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opencc-zeroMar 2023View details →

Post-glacial colonization of the Fennoscandian coast by a plant parasitic insect with an unusual life history

Species that exhibit very peculiar ecological traits combined with limited dispersal ability pose a challenge to our understanding of ecological and evolutionary mechanisms. This is especially true when they have managed to spread over long distances, overcome physical barriers and colonise large areas. Climate and landscape changes, trophic web relations as well as life history all interact to shape migration routes and present-day species distributions and their population genetic structures. Here we analysed the post-glacial colonization of northern Europe by the gall midge Contarinia vincetoxici, which is a monophagous parasite on the perennial herb White swallowwort (Vincetoxicum hirundinaria). This insect not only has a narrow feeding niche but also limited dispersal ability and an exceptionally long dormancy. Gall midge larvae (n = 329) were collected from 16 sites along its distribution range in Denmark, Sweden, and Finland. Using microsatellite loci and knowledge of the species and the regions' history, we investigated the role of landscape change, host plant distribution, insect population dynamics, and life history in shaping the population genetic structure of the insect. We devoted particular interest to the role of the insect's presumed poor dispersal capacity in combination with its exceptionally extended diapause. We found significant levels of local inbreeding (95% highest posterior density interval = 0.42–0.47), low level within-population heterozygosity (mean HE = 0.45, range 0.20–0.61) with private alleles in all populations except two. We also found significant (p < 0.001) regional isolation-by-distance patterns, suggesting regularly recurring mainly short-distance dispersal. According to approximate Bayesian computations, C. vincetoxici appears to have colonized the study area via wind-aided flights from remote areas approximately 4600 to 700 years before present when the land has gradually risen above the sea level. Extremely long dormancy periods have allowed the species to "disperse in time", thereby aiding population persistence despite generally low census population sizes.

openother-openJan 2023View details →

Gene/Protein BridgeDb ID Mapping Database (Ensembl Plants 52)

Mapping databases derived from Ensembl Plants 52. These files can be used with BridgeDb. This version doesn't have the issue of not could be searched using gene names (e.g. in PathVisio). The scripts which were used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.

A unified meta-ecosystem dynamics model: Integrating herbivore-plant subwebs with the intermittent upwelling hypothesis

Determining the relative influence of biotic and abiotic processes in structuring communities at local to large spatial scales is best understood using a biogeographic comparative-experimental approach. Using this approach, previous work suggests that intertidal community dynamics (top-down and bottom-up effects) vary unimodally along an upwelling-based productivity gradient, termed the Intermittent Upwelling Hypothesis (IUH). Evidence consistent with the IUH comes from the sessile invertebrate/predator (SIP) subweb in certain rocky intertidal communities, but whether this pattern extends to macrophyte/herbivore (MH) subwebs is unknown. Here we ask: Are MH subwebs also structured as predicted by the IUH? What is the relative importance of herbivory and predation in structuring these communities? Under what conditions do ecological subsidies like nutrients or propagule production drive community dynamics? And are omnivorous interactions important? We hypothesize that MH subwebs are driven by a new construct, the Grazing-Weakening Hypothesis (GWH), which states that MH interactions weaken monotonically with increasing nutrients, with strong (weak) herbivory and low (high) macrophyte productivity at low (high) nutrients. We explored local-to-large spatial scale dynamics of both subwebs using a biogeographic comparative-experimental factorial field experiment testing joint and separate effects of herbivores and predators between two continents. Experiments at ten sites ranging across from persistent upwelling to persistent downwelling regimes ran for 26-29 months in Oregon and California, and New Zealand South Island. For the MH subweb, results were consistent with the GWH: herbivory declined and macrophytes increased with increasing nutrients. As expected, results for the SIP subweb were consistent with the IUH: predator effect size was unimodally related to upwelling. Overall, herbivory explained more variation in community structure than did predation, especially in New Zealand. Omnivory was weak, sessile invertebrates outcompeted macrophytes, and ocean-driven subsidies provided the basic template driving ecosystem dynamics. We propose a unified Meta-Ecosystem Dynamics Model (MEcoDynaMo) combining MH and SIP results: with increased upwelling, sessile invertebrates and underlying dynamics vary unimodally (as in the IUH), while herbivory decreases and macrophytes generally increase. While this model was based on research in temperate ecosystems varying in upwelling regime, its wider applicability remains to be tested.

Plant dieback in Mediterranean shrublands under 2014 extreme drought (Alicante, Spain)

Field data from four Mediterranean shrublands monitored during an extreme drought in 2014 (hydrological year) in SE Spain. Data are plant dieback of the total plant community and main plant biotypes (shrubs, subshrubs and grasses), vegetation structure attributes (phytovolume, plant height, LAI, and sizes of patch and inter-patch areas), soil properties (soil depth and soil surface cover types) and water availability indicators (soil moisture and environmental variables).

opencc-by-4.0Mar 2023View details →

Figures: The wind farm as a sensor: learning and explaining orographic and plant-induced flow heterogeneities from operational data

Python figures in pickle format matplotlib version 3.5.1

opencc-by-4.0Feb 2023View details →

Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response

We examined the role of the plant vs the environment in selecting for beneficial microbes to plants in their home moisture environment, in either wet vs dry conditions. To this end, we first conditioned soil microbial communities, selecting for either dry- or wet-adapted soil microbial communities, either with or without plants. After 3 plant generations, we conducted a full reciprocal transplant of each soil community onto wet- and dry-treated plants, using the soil from the prior 3 generations as an inoculum. From plants inoculated with these ‘evolved’ soils, we measured plant biomass and height. We also measured soil nitrogen of the inoculum, and measured inoculum respiration across a water content gradient.

Temperature and plants disease simulation to 2038

In this datasets we combined temperatures data broken down by NUTS Level 3 from 1989 to 2018 (link to data: https://doi.org/10.5281/zenodo.5789430) with disease observed in laboratory from scientists of the University of Torin (link to data: https://doi.org/10.5281/zenodo.6323408). We computed the prediction of temperature using an LSTM algorithm to year 2038 and we associated the result with plant disease evolution observed in the laboratory. The main purpose of this project is to better understand possible scenario related to increasing of temperatures and plant disease spreading.

Patterns of host plant use do not explain mushroom body expansion in Heliconiini butterflies

The selective pressures leading to the elaboration of downstream, integrative processing centres, such as the mammalian neocortex or insect mushroom bodies, are often unclear. In Heliconius butterflies, the mushroom bodies are three to four times larger than their Heliconiini, and the largest known in Lepidoptera. Heliconiini lay almost exclusively on Passiflora, which exhibit a remarkable diversity of leaf shape, and it has been suggested that the mushroom body expansion of Heliconius may have been driven by the cognitive demands of recognising and learning the leaf shapes of local host plants. We test this hypothesis using two complementary methods: i) phylogenetic comparative analyses to test whether variation in mushroom body size is associated with the morphological diversity of host plants exploited across the Heliconiini; and ii) shape learning experiments using six Heliconiini species. We found that variation in the range of leaf morphologies used by Heliconiini was not associated with mushroom body volume. Similarly, we find interspecific differences in shape learning ability, but Heliconius are not overall better shape learners than other Heliconiini. Together these results suggest that the visual recognition and learning of host plants was not a main factor driving the diversity of mushroom body size in this tribe.

Data for: No physiological costs of dual sequestration of chemically different plant toxins in the milkweed bug Spilostethus saxatilis (Heteroptera: Lygaeidae)

Many herbivorous insects not only cope with plant toxins but also sequester them as a defense against predators and parasitoids. Sequestration is a product of the evolutionary arms race between plants and herbivorous insects and has been hypothesized to incur physiological costs due to specific adaptations required. Contradictory evidence about these costs exists for insects sequestering only one class of toxin, but very little is known about the physiological implications for species sequestering structurally different classes of compounds. Spilostethus saxatilis is a milkweed bug belonging to the cardenolide-sequestering heteropteran subfamily Lygaeinae (Heteroptera: Lygaeidae) that has shifted to the colchicine-containing plant Colchicum autumnale, a resource of chemically unrelated alkaloids. Using feeding-assays on artificial diet and chemical analysis, we assessed whether S. saxatilis is still able to sequester cardenolides apart from colchicine and related metabolites (colchicoids), and tested the effect of (1) either a natural cardenolide concentration (using ouabain as a model compound) or a natural colchicine concentration, (2) an increased concentration of both toxins, and (3) seeds of either Asclepias syriaca (cardenolides) or C. autumnale (colchicoids) on a set of life-history traits. For comparison, we assessed the same life-history traits in the milkweed bug Oncopeltus fasciatus exposed to cardenolides only. Although cardenolides and colchicoids have different physiological targets (Na+/K+-ATPase vs tubulin) and thus require different resistance traits, chronic exposure and sequestration of both isolated toxins caused no physiological costs such as reduced growth, increased mortality, lower fertility, or shorter adult life span in S. saxatilis. Indeed, an increased performance was observed in O. fasciatus and an according trend was found in S. saxatilis when feeding on isolated ouabain and isolated colchicine, respectively. Positive effects were even more pronounced when insects were provided with natural toxic seeds (i.e. C. autumnale for S. saxatilis and A. syriaca for O. fasciatus), especially in O. fasciatus. Our findings suggest, that S. saxatilis can sequester two chemically unrelated classes of plant compounds at a cost-free level, and that colchicoids may even play a beneficial role in terms of fertility.

Novel cropping system strategies in China can increase plant protein with higher economic value but lower greenhouse gas emissions and water use

This database contains the average crop residue, manure nitrogen, manure organic carbon, net greenhouse gas emissions, and cropland area for 17 cropping systems at prefecture level during the period 2014-2018. In addition, it contained the changes of net greenhouse gas emissions caused by the optimization at prefecture level and province level.     We also shared the key code for optimizing cropping systems at prefecture level and provided the all data. Users can run it the Matlab platform.

Developmental parameters of Opisina arenosella Walker (Lepidoptera: Oecophoridae) on alternative host plants

Survival and development of Opisina arenosella Walker (Lepidoptera: Oecophoridae), the leaf eating caterpillar of coconut, were studied on three host plants on which comparatively high feeding rates were observed: Artocarpus heterophyllus Lam. (Jack fruit), Elaeis guineensis Jacq. (Oil palm) and Anacardium occidentale L. (Cashew), plus coconut palm (Cocos nucifera L.). A freshly hatched first instar O. arenosella larva was transferred onto the leaf in a glass beaker and reared on them. Fresh leaves were provided every 48 h until pupation of O. arenosella larvae. The larval period, pupal period and the longevity of the successfully developing adult female moths were recorded. For each plant species, there were ten replicates yielding adult moths. Data on the length of O. arenosella developmental stages and adult longevity had homogenous variance (Bartlett’s test on residuals from ANOVA of developmental time across plant species: Larval period, v2 = 5.13, df = 3, P = 0.163; Pupal period, v2 = 0.15, df = 3, P = 0.986; Longevity, v2 = 1.58, df = 3, P = 0.664) and were normally distributed (Shapiro–Wilk test: Larval period, W = 0.978, P = 0.632; Pupal period, W = 0.981, P = 0.714; Longevity, W = 0.974, P = 0.472). Thus, the effects of plant species on each of these measures were tested using one-way ANOVA in GenStat. Aggregation of factor levels was used to evaluate differences between treatments when overall results were significant (Crawley 1993). The larval period differed significantly across all four plant species presented and was shortest when on coconut. Pupal periods were also shortest on coconut but did not differ among larvae fed on the three intercrops. The longevity of adult females was unaffected by the species of plant on which larvae had fed.

Do plant-soil feedbacks promote coexistence in a sagebrush steppe?

Recent studies have shown the potential for negative plant-soil feedbacks (PSFs) to promote stable coexistence but have not quantified the stabilizing effect relative to other coexistence mechanisms. We conducted a field experiment to test the role of PSFs in stabilizing coexistence among four dominant sagebrush steppe species that appear to coexist stably, based on previous work with observational data and models. We then integrated the effects of PSF treatments on focal species across germination, survival, and first-year growth. To contribute to stable coexistence, soil microbes should have host-specific effects that result in negative feedbacks. Over two replicated growing seasons, our experiments consistently showed that soil microbes have negative effects on plant growth, but these effects were rarely host-specific. The uncommon host-specific effects were mostly positive at the germination stage and negative for growth. Integrated effects of PSF across early life-stage vital rates showed that PSF-mediated self-limitation occasionally had large effects on projected plant biomass but occurred inconsistently between years. Our results suggest that while microbially-mediated PSF may not be a common mechanism of coexistence in this community, it may still affect the relative abundance of dominant plant species via changes in host fitness. Our work also serves as a blueprint for future investigations that aim to identify underlying processes and test alternative mechanisms to explain important patterns in community ecology.

Data from: A meta-analysis of plant tissue O2 dynamics

This dataset includes 1,567 recorded tissue O2 levels from 112 plant species extracted from published literature. The data forms the basis of the publication "A meta-analysis of plant tissue O2 dynamics" with the following abstract: Adequate tissue O2 supply is crucial for plant functioning. We therefore aimed at identifying environmental conditions and plant characteristics affecting plant tissue O2 status. We extracted data and performed meta-analysis on > 1,500 published tissue O2 measurements from 112 species. Tissue O2 status ranged from anoxic conditions in especially roots, to > 53 kPa in submerged, photosynthesizing shoots. Using information-theoretic model selection, we identified 'submergence', 'light', 'tissue type' as well as 'light × submergence' interaction as significant drivers of tissue O2 status. Median O2 status was especially low (< 50% of atmospheric equilibrium) in belowground rhizomes, potato tubers and root nodules. Mean shoot and root O2 was ~25% higher in light than in dark when shoots had atmospheric contact. However, light showed a significant interaction with submergence on plant O2, with a submergence-induced 44% increase in light, compared with a 42% decline in dark, relative to plants with atmospheric contact. During submergence, ambient water column O2 and shoot tissue O2 correlated stronger in darkness than in light conditions. Although miniaturised Clark-type O2 electrodes in particular have resulted in enhanced understanding of plant O2 dynamics, the use of non-invasive methods is still lacking behind its widespread use in mammalian tissues.

Effects of long-term mowing on leaf- and root-associated bacterial community structures are linked to functional traits in 11 plant species from a temperate steppe

<ol> <li>Long-term mowing can cause morphological stuntedness of plants, thus reducing grassland productivity and exacerbating grassland degradation. Although plant microbiomes can enhance plant resistance against disturbance, considerable uncertainty exists regarding how mowing and mowing-induced plant trait plasticity affect plant microbiomes in natural grasslands. </li> <li>Here we examined the responses of leaf-/root-associated bacterial (LAB/RAB) communities of 11 dominant herbaceous perennials (6 replicates per species) to a 17-year mowing treatment in a temperate grassland. We also measured leaf/root physiological and morphological traits and analyzed the relationships among mowing practice, bacterial community structures, and leaf/root trait parameters. </li> <li>We found that both leaf and root functional traits showed interspecific variations (variations across different plant species), while only the leaf traits exhibited intraspecific variation (treatment-induced variations within plant species) between the treatments. Similarly, the LAB community structure was more sensitive to mowing but less influenced by host species identity, compared to the RAB community. The RAB community structure was primarily shaped by host species identity, while mowing was a secondary influencing factor. </li> <li> The different patterns of LAB and RAB communities in response to mowing could be specifically explained by the inter-/intraspecific variations of the related leaf and root traits. The LAB community was strongly correlated with the leaf traits which exhibited mowing-induced plasticity (intraspecific variation), with the correlations with nitrogen resorption efficiency and aboveground dry weight being the greatest. The root traits were important indicators of bacterial community structure in the root compartment across the hosts, rather than between the treatments. Root tissue density showed the strongest interspecific variation, and was identified as an overwhelming driver of the RAB community. The shifts in LAB/RAB communities under mowing were largely attributed to the increased proportions of Actinobacteria. The high mowing sensitivity of the LAB community was associated with the enrichment of soil-derived Actinobacteria in leaves under mowing. Actinobacteria were also the main keystone taxa in the bacterial community networks under mowing. </li> <li>Our results demonstrate that the magnitude of plant-associated microbial community response to long-term mowing is plant compartment- and trait-variation-dependent, and advance our understanding of the leaf/root microbiome-trait relationships in complex plant communities.</li> </ol>

Plant–hummingbird pollination networks exhibit limited rewiring after experimental removal of a locally abundant plant species

In this study, we simulated the local extinction of a hummingbird-pollinated understory plant, Heliconia tortuosa, from tropical forest fragments using a replicated Before-After-Control-Impact (BACI) experimental design while quantifying plant-hummingbird interactions through two parallel techniques: pollen collected from individual hummingbirds ('pollen networks', created from >300 pollen samples) and observations of hummingbirds visiting focal plants ('camera networks', created from >19,000 observation hours). Each response variable was measured during each experimental period (pre and post) in sites with and without H. tortuosa removal (treatment and control).

Elevated atmospheric CO2 suppresses silicon accumulation and exacerbates endophyte reductions in plant phosphorus

Many temperate grasses are both hyper-accumulators of silicon (Si) and hosts of Epichloë fungal endophytes; functional traits which may alleviate environmental stresses such as herbivore attack. Si accumulation and endophyte infection may operate synergistically, but this has not been tested in a field setting, nor in the context of changing environmental conditions. Predicted increases in atmospheric CO2 concentrations can affect both Si accumulation and endophyte function, but these have not been studied in combination. We investigated how elevated atmospheric CO2 (eCO2), Si supplementation, endophyte-presence and insect herbivory impacted plant growth, stoichiometry (C, N, P and Si), leaf gas exchange (rates of photosynthesis, stomatal conductance, transpiration rates) and endophyte production of anti-herbivore defences (alkaloids) of an important pasture grass (tall fescue; Lolium arundinaceum) in the field. eCO2 and Si supplementation increased shoot biomass (+52% and +31%, respectively), whereas herbivory reduced shoot biomass by at least 35% and induced Si accumulation by 24%. Shoot Si concentrations, in contrast, decreased by 17–21% under eCO2. Si supplementation and herbivory reduced shoot C concentrations. eCO2 reduced shoot N concentrations which led to increased shoot C:N ratios. Overall, shoot P concentrations were 26% lower in endophytic plants compared to non-endophytic plants, potentially due to decreased mass flow (i.e. observed reductions in stomatal conductance and transpiration). Alkaloid production was not discernibly affected by any experimental treatment. The negative impacts of endophytes on P uptake were particularly strong under eCO2. We show that eCO2 and insect herbivory reduce and promote Si accumulation, respectively, incorporating some field conditions for the first time. This indicates that these drivers operate in a more realistic ecological context than previously demonstrated. Reduced uptake of P in endophytic plants may adversely affect plant productivity in the future, particularly if increased demand for P due to improved plant growth under eCO2 cannot be met.

Foliar N, P and K global upscaled maps in woody plants

Global foliar N,  P and K maps in woody plants. Further details in: Vallicrosa, H., Sardans, J., Maspons, J., Zuccarini, P., Fernández-Martínez, M., Bauters, M., Goll, D.S., Ciais, P., Obersteiner, M., Janssens, I.A. and Peñuelas, J. (2022), Global maps and factors driving forest foliar elemental composition: the importance of evolutionary history. New Phytol, 233: 169-181. <a href="https://doi.org/10.1111/nph.17771">https://doi.org/10.1111/nph.17771</a>

Data and code: Plants cultivated for ecosystem restoration can evolve towards a domestication syndrome

Data and code to the publication Conrady et al (2023): Plants cultivated for ecosystem restoration can evolve towards a domestication syndrome, PNAS.

Drought neutralizes positive effects of long-term grazing on grassland productivity through altering plant-soil interactions

Livestock grazing is among the most intensive land-use activities in grasslands and can affect plant communities directly or indirectly via grazing-induced soil legacies. Under climate change, grasslands are threatened globally by recurrent drought. However, the extent to which drought influences grazing-induced soil legacy effects on plant biomass production and community composition remains largely unexplored. We grew five naturally co-occurring plant species (three dominants and two subordinates) in mixed communities in a glasshouse experiment in live and sterilized soil that had or had not been subjected to 19 years of grazing; these plant communities were then exposed to a subsequent drought. We tested the treatment effects on plant community biomass, proportional aboveground biomass of individual species, arbuscular mycorrhizal (AM) fungal root colonization, and soil nutrient availability. Under drought-free conditions, soils from grazed plots produced significantly higher plant aboveground and total community biomass compared to soils from ungrazed plots. In contrast, plant aboveground and total community biomass were similar between grazed and ungrazed soils under drought conditions. Similarly, soils from grazed plots increased the proportional biomass of dominant species but decreased the proportion of subordinate species; however, the proportional biomass of dominant and subordinate species was similar between grazed and ungrazed soils under drought conditions. Soil NO3--N in grazed soil was significantly higher compared to ungrazed soil. Drought dramatically increased soil NO3--N in sterilized soil and had a more pronounced increase in grazed soil than in ungrazed soil. Arbuscular mycorrhizal fungal root colonization from grazed soil was lower compared to ungrazed soil. Drought significantly increased the soil available phosphorus concentration, as well as plant community AM fungal root colonization. Synthesis. Our study suggests that drought can neutralize positive grazing effects on plant community biomass production via altered plant-soil interactions. Also, we found that drought can alleviate the negative effects of grazing legacies on subordinate species by reducing the competitiveness of dominant species. Our study provides new insights for understanding the underlying mechanisms of grazing effects on grassland productivity under climate change.

Datasets of eponyms for South American plants and Mozambican terrestrial vertebrates

Two datasets containing information on the Eponyms of South American plants and Mozambique's terrestrial vertebrates.