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neytiri

05065

05165

• gaia
  james lovelock and our relationship to the earth as a living process

• the gaia hypothesis: science on a pagan planet
  michael ruse 2013 978-0-226-06039-2

  • “The Vanishing Face of Gaia: A Final Warning (2009). A year or two earlier, Lynn Margulis was writing an enthusiastic introduction (“inclusive, tolerant and enlightened”) to a book on Gaia called Animate Earth: Science, Intuition, and Gaia (2006) by Stephan Harding. And then there are The Gaia Project: 2012; The Earth’s Coming Great Changes (2007), by Hwee-Yong Jang (“the Earth is already undergoing a purification process”); and Earthy Realism: The Meaning of Gaia (2007), an edited volume including “Can Gaia Forgive Us,” by Anne Primavesi (“We have hurt, victimized, damaged the more-than-human community of life on Earth. If so, Gaia’s purposes and ours will be served by a repentance that acknowledges the wrong done and effects [sic] change in our lives that will heal relationships with the members of that community”). At a somewhat more practical level, there is Gaia’s Garden, Second Edition: A Guide to Home-Scale Permaculture (2009), by Toby Hemenway”
  • “Rupert Sheldrake is even more beyond the pale. He diverted the makings of a brilliant scientific career—double first (first class in two subjects) from Cambridge, research fellow of the Royal Society—into the writing of A New Science of Life: The Hypothesis of Morphic Resonance (1981). The editor of Nature wrote that his book was “an exercise in pseudo science” and asked if this was “a book for burning?” A follow-up book, The Rebirth of Nature: The Greening of Science and God, has Gaian fingerprints on virtually every page: “Mother Nature is reasserting herself whether we like it or not. In particular, the acknowledgement that our planet is a living organism, Gaia, Mother Earth, strikes a responsive chord in millions of people; it reconnects us both with our personal, intuitive experience of nature and with the traditional understanding of nature as alive” (Sheldrake 1991, 10).”
  • spencer: survival of the fittest
  • For Darwin, we will always have Malthus with us. For Spencer, in the end Malthus will become irrelevant (Young 1985).

• verde brillante: sensibilità e intelligenza del mondo vegetale
  brilliant green: the surprising history and science of plant intelligence
  stefano mancuso & alessandra viola 2013

  • “What brilliant researcher would devote herself to plants instead of animals, knowing that she will be excluded from the majority of scientific awards?
    As we have seen, this state of affairs is a natural outcome of our culture. In life as in science, the common scale of values relegates plants to last place among living things. An entire realm, the plant world, is underappreciated, despite the fact that our survival on the planet and our future depend on it.”

  • “in a liana native to Cuba, the Marcgravia evenia, circular leaves shaped like real satellite dishes have been described, whose only purpose appears to be to signal the presence of flowers to bats’ sonar.”

  • “Botanists and entomologists know very well that a bee will stay all day on the same species of flower it visited in the morning.”

• not yet read

  • homage to gaia: the life of an independent scientist
    james lovelock 2014

  • a rough ride to the future
    james lovelock 2015

  • the vanishing face of gaia: a final warning
    james lovelock 2009

  • gaia: a new look at life on earth
    james lovelock 1978

05265

• life in deep earth totals 15 to 23 billion tonnes of carbon—hundreds of times more than humans
  2018
  deepcarbon.net/life-deep-earth-totals-15-23-billion-tonnes-carbon

  • the biomass and biodiversity of the continental subsurface
    c. magnabosco et al. 2018
    doi.org/10.1038/s41561-018-0221-6

    • absrtact Despite accounting for a significant portion of the Earth’s prokaryotic biomass, controls on the abundance and biodiversity of microorganisms residing in the continental subsurface are poorly understood. To redress this, we compiled cell concentration and microbial diversity data from continental subsurface localities around the globe. Based on considerations of global heat flow, surface temperature, depth and lithology, we estimated that the continental subsurface hosts 2 to 6 × 1029 cells and found that other variables such as total organic carbon and groundwater cellular abundances do not appear to be predictive of cell concentrations in the continental subsurface. Although we were unable to identify a reliable predictor of species richness in the continental subsurface, we found that bacteria are more abundant than archaea and that their community composition was correlated to sample lithology. Using our updated continental subsurface cellular estimate and existing literature, we estimate that the total global prokaryotic biomass is approximately 23 to 31 Pg of carbon C (PgC), roughly 4 to 10 times less than previous estimates.

• kinetics and identities of extracellular peptidases in subsurface sediments of the white oak river estuary, nc
  andrew d. steen et al. 2019
  doi.org/10.1128/aem.00102-19

  • "These microbes live incredibly slow lives, with cells multiplying somewhere between every 10 years and every 10,000 years, but we aren't sure how," said Steen. "Our work shows that those microbes are living the same way any other microbe does, just way more slowly and with some improved ability to eat the low-quality food in their environment."
  • abstract Anoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily slow rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities (Vmax) decreased with increasing sediment depth, although Vmax expressed on a per cell basis was approximately the same at all depths. Half-saturation constants (Km) decreased with depth, indicating peptidases that functioned more efficiently at low substrate concentrations. Potential activities of extracellular peptidases acting on molecules that are enriched in degraded organic matter (D-phenylalanine and L-ornithine) increased relative to enzymes that act on L-phenylalanine, further suggesting microbial community adaptation to access degraded organic matter. Nineteen classes of predicted, exported peptidases were identified in genomic data from the same site, of which genes for class C25 (gingipain-like) peptidases represented more than 40% at each depth. Methionine aminopeptidases, zinc carboxypeptidases, and class S24-like peptidases, which are involved in single-stranded DNA repair, were also abundant. These results suggest a subsurface heterotrophic microbial community that primarily accesses low-quality detrital organic matter via a diverse suite of well-adapted extracellular enzymes.
    Importance Burial of organic carbon in marine and estuarine sediments represents a long-term sink for atmospheric carbon dioxide. Globally, ∼40% of organic carbon burial occurs in anoxic estuaries and deltaic systems. However, the ultimate controls on the amount of organic matter that is buried in sediments, versus oxidized into CO2, are poorly constrained. Here we used a combination of enzyme assays and metagenomic analysis to identify how subsurface microbial communities catalyze the first step of proteinaceous organic carbon degradation. Our results show that microbial communities in deeper sediments are adapted to access molecules characteristic of degraded organic matter, suggesting that those heterotrophs are adapted to life in the subsurface.

• forearc carbon sink reduces long-term volatile recycling into the mantle
  p. h. barry et al. 2019
  doi.org/10.1038/s41586-019-1131-5

  • At a subduction zone there is communication between Earth's surface and interior. Two plates collide and the denser plate sinks, transporting material from the surface into Earth's interior. Showing that the microbes at the near-surface are playing a fundamental role in how carbon and other elements are being locked up into the crust provides a profound new understanding of Earth processes and helps researchers model how Earth's interior may develop over time.

    Co-author, Professor Chris Ballentine, Head of the Department of Earth Sciences at the University of Oxford, said: 'What we've shown in this study is that in areas that are critically important for putting chemicals back down into the planet -- these big subduction zones -- life is sequestering carbon. On geological timescales life might be controlling the chemicals at the surface and storing elements like carbon in the crust.'

    This is the first evidence that subterranean life plays a role in removing carbon from subduction zones. It has been well established that microbes are capable of taking carbon dissolved in water and converting it into a mineral within the rocks. This study demonstrates that the process is happening on a large scale across a subduction zone. It is a natural CO2 sequestration process which can control the availability of carbon on Earth's surface.

    Lead author, Dr Peter Barry, who carried out the research while at the Department of Earth Sciences, Oxford University, said: 'We found that a substantial amount of carbon is being trapped in non-volcanic areas instead of escaping through volcanoes or sinking into Earth's interior.

    'Until this point scientists had assumed that life plays little to no role in whether this oceanic carbon is transported all the way into the mantle, but we found that life and chemical processes work together to be the gatekeepers of carbon delivery to the mantle.'

    During the 12-day expedition, the 25-person group of multi-disciplinary scientists collected water samples from thermal springs throughout Costa Rica. Scientists have long predicted that these thermal waters spit out ancient carbon molecules, subducted millions of years before. By comparing the relative amounts of two different kinds of carbon -- called isotopes -- the scientists showed that the predictions were true and that previously unrecognized processes were at work in the crust above the subduction zone, acting to trap large amounts of carbon.

    Following their analyses, the scientists estimated that about 94 percent of that carbon transforms into calcite minerals and microbial biomass.

    Senior author, Karen Lloyd, Associate Professor of Microbiology at the University of Tennessee, Knoxville, said: 'These microbes are literally sequestering carbon. Scientists are actively working on carbon sequestration to mitigate climate change and carbon capture and storage as a means to bury greenhouse gases over long time periods. Our study is a really good example of where this is happening naturally, and it was previously unrecognised. This study shows that this happens on a big, reservoir scale.'

    Maarten de Moor, co-author and professor at the National University of Costa Rica's Observatory of Volcanology and Seismology, said: 'It is amazing to consider that tiny microbes can potentially influence geological processes on similar scales as these powerful and visually impressive volcanoes, which are direct conduits to Earth's interior. The processes that we have identified in this study are less obvious, but they are important because they are operating over huge spatial areas in comparison to volcanoes.'

    The researchers now plan to investigate other subduction zones to see if this trend is widespread. If these biological and geochemical processes occur worldwide, they would translate to 19 percent less carbon entering the deep mantle than previously estimated.

    Co-author Donato Giovannelli, Assistant Professor at the University of Naples Federico II and affiliated scientist at the CNR-IRBIM and Rutgers University, said: 'There are likely even more ways that biology has had an outsized impact on geology, we just haven't discovered them yet.'

    Dr Peter Barry, now an Associate Scientist at Woods Hole Oceanographic Institution, added: 'We have people from three different fields working together and only with such an interdisciplinary approach can you make such breakthroughs. Moving forward, this will change how people look at these systems. For me that is thrilling.'

  • abstract Carbon and other volatiles in the form of gases, fluids or mineral phases are transported from Earth’s surface into the mantle at convergent margins, where the oceanic crust subducts beneath the continental crust. The efficiency of this transfer has profound implications for the nature and scale of geochemical heterogeneities in Earth’s deep mantle and shallow crustal reservoirs, as well as Earth’s oxidation state. However, the proportions of volatiles released from the forearc and backarc are not well constrained compared to fluxes from the volcanic arc front. Here we use helium and carbon isotope data from deeply sourced springs along two cross-arc transects to show that about 91 per cent of carbon released from the slab and mantle beneath the Costa Rican forearc is sequestered within the crust by calcite deposition. Around an additional three per cent is incorporated into the biomass through microbial chemolithoautotrophy, whereby microbes assimilate inorganic carbon into biomass. We estimate that between 1.2 × 108 and 1.3 × 1010 moles of carbon dioxide per year are released from the slab beneath the forearc, and thus up to about 19 per cent less carbon is being transferred into Earth’s deep mantle than previously estimated.

05365

• plants for a future: edible & useful plants for a healthier world
  ken fern 2000 9781856230117

• the incredible journey of plants
  stefano mancuso 2020

05465

• scenario planning with linked land-sea models inform where forest conservation actions will promote coral reef resilience
  j. m. s. delevaux et al. 2018
  doi.org/10.1038/s41598-018-29951-0

  • We developed a linked land-sea modeling framework based on remote sensing and empirical data, which couples sediment export and coral reef models at fine spatial resolution. This spatially-explicit (60 × 60 m) framework simultaneously tracks changes in multiple benthic and fish indicators as a function of land-use and climate change scenarios. We applied this framework in Kubulau District, Fiji, to investigate the effects of logging, agriculture expansion, and restoration on coral reef resilience. Under the deforestation scenario, models projected a 4.5-fold sediment increase (>7,000 t. yr−1) coupled with a significant decrease in benthic habitat quality across 1,940 ha and a reef fish biomass loss of 60.6 t. Under the restoration scenario, models projected a small (<30 t. yr−1) decrease in exported sediments, resulting in a significant increase in benthic habitat quality across 577 ha and a fish biomass gain of 5.7 t. The decrease in benthic habitat quality and loss of fish biomass were greater when combining climate change and deforestation scenarios. We evaluated where land-use change and bleaching scenarios would impact sediment runoff and downstream coral reefs to identify priority areas on land, where conservation or restoration could promote coral reef resilience in the face of climate change.

05565

• tomato seeds preferably transmit plant beneficial endophytes
  alessandro bergna et al. 2019
  doi.org/10.1094/pbiomes-06-18-0029-r

  • seed endophytes (microorganisms found in inner seed tissues) have distinct compositions and harbor different beneficial bacteria. The team also found that plant seeds were an important vector for the transmission of beneficial microorganisms across generations. Notably, they found that the seed is an important vehicle of plant growth-promoting bacteria.

    This novel discovery has an impact for the design of seed treatment. Cernava explains: "These findings provide a basis to further explore how plant seeds can be specifically equipped with beneficial microorganisms and provide the basis to develop sustainable alternative to chemical inputs, such as fertilizers and pesticides, in agriculture."

  • abstract Endophytes with plant growth-promoting activity can improve the health and development of plants during all life stages. However, less is known about their stability and transmission across plant genotypes, habitats, and generations. By combining community and isolate analyses, we found that each plant habitat and genotype harbored distinct bacterial communities and plant growth-promoting bacteria (PGPB). Soil, root endosphere, and rhizosphere were the habitats with the highest bacterial diversity, while seeds hosted more selective communities. Seeds generated under field conditions showed traces of a bacterial community composition connected to the suppression of plant pathogens. In contrast, seeds of the successive generation grown in a pathogen-free and low-nutrient environment showed a predominance of bacteria that facilitate the uptake of nutrients. These modifications of the microbiome can be explained by an adaptation to prevalent environmental conditions. Cultivation approaches revealed microhabitat-specific PGPB that were assigned to various species of Bacillus, Stenotrophomonas, and Ralstonia. Tracking down these bacteria among the whole tomato plant allowed us to identify the seed as a primary vehicle of PGPB transmission. This previously undescribed vertical transmission of PGPB represents a strategy to maintain plant beneficial bacteria over generations and has an impact for the design of seed treatments.

• advantage of leakage of essential metabolites for cells
  jumpei f. yamagishi et al. 2020
  doi.org/10.1103/physrevlett.124.048101

  • “It is in the nature of membranes to leak, but if leaking is undesirable, why has evolution not stopped it? This question of ‘Why?’ was never solved,” said Professor Kunihiko Kaneko, a theoretical biology expert from the University of Tokyo Research Center for Complex Systems Biology.
    The research team used calculations that can measure the changes of multiple factors over time, called dynamical-system modeling, in combination with computer simulations. In this modeling, the researchers considered the nonlinear processes for cell growth where a cell takes in external nutrients and converts them to cellular body and energy by intracellular chemical reactions, by representing the cellular state as the concentrations of intracellular chemicals including nutrients, enzymes, and components to synthesize cellular body. All calculations assumed that the model cells were in a steady state of growth where their internal metabolism and relative concentration of chemicals inside the cells were all stable.
    The calculations were designed to identify what types of chemical synthesis pathways would become more efficient if some of their components leaked out to the environment. The mathematical models of chemical synthesis paths are simpler than the complex branching pathways in living cells, but allow researchers to look for fundamental patterns.
    Researchers identified two such model chemical pathways with catalytic reactions that use enzymes to enhance the reaction rate, which they call the “flux control” and “growth-dilution” mechanisms. In both mechanisms, leaking one essential upstream chemical component of the pathway allows the end product to be produced more efficiently. Thus, leaking is something cells do to selfishly enhance their own growth.
    “In theory, the flux control mechanism enhances the pathway for biomass synthesis by the leakage of an essential chemical in an alternative branching pathway, whereas the growth-dilution mechanism enhances the biomass synthesis by the leakage of the precursors of biomass (e.g., amino acids) essential for cell growth. These are a result of the balance between chemical reactions and concentration dilution associated with cellular volume growth,” said Jumpei Yamagishi, a first-year graduate student who has worked in Kaneko’s laboratory since his undergraduate years.
    The models that the research team created so far only consider one type of cell at a time. However, leaking upstream components might become a problem for cells living only with identical types of cells leaking the same components.
    “In many cases, if all cells are leaking the same molecule, their environment will become ‘polluted.’ But if multiple cell types live together, then they can leak one chemical and use a different chemical leaked by the others,” said Kaneko.
    This mutually beneficial exchange of leaked essential nutrients may be a selfless way to enhance the growth of the whole community of cells.
    “Our work may partially answer why the natural environment is so different from artificial lab conditions where bacteria are grown in pure monocultures, but we will need additional models to be sure,” said Yamagishi.
    The researchers are planning to design more complex mathematical calculations to better simulate natural conditions where multiple types of cells coexist to see if that reveals other types of synthesis pathways that benefit from leaking.

  • abstract Microbial cells generally leak various metabolites including those necessary to grow. Why cells secrete even essential chemicals so often is, however, still unclear. Based on analytical and numerical calculations, we show that if the intracellular metabolism includes multibody (e.g., catalytic) reactions, leakage of essential metabolites can promote the leaking cell’s growth. This advantage is typical for most metabolic networks via “flux control” and “growth-dilution” mechanisms, as a general consequence of the balance between synthesis and growth-induced dilution with autocatalytic reactions. We further argue that this advantage may lead to a novel form of symbiosis among diverse cells.

05665

• the minds of plants: from the memories of flowers to the sociability of trees, the cognitive capacities of our vegetal cousins are all around us
  laura ruggles 2017
  aeon.co/essays/beyond-the-animal-brain-plants-have-cognitive-capacities-too

• decision-making in plants under competition
  michal gruntman et al. 2017
  doi.org/10.1038/s41467-017-02147-2

  • Plants can plastically respond to light competition in three strategies, comprising vertical growth, which promotes competitive dominance; shade tolerance, which maximises performance under shade; or lateral growth, which offers avoidance of competition. Here, we test the hypothesis that plants can ‘choose’ between these responses, according to their abilities to competitively overcome their neighbours. We study this hypothesis in the clonal plant Potentilla reptans using an experimental setup that simulates both the height and density of neighbours, thus presenting plants with different light-competition scenarios. Potentilla reptans ramets exhibit the highest vertical growth under simulated short-dense neighbours, highest specific leaf area (leaf area/dry mass) under tall-dense neighbours, and tend to increase total stolon length under tall-sparse neighbours. These responses suggest shifts between ‘confrontational’ vertical growth, shade tolerance and lateral-avoidance, respectively, and provide evidence that plants adopt one of several alternative plastic responses in a way that optimally corresponds to prevailing light-competition scenarios.

05765

• plant communication and sensing

  • das geheime leben der bäume
    the hidden life of trees
    peter wollheben 2015 9781771642491

  • how trees talk to each other
    suzanne simard 2016
    ted.com/talks/suzanne_simard_how_trees_talk_to_each_other#t-63012

  • interplant communication of tomato plants through underground common mycorrhizal networks
    song yy et al. 2010
    doi.org/10.1371/journal.pone.0013324

    • http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013324
    • Song et al. (Guangzhou, China; PLoS ONE) demonstrate interplant communication through mycorrhiza; good design of control experiments.

  • reconsidering plant memory: intersections between stress recovery, rna turnover, and epigenetics
    crisp et al. 2016
    doi: 10.1126/sciadv.1501340
    Link: advances.sciencemag.org/content/2/2/e1501340.full

    • plant memory and forgetting
    • some plants also appear to have a type of short-term memory that is not related to either DNA or RNA, but thus far it is not understood, primarily, because it has not yet been studied.

  • salivary cues: simulated roe deer browsing induces systemic changes in phytohormones and defence chemistry in wild-grown maple and beech saplings
    bettina ohse, almuth hammerbacher, carolin seele, stefan meldau, michael reichelt, sylvia ortmann, christian wirth 2016
    http://dx.doi.org/10.1111/1365-2435.12717
    Link: dx.doi.org/10.1111/1365-2435.12717

    • Tree saplings in temperate forests world-wide experience intense browsing from deer and other mammalian herbivores. However, when compared to insect herbivory, our knowledge about the cues that trigger mammalian-induced defence responses in trees is limited.
      We studied responses of field-grown saplings of European beech (Fagus sylvatica L.) and Sycamore maple (Acer pseudoplatanus L.) to simulated browsing by (i) clipping apical buds or leaves and (ii) additionally applying roe deer (Capreolus capreolus L.) saliva to the cut surface. We analysed induced changes in phytohormones and phenolics in the saplings’ remaining buds or leaves, respectively.
      In both species, jasmonates were activated after clipping of buds and leaves. Importantly, additional saliva application activated salicylic acid in beech leaves and led to increases in cytokinins in beech buds. Saliva application also led to an increased biosynthesis of several hydrolysable tannins (mainly ellagitannins) and flavonols in maple leaves. Condensed tannins, the most abundant phenolics in beech buds and leaves, did not change after either clipping or saliva application. However, clipping with additional saliva application decreased levels of phenolic acids (cinnamic acid derivatives) in beech buds.
      We conclude that the two tree species perceive and respond to unknown elicitors in the deer saliva, resulting in changes in phytohormone levels and defence-associated secondary metabolites.
      We suggest that variation in induced defence responses between tree species as well as between buds and leaves is related to differences in morphological traits, which interrelate with chemical traits and result in species-specific strategies to respond to mammalian herbivory.

  • the intelligent plant: scientists debate a new way of understanding flora
    michael pollan 2016
    http://www.newyorker.com/magazine/2013/12/23/the-intelligent-plant
    Link: newyorker.com/magazine/2013/12/23/the-intelligent-plant

  • spatially-dependent alkyl quinolone signaling responses to antibiotics in pseudomonas aeruginosa swarms
    nydia morales-soto et al. 2018
    http://dx.doi.org/10.1074/jbc.ra118.002605

    • There is a general lack of understanding about how communities of bacteria respond to exogenous toxins such as antibiotics. Most of our understanding of community-level stress responses comes from the study of stationary biofilm communities. Although several community behaviors and production of specific biomolecules affecting biofilm development and associated behavior have been described for Pseudomonas aeruginosa and other bacteria, we have little appreciation for the production and dispersal of secreted metabolites within the 2D and 3D spaces they occupy as they colonize, spread, and grow on surfaces. Here we specifically studied the phenotypic responses and spatial variability of alkyl quinolones, including the Pseudomonas quinolone signal (PQS) and members of the alkyl hydroxyquinoline (AQNO) subclass, in P. aeruginosa plate-assay swarming communities. We found that PQS production was not a universal signaling response to antibiotics as tobramycin elicited an alkyl quinolone response while carbenicillin did not. We also found that PQS and AQNO profiles in response to tobramycin were markedly distinct and influenced these swarms on different spatial scales. The distribution of alkyl quinolones varied by several orders of magnitude within the same swarm. At some tobramycin exposures, P. aeruginosa swarms produced alkyl quinolones in the range of 150 µM PQS and 400 µM AQNO that accumulated as aggregates. Our collective findings show that the distribution of alkyl quinolones can vary by several orders of magnitude within the same swarming community.  More notably, our results suggest that multiple intercellular signals acting on different spatial scales can be triggered by one common cue.

  • circadian entrainment in arabidopsis by the sugar-responsive transcription factor bzip63
    alexander frank et al. 2018
    http://dx.doi.org/10.1016/j.cub.2018.05.092

    • The transcription factor bZIP63 binds and regulates the circadian clock gene PRR7
      bZIP63 is required for adjustment of circadian period by sugars
      Trehalose-6-phosphate metabolism and KIN10 signaling regulate circadian period
      Sugar signals establish the correct circadian phase in light and dark cycles

      Synchronization of circadian clocks to the day-night cycle ensures the correct timing of biological events. This entrainment process is essential to ensure that the phase of the circadian oscillator is synchronized with daily events within the environment 1, to permit accurate anticipation of environmental changes [2, 3]. Entrainment in plants requires phase changes in the circadian oscillator, through unidentified pathways, which alter circadian oscillator gene expression in response to light, temperature, and sugars [4, 5, 6]. To determine how circadian clocks respond to metabolic rhythms, we investigated the mechanisms by which sugars adjust the circadian phase in Arabidopsis 5. We focused upon metabolic regulation because interactions occur between circadian oscillators and metabolism in several experimental systems [5, 7, 8, 9], but the molecular mechanisms are unidentified. Here, we demonstrate that the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) regulates the circadian oscillator gene PSEUDO RESPONSE REGULATOR7 (PRR7) to change the circadian phase in response to sugars. We find that SnRK1, a sugar-sensing kinase that regulates bZIP63 activity and circadian period [10, 11, 12, 13, 14] is required for sucrose-induced changes in circadian phase. Furthermore, TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1), which synthesizes the signaling sugar trehalose-6-phosphate, is required for circadian phase adjustment in response to sucrose. We demonstrate that daily rhythms of energy availability can entrain the circadian oscillator through the function of bZIP63, TPS1, and the KIN10 subunit of the SnRK1 energy sensor. This identifies a molecular mechanism that adjusts the circadian phase in response to sugars.

05865

• why are plants green?
  quieting a noisy antenna reproduces photosynthetic light-harvesting spectra
  trevor b. arp et al. 2020
  doi.org/10.1126/science.aba6630

  • model that reproduces a general feature of photosynthetic light harvesting, observed across many photosynthetic organisms.
    Light harvesting is the collection of solar energy by protein-bound chlorophyll molecules. In photosynthesis — the process by which green plants and some other organisms use sunlight to synthesize foods from carbon dioxide and water — light energy harvesting begins with sunlight absorption.
    The researchers’ model borrows ideas from the science of complex networks, a field of study that explores efficient operation in cellphone networks, brains, and the power grid. The model describes a simple network that is able to input light of two different colors, yet output a steady rate of solar power. This unusual choice of only two inputs has remarkable consequences.
    “Our model shows that by absorbing only very specific colors of light, photosynthetic organisms may automatically protect themselves against sudden changes — or ‘noise’ — in solar energy, resulting in remarkably efficient power conversion,” said Gabor, an associate professor of physics and astronomy, who led the study appearing today in the journal Science. “Green plants appear green and purple bacteria appear purple because only specific regions of the spectrum from which they absorb are suited for protection against rapidly changing solar energy.”
    Gabor first began thinking about photosynthesis research more than a decade ago, when he was a doctoral student at Cornell University. He wondered why plants rejected green light, the most intense solar light. Over the years, he worked with physicists and biologists worldwide to learn more about statistical methods and the quantum biology of photosynthesis.
    Richard Cogdell, a botanist at the University of Glasgow in the United Kingdom and a coauthor on the research paper, encouraged Gabor to extend the model to include a wider range of photosynthetic organisms that grow in environments where the incident solar spectrum is very different.
    “Excitingly, we were then able to show that the model worked in other photosynthetic organisms besides green plants, and that the model identified a general and fundamental property of photosynthetic light harvesting,” he said. “Our study shows how, by choosing where you absorb solar energy in relation to the incident solar spectrum, you can minimize the noise on the output — information that can be used to enhance the performance of solar cells.”
    Coauthor Rienk van Grondelle, an influential experimental physicist at Vrije Universiteit Amsterdam in the Netherlands who works on the primary physical processes of photosynthesis, said the team found the absorption spectra of certain photosynthetic systems select certain spectral excitation regions that cancel the noise and maximize the energy stored.
    “This very simple design principle could also be applied in the design of human-made solar cells,” said van Grondelle, who has vast experience with photosynthetic light harvesting.
    Gabor explained that plants and other photosynthetic organisms have a wide variety of tactics to prevent damage due to overexposure to the sun, ranging from molecular mechanisms of energy release to physical movement of the leaf to track the sun. Plants have even developed effective protection against UV light, just as in sunscreen.
    “In the complex process of photosynthesis, it is clear that protecting the organism from overexposure is the driving factor in successful energy production, and this is the inspiration we used to develop our model,” he said. “Our model incorporates relatively simple physics, yet it is consistent with a vast set of observations in biology. This is remarkably rare. If our model holds up to continued experiments, we may find even more agreement between theory and observations, giving rich insight into the inner workings of nature.”
    To construct the model, Gabor and his colleagues applied straightforward physics of networks to the complex details of biology, and were able to make clear, quantitative, and generic statements about highly diverse photosynthetic organisms.
    “Our model is the first hypothesis-driven explanation for why plants are green, and we give a roadmap to test the model through more detailed experiments,” Gabor said.
    Photosynthesis may be thought of as a kitchen sink, Gabor added, where a faucet flows water in and a drain allows the water to flow out. If the flow into the sink is much bigger than the outward flow, the sink overflows and the water spills all over the floor.
    “In photosynthesis, if the flow of solar power into the light harvesting network is significantly larger than the flow out, the photosynthetic network must adapt to reduce the sudden over-flow of energy,” he said. “When the network fails to manage these fluctuations, the organism attempts to expel the extra energy. In doing so, the organism undergoes oxidative stress, which damages cells.”
    The researchers were surprised by how general and simple their model is.
    “Nature will always surprise you,” Gabor said. “Something that seems so complicated and complex might operate based on a few basic rules. We applied the model to organisms in different photosynthetic niches and continue to reproduce accurate absorption spectra. In biology, there are exceptions to every rule, so much so that finding a rule is usually very difficult. Surprisingly, we seem to have found one of the rules of photosynthetic life.”
    Gabor noted that over the last several decades, photosynthesis research has focused mainly on the structure and function of the microscopic components of the photosynthetic process.
    “Biologists know well that biological systems are not generally finely tuned given the fact that organisms have little control over their external conditions,” he said. “This contradiction has so far been unaddressed because no model exists that connects microscopic processes with macroscopic properties. Our work represents the first quantitative physical model that tackles this contradi

  • abstract Photosynthesis achieves near unity light-harvesting quantum efficiency yet it remains unknown whether there exists a fundamental organizing principle giving rise to robust light harvesting in the presence of dynamic light conditions and noisy physiological environments. Here, we present a noise-canceling network model that relates noisy physiological conditions, power conversion efficiency, and the resulting absorption spectra of photosynthetic organisms. Using light conditions in full solar exposure, light filtered by oxygenic phototrophs, and light filtered under seawater, we derived optimal absorption characteristics for efficient solar power conversion. We show how light-harvesting antennae can be tuned to maximize power conversion efficiency by minimizing excitation noise, thus providing a unified theoretical basis for the observed wavelength dependence of absorption in green plants, purple bacteria, and green sulfur bacteria.

05965

• understanding the molecular basis of salt sequestration in epidermal bladder cells of chenopodium quinoa
  jennifer böhm et al. 2018
  http://dx.doi.org/10.1016/j.cub.2018.08.004

  • HKT1-type channels mediate a one-way sodium load into quinoa bladder cells
    ClC transporters operate in the Cl− sequestration into vacuoles of bladder cells
    The bladder cytoplasm is osmotically balanced by potassium and proline import
    On the transcript level, bladders are “constitutively active” for salt sequestration

    Soil salinity is destroying arable land and is considered to be one of the major threats to global food security in the 21st century. Therefore, the ability of naturally salt-tolerant halophyte plants to sequester large quantities of salt in external structures, such as epidermal bladder cells (EBCs), is of great interest. Using Chenopodium quinoa, a pseudo-cereal halophyte of great economic potential, we have shown previously that, upon removal of salt bladders, quinoa becomes salt sensitive. In this work, we analyzed the molecular mechanism underlying the unique salt dumping capabilities of bladder cells in quinoa. The transporters differentially expressed in the EBC transcriptome and functional electrophysiological testing of key EBC transporters in Xenopus oocytes revealed that loading of Na+ and Cl− into EBCs is mediated by a set of tailored plasma and vacuole membrane-based sodium-selective channel and chloride-permeable transporter.

06065

• caroline merchant
  • radical ecology
  • the death of nature

06165

• biochar

  • short-term changes in physical and chemical properties of soil charcoal support enhanced landscape mobility
    lacey a. pyle et al. 2017
    http://dx.doi.org/10.1002/2017jg003938

    • Charcoal is a major component of the stable soil organic carbon reservoir, and the physical and chemical properties of charcoal can sometimes significantly alter bulk soil properties (e.g., by increasing soil water holding capacity). However, our understanding of the residence time of soil charcoal remains uncertain, with old measured soil charcoal ages in apparent conflict with relatively short modeled and measured residence times. These discrepancies may exist because the fate of charcoal on the landscape is a function not just of its resistance to biological decomposition but also its physical mobility. Mobility may be important in controlling charcoal landscape residence time and may artificially inflate estimates of its degradability, but few studies have examined charcoal vulnerability to physical redistribution. Charcoal landscape redistribution is likely higher than other organic carbon fractions owing to charcoal’s low bulk density, typically less than 1.0 g/cm3. Here we examine both the physical and chemical properties of soil and charcoal over a period of two years following a 2011 wildfire in Texas. We find little change in properties with time; however, we find evidence of enhanced mobility of charcoal relative to other forms of soil organic matter. These data add to a growing body of evidence that charcoal is preferentially eroded, offering another explanation for variations observed in its environmental residence times.

• uncoupling human and climate drivers of late holocene vegetation change in southern brazil
  mark robinson et al. 2018
  http://dx.doi.org/10.1038/s41598-018-24429-5

  • In the highlands of southern Brazil an anthropogenitcally driven expansion of forest occurred at the expense of grasslands between 1410 and 900 cal BP, coincident with a period of demographic and cultural change in the region. Previous studies have debated the relative contributions of increasing wetter and warmer climate conditions and human landscape modifications to forest expansion, but generally lacked high resoltiuon proxies to measure these effects, or have relied on single proxies to reconstruct both climate and vegetation. Here, we develop and test a model of natural ecosystem distribution against vegetation histories, paleoclimate proxies, and the archaeological record to distinguish human from temperature and precipitation impacts on the distribution and expansion of Araucaria forests during the late Holocene. Carbon isotopes from soil profiles confirm that in spite of climatic fluctuations, vegetation was stable and forests were spatially limited to south-facing slopes in the absence of human inputs. In contrast, forest management strategies for the past 1400 years expanded this economically important forest beyond its natural geographic boundaries in areas of dense pre-Columbian occupation, suggesting that landscape modifications were linked to demographic changes, the effects of which are still visible today.

06265

• edge fires drive the shape and stability of tropical forests
  laurent hébert-dufresne et al. 2018
  http://dx.doi.org/10.1111/ele.12942

  • In tropical regions, fires propagate readily in grasslands but typically consume only edges of forest patches. Thus, forest patches grow due to tree propagation and shrink by fires in surrounding grasslands. The interplay between these competing edge effects is unknown, but critical in determining the shape and stability of individual forest patches, as well the landscape‐level spatial distribution and stability of forests. We analyze high‐resolution remote‐sensing data from protected Brazilian Cerrado areas and find that forest shapes obey a robust perimeter–area scaling relation across climatic zones. We explain this scaling by introducing a heterogeneous fire propagation model of tropical forest‐grassland ecotones. Deviations from this perimeter–area relation determine the stability of individual forest patches. At a larger scale, our model predicts that the relative rates of tree growth due to propagative expansion and long‐distance seed dispersal determine whether collapse of regional‐scale tree cover is continuous or discontinuous as fire frequency changes.

06365

• the fate of rome: climate, disease, and the end of an empire
  kyle harper 2017 9781400888917

  • “The ancients revered the frightful sway of the goddess Fortuna, aware, in their own way, that the presiding powers of history seem to be a volatile mix of structure and chance, laws of nature and sheer luck. The Romans lived at a fateful juncture in the human story, and the civilization they built was, in ways the Romans could not have imagined, the victim both of its own success and the caprice of the environment. The enduring power of the Romans to enchant us derives, at least in part, from the poignancy of our knowledge that they stood on the invisible edge of unsuspected change. The long, intertwined story of humanity and nature is full of paradox, surprise, and blind chance. That is why the particularity of history matters. Nature, like humanity, is cunning, but constrained by the circumstances of the past. Our story, and the story of the planet, are inseparable.”
  • The Romans knew that life was evanescent, and that the winds of death could sweep back their hard-fought gains in a moment.

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• pathways of influence in emotional appeals: benefits and tradeoffs of using fear or humor to promote climate change-related intentions and risk perceptions
  christofer skurka et al. 2018
  http://dx.doi.org/10.1093/joc/jqx008

  • Though fear appeals have largely been the default emotional appeal to motivate prosocial behaviors, research indicates that other emotionally charged messages, like those using humor, may also be effective. We conducted an experiment to compare the effects of fear and humor appeals on climate change-related behavioral intentions and perceived risk of climate change. We randomly assigned young adults to view one of three videos about climate change (fear, humor, informational) or a control video. Compared to control, viewing the fear or humor appeal produced greater climate change activism intentions, but only the fear appeal directly affected risk perceptions. Mediation analyses highlighted tradeoffs for fear and humor appeals, and moderation analyses demonstrated an age-by-appeal interaction effect on intentions and perceived risk.

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• african biomass burning is a substantial source of phosphorus deposition to the amazon, tropical atlantic ocean, and southern ocean
  anne e. barkley et al. 2019
  http://dx.doi.org/10.1073/pnas.1906091116

  • Nutrients found in atmospheric particles, called aerosols, are transported by winds and deposited to the ocean and on land where they stimulate the productivity of marine phytoplankton and terrestrial plants leading to the sequestration of atmospheric carbon dioxide.

    "It had been assumed that Saharan dust was the main fertilizer to the Amazon Basin and Tropical Atlantic Ocean by supplying phosphorus to both of these ecosystems," said the study's senior author Cassandra Gaston, an assistant professor in the Department of Atmospheric Sciences at the UM Rosenstiel School. "Our findings reveal that biomass burning emissions transported from Africa are potentially a more important source of phosphorus to these ecosystems than dust."

    To conduct the study, the researchers analyzed aerosols collected on filters from a hilltop in French Guiana, at the northern edge of the Amazon Basin, for mass concentrations of windborne dust and their total and soluble phosphorus content. They then tracked the smoke moving through the atmosphere using satellite remote sensing tools to understand the long-range transport of smoke from Africa during time periods when elevated levels of soluble phosphorus were detected. They were then able to estimate the amount of phosphorus deposited to the Amazon Basin and the global oceans from African biomass burning aerosols using a transport model.

    The analysis concluded that the smoke from widespread biomass burning in Africa, mostly the result of land clearing, brush fires and industrial combustion emissions, is potentially a more important source of phosphorus to the Amazon rainforest and Tropic Atlantic and Southern oceans than dust from the Sahara Desert.

    "To our surprise, we discovered that phosphorus associated with smoke from southern Africa can be blown all the way to the Amazon and, potentially, out over the Southern Ocean where it can impact primary productivity and the drawdown of carbon dioxide in both ecosystems," said UM Rosenstiel School graduate student Anne Barkley, lead author of the study.

    "Aerosols play a major role in Earth's climate, however, there is a lot that we don't understand regarding how they affect radiation, clouds, and biogeochemical cycles, which impedes our ability to accurately predict future increases in global temperature," said Gaston. "These new findings have implications for how this process might look in the future as combustion and fire emissions in Africa and dust transport patterns and amounts change with a changing climate and an increasing human population."

  • abstract The deposition of phosphorus (P) from African dust is believed to play an important role in bolstering primary productivity in the Amazon Basin and Tropical Atlantic Ocean (TAO), leading to sequestration of carbon dioxide. However, there are few measurements of African dust in South America that can robustly test this hypothesis and even fewer measurements of soluble P, which is readily available for stimulating primary production in the ocean. To test this hypothesis, we measured total and soluble P in long-range transported aerosols collected in Cayenne, French Guiana, a TAO coastal site located at the northeastern edge of the Amazon. Our measurements confirm that in boreal spring when African dust transport is greatest, dust supplies the majority of P, of which 5% is soluble. In boreal fall, when dust transport is at an annual minimum, we measured unexpectedly high concentrations of soluble P, which we show is associated with the transport of biomass burning (BB) from southern Africa. Integrating our results into a chemical transport model, we show that African BB supplies up to half of the P deposited annually to the Amazon from transported African aerosol. This observational study links P-rich BB aerosols from Africa to enhanced P deposition in the Amazon. Contrary to current thought, we also show that African BB is a more important source of soluble P than dust to the TAO and oceans in the Southern Hemisphere and may be more important for marine productivity, particularly in boreal summer and fall.

• pervasive phosphorus limitation of tree species but not communities in tropical forests
  benjamin l. turner et al. 2018
  http://dx.doi.org/10.1038/nature25789

  • Phosphorus availability is widely assumed to limit primary productivity in tropical forests7,8, but support for this paradigm is equivocal9. Although biogeochemical theory predicts that phosphorus limitation should be prevalent on old, strongly weathered soils10,11, experimental manipulations have failed to detect a consistent response to phosphorus addition in species-rich lowland tropical forests12,13,14,15. Here we show, by quantifying the growth of 541 tropical tree species across a steep natural phosphorus gradient in Panama, that phosphorus limitation is widespread at the level of individual species and strengthens markedly below a threshold of two parts per million exchangeable soil phosphate. However, this pervasive species-specific phosphorus limitation does not translate into a community-wide response, because some species grow rapidly on infertile soils despite extremely low phosphorus availability. These results redefine our understanding of nutrient limitation in diverse plant communities and have important implications for attempts to predict the response of tropical forests to environmental change.

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• aux1-mediated root hair auxin influx governs scftir1/afb -type ca2 signaling
  julian dindas et al. 2018
  ncbi.nlm.nih.gov/pmc/articles/pmid/29563504/
  http://dx.doi.org/10.1038/s41467-018-03582-5

  • Auxin is a key regulator of plant growth and development, but the causal relationship between hormone transport and root responses remains unresolved. Here we describe auxin uptake, together with early steps in signaling, in Arabidopsis root hairs. Using intracellular microelectrodes we show membrane depolarization, in response to IAA in a concentration- and pH-dependent manner. This depolarization is strongly impaired in aux1 mutants, indicating that AUX1 is the major transporter for auxin uptake in root hairs. Local intracellular auxin application triggers Ca2+ signals that propagate as long-distance waves between root cells and modulate their auxin responses. AUX1-mediated IAA transport, as well as IAA- triggered calcium signals, are blocked by treatment with the SCFTIR1/AFB - inhibitor auxinole. Further, they are strongly reduced in the tir1afb2afb3 and the cngc14 mutant. Our study reveals that the AUX1 transporter, the SCFTIR1/AFB receptor and the CNGC14 Ca2+ channel, mediate fast auxin signaling in roots.

• glutamate triggers long-distance, calcium-based plant defense signaling
  masatsugu toyota et al. 2018
  http://dx.doi.org/10.1126/science.aat7744

  • A plant injured on one leaf by a nibbling insect can alert its other leaves to begin anticipatory defense responses. Working in the model plant Arabidopsis, Toyota et al. show that this systemic signal begins with the release of glutamate, which is perceived by glutamate receptor–like ion channels. The ion channels then set off a cascade of changes in calcium ion concentration that propagate through the phloem vasculature and through intercellular channels called plasmodesmata. This glutamate-based long-distance signaling is rapid: Within minutes, an undamaged leaf can respond to the fate of a distant leaf.

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07165

• drivers of vegetative dormancy across herbaceous perennial plant species
  richard p. shefferson et al. 2018
  http://dx.doi.org/10.1111/ele.12940

  • Vegetative dormancy, that is the temporary absence of aboveground growth for ≥ 1 year, is paradoxical, because plants cannot photosynthesise or flower during dormant periods. We test ecological and evolutionary hypotheses for its widespread persistence. We show that dormancy has evolved numerous times. Most species displaying dormancy exhibit life‐history costs of sprouting, and of dormancy. Short‐lived and mycoheterotrophic species have higher proportions of dormant plants than long‐lived species and species with other nutritional modes. Foliage loss is associated with higher future dormancy levels, suggesting that carbon limitation promotes dormancy. Maximum dormancy duration is shorter under higher precipitation and at higher latitudes, the latter suggesting an important role for competition or herbivory. Study length affects estimates of some demographic parameters. Our results identify life historical and environmental drivers of dormancy. We also highlight the evolutionary importance of the little understood costs of sprouting and growth, latitudinal stress gradients and mixed nutritional modes.

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07665

• a lignin molecular brace controls precision processing of cell walls critical for surface integrity in arabidopsis
  yuree lee et al. 2018
  http://dx.doi.org/10.1016/j.cell.2018.03.060

  • •Two neighboring cell types coordinate cellular activities for organ separation
    •A honeycomb structure of lignin acts as a “molecular brace”
    •The lignin brace spatially restricts cell wall breakdown
    •Lignin deposition ensures surface integrity of transdifferentiated epidermal cells

    The cell wall, a defining feature of plants, provides a rigid structure critical for bonding cells together. To overcome this physical constraint, plants must process cell wall linkages during growth and development. However, little is known about the mechanism guiding cell-cell detachment and cell wall remodeling. Here, we identify two neighboring cell types in Arabidopsis that coordinate their activities to control cell wall processing, thereby ensuring precise abscission to discard organs. One cell type produces a honeycomb structure of lignin, which acts as a mechanical “brace” to localize cell wall breakdown and spatially limit abscising cells. The second cell type undergoes transdifferentiation into epidermal cells, forming protective cuticle, demonstrating de novo specification of epidermal cells, previously thought to be restricted to embryogenesis. Loss of the lignin brace leads to inadequate cuticle formation, resulting in surface barrier defects and susceptible to infection. Together, we show how plants precisely accomplish abscission.

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• previsual symptoms of xylella fastidiosa infection revealed in spectral plant-trait alterations
  p. j. zarco-tejada et al. 2018
  http://dx.doi.org/10.1038/s41477-018-0189-7

  • Plant pathogens cause significant losses to agricultural yields and increasingly threaten food security17, ecosystem integrity and societies in general2,3,4,21. Xylella fastidiosa is one of the most dangerous plant bacteria worldwide, causing several diseases with profound impacts on agriculture and the environment22. Primarily occurring in the Americas, its recent discovery in Asia and Europe demonstrates that X. fastidiosa’s geographic range has broadened considerably, positioning it as a reemerging global threat that has caused socioeconomic and cultural damage23,8. X. fastidiosa can infect more than 350 plant species worldwide9, and early detection is critical for its eradication8. In this article, we show that changes in plant functional traits retrieved from airborne imaging spectroscopy and thermography can reveal X. fastidiosa infection in olive trees before symptoms are visible. We obtained accuracies of disease detection, confirmed by quantitative polymerase chain reaction, exceeding 80% when high-resolution fluorescence quantified by three-dimensional simulations and thermal stress indicators were coupled with photosynthetic traits sensitive to rapid pigment dynamics and degradation. Moreover, we found that the visually asymptomatic trees originally scored as affected by spectral plant-trait alterations, developed X. fastidiosa symptoms at almost double the rate of the asymptomatic trees classified as not affected by remote sensing. We demonstrate that spectral plant-trait alterations caused by X. fastidiosa infection are detectable previsually at the landscape scale, a critical requirement to help eradicate some of the most devastating plant diseases worldwide.

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• transient phenomena in ecology
  alan hastings et al. 2018
  http://dx.doi.org/10.1126/science.aat6412

  • Ecological systems sometimes experience sudden changes in their properties or function which often results in species extinction and significant loss of biodiversity.
    Understanding why these significant changes occur remains a challenge, in particular because transitions often happen under apparently steady, constant conditions and therefore cannot be directly linked to a specific environmental change.
    By bringing together empirical data, insights from ecological theory and mathematical models, the team has revealed that abrupt transitions in an ecosystem can occur as a result of long-term transient dynamics, including ‘ghost attractors’ and ‘crawl-bys’.
    An attractor is an ‘end-state’ of a given ecosystem, that is where it expected to be found over an infinitely long period of time and/or where it returns after small perturbations.
    A ‘ghost attractor’ is a special configuration of a dynamical system that exhibits the same behaviour as an attractor but only for a finite time within an ecosystem. After that time, the system would normally experience a fast evolution or transition to another state which can have very different properties. Such transition would therefore correspond to a catastrophe or major ecological shift.
    ‘Crawl-bys’, on the other hand, exist when changes to the dynamic of an ecosystem happen slowly over a long period of time.
    Professor Petrovskii explained: “An ecological catastrophe emerging from a ‘ghost attractor’ or a ‘crawl-by’ may be a debt that we have to pay for the actions or mistakes — for example unsustainable use of natural resources — made many generations ago.
    “Our research shows that a healthy ecosystem will not necessarily remain healthy, even in the absence of any significant environmental change. Therefore, better monitoring of the state of an ecosystem is required to mitigate potential disasters.
    “We also can predict an approaching catastrophe in the sense that our study advises where to look for its signs and what is the relevant time scale: the environmental change (whether it is natural or human-made) that will finally lead to big changes might have happened a very long time ago.
    “These findings create a new paradigm as well as a powerful theoretical framework for understanding — and potentially predicting — ecological catastrophes and for their efficient management.”

08265

• a separated vortex ring underlies the flight of the dandelion
  cathal cummins et al. 2018
  http://dx.doi.org/10.1038/s41586-018-0604-2

  • Wind-dispersed plants have evolved ingenious ways to lift their seeds24,25. The common dandelion uses a bundle of drag-enhancing bristles (the pappus) that helps to keep their seeds aloft. This passive flight mechanism is highly effective, enabling seed dispersal over formidable distances26,27; however, the physics underpinning pappus-mediated flight remains unresolved. Here we visualized the flow around dandelion seeds, uncovering an extraordinary type of vortex. This vortex is a ring of recirculating fluid, which is detached owing to the flow passing through the pappus. We hypothesized that the circular disk-like geometry and the porosity of the pappus are the key design features that enable the formation of the separated vortex ring. The porosity gradient was surveyed using microfabricated disks, and a disk with a similar porosity was found to be able to recapitulate the flow behaviour of the pappus. The porosity of the dandelion pappus appears to be tuned precisely to stabilize the vortex, while maximizing aerodynamic loading and minimizing material requirements. The discovery of the separated vortex ring provides evidence of the existence of a new class of fluid behaviour around fluid-immersed bodies that may underlie locomotion, weight reduction and particle retention in biological and manmade structures.

• a novel adaptation facilitates seed establishment under marine turbulent flows
  gary a. kendrick et al. 2020
  http://dx.doi.org/10.1038/s41598-019-56202-7

  • one group of seagrasses, Australian species of the genus Posidonia, have evolved yet another remarkable adaptation for ocean survival: a winged seed whose shape harnesses the force of underwater currents to hold it on the seafloor for rooting.
    Results of the study offer valuable insights for efforts to restore seagrass populations in Australia, the Chesapeake Bay, and elsewhere. Seagrass meadows, which provide important nursery and feeding habitat for other marine life and play a key role in maintaining water quality, are under threat worldwide from warming and over-fertilization of coastal waters.
    Published in a recent issue of Scientific Reports, the seagrass study is the first to record a winged seed among marine angiosperms, and to experimentally determine its adaptive benefit. It also shows that seeds of Posidonia species in areas with stronger currents have larger wings, further evidence of the trait’s utility.
    Lead author on the report was Dr. Gary Kendrick of the University of Western Australia. The research emerged from a long-term collaboration between Kendrick and Dr. Robert “JJ” Orth of William & Mary’s Virginia Institute of Marine Science, a pioneer in monitoring and restoring seagrasses in the Chesapeake Bay and mid-Atlantic coastal lagoons. Also contributing to the study were Marion Cambridge, Jeremy Shaw, Lukasz Kotula, and Ryan Lowe of UWA and Andrew Pomeroy of the Australian Institute for Marine Science.
    “Understanding the basic biology of seeds and their establishment allows us to optimize our seed-based restoration practices,” says Kendrick. “Working with JJ and the team at VIMS — using their deep understanding of the world the seed experiences — has resulted in a truly interdisciplinary outcome that combines the skills of seagrass and restoration biologists, plant anatomists, and hydrodynamic modelers.”
    A serendipitous seed story

    Winged seeds are commonly used by land plants for dispersal by wind, with the helicopter-like seeds of maple and ash trees a familiar example. So when Orth first noted the wing-like structure on Posidonia seeds during Australian fieldwork in the mid-1990s, his initial thought was that it served a similar function.
    “My preliminary hypothesis was that [the wing] would serve to move the seed farther away from the parent plant when it was released from the fruit,” says Orth. Posidonia produces large buoyant fruits that break off from the adult plant and can float kilometers away, releasing seeds as they mature.
    But years of painstaking research showed the opposite. “When released from the fruit,” says Orth, “the seeds drop really fast.”
    Based on that finding, Orth and colleagues developed a second working hypothesis, that the purpose of the wing was to get the seed to the bottom quickly, before it could be eaten by predators. But field research again proved them wrong. “It turns out not many creatures like to eat these seeds, except for crabs and other small crustaceans,” says Orth.
    The third time’s the charm
    The researchers’ path to discovering the wing’s true function began when Dr. Marion Cambridge of UWA’s Oceans Institute suggested a third hypothesis — that the wing keeps the seed at the sediment surface until it can grow anchoring roots.

    To test this hypothesis, the team carefully measured the surface area of the seeds using both scanning electron microscopy and X-ray tomography, gauged the flow of currents around seeds placed in a flume, and used these data to build a computer model of the relevant hydrodynamic forces.
    “When we brought in Andrew [Pomeroy], a hydrodynamics expert, he got pretty excited about what he saw,” says Orth. “He launched the modeling effort that’s highlighted in the paper. Together with our microscopy and flume data, it clearly supports the idea that the wing helps the seed maintain its position on the bottom, very similar to how flatfishes can stay on the bottom in strong currents.”
    In sum, rather than helping to lift and disperse the seeds as with maples, the team’s research shows that evolution has engineered the Posidonia wing to push the seed against the seafloor, like the downforce generated by the wing on the rear of a race car.
    Stronger currents, larger wings
    Further support for the team’s hypothesis comes from their comparison of wing width in the seeds of Australia’s three Posidonia species, which inhabit a gradient of coastal habitats from current-scoured open shorelines to more sheltered bays.
    “The neatest thing about the project,” says Orth, “is that the width of the wing differs in the three species that dominate the west coast of Australia, and correlates with each species’ environment. Posidonia coriacea, which lives in the most wave-swept areas, has the widest wing, while the other two species — australis and sinuosa — live under calmer conditions and have smaller wings.” This correlation extends all the way to the quiet waters of the Mediterranean, where a relict population of the same genus (P. oceanica) has seeds with barely any wing at all.

  • abstract Seeds of Australian species of the seagrass genus Posidonia are covered by a membranous wing that we hypothesize plays a fundamental role in seed establishment in sandy, wave swept marine environments. Dimensions of the seed and membrane were quantified under electron microscopy and micro-CT scans, and used to model rotational, drag and lift forces. Seeds maintain contact with the seabed in the presence of strong turbulence: the larger the wing, the more stable the seed. Wing surface area increases from P. sinuosa < P. australis < P.coriacea correlating with their ability to establish in increasingly energetic environments. This unique seed trait in a marine angiosperm corresponds to adaptive pressures imposed on seagrass species along 7,500 km of Australia’s coastline, from open, high energy coasts to calmer environments in bays and estuaries.
    Progress: 100%

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• field analysis of psychological effects of urban design: a case study in vancouver
  hanna r. negami et al. 2019
  http://doi.org/10.1080/23748834.2018.1548257

  • Researchers found that green spaces and colourful, community-driven urban design elements were associated with higher levels of happiness, greater trust of strangers, and greater environmental stewardship than locations without those amenities.

    "The urban design interventions we studied are relatively simple and low-cost, but show great potential to improve individuals' emotional and social lives," says Hanna Negami, lead author and PhD candidate in cognitive neuroscience. "Something as simple as adding greenery to a concrete lane or painting a rainbow crosswalk could help to enrich urban public spaces."

    For the study, participants were taken on walking tours of Vancouver's West End neighbourhood and asked to complete a questionnaire via a smartphone application at six stops, including a pair of laneways (one green, one concrete), crosswalks (one painted rainbow, one standard zebra), and a pair of greenspaces (one wild community garden and one manicured greenspace).

    The addition of greenspace and place-making initiatives can help promote social connections for citizens, and help to mitigate social isolation. Researchers hope that these findings will ultimately help improve the experiences of people living in cities.

    "We know that the design of a city has direct, measurable, psychological impact on its citizens," says Colin Ellard, professor of psychology and director of the Urban Realities Lab. "We've been able to show how such impact can be measured and what it can tell us about good, psychologically sustainable design."

  • abstract City densification is associated with increased social isolation and poorer physical and mental health. As an important environmental and social context, the urban environment has great potential to shape residents’ experiences and social interactions, as well as to mitigate social isolation by promoting trust and sociability. The current study examines the effects of urban design interventions, such as colorful crosswalks and greenery, on participants’ mental well-being, sociability and feelings of environmental stewardship. Participants were led on walks of Vancouver’s West End neighborhood, stopping at six sites (three intervention and three comparison sites) to indicate their emotional response to and perception of the environment using a smartphone application. Spaces with greenery and spaces with a colorful, community-driven urban intervention were associated with higher levels of happiness, trust, stewardship and attraction to the sites than their more standard comparison sites. Our findings demonstrate that simple urban design interventions can increase subjective well-being and sociability among city residents. Further, our experiment presents a novel environmental-psychological field methodology for collecting empirical affective and cognitive data on how individuals respond to urban design.

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• the balance of interaction types determines the assembly and stability of ecological communities
  jimmy j. qian, erol akçay 2020
  http://dx.doi.org/10.1038/s41559-020-1121-x

  • For half a century, scientists who have developed models of how ecological communities function have arrived at an unsettling conclusion. Their models’ predictions — seen as classic tenets of community ecology — suggested that mutualistic interactions between species, such as the relationship between plants and pollinators, would lead to unstable ecosystems.

    “In one of these classic theories,” says Erol Akçay, an assistant professor of biology at Penn, “it says that if you have a lot of these mutualistic interactions, where if you increase the abundance of one species it will lead to an increase in the other, things tend to go out of equilibrium.”
    In a paper published this week in Nature Ecology and Evolution, Akçay and Jimmy Qian, a 2019 Penn graduate who worked in Akçay’s lab when he was a student, challenge those assumptions. Their work shows that mutualism is compatible with stable communities and that the balance of mutualism with other types of interactions, including competitive and exploitative, plays determinative roles in the makeup, size, and stability of those communities.
    “We argue that mutualisms are not inherently destabilizing,” says Qian, now a medical student at Stanford University. “It’s all about the balance of how much mutualism there is and how unique those mutualistic benefits are.”
    As an undergraduate, Qian worked with Akçay for more than two years on projects related to health and medicine. The current project emerged from initial attempts to model the community dynamics of a human microbiome.
    “As we started reading the literature and building models, we realized there were questions in microbiome ecology that were generalizable to community ecology as a whole, which is where this paper ended up,” says Qian.

    Specifically, the researchers started looking more closely at the seminal work of Robert May, a renowned ecologist and physicist who argued that larger, more complex communities tend to be less stable. Stability in these models is a measurement of how likely a system is to return to an equilibrium if nudged away from it. For example, a stable community could withstand a disease reducing numbers of one of its species and come out the other side of the infection with its same species composition intact.
    In earlier studies, scientists showed that mutualistic interactions had destabilizing effects on communities and thus must only play a small role in ecosystems, alongside interactions that are either competitive or exploitative, like a predator-prey dynamic.
    Yet one needn’t look further than a coral reef or rainforest to see that the world is full of complex ecosystems. And from plant-pollinator interactions to human-microbiome relationships, mutualistic interactions also abound. So Akçay and Qian decided to dig deeper to see what these earlier models may have missed when it came to mutualism and ecosystem stability.
    One thing they noticed was that earlier studies had assumed mutualistic interactions benefited the species involved in a linear fashion, without any saturation point. But in reality, the benefits of mutualism have a limit. For example, says Akçay, if you have more bees in an ecosystem, plants might get pollinated more and might produce more fruits. “But at some point,” he says, “if the area is filled with bees and the plants are all pollinated, the plants will be limited by something else.”
    In addition to including this saturation point, Akçay and Qian attempted to make their new model more closely mimic the natural world by allowing the ecosystem to assemble gradually, adding species in a sequential manner. The classical models, in contrast, assumed that all the species came together in one fell swoop and then reached equilibrium.

    “Of course, real communities don’t assemble that way,” says Akçay.
    Their sequential assembly technique also allowed them to measure a different type of stability from the internal stability normally measured in these models, which they call external stability, or the ability of a community to resist invasion by a new species.
    In their model, each time they added a species they would randomly assign it an interaction type — mutualistic, exploitative, or competitive — with all the other species in the community.
    Their findings support the intuitive notion that mutualistic interactions have a place in a stable society.
    “It’s really the balance of the different interaction types between species that governs the community dynamics and stability,” Qian says.
    In their model, more mutualisms did not mean less internal stability, in contrast to what the classic models predicted. And mutualisms enhanced external stability in their analysis.
    “So, they are actually more stable in an external sense because they are more resistant to invasions from outside,” says Akçay. “And the reason is blindingly obvious in retrospect. If you have a community where most of the species are helping each other, each species will be abundant. If you are at this tiny population size and are trying to invade this community, it will be hard because your competitors are thriving.”
    While the new model is relatively simple and has room to be refined, Akçay and Qian say the results seem to be part of a shift in the community ecology field toward understanding that positive interactions in communities don’t necessarily unsettle communities.
    “These old, classical ecology questions still have legs,” Akçay says.

  • abstract What determines the assembly and stability of complex communities is a central question in ecology. Past work has suggested that mutualistic interactions are inherently destabilizing. However, this conclusion relies on the assumption that benefits from mutualisms never stop increasing. Furthermore, almost all theoretical work focuses on the internal (asymptotic) stability of communities assembled all at once. Here, we present a model with saturating benefits from mutualisms and sequentially assembled communities. We show that such communities are internally stable for any level of diversity and any combination of species interaction types. External stability, or resistance to invasion, is thus an important but overlooked measure of stability. We demonstrate that the balance of different interaction types governs community dynamics. A higher fraction of mutualistic interactions can increase the external stability and diversity of communities as well as species persistence, if mutualistic interactions tend to provide unique benefits. Ecological selection increases the prevalence of mutualisms, and limits on biodiversity emerge from species interactions. Our results help resolve long-standing debates on the stability, saturation and diversity of communities.

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• mildew locus o facilitates colonization by arbuscular mycorrhizal fungi in angiosperms
  catherine n. jacott et al. 2020
  http://dx.doi.org/10.1111/nph.16465

  • the Mildew Locus O (MLO) gene causes the majority of major crops to be susceptible to the fungal leaf pathogen powdery mildew. Loss of the gene causes durable and robust resistance to the pathogen.
    But if this gene is disadvantageous to the host, why has it been conserved throughout evolutionary history? Does this susceptibility factor also fulfil some other beneficial role?
    In a joint project between the John Innes Centre and the Shanghai Institute of Plant Physiology and Ecology, scientists found that the MLO gene needed by the powdery mildew pathogens is also used by symbiotic mycorrhizal fungi that help plants obtain nutrients from the soil.
    Mycorrhizal fungi are beneficial soil microorganisms that establish symbiotic interactions in plant roots and contribute to nutrient uptake. Powdery mildews are serious leaf fungal pathogens that infect many different plant genera and cause significant crop losses in agriculture.
    Importantly, the MLO gene and mycorrhizal symbiosis appeared very early in the evolution of land plants, millions of years before the occurrence of powdery mildew fungi.
    In this study, experiments showed that mycorrhizal colonisation was reduced in mutant plants of barley, wheat and Medicago truncatula which did not express the MLO gene. This was accompanied by a pronounced decrease in the expression of many key genes required for accommodation of arbuscular mycorrhizal fungi inside plant cells. The findings suggest the primary role for MLO in flowering plants is in colonisation by the arbuscular mycorrhizal fungi, and that this role has been appropriated by powdery mildew.

  • abstract Loss of barley Mildew Resistance Locus O (MLO) is known to confer durable and robust resistance to powdery mildew (Blumeria graminis), a biotrophic fungal leaf pathogen. Based on the increased expression of MLO in mycorrhizal roots and its presence in a clade of the MLO family that is specific to mycorrhizal‐host species, we investigated the potential role of MLO in arbuscular mycorrhizal interactions.
    Using mutants from barley (Hordeum vulgare), wheat (Triticum aestivum), and Medicago truncatula, we demonstrate a role for MLO in colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis.
    Early mycorrhizal colonization was reduced in mlo mutants of barley, wheat, and M. truncatula, and this was accompanied by a pronounced decrease in the expression of many of the key genes required for intracellular accommodation of arbuscular mycorrhizal fungi.
    These findings show that clade IV MLOs are involved in the establishment of symbiotic associations with beneficial fungi, a role that has been appropriated by powdery mildew.

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• woman in the wilderness
  miriam lancewood 2017 978-0349418247

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• not yet read

  • facing gaia: eight lectures on the new climatic regime
    bruno latour 2018

  • half-earth: our planet’s fight for life
    edward o. wilson 2016

  • the poetic species: a conversation with edward o. wilson and robert hass 2014

  • convergence with nature: a daoist perspective
    david cooper 2012

  • weeds
    nina edwards 2015

  • the plant messiah: adventures in search of the world’s rarest species
    carlos magdalena 2017

  • the man who climbs trees
    james aldred 2018

  • the wisdom of trees
    max adams 2014

  • dirt work: an education in the woods
    christine byl 2017

  • what a plant knows: a field guide to the senses
    daniel chamovitz 2012

  • the weather detective: rediscovering nature’s secret signs
    peter wohlleben 2018

  • science and spiritual practices: transformative experiences and their effects on our bodies, brains and health
    rupert sheldrake 2017

  • the philosopher’s plant: an intellectual herbarium
    michael marder, mathilde roussel 2019

  • the revolutionary genius of plants: a new understanding of plant intelligence and behavior
    stefano manucso 2017

  • entangled life: how fungi make our worlds, change our minds & shape our futures
    merlin sheldrake 2020

  • think little
    wendell berry 2020

  • diary of a young naturalist
    dara mcanulty 2020

09965

• not recommended
  • novacene: the coming age of hyperintelligence
    james lovelock 2019

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• “ranger rick” and ecology

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• i see you
  leona lewis

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• der ewiger kreis
  jocelyn smith

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• we are the world
  various

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• terbium Tb (ytterby, in sweden)
• neytiri
  • riding black thanator
  • hometree
• FE
• http link back to 00100

live

千と千尋の神隠し

spirited away

魔女の宅急便

kiki’s delivery service

耳をすませば

whisper of the heart

天空の城ラピュタ

laputa

groundhog day

double star

宇宙のステルヴィア

stellvia

calvin and hobbes

die

生きる

ikiru

the little match girl

the little mermaid (1974 tv)

le petit prince

flowers for algernon

stranger in a strange land

トップをねらえ!

gunbuster

i will fear no evil

魔法騎士 レイアース

rayearth

district 9

never let me go

el laberinto del fauno

pan’s labyrinth

魔法少女まどか☆マギカ

madoka magika

choice

desert

the lorax

citizen of the galaxy

emergence

gladiator–at–law

もののけ姫

mononoke

friday

the moon is a harsh mistress

earth abides

our

forest

となりのトトロ

totoro

崖の上のポニョ

ponyo

the wombles

maleficent

avatar

風の谷のナウシカ

nausicaä

the mouse and his child

• where i first heard of the concept of a “mental leap”, among other great concepts

無人惑星サヴァイヴ

mujin wakusei survive

未来少年コナン

future boy conan

walden

desert solitaire