The Week in Botany September 15, 2025
Unfortunately, there’s some bad news this week. The in silico Plants editor, Stephen Long, has died. A brief obituary has been posted to Illinois’s website, and I’m sure more lengthier obituaries will appear when the news sinks in.
While scientific journal editors are ideally active researchers, he and his team are at the top of his field. Here I might link to a few recent papers, but his Google Scholar page shows ten from 2025 so far. If you were to describe in a word, prolific might be it. But he didn’t just publish papers, he produced journals.
I met him a few times while he edited in silico Plants, a journal he founded to provide a venue for papers in plant modelling. He was also the founder of Global Change Biology and GCB Bioenergy and announced last month a new journal GCB Communications. Together the journals have amassed nearly a million citations, which shows he knew what science people wanted to talk about.
But there’s more to impact than numbers. It’s easy to get lost in the numbers of publications and journals, and each one of those was built on human interactions. It says a lot about him that he could connect with so many people and encourage them to work alongside him. I looked forward to meetings when I knew he was going to be there, because I knew there was always going to be something to be excited about. I’ll miss that, and I’m certain I won’t be alone.
It’s another shorter email, as I was away on family business again this week. Next week, for a change, I have a hospital visit that will take some time. However, I’ll make sure there’s time to send another email of the papers and the news stories you’re sharing on Mastodon and Bluesky at the same time next week. Until next time, take care.
Alun (webmaster@botany.one)
On Botany One
How the Tlahuica-Pjiekakjoo Keep Their Mycological Heritage Thriving
A decade-long collaboration reveals how an endangered Indigenous group holds unparalleled knowledge of wild fungi, and how they’re passing it on to future generations.
Ramiro Aguilar: “Plants Are the Most Incredible Organisms”
Botany One interviews Dr. Ramiro Aguilar, who was sponsored by Annals of Botany to speak at ATBC 2025.
Thriving in Allchar: Arsenic and Thallium Tolerance in Viola Species
Viola metallophytes have evolved the rare capacity to tolerate toxic metals, allowing them to thrive in the harsh soils of Allchar, North Macedonia.
Invasive Species Outperform Natives by Flowering Out of Season
A new study reveals how off-season flowering helps invasive plants outcompete native species.
…and last’s week’s Week in Botany with a loss of immunity, a gain of parasites and untold stories of plant evolution.
News & Views
The legacy lost when Forest Service offices shut down
After 117 years of operation, the U.S. Forest Service’s Southwest Regional Office in Albuquerque is closing by order of the secretary of agriculture. Since 1908, this office has directed the management of over 20 million acres of national forests in Arizona and New Mexico. Top leadership has already departed, and many staff have retired, been transferred or fired.
Why would anyone want to be a scientist?
It is difficult to fathom why anyone intelligent enough to be a scientist would actually choose to be one. Doing good science requires the utmost exertion of body, mind and spirit, yet is consistently filled with failure and rejection. But, strange even to myself, I not only don't question the unfavorable risk-to-reward ratio but consider myself astonishingly lucky to be a scientist. There are three fundamental pleasures that have sustained me through 50 years of this madness.
Can researchers stop AI making up citations?
OpenAI’s GPT-5 hallucinates less than previous models do, but cutting hallucination completely might prove impossible.
A Eulogy for Teakettle
Justice William O. Douglas, in his dissenting opinion of the Supreme Court’s decision in Sierra Club v. Morton, said “Contemporary public concern for protecting nature’s ecological equilibrium should lead to the conferral of standing upon environmental objects to sue for their own preservation.” His opinion goes on to state that corporations are given personhood and so should natural systems. Today I want to give voice to the Teakettle Experimental Forest, a place that burned in the first few days of September 2025.
Talented early-career researcher receives major Wellcome Trust funding
The innovative research project of an early-career plant scientist at the John Innes Centre has attracted a prestigious funding award from a global health charity. Dr Miguel Montez, a post-doctoral scientist in the group of Professor Caroline Dean FRS, has received the Early-Career Award from the Wellcome Trust.
Garnet fire burns into grove of giant sequoias; several behemoths are in flames
A blaze raging through the Sierra National Forest in Fresno County has burned through part of a large grove of giant sequoias, setting at least a few of the rare, towering trees on fire.
Scientists take on Trump: these researchers are fighting back
Through lawsuits, grant tracking, whistle-blowing and more, resistance to the US war on science is growing.
Delivering your daily dose of fungi
Nigel Chaffey reviews Mushroom day: A story of 24 hours and 24 fungal lives, by Alison Pouliot.
New pathway engineered into plants lets them suck up more CO₂
Engineered pathway lets carbon be plugged directly into key metabolic pathways.
This Week in Botany
5 Years Ago: Two evolution pathways acted on the “genomic fossils” in the tea plant genus, Camillia
10 Years Ago: Plants vs mobile ’phones
15 Years Ago: Lucky heather? No, clover!
Scientific Papers
Knockout of an SPX-related gene for polyphosphate synthetase accelerates phosphate starvation responses in the oleaginous microalga Nannochloropsis oceanica ($)
SPX domain-containing proteins are important for phosphate (Pi) signaling and homeostasis in various eukaryotes. Genomic and transcriptomic analyses of the oleaginous microalga Nannochloropsis oceanica identified four genes encoding SPX family members with distinct domain architectures: SPX (NoSPX1), SPX-VTC(NoSPX2), SPX-EXS (NoSPX3), and SPX-MFS (NoSPX4). These NoSPX genes responded differentially to Pi deprivation, with NoSPX1 and NoSPX2 expression being significantly up-regulated.
Engineering the plant circadian clock for latitudinal adaptation as a strategy to secure agricultural productivity on a changing planet (FREE)
Gerhardt & Mehta argue that rapid latitudinal adaptation of crops in the future is possible via the targeted engineering of morning-, afternoon-, and evening-expressed circadian regulators in crop plants with distinct phenologies.
Precision plant epigenome editing: what, how, and why ($)
Advances in genome engineering have paved the way for targeted epigenome engineering, providing fundamental insights into the role of epigenetic modifications in trait inheritance. Engineered epialleles have already delivered stable, heritable changes in agronomic traits. Despite this capacity, progress in the field has not yet achieved its potential, leaving many avenues of research unexplored. Leech et al examine the factors influencing this progress, including the advances in current epigenome editing techniques, the key research goals and translational applications, and the challenges in the selection of ideal target loci.
Evolutionary consequences of extreme climate events ($)
Baeckens & Donihue review the evolutionary outcomes of extreme climate events and show how they depend on the characteristics of the events themselves, the traits under selection, the adaptive capacity of affected populations and the ecological context of selection.
What Large Language Models Know About Plant Molecular Biology (FREE)
Large language models (LLMs) are rapidly permeating scientific research, yet their capabilities in plant molecular biology remain largely uncharacterized. Fernandez Burda et al present MoBiPlant, the first comprehensive benchmark for evaluating LLMs in this domain, developed by a consortium of 112 plant scientists across 19 countries.
High tree diversity exposed to unprecedented macroclimatic conditions even under minimal anthropogenic climate change ($)
Trees play key roles in terrestrial ecosystems but are sensitive to large climatic changes. Boonman et al quantify end-of-century climate change exposure–shifts to species’ currently unoccupied climate zones–for 32,089 tree species globally.
Conserved transcriptional reprogramming in nematode infected root cells (FREE)
Saura-Sanchez et al developed a comparative host-pathogen framework to study the nematode infection process in Arabidopsis and rice. Using a cross-species single-cell transcriptomics approach, they identified a unique molecular signature in infected root cells and show that the cellular reprogramming during these early stages is highly conserved across both host-pathogen interactions.
A multigenic quantitative trait locus underlies natural variation in Arabidopsis thaliana root system architecture and transcriptional responses to microbiota-derived Pseudomonas (FREE)
Plants interact with structured microbial communities called the microbiota, which can have a profound impact on plant growth and health. However, how plants perceive and respond to specific core microbiota members at a molecular level is still unclear. Copeland et al identified natural variation in Arabidopsis thaliana root responses to bacterial strains of the genus Pseudomonas, a core genus of the plant microbiota.
Roots: metabolic architects of beneficial microbiome assembly (FREE)
Uribe-Acosta et al highlight the multifaceted role of plant metabolites in root microbiome assembly, focusing on their dynamic regulation by plant genotype, environmental conditions, and immune responses. They discuss the emerging concept of roots as metabolic architects of their associated microbiomes, wherein plant–metabolite–microbiome interactions coevolved alongside critical life-support systems such as immunity and nutrient acquisition.
Distal to proximal: a continuum of drivers shaping tree growth and carbon partitioning (FREE)
The relationship between tree carbon (C) assimilation and growth is central to understanding tree functioning and forecasting forest C sequestration, yet remains unresolved. The long-standing debate over C source vs sink limits to growth has yielded invaluable insight, but rests on a false dichotomy. Reframing this issue in terms of distal-to-proximal processes driving sink activity and placing it within a broader understanding of C partitioning offers new insights.
In AoBC Publications
Careers
Note: These are posts that have been advertised around the web. They are not posts that I personally offer, nor can I arrange the visa for you to work internationally.
JXB Editorial Internships – Call for Applicants
We are excited to announce that we are inviting applications for the fourth round of JXB Editorial Internships. The aim of these internships is to provide early career researchers with experience of scientific publishing from the editorial side, as an opportunity for career development as a researcher, or with a view to a career in scientific publishing.
Senior Research Officer (Postdoctoral Research Associate), Essex
PlantPlug is an ambitious, ARIA-funded initiative led by Dr Pallavi Singh that is redefining the role of parasitic plants as programmable living biointerfaces. This is a rare opportunity to work at the cutting edge of synthetic biology, developmental plant science, and interspecies communication, using mistletoe as an entirely novel chassis for trait transfer between plants. The successful candidate will play a pivotal role in building and delivering the experimental and technical foundations of this pioneering grant, from in-vitro mistletoe germination and propagation to genetic transformation and host-integration assays.
Tenure-Track Professor for Plant Biochemistry, Tübingen
The successful candidate is expected to develop and carry out an independent research program at the Center for Plant Molecular Biology (ZMBP) on plant biochemistry. The focus of the research program should be on the biochemical aspects of the composition, structure, dynamics and regulation of plant protein complexes and associated molecules.
Professorship in Plant Genetics, Kiel
We are searching for a scientist with an excellent international track record and pioneering research activities in the fields of plant genetics, such as the regulation of stress responses in natural environments and the role of epigenetic factors in stress adaptations. We are looking for a scientist with a focus on fundamental aspects of plant genetics through research work with plants in relation to their natural habitat. The particular expertise in research is underpinned by outstanding publications and successful acquisition of third-party funded projects.
Universitätsprofessor(in) (m/w/d) für Pflanzengenetik, Würzburg
We are looking for an excellent researcher with an international profile in plant genetics within the context of plant evolution, development, and adaptation. The candidate should work experimentally and bioinformatically, and cooperate interdisciplinarily.
Postdoctoral Research Fellow in Forest Monitoring, Sydney
Join a pioneering project funded by the Australian Forest & Wood Innovation Centre for Climate-Smart Forestry, where your expertise will help shape the future of forest monitoring across Australia. This newly created position plays a central role in developing a prototype open-data platform to monitor the structure, condition, and carbon stocks of Australian forests. You’ll work with ground-based and remotely-sensed datasets and contribute to a national roadmap for forest monitoring.
Assistant Professor of Global Change Biology, Montréal
The successful candidate will contribute to faculty excellence through teaching, research, and service. They will develop a research programme, teach and supervise students, and participate in departmental and university activities.