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Phage selection drives resistance-virulence trade-offs in Ralstonia solanacearum plant pathogenic bacterium irrespective of the growth temperature

While temperature has been shown to affect the survival and growth of bacteria and their phage parasites, it is unclear if trade-offs between phage resistance and other bacterial traits depend on the temperature. Here, we experimentally compared the evolution of phage resistance-virulence trade-offs and underlying molecular mechanisms in phytopathogenic Ralstonia solanacearum bacterium at 25 °C and 35 °C temperature environments. We found that experimental growth conditions selected for small colony variants (SCVs) with increased growth rate and mutations in the quorum-sensing (QS) signalling receptor gene, phcS. Interestingly, SCVs were also phage-resistant and reached higher frequencies in the presence of phages in both temperature environments. Evolving phage resistance was costly in terms of reduced carrying capacity, biofilm formation and reduced virulence in planta possibly due to loss of QS-mediated expression of key virulence genes. We also observed mucoid phage-resistant colonies that showed loss of virulence and reduced twitching motility likely due to parallel mutations in prepilin peptidase gene pilD. Moreover, phage-resistant SCVs from 35 °C-phage treatment had parallel mutations in genes encoding type II secretion system (T2SS) genes (gspE and gspF), indicating that defects in pseudopilus made bacterium resistant to the phage. Additional transcriptomic analysis revealed upregulation of CBASS and type Ⅰ restriction-modification phage defence systems in response to phage exposure, which coincided with reduced expression of motility and virulence-associated genes, including pilD and type II and III secretion systems. Together, these results suggest that phage resistance-virulence trade-offs are not affected by the growth temperature but can be mediated through both pre- and post-infection phage resistance mechanisms.

ChinaSoyArea10m: a dataset of soybean planting areas with a spatial resolution of 10 m across China from 2017 to 2021

This dataset provides 10m-resolution maps of soybean planting areas in China during 2017-2021.*** The data file is in ".tif" format*** Temporal Resolution: Annually*** Temporal coverage: 2017-2021*** Pixel size: 10 m*** Projection information: EPSG: 4326The map boundary employed in this database does not imply the expression of any opinion whatsoever on the part of us concerning the legal status of any country, territory, city or area or its authorities, or concerning the delimitation of its frontiers or boundaries.

Elevational and seasonal patterns of plant pollinator networks in two highland tropical ecosystems in Costa Rica

Plant pollinator interaction matrices used to construct plant-pollinator interaction networks in two highland tropical ecosystems in Costa Rica. Numbers in matrices indicates the number of interactions recorded. The names of the files indicates the collect site (MF: Montane Forest; PAR= Paramo) and the season of the year (Dry and Rainy seasons, respectively).

opencc-by-4.0Aug 2022View details →

Text-fig. 1. Situation of Early Miocene plant localities. a: Central Europe with Brno area and other fossil sites mentioned in text (1 – Znojmo and Přímětice, 2 – Oberdorf, 3 – Modrý Kameň Basin, 4 – Lipovany, 5 – Ipolytarnóc; CZ – the Czech Republic, PL – Poland, SK – Slovakia, H – Hungary, A – Austria, D – Germany). b: Brno area with Líšeň municipal district indicated. c: Líšeň municipal district with fossil sites indicated by asterisk. in A New Early Miocene (Ottnangian) Flora Of The "Rzehakia Beds" From Brno-Líšeň

Text-fig. 1. Situation of Early Miocene plant localities. a: Central Europe with Brno area and other fossil sites mentioned in text (1 – Znojmo and Přímětice, 2 – Oberdorf, 3 – Modrý Kameň Basin, 4 – Lipovany, 5 – Ipolytarnóc; CZ – the Czech Republic, PL – Poland, SK – Slovakia, H – Hungary, A – Austria, D – Germany). b: Brno area with Líšeň municipal district indicated. c: Líšeň municipal district with fossil sites indicated by asterisk.

Impact of Phytophthora cinnamomi on the taxonomic and functional diversity of forest plants in a mediterranean-type biodiversity hotspot

Aim Diversity-rich mediterranean-type sclerophyllous forests are home to 20% of described species on Earth. In the Eucalyptus marginata (jarrah) forest of southwest of Western Australia diversity is being reduced by extensive human use and the introduction of the plant pathogen Phytophthora cinnamomi. This study investigated the influence of P. cinnamomi infestation on the structure, taxonomic and functional diversity, and species composition of the forest. Location: Jarrah forest of southwestern Australia Methods Species abundance, understorey cover and canopy cover were assessed along 22, 30-m long transects which crossed infested and non-infested zones in five reserves in the jarrah forest. A trait database was assembled for 137 plants using 13 traits related to nutrient- and carbon acquisition, disturbance tolerance and reproduction. The responses of canopy cover, understorey cover, species richness, Shannon diversity, evenness, abundance, and functional diversity for trait groups, and all groups combined were modelled against reserve and zone as fixed effects and transect and transect section as random effects. To assess the species composition, NMDS ordination based on Bray Curtis resemblance and indicator species analyses were used. Results Significantly higher understorey cover, species richness, Shannon diversity and evenness were recorded in non-infested compared to infested zones, but there were no changes in the canopy cover and overall abundance. In non-infested zones, the functional diversity of nutrient acquisition and reproductive traits was higher, but the functional diversity of carbon acquisition traits was lower. No difference in functional diversity was recorded in disturbance tolerance and overall traits between the two zones. NMDS ordination and ANOSIM revealed a significant difference in the species composition between the two zones, and 11 indicator species significantly associated with infested and non-infested zones were identified. Conclusion Phytophthora cinnamomi has significantly affected the forest structure, taxonomic and functional diversity, and species composition. Contrasting responses of functional trait groups obscured overall trait responses to P. cinnamomi.

Presence and proportion of plants in biodiversity inventories conducted by undergraduate students enrolled in animal-related courses

Dataset on biodiversity inventories conducted by 110 undergraduate students enrolled in animal-related courses using the iNaturalist platform.

opencc-by-4.0Aug 2023View details →

Figures 1–4. Plants associated with the sineguelas leaf beetle 1 in Biology of the sineguelas leaf beetle, Podontia quatuordecimpunctata (L.) (Chrysomelidae: Galerucinae: Alticini), on Spondias purpurea L. (Anacardiaceae) in the Philippines

Figures 1–4. Plants associated with the sineguelas leaf beetle 1) A typical sineguelas tree (Spondias purpurea (L.) with foliage (June to November). 2) Fruits (April to June) in the Philippines. 3) Fruits of yellow sineguelas (Spondias dulcis Parkinson). 4) Fruits of "Libas" (Spondias pinnata (L.f.) Kurz). (Photographs courtesy of SLB project).

Data and code corresponding to the article "Interaction network structure explains species temporal persistence in empirical plant-pollinator communities"

This upload contains the Datasets and code to generate the results of the article "Interaction network structure explains species temporal persistence in empirical plant-pollinator communities".The database comprises two files containing the abundances of plants and pollinators, and one containing the interaction networks among plants and pollinators. The code folder contains the code to generate the results, and to generate the figures of the manuscript.

Data from: Herbivores disrupt clinal variation in plant responses to water limitation

Plasticity in plant traits, including secondary metabolites, is critical to plant survival and competitiveness under stressful conditions. The ability of a plant to respond effectively to combined stressors can be impacted by crosstalk in biochemical pathways, resource availability, and evolutionary history, but such responses remain underexplored. In particular, we know little about intraspecific variation in response to combined stressors or whether such variation is associated with the stress history of a given population. Here, we investigated the consequences of combined water and herbivory stress for plant traits, including relative growth rate, leaf morphology, and various measures of phytochemistry, using a common garden of Asclepias fascicularis milkweeds. To examine how plant trait means and plasticities depend on the history of environmental stress, seeds for the experiment were collected from across a gradient of aridity in the Great Basin, USA. We then conducted a factorial experiment crossing water limitation with herbivory. Plants responded to water limitation alone by increasing the evenness of UV-absorbent secondary metabolites, and to herbivory alone by increasing the richness of metabolites. However, plants that experienced combined water and herbivory stress exhibited similar phytochemical diversity to well-watered control plants. This lack of plasticity in phytochemical diversity in plants experiencing combined stressors was associated with a reduction in relative growth rates. Leaf chemistry means and plasticities exhibited clinal variation corresponding to seed-source water deficits. The total concentration of UV-absorbent metabolites decreased with increasing water availability among seed sources, driven by higher concentrations of flavonol glycosides, which are hypothesized to act as antioxidants, among plants from drier sites. Plants sourced from drier sites exhibited higher plasticity in flavonol glycoside concentrations in response to water limitation, which increased phytochemical evenness, but simultaneous herbivory dampened plant responses to water limitation irrespective of seed source. Synthesis: These results suggest that climatic history can affect intraspecific phytochemical plasticity, which may confer tolerance to water limitation, but that co-occurring herbivory disrupts such patterns. Global change is increasing the frequency and intensity of stress combinations, such that understanding intraspecific responses to combined stressors is critical for predicting the persistence of plant populations.

opencc-zeroAug 2023View details →

The Genome Project of Trib. Coreopsideae Plants

This project aims to construct the reference genomes of three plants from Trib. Coreopsideae in Asteraceae, including Dahlia pinnata, Cosmos bipinnata and Bidens alba.

Fig. 4 in Favourite plants of wild bees

Fig. 4. Favourite plants as pollen hosts. Scaled pollen scores for each of the identified 34 "high visitor richness" plant species (according to Fig. 3). The scaled pollen score for one plant species is the percentage of other plant species that are visited by a lower number of bee species, e.g. a scaled pollen score of 100 shows that all other plant species in the database were visited by a lower number of bee species. The maximum number of bee species visiting one plant species is 71 and the total number of plant species described in Westrich (2018) is 494. The average scaled pollen score of 50 is indicated by the dashed red line.

Fig. 6 in Favourite plants of wild bees

Fig. 6. Favourite plants in existing seed mixtures. Percentage of commercial seed mixtures containing seeds of the identified 34 "high visitor richness" plant species (according to Fig. 3). Total number of seed mixtures n = 55.

Fig. 5 in Favourite plants of wild bees

Fig. 5. Favourite plants as hosts for polylectic, oligolectic and threatened species. Percentage of wild bee species visiting each of the identified 34 "high visitor richness" species (according to Fig. 3). 100% of observed bee species is the total number of polylectic, oligolectic and threated species that are included in the Wildbienen-Kataster dataset, which includes ~ 75% of all wild bee species in Germany (440 species in total, containing 87 oligolectic and 177 red-listed species). The percentage of wild bee species for plants that are not widespread in the study area, such as Chondrilla juncea or Ballota nigra, are underestimated.

Fig. 2 in Favourite plants of wild bees

Fig. 2. Overview of the way that the datasets were combined in the analyses (detailed descriptions are given in the Material & Methods section).

Fig. 3 in Favourite plants of wild bees

Fig. 3. Favourite plants of bees. Plant species are grouped into "high visitor richness", "medium visitor richness" and "low visitor richness" based on the bee visits observed in the BienABest-project. On each sampling date and each habitat and location, the plant species were ranked based on the increasing number of visiting bee species. Mean ranks ¯R i for each plant species during all months (yellow), during April and May (green), during June (blue) and during July and August (purple) are shown. As the BienABest dataset contains a high proportion of interactions of polylectic and common species (male and female individuals), we additionally highlighted the top plant species with the greatest number of visiting oligolectic (+, n = 18 plant species) and red listed wild bee species (*, n = 17 plant species) according to Wildbienen-Kataster dataset.

Figure 4 in Oviposition of Quesada gigas (Hemiptera: Cicadidae) in coffee plants

Figure 4. Percentage of branches with Quesada gigas egg nest in the two areas of the experiment, in different thirds of the coffee plant height and in the collection periods of the branches. São Sebastião do Paraíso, Minas Gerais, Brazil. 2008.

Figure 3 in Oviposition of Quesada gigas (Hemiptera: Cicadidae) in coffee plants

Figure 3. Quesada gigas eggs collected from dry coffee-plant branches. Scale: 1 mm. São Sebastião do Paraíso, Minas Gerais, Brazil. 2008.

Figure 2 in Oviposition of Quesada gigas (Hemiptera: Cicadidae) in coffee plants

Figure 2. Oviposition by Quesada gigas on a dry coffee-plant branch. A. Female depositing eggs inside the branch. B. Insertion point of ovipositor that was sealed after egg-laying. C. Mass of eggs shown from upper view. D. Mass of eggs shown in lateral view. São Sebastião do Paraíso, Minas Gerais, Brazil. 2008.

Figure 1 in Oviposition of Quesada gigas (Hemiptera: Cicadidae) in coffee plants

Figure 1. Distribution of the sampling points by block in each analysed area. São Sebastião do Paraíso, Minas Gerais, Brazil. 2008.

Unveiling the genetic networks: Exploring the dynamic interaction of photosynthetic phenotypes in woody plants across varied light gradients

Background: Understanding the mechanisms by which genes control and regulate complex quantitative traits during periods of fluctuating resources remains a challenging and uncertain task in photosynthesis studies. Most studies have focused on the structure of photosynthesis, the photosynthetic response under stress, or the genetic mechanisms involved in photosynthetic effects and neglected the interactive genetic mechanism that governs various traits through significant quantitative trait loci (QTLs). Results In this study, we have developed a differential dynamic system that enables the identification of QTLs based on the photosynthetic phenotypic and genotypic data under varying levels of light intensity gradients. The framework not only allows for the assessment of the direct effects of QTLs on phenotypes but also captures how they influence interactions among phenotypes as light intensities change. We have analyzed the genetic effects and genetic variance, visualized the genetic network associated with photosynthesis interactions, and validated the effectiveness and stability of the DDS framework. Pivotal QTLs were identified individually to uncover the process and pattern of interaction. Through functional annotation, we made an intriguing discovery that seemingly unimportant QTLs can still have significant genetic effects on phenotypic changes through their regulation with other QTLs. Conclusions This finding emphasizes the significance of considering the interactive genetic architecture when seeking to understand the genetic interaction mechanism of photosynthesis in natural populations of woody plants. Moreover, our research provides a novel framework that can be extended to explore the interactive genetic architecture among organisms, contributing to a deeper understanding of stress resistance mechanisms in woody plants.