Entanglements of art and ecology
Ros Gray
To see a World in a Grain of Sand And a Heaven in a Wild Flower, Hold Infinity in the palm of your hand And Eternity in an hour. William Blake (1757-1827)
Entanglements of art and ecology
Ros Gray
A diverse and distinct microbiome inside living trees
Arnold et al., preprint
Despite significant advances in microbiome research across various environments, the microbiome of Earth’s largest biomass reservoir– the wood of living trees– remains largely unexplored. This oversight neglects a critical aspect of global biodiversity and potentially key players in tree health and forest ecosystem functions. Here we illuminate the microbiome inhabiting and adapted to wood, and further specialized to individual host species. We demonstrate that a single tree can host approximately a trillion microbes in its aboveground internal tissues, with microbial communities partitioned between heartwood and sapwood, each maintaining a distinct microbiome with minimal similarity to other plant tissues or nearby ecosystem components. Notably, the heartwood microbiome emerges as a unique ecological niche, distinguished in part by endemic archaea and anaerobic bacteria that drive consequential biogeochemical processes. Our research supports the emerging idea of a plant as a “holobiont”—a single ecological unit comprising host and associated microorganisms—and parallels human microbiome research in its implications for host health, disease, and functionality. By mapping the structure, composition, and potential sources and functions of the tree internal microbiome, our findings pave the way for novel insights into tree physiology and forest ecology, and establish a new frontier in environmental microbiology.
Discover network dynamics with neural symbolic regression
Yu et al., 2025
Network dynamics are fundamental to analyzing the properties of high-dimensional complex systems and understanding their behavior. Despite the accumulation of observational data across many domains, mathematical models exist in only a few areas with clear underlying principles. Here we show that a neural symbolic regression approach can bridge this gap by automatically deriving formulas from data. Our method reduces searches on high-dimensional networks to equivalent one-dimensional systems and uses pretrained neural networks to guide accurate formula discovery. Applied to ten benchmark systems, it recovers the correct forms and parameters of underlying dynamics. In two empirical natural systems, it corrects existing models of gene regulation and microbial communities, reducing prediction error by 59.98% and 55.94%, respectively. In epidemic transmission across human mobility networks of various scales, it discovers dynamics that exhibit the same power-law distribution of node correlations across scales and reveal country-level differences in intervention effects. These results demonstrate that machine-driven discovery of network dynamics can enhance understandings of complex systems and advance the development of complexity science.
AI is helping to decode animals’ speech. Will it also let us talk with them?
Rachel Fieldhouse
Deep in the rainforests of the Democratic Republic of the Congo, Mélissa Berthet found bonobos doing something thought to be uniquely human.
During the six months that Berthet observed the primates, they combined calls in several ways to make complex phrases1. In one example, bonobos (Pan paniscus) that were building nests together added a yelp, meaning ‘let’s do this’, to a grunt that says ‘look at me’. “It’s really a way to say: ‘Look at what I’m doing, and let’s do this all together’,” says Berthet, who studies primates and linguistics at the University of Rennes, France.
In another case, a peep that means ‘I would like to do this’ was followed by a whistle signalling ‘let’s stay together’. The bonobos combine the two calls in sensitive social contexts, says Berthet. “I think it’s to bring peace.”
The study, reported in April, is one of several examples from the past few years that highlight just how sophisticated vocal communication in non-human animals can be. In some species of primate, whale and bird, researchers have identified features and patterns of vocalization that have long been considered defining characteristics of human language. These results challenge ideas about what makes human language special — and even how ‘language’ should be defined.
Perhaps unsurprisingly, many scientists turn to artificial intelligence (AI) tools to speed up the detection and interpretation of animal sounds, and to probe aspects of communication that human listeners might miss. “It’s doing something that just wasn’t possible through traditional means,” says David Robinson, an AI researcher at the Earth Species Project, a non-profit organization based in Berkeley, California, that is developing AI systems to decode communication across the animal kingdom.
As the research advances, there is increasing interest in using AI tools not only to listen in on animal speech, but also to potentially talk back.
Continue reading:
https://www.nature.com/articles/d41586-025-02917-9
Common mycorrhizal networks facilitate plant disease resistance by altering rhizosphere microbiome assemblyAuthor links open overlay panel
Zhang et al., 2025
Arbuscular mycorrhizal fungi can interconnect the roots of individual plants by forming common mycorrhizal networks (CMNs). These symbiotic structures can act as conduits for interplant communication. Despite their importance, the mechanisms of signal transfer via CMNs and their implications for plant community performance remain unknown. Here, we demonstrate that CMNs act as a pathway to elicit defense responses in healthy receiver plants connected to pathogen-infected donors. Specifically, we show that donor plants infected by the phytopathogen Botrytis cinerea transfer jasmonic acid via CMNs, which then act as a chemical signal in receiver plants. This signal transfer to receiver plants induces shifts in root exudates, promoting the recruitment of specific microbial taxa (Streptomyces and Actinoplanes) that are directly linked to the suppression of B. cinerea infection. Collectively, our study reveals that CMNs act as interplant chemical communication conduits, transferring signals that contribute to plant disease resistance via modulation of the rhizosphere microbiota.
https://www.sciencedirect.com/science/article/pii/S1931312825003427
Meta-analysis shows that planting nitrogen-fixing species increases soil organic carbon stock
Sun et al., 2025
Nitrogen (N)-fixing species are widely used in forestation and agriculture. The effects of planting N-fixing species on soil organic carbon (SOC) stock, however, remain uncertain, limiting policy development and their application towards a possible climate change mitigation strategy. Here we conduct a global meta-analysis of 385 datapoints from 136 studies comparing SOC stock with planting N-fixing versus non-N-fixing species. Planting N-fixing species increases SOC stock by 16% compared with non-N-fixing species. This SOC increase is closely accompanied by soil N increases, with an average accumulation of 7.8 g of SOC per gram of soil N increase. Climate mediates SOC responses, with greater SOC sequestration observed in drier and warmer regions, particularly in the tropics. We estimate that an additional increase of 0.29–0.75 PgC yr−1 in global SOC stock could be achieved by adopting N-fixing species for forestation, agriculture and regeneration of marginal lands, highlighting their potential for climate change mitigation.
Global distribution of the selected studies testing the effects of planting N-fixing species on SOC stock in this meta-analysis. Green and orange dots represent the geographic locations of studies on tree and crop planting, respectively. The green and orange shaded areas show the distribution ranges of planted forests and croplands, respectively. Inset: the distribution of the sites in the global biomes based on climatic conditions: MAT and MAP. Black dots indicate study sites in this meta-analysis.
Advances in microbial based bio-inoculum for amelioration of soil health and sustainable crop production
Samantaray et al., 2024
Mutualism provides a basis for biodiversity in eco-evolutionary community assembly
Gui Araujo,Miguel Lurgi
Ecological communities are considerably more complex than simple collections of species sharing the same environment. The large number of ecological interactions among species drives changes in populations through time that dictate the persistence of the entire community. Most research into the mechanisms of biodiversity considers different interaction types (mutualism, competition, consumer-resource) in isolation in either ecological or evolutionary contexts. In this study, we developed a community growth model that incorporates mutualism, competition, and consumer-resource interactions and considers both ecological and evolutionary mechanisms of assembly together. We found that communities formed via evolutionary speciation can reach higher species richness and exhibit greater proportions of mutualistic interactions than purely ecological models, resulting in more complex community structures. High levels of mutualism lead to communities more resilient to disturbances, such as the arrival of new species or sudden changes in abundances. Our research extends previous efforts by aiming to understand how evolutionary processes shape the diversity of ecological interactions and the role of these interactions in species persistence. Such knowledge is essential for preserving and restoring ecosystems in the face of growing environmental degradation.
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013402
Application of microbial inoculants significantly enhances crop productivity: A meta-analysis of studies from 2010 to 2020
Li et al, 2022
Abstract
Introduction
With the rapid development of microbial technology, microbial inoculant is considered as a promising tool in sustainable agricultural systems. Mechanisms by which microbial inoculants improve crop yield include improving plant nutrient availability and alleviating abiotic/biotic stresses (e.g., drought, salt and disease). However, the field efficacy of microbial inoculants remains inconsistent, which constrains large-scale adoptions. Identity of dominant mechanisms that underpin the positive impacts of different microbial inoculants is limited. Thus, a comprehensive quantitative assessment of known inoculants on crop performance is needed to provide guidance for the development of effective microbial tools from both research and commercial perspectives.
Materials and Methods
Based on 97 peer-reviewed publications, we conducted a meta-analysis to quantify the benefits of different microbial inoculants on crop yield, and to identify the key mechanisms that underpin enhanced crop yield.
Results
Result showed that (i) alleviation of stresses was the major mechanism (53.95%, n = 53) by which microbial inoculants enhance crop yield, while improving plant nutrient availability accounted for 22.25% (n = 58) of crop yield enhancement. (ii) Pseudomonas was the most effective microbial inoculant in enhancing crop yield through alleviating stresses (63.91%, n = 15), whereas Enterobacter was the most effective in improving plant nutrient availability (27.12%, n = 5). (iii) Considering both mechanisms together, Pseudomonas (49.94%, n = 21), Enterobacter (27.55%, n = 13) and Bacillus (25.66%, n = 32) were the largest sources of microbial inoculants to enhance crop yield, and the combination of diazotroph Burkholderia with its legume host had the highest effect on improving the yield (by 196.38%). Microbial inoculants also improve nutritional quality by enhancing mineral contents in the produce.
Conclusion
Our analysis provides evidence that microbial inoculants can enhance agricultural productivity and nutritional quality and can be used either alone or in combination with reduced amount of agrochemicals to promote sustainable agriculture.
Revisiting the cry-for-help hypothesis in plant–microbe interactions
Tharp et al., 2025
The ‘cry-for-help hypothesis’ (CHH) is broadly used to study how root exudate modulation under stress influences recruitment of beneficial microbes in the rhizosphere. Here, we explored common misconceptions and limitations of the CHH and advocate for the reassessment of this prevalent hypothesis to unfold the ecological complexities of plant–microbe interactions.
https://www.cell.com/trends/plant-science/abstract/S1360-1385(25)00223-7
Linalool-triggered plant-soil feedback drives defense adaptation in dense maize plantings
Guo et al., 2025
Structured Abstract
INTRODUCTION
Planting crops more densely increases overall yields, but it also raises the risk of pest and pathogen outbreaks. Although plants can modify their architecture to adapt to crowded conditions, how they adjust their immune responses remains largely unknown. Understanding how plants manage these trade-offs is critical for sustainable agriculture, especially in the context of increasing global food demands.
RATIONALE
Plants release chemical cues, such as volatiles, that inform neighbors of environmental conditions. One such compound, linalool, is a constitutively emitted leaf volatile in maize and other grasses. We hypothesized that linalool could act as a signal in densely planted fields, triggering plant-soil feedback that prepares neighboring plants for potential biotic stress. We explored how linalool shapes root signaling, soil microbiota, and ultimately plant defense and growth.
RESULTS
Field surveys revealed that maize plants in the inner rows of densely planted fields suffered less herbivore damage than those at the edges but that they also had reduced growth. Laboratory soil–transplantation experiments confirmed that soils conditioned by high-density plantings decreased plant biomass while enhancing resistance to insects, nematodes, and pathogens. These effects extended across genotypes and species.
Volatile profiling identified linalool as a key compound increasing with planting density. Exposure of maize to synthetic linalool reproduced the feedback effects, which required the presence of a living plant. Mechanistically, linalool activated jasmonate signaling in roots and up-regulated genes that drive the biosynthesis and exudation of the specialized metabolite HDMBOA-Glc. This exudate reshaped the rhizosphere microbiome, selectively enriching bacteria that suppressed plant growth but increased resistance in subsequently grown plants. Soil sterilization and microbial inoculation confirmed that these microbes were essential for the feedback loop.
In plants grown in linalool-conditioned soil, defense-related signaling, particularly salicylic acid signaling, was up-regulated, whereas growth-promoting metabolic pathways were down-regulated. Plants lacking salicylic acid signaling did not show growth-defense trade-offs, confirming salicylic acid’s role in expressing the feedback-triggered defense.
CONCLUSION
This study uncovers a volatile-triggered feedback mechanism through which maize adapts its defense in crowded environments. The constitutive emission of linalool primes neighboring plants by activating root jasmonate signaling, promoting HDMBOA-Glc exudation, and altering the rhizosphere microbiome. This, in turn, leads to elevated defense and suppressed growth in subsequent plants through salicylic acid signaling. These findings shed light on how plants integrate aboveground cues and belowground processes to optimize defense in high-density settings. Harnessing this natural defense pathway through breeding, microbial inoculants, or synthetic biology could enable the development of crops that are more resilient and require fewer chemical inputs.
https://www.science.org/doi/10.1126/science.adv6675
The Bird and The Tree
Cornell Lab of Ornithology
Law of complexity
Robert Hazen and Michael Wong
Maximum Entropy is a Foundation for Complexity Science
John Harte
The Hive Architect | Saving Britain's Wild Bees
Farmer-led Research on Europe’s Full Productivity
This report presents the results of the first phase of European Alliance for Regenerative Agriculture (EARA) ongoing farmer-led research program, introducing a groundbreaking way to measure real-world agricultural success through the Regenerating Full Productivity (RFP) index. Developed with and for farmers, the RFP captures both agronomic and ecological performance in a single, practical tool.
Tested across 14 countries from 2021 to 2023, this first phase reveals compelling results:
Full Report:
Impacts of climate change on global agriculture accounting for adaptation
Hultgren et al., 2025
Climate change threatens global food systems, but the extent to which adaptation will reduce losses remains unknown and controversial. Even within the well-studied context of US agriculture, some analyses argue that adaptation will be widespread and climate damages small, whereas others conclude that adaptation will be limited and losses severe. Scenario-based analyses indicate that adaptation should have notable consequences on global agricultural productivity, but there has been no systematic study of how extensively real-world producers actually adapt at the global scale. Here we empirically estimate the impact of global producer adaptations using longitudinal data on six staple crops spanning 12,658 regions, capturing two-thirds of global crop calories. We estimate that global production declines 5.5 × 1014 kcal annually per 1 °C global mean surface temperature (GMST) rise (120 kcal per person per day or 4.4% of recommended consumption per 1 °C; P < 0.001). We project that adaptation and income growth alleviate 23% of global losses in 2050 and 34% at the end of the century (6% and 12%, respectively; moderate-emissions scenario), but substantial residual losses remain for all staples except rice. In contrast to analyses of other outcomes that project the greatest damages to the global poor, we find that global impacts are dominated by losses to modern-day breadbaskets with favourable climates and limited present adaptation, although losses in low-income regions losses are also substantial. These results indicate a scale of innovation, cropland expansion or further adaptation that might be necessary to ensure food security in a changing climate.
a–f, Colours indicate central estimate in a high-emissions scenario (RCP 8.5), net of adaptation costs and benefits, for maize (a), soybean (b), rice (c), wheat (d), cassava (e) and sorghum (f) for 2089–2098. Projections computed for 24,378 subnational units relative to counterfactual yields, uncropped regions are shaded in grey. Wheat shows winter wheat and spring wheat projections combined, weighted by their area share in each region. Estimates in each location are ensemble means across climate and statistical uncertainty. Incomes from SSP3.
https://www.nature.com/articles/s41586-025-09085-w
The Tipping Points of Climate Change — and Where We Stand
Johan Rockström
Les invasions biologiques
Franck Courchamp
Peter Singer: Animal suffering is human responsibility
Regenerative agriculture: The evidence
British Ecological Society
What's Happening At Göbekli Tepe
An update with Field Director Dr Lee Clare
Soil microbial effects on plant community responses to fire in longleaf pine savannas
Anita Simha and Gaurav Kandlikar
Trajectories of the Earth System in the Anthropocene
Steffen et al., 2018
We explore the risk that self-reinforcing feedbacks could push the Earth System toward a planetary threshold that, if crossed, could prevent stabilization of the climate at intermediate temperature rises and cause continued warming on a “Hothouse Earth” pathway even as human emissions are reduced. Crossing the threshold would lead to a much higher global average temperature than any interglacial in the past 1.2 million years and to sea levels significantly higher than at any time in the Holocene. We examine the evidence that such a threshold might exist and where it might be. If the threshold is crossed, the resulting trajectory would likely cause serious disruptions to ecosystems, society, and economies. Collective human action is required to steer the Earth System away from a potential threshold and stabilize it in a habitable interglacial-like state. Such action entails stewardship of the entire Earth System—biosphere, climate, and societies—and could include decarbonization of the global economy, enhancement of biosphere carbon sinks, behavioral changes, technological innovations, new governance arrangements, and transformed social values.
Stability landscape showing the pathway of the Earth System out of the Holocene and thus, out of the glacial–interglacial limit cycle to its present position in the hotter Anthropocene. The fork in the road is shown here as the two divergent pathways of the Earth System in the future (broken arrows). Currently, the Earth System is on a Hothouse Earth pathway driven by human emissions of greenhouse gases and biosphere degradation toward a planetary threshold at ∼2 °C, beyond which the system follows an essentially irreversible pathway driven by intrinsic biogeophysical feedbacks. The other pathway leads to Stabilized Earth, a pathway of Earth System stewardship guided by human-created feedbacks to a quasistable, human-maintained basin of attraction. “Stability” (vertical axis) is defined here as the inverse of the potential energy of the system. Systems in a highly stable state (deep valley) have low potential energy, and considerable energy is required to move them out of this stable state. Systems in an unstable state (top of a hill) have high potential energy, and they require only a little additional energy to push them off the hill and down toward a valley of lower potential energy
Global Food Quantity and Diversity to Drop by More than Half with Our Accelerated Climate Warming
Paul Beckwith
The formal demography of kinship: Demographic stochasticity in the kinship network
Hal Caswell
Le hasard pris sur l'aile, préservé, reproduit par la machinerie de l'invariance et ainsi converti en ordre, règle et nécessité. Un processus totalement aveugle peut par définition conduire à n'importe quoi ; il peut même conduire à la vision elle-même.
Jacques Monod. 1970. Le Hasard et la Nécessité : Essai sur la philosophie naturelle de la biologie moderne, Paris, Éditions du Seuil, coll.
The Secret Language of Plants: The Incredible Intelligence of Plants
“𝘐 𝘭𝘪𝘬𝘦 𝘨𝘢𝘳𝘥𝘦𝘯𝘴, 𝘵𝘳𝘦𝘦𝘴, 𝘢𝘯𝘥 𝘶𝘯𝘮𝘦𝘤𝘩𝘢𝘯𝘪𝘻𝘦𝘥 𝘧𝘢𝘳𝘮𝘭𝘢𝘯𝘥𝘴; 𝘐 𝘴𝘮𝘰𝘬𝘦 𝘢 𝘱𝘪𝘱𝘦, 𝘢𝘯𝘥 𝘭𝘪𝘬𝘦 𝘨𝘰𝘰𝘥 𝘱𝘭𝘢𝘪𝘯 𝘧𝘰𝘰𝘥...”
The Letters of J. R. R. Tolkien, pp. 288-89.
En esta lista de videos se explora la importancia que tienen las interacciones ecológicas en el funcionamiento de los ecosistemas. Se parte de los casos más simples y conocidos, para posteriormente ir explorando fenómenos menos conocidos y más complejos.
Lista completa de videos:
https://www.youtube.com/playlist?list=PLAVCc09jUR88NecBkTEDk2Mjp2QEhTk0x
.
The Origins of Modern Maize - Jeff Ross-Ibara
Life, its origin, and its distribution: a perspective from the Conway-Kochen Theorem and the Free Energy Principle
Chris Fields aand Michael Levin
We argue here that the Origin of Life (OOL) problem is not just a chemistry problem but is also, and primarily, a cognitive science problem. When interpreted through the lens of the Conway-Kochen theorem and the Free Energy Principle, contemporary physics characterizes all complex dynamical systems that persist through time as Bayesian agents. If all persistent systems are to some – perhaps only minimal – extent cognitive, are all persistent systems to some extent alive, orare living systems only a subset of cognitive systems? We argue that no bright line can be drawn, and we re-assess, from this perspective, the Fermi paradox and the Drake equation. We conclude that improving our abilities to recognize and communicate with diverse intelligences in diverse embodiments, whether based on familiar biochemistry or not, will either resolve or obviate the OOL problem.
https://www.tandfonline.com/doi/epdf/10.1080/19420889.2025.2466017
WILD CLOCKS
by David Farrier
Attentive to the loss of age-old ecological relationships as “wild clocks” fall out of synchronization with each other, David Farrier imagines an opportunity to renew the rhythms by which we live.

These Lizards Have Been Playing Rock-Paper-Scissors for 15 Million Years
Winds of Change - Breathing a New Disciplinary Matrix Into Biology
Seth Bordenstein
Haulout
Maxim Arbugaev, Evgenia Arbugaeva (2022)
Understanding Relationships and Ecology
Fritjof Capra
How trees eat salmon: The circle of life, explained
Sean B. Carroll
Uniendo los Puntos:
Diego Griffon Briceño
Doctor en Ecología, Magíster en Entomología e Ingeniero Agrónomo. Consultor en modelaje matemático, simulación de procesos ecológicos, análisis de datos y aprendizaje estadístico en agroecosistemas. Profesor en la Universidad Central de Venezuela (cátedras Ecología de Poblaciones y Evolución) e investigador en las áreas de Ecología Teórica, Ecología Matemática y Agroecología.
Correo: diego.griffon@ciens.ucv.ve
Este blog tiene por objetivo la discusión de temas relacionados con Agroecología, Ecología social y Biocomplejidad.
Interacciones en la Agroecología
Número especial de la revista Acta Biologica Venezuelica
La Reina Roja
Reflexiones sobre el estado actual de la agricultura
"None of the human faculties should be excluded from scientific activity. The depths of intuition, a sure awareness of the present, mathematical profundity, physical exactitude, the heights of creative reason and sharpness of understanding, together with a versatile and ardent imagination and a loving delight in the world of the senses, they are all essential for a lively and productive apprehension of the moment."
J. W. Goethe (1749 - 1832)
No es una mercancía from Diego Griffon on Vimeo.
-----------------------o-----------------------
Si me vas a pegar no me grites
Película experimental en la cual se explora la conexión existente entre el modelo civilizatorio hegemónico actual y el surgimiento de formas particulares de relación del ser humano con el resto de la naturaleza. La película está construida como un collage, en el cual la visión crítica de la ecología social sirve de hilo conductor. En ella se utiliza a la agricultura para mostrar como el modelo civilizatorio hegemónico determina la materialización de tipos particulares de relaciones sociales, a la par que conduce a formas específicas de comprender y vincularse con la naturaleza. En la película también se muestra que existen alternativas a la lógica dominante, alternativas que actualmente coexisten en resistencia, luchando por sobrevivir.
-----------------------o-----------------------
......
.....Omnibus Dubitandum
.
La orquídea de noche esconde
en su perfume
el blanco de su flor.
Yosa Buson (1716-1783)
Ecology has been eminently a descriptive science despite some pioneering work by theoreticians such as Lotka, Volterra, Nicholson, and others. Description is a first step toward understanding a system. However, such a first step needs to be accompanied by the development of a theoretical framework in order to achieve real insight and, whenever possible, predictive power.
Ricard V. Solé and Jordi Bascompte, 2006 (Self-Organization in Complex Ecosystems).
"Toda pregunta es siempre más que una pregunta, está probando una carencia, una ansiedad por llenar un hueco intelectual o psicológico, y hay muchas veces en que el hecho de encontrar una respuesta es menos importante que haber sido capaz de vivir a fondo la pregunta, de avanzar ansiosamente por las pistas que tiende a abrir en nosotros"
Julio Cortázar. Desafíos.