequality in plant diversity knowledge and unrecorded plant extinctions: An example from the grasses of Madagascar
Plants are essential for all life, providing the infrastructure and energy for our ecosystems. A recent report indicates that more than 500 plant species are already presumed extinct and many more could have been lost without anyone being aware, especially in species‐rich areas with high levels of human impact, and where botanical knowledge is poor. Inequality in the availability and accessibility of biodiversity data, professional expertise, and funding interact to produce chronic differences in knowledge between countries. Vorontsova et al. illustrate this using an example from Madagascar. Understanding these knowledge inequalities will strengthen our ability to improve the situation for people as well as for plants.
Plants, People, Planet

Extracellular proteolytic cascade in tomato activates immune protease Rcr3
The secretion of papain-like cysteine proteases (PLCPs) is an important component of the immune response across the plant kingdom. Paulus et al. show that immune protease Rcr3, a secreted PLCP of tomato, is activated by secreted subtilisins, which are common serine proteases in plants.
PNAS

CDKD-dependent activation of CDKA;1 controls microtubule dynamics and cytokinesis during meiosis
Sofroni et al. reveal that the central cell cycle regulator CYCLIN DEPENDENT KINASE A;1 (CDKA;1), the Arabidopsis homologue of Cdk1 and Cdk2, partially in conjunction with CYCLIN B3;1 (CYCB3;1), is a key regulator of the microtubule cytoskeleton in meiosis. For full CDKA;1 activity, the function of three redundantly acting CDK-activating kinases (CAKs), CDKD;1, CDKD;2, and CDKD;3, is necessary. Progressive loss of these genes in combination with a weak loss-of-function mutant in CDKA;1 allowed a fine-grained dissection of the requirement of cell-cycle kinase activity for meiosis. Notably, a moderate reduction of CDKA;1 activity converts the simultaneous cytokinesis in Arabidopsis, i.e., one cytokinesis separating all four meiotic products concurrently into two successive cytokineses with cell wall formation after the first and second meiotic division, as found in many monocotyledonous species.
Journal of Cell Biology

The Impact of Bt Corn on Aflatoxin-Related Insurance Claims in the United States
Previous field studies have reached no collective consensus on whether Bt corn, the most commonly planted transgenic crop worldwide, has significantly lower aflatoxin levels than non-Bt isolines. Aflatoxin, a mycotoxin contaminating corn and other commodities, causes liver cancer in humans and can pose severe economic losses to farmers. Yu et al. found that from 2001–2016, a significant inverse correlation existed between Bt corn planting and aflatoxin-related insurance claims in the United States, when controlling for temperature and drought.
Scientific Reports

Plant Breeding Capacity in U.S. Public Institutions
Several studies in recent decades have warned that plant breeding capacity in U.S. institutions may be declining, placing our food system at risk. To further understand the status, trajectory and needs of these programs, a national survey was conducted in 2018. Public sector plant breeding programs (n = 278) in 44 U.S. states responded to questions about staffing levels, budgets, access to needed personnel, and access to technology for selective breeding. Almost half of program leaders were nearing retirement age. Programs reported significantly declining estimates of hours spent on program activities by program leaders and technical support staff. On average, programs reported devoting 2.78 FTE to plant breeding research in the most recent fiscal year (including all types of personnel); for germplasm enhancement activities and variety development, mean estimated hours per program totaled 1.58 FTE and 2.20 FTE, respectively.
Crop Science


     

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