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Microbe‐associated molecular pattern (MAMP)‐triggered immunity (MTI) research has traditionally centred around signal transduction pathways originating from activated membrane‐localized pattern recognition receptors (PRRs), culminating in nuclear transcription and posttranslational modifications. More recently, chloroplasts have emerged as key immune signalling hubs, playing a central role in integrating environmental signals. Notably, MAMP recognition induces chloroplastic reactive oxygen species (cROS) that is suppressed by pathogen effectors, which also modify the balance of chloroplast‐synthesized precursors of the defence hormones, jasmonic acid, salicylic acid (SA) and abscisic acid. This study focuses on how well‐characterized PRRs and coreceptors modulate chloroplast physiology, examining whether diverse signalling pathways converge to similarly modulate chloroplast function. Pretreatment of receptor mutant plants with MAMP and D(Damage)AMP peptides usually protect against effector modulation of chlorophyll fluorescence and prevent Pseudomonas syringae effector‐mediated quenching of cROS and suppression of maximum dark‐adapted quantum efficiency (the ratio of variable/maximum fluorescence [Fv/Fm]). The MTI coreceptor double mutant, bak1‐5/bkk1‐1, exhibits a remarkable decrease in Fv/Fm compared to control plants during infection, underlining the importance of MTI‐mediated signalling in chloroplast immunity. Further probing the role of the chloroplast in immunity, we unexpectedly found that even moderate changes in light intensity can uncouple plant immune signalling.

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/land12050986/s1. File S1 Glossary of abbreviations used in the paper., This research was funded by the TERRANOVA Project, H2020 Marie Sklodowska-Curie grant agreement no. 813904., Reliable quantitative vegetation reconstructions for Europe during the Holocene are crucial to improving our understanding of landscape dynamics, making it possible to assess the past effects of environmental variables and land-use change on ecosystems and biodiversity, and mitigating their effects in the future. We present here the most spatially extensive and temporally continuous pollen-based reconstructions of plant cover in Europe (at a spatial resolution of 1° × 1°) over the Holocene (last 11.7 ka BP) using the ‘Regional Estimates of VEgetation Abundance from Large Sites’ (REVEALS) model. This study has three main aims. First, to present the most accurate and reliable generation of REVEALS reconstructions across Europe so far. This has been achieved by including a larger number of pollen records compared to former analyses, in particular from the Mediterranean area. Second, to discuss methodological issues in the quantification of past land cover by using alternative datasets of relative pollen productivities (RPPs), one of the key input parameters of REVEALS, to test model sensitivity. Finally, to validate our reconstructions with the global forest change dataset. The results suggest that the RPPs.st1 (31 taxa) dataset is best suited to producing regional vegetation cover estimates for Europe. These reconstructions offer a long-term perspective providing unique possibilities to explore spatial-temporal changes in past land cover and biodiversity., H2020 Marie Sklodowska-Curie TERRANOVA Project 813904, Swiss National Science Foundation, Swiss Academy of Sciences, U.S. National Science Foundation, Chinese Academy of Science, Linnaeus University’s, MERGE PRG323, ETF PRG323

In high-throughput phenotyping, recognizing individual plant categories is a vital support process for plant breeding. However, different plant categories have different fine-grained characteristics, i.e., intra-class variation and inter-class similarity, making the process challenging. Existing deep learning-based recognition methods fail to effectively address this recognition task under challenging requirements, leading to technical difficulties such as low accuracy and lack of generalization robustness. To address these requirements, this paper proposes PlantNet, a fine-grained network for plant recognition based on transfer learning and a bilinear convolutional neural network, which achieves high recognition accuracy in high-throughput phenotyping requirements. The network operates as follows. First, two deep feature extractors are constructed using transfer learning. The outer product of the different spatial locations corresponding to the two features is then calculated, and the bilinear convergence is computed for the different spatial locations. Finally, the fused bilinear vectors are normalized via maximum expectation to generate the network output. Experiments on a publicly available Arabidopsis dataset show that the proposed bilinear model performed better than related state-of-the-art methods. The interclass recognition accuracy of the four different species of Arabidopsis Sf-2, Cvi, Landsberg and Columbia are found to be 98.48%, 96.53%, 96.79% and 97.33%, respectively, with an average accuracy of 97.25%. Thus, the network has good generalization ability and robust performance, satisfying the needs of fine-grained plant recognition in agricultural production.

Graphical abstract, Environmental structure describes physical structure that can determine heterogenous spatial distribution of biotic and abiotic (nutrients, stressors etc.) components of a microorganism’s microenvironment. This study investigated the impact of micrometre-scale structure on microbial stress sensing, using yeast cells exposed to copper in microfluidic devices comprising either complex soil-like architectures or simplified environmental structures. In the soil micromodels, the responses of individual cells to inflowing medium supplemented with high copper (using cells expressing a copper-responsive pCUP1-reporter fusion) could be described neither by spatial metrics developed to quantify proximity to environmental structures and surrounding space, nor by computational modelling of fluid flow in the systems. In contrast, the proximities of cells to structures did correlate with their responses to elevated copper in microfluidic chambers that contained simplified environmental structure. Here, cells within more open spaces showed the stronger responses to the copper-supplemented inflow. These insights highlight not only the importance of structure for microbial responses to their chemical environment, but also how predictive modelling of these interactions can depend on complexity of the system, even when deploying controlled laboratory conditions and microfluidics.

Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We resequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared with a previous version. Our annotation of the new assembly, aided by RNA-sequencing information, revealed a 175% expansion (40 to 110) in the CHxC effector class, which we redefined as “CCG” based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and, particularly, the role of CCG effectors in virulence and avirulence on different hosts. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

SummaryPrevious work within the community led to the identification of a single dominant allele that controls the everbearing trait. However, frequent observations have indicated that crosses do not segregate in a Mendelian fashion, as would be expected for a trait controlled by a single dominant gene. Therefore, it was hypothesised that one or more unidentified epistatic alleles interact with the major gene.A GWAS was conducted on 587 June-bearers and 207 everbearers to assess the genetic components associated with flowering habit. The segregation ratios of parental strawberry lines with known phenotypes were used to validate the identified alleles.Three loci including the known, major FaPFRU locus and two epistatic modifiers were identified. These modifiers function as enhancers of the everbearing trait in individuals containing a single copy of the FaPFRU everbearing allele and appear to be functionally redundant. Principally, heterozygous individuals required the presence of two modifying alleles in order to allow expression of the everbearing trait.Inclusion of the epistatic alleles improved the prediction of everbearing segregation ratios, beyond that of a single allele model, however, a large proportion of the variation remained unexplained. Future work should identify the additional repressor and enhancer modifiers not identified here. Discovering the genetic components controlling the everbearing trait can enable genetic informed strawberry improvement.Society Impact StatementUntil the 1970s, the majority of commercial strawberry varieties produced a single bloom of flowers. However, continuously flowering, everbearing strawberries are now routinely cultivated and use is increasing. Indeed, introgression of the everbearing flowering trait can lead to economic benefits for growers through the production of a continual crop from the same plant. Utilising genetic guided improvement has the power to streamline everbearing generation. As such, utilising the genetic markers reported here, can help to identify everbearing individuals at an early time point in the breeding process. Furthermore, these markers can help to improve the predictions of progeny segregation ratios.

The Turks and Caicos Islands (TCI) have been affected by sargassum inundations, with impacts on the economy and environment. Sargassum removal can be costly, but sargassum use and valorisation may generate income and offset environmental damage. A significant barrier to the valorisation of sargassum is insufficient knowledge of its chemical makeup, as well as its seasonal variation and decay after stranding. The chemical characterisation of mixed sargassum and its constituent species and morphotypes (S. natans I, S.natans VIII and S. fluitans) collected from TCI between September 2020 and May 2021 and changes in the composition of sargassum decaying (over 147 days) were studied. High ash (24.61–51.10% dry weight (DW)) and arsenic (49–217 mg kg−1) could severely hamper the use of this seaweed for food or feed purposes. Although there was some reduction in arsenic levels in decaying sargassum, levels remained high (>49 mg kg−1). Biomethane production by anaerobic digestion (AD) is a potential option. Nevertheless, the exploitation of sargassum for biogas, either fresh or as it decays on the beach, is challenging due to low methane yields (

Since 2011, holopelagic Sargassum fluitans and natans have been arriving en masse to the wider Caribbean region and West Africa, impacting near-shore habitats and coastal communities. We examined the impacts of the Sargassum influx on tourism-related businesses through face-to-face interviews and focus groups and on near-shore seagrass beds through in-water surveys in the Turks and Caicos Islands (TCI). Substantial accumulations of sargassum were found on the beaches of South Caicos and Middle Creek Cay in 2018 and 2019, including a Sargassum brown tide in 2018. A variety of different approaches to removing sargassum from the beaches were mentioned and a desire from local businesses as well as local authorities to find a sustainable, cost-effective solution to what is viewed by many as a serious problem. The brown tide and sargassum accumulating as a layer on the benthos inside the seagrass beds caused significant loss of Thalassia testudinum. Halodule wrightii, macroalgae and sand plains were found in the areas lost by T. testudinum. This finding suggests that, if a cost-effective end use for sargassum could be identified, harvesting material in inshore waters rather than when it has arrived on the beach would have dual benefits.

Waxy corn starch is widely used in food and papermaking industries due to its unique properties. In this work, the structural and functional properties of starch isolated from waxy corn at different stages of kernel growth were investigated and their relationships were clarified. The results showed that with kernel growth, the surface of starch granules became smooth gradually, and the inner growth rings and the porous structure grew and became clear. Meanwhile, the weight-average molecular mass (Mw), root mean square radius (Rg), and average particle size increased while the amylose content decreased, which should account for the decreased pasting temperature (from 71.37 to 67.44 °C) and increased peak viscosity (1574.2 to 1883.1 cp) and breakdown value observed. Besides, the contents of slowly digestible starch (SDS) and resistant starch (RS) in waxy corn starch decreased significantly (from 44.01% to 40.88% and from 16.73% to 9.80%, respectively, p < 0.05) due to decreases in the double helix content, crystallinity, and structural order, and increases in the semi-crystalline lamellae thickness and the amorphous content. This research provides basic data for the rational utilization of waxy corn starch at different stages of kernel growth.\ud \ud

The beet army worm, Spodoptera exigua, is a widely distributed polyphagous pest of economically important crops worldwide.\ud The management of this pest insect continues to face many challenges. Despite synthetic chemicals posing a serious\ud threat to the environment, these remain the conventional approach for controlling S. exigua in the field. An over-reliance on\ud chemical control has not only led to selection for resistance to insecticides and to a reduction of natural enemies, but has also\ud polluted various components of ecosystem. Given these increasing pressures on the ecosystem, there is a need to implement\ud integrated pest management (IPM) approaches exploiting a wider range of tools (biotechnological approaches, microbial\ud control, biological control, cultural control, and use of host plant resistance) for an alternative to chemical control. The IPM\ud approach can not only reduce the hazard of chemical residues in the environment and associated health problems, but may\ud also provide best strategies to control insect pests. This review synthesizes published information on insecticide resistance\ud of S. exigua and explores alternative IPM approaches to control S. exigua.

Cleavage of dimethylsulfoniopropionate (DMSP) can deter herbivores in DMSP-producing eukaryotic algae; however, it is unclear whether a parallel defence mechanism operates in marine bacteria. Here we demonstrate that the marine bacterium Puniceibacterium antarcticum SM1211, which does not use DMSP as a carbon source, has a membrane-associated DMSP lyase, DddL. At high concentrations of DMSP, DddL causes an accumulation of acrylate around cells through the degradation of DMSP, which protects against predation by the marine ciliate Uronema marinum. The presence of acrylate can alter the grazing preference of U. marinum to other bacteria in the community, thereby influencing community structure. The marine bacterium Puniceibacterium antarcticum SM1211 can produce acrylate from dimethylsulfoniopropionate (DMSP) cleavage by the DMSP lyase, DddL, which protects against grazing by a ciliate predator.

Water is one of the principal constituents by mass of living plant cell walls. However, its role and interactions with secondary cell wall polysaccharides and the impact of dehydration and subsequent rehydration on the molecular architecture are still to be elucidated. This work combines multidimensional solid-state 13C magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) with molecular dynamics modeling to decipher the role of water in the molecular architecture of softwood secondary cell walls. The proximities between all main polymers, their molecular conformations, and interaction energies are compared in never-dried, oven-dried, and rehydrated states. Water is shown to play a critical role at the hemicellulose–cellulose interface. After significant molecular shrinkage caused by dehydration, the original molecular conformation is not fully recovered after rehydration. The changes include xylan becoming more closely and irreversibly associated with cellulose and some mannan becoming more mobile and changing conformation. These irreversible nanostructural changes provide a basis for explaining and improving the properties of wood-based materials.

The dissolution behavior of cellulose in the mixtures of dimethyl sulfoxide (DMSO) and different ionic liquids (ILs) at 25 °C was studied. High solubility of cellulose was reached in the mixtures of ILs and DMSO at mole fractions of 1:2, 1:2, and 1:1 for 1-butyl-3-methylimidazolium acetate, 1-propyl-3-methylimidazolium acetate, and 1-ethyl-3-methylimidazolium acetate, respectively. At high DMSO/IL molar ratios (10:1–2:1), a longer alkyl chain of the IL cation led to higher cellulose solubility. However, shorter cation alkyl chains favored cellulose dissolution at 1:1. Rheological, Fourier transform infrared spectroscopy (FTIR), and nuclear magnetic resonance (NMR) measurements were used to understand cellulose dissolution. It was found out that the increase of the DMSO ratio in binary mixtures caused higher cellulose solubility by decreasing the viscosity of systems. For cations with longer alkyl chains, stronger interaction between the IL and cellulose and higher viscosity of DMSO/IL mixtures were observed. The new knowledge obtained here could be useful to the development of cost-effective solvent systems for biopolymers.\ud \ud

The flower pollination algorithm (FPA) is a highly efficient metaheuristic optimization algorithm that is inspired by the pollination process of flowering species. FPA is characterised by simplicity in its formulation and high computational performance. Previous studies on FPA assume fixed parameter values based on empirical observations or experimental comparisons of limited scale and scope. In this study, a comprehensive effort is made to identify appropriate values of the FPA parameters that maximize its computational performance. To serve this goal, a simple non-iterative, single-stage sampling tuning method is employed, oriented towards practical applications of FPA. The tuning method is applied to the set of 28 functions specified in IEEE-CEC'13 for real-parameter single-objective optimization problems. It is found that the optimal FPA parameters depend significantly on the objective functions, the problem dimensions and affordable computational cost. Furthermore, it is found that the FPA parameters that minimize mean prediction errors do not always offer the most robust predictions. At the end of this study, recommendations are made for setting the optimal FPA parameters as a function of problem dimensions and affordable computational cost. [Abstract copyright: © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2021.]

The high-capacity tensiometer and thermocouple psychrometer measure xylem water potential with high accuracy and adequate response time, as demonstrated by simultaneous measurements on sapling stems., The pressure chamber, the most popular method used to measure xylem water potential, is a discontinuous and destructive technique and is therefore not suitable for automated monitoring. Continuous non-destructive monitoring could until very recently be achieved only by use of the thermocouple psychrometer (TP). Here we present the high-capacity tensiometer (HCT) as an alternative method for continuous non-destructive monitoring. This provided us with a unique chance to cross-validate the two instruments by installing them simultaneously on the same sapling stem. The HCT and the TP showed excellent agreement for xylem water potential less than –0.5 MPa. Response to day/night cycles and watering was remarkably in phase, indicating excellent response time of both instruments despite substantially different working principles. For xylem water potential greater than –0.5 MPa, the discrepancies sometimes observed between the HCT and TP were mainly attributed to the kaolin paste used to establish contact between the xylem and the HCT, which becomes hydraulically poorly conductive in this range of water potential once dried beyond its air-entry value and subsequently re-wetted. Notwithstanding this limitation, which can be overcome by selecting a clay paste with higher air-entry value, the HCT has been shown to represent a valid alternative to the TP.

We investigated the role of plant host and soil variables in determining arbuscular mycorrhizal fungi (AMF) community composition in plant roots of two spatially separated mangrove estuaries on the rivers Aghanashini (14° 30′ 30″ N–74° 22′ 44″ E) and Gangavali (14° 35′ 26″ N–74° 17′ 51″ E) on the west coast of India. Both mangrove estuaries had similar plant species composition but differed in soil chemistries. We amplified a 550-bp portion of 18S small subunit (SSU) rDNA from mangrove plant roots and analysed it by restriction fragment length polymorphism (RFLP). Clones representing unique RFLP patterns were sequenced. A total of 736 clones were obtained from roots of seven and five plant species sampled at Aghanashini and Gangavali, respectively. AMF phylotype numbers in plant roots at Aghanashini (12) were higher than at Gangavali (9) indicating quantitative differences in the AMF community composition in plant roots at the two mangrove estuaries. Because both estuaries had similar plant species composition, the quantitative difference in AMF communities between the estuaries could be an attribute of the differences in rhizospheric chemistry between the two sites. Non-metric multidimensional scaling (NMDS) revealed overlap in the AMF communities of the two sites. Three and two AMF phylotypes had significant indicator value indices with specific hosts at Aghanashini and Gangavali, respectively. Environmental vector fitting to NMDS ordination did not reveal a significant effect of any soil variable on AMF composition at the two sites. However, significant effects of both plant hosts and sites were observed on rhizospheric P. Our results indicate that root AMF community composition may be an outcome of plant response to rhizospheric variables. This suggests that plant identity may have a primary role in shaping AMF communities in mangroves.

Funding: KL was funded by a BBSRC EASTBIO DTP studentship provided through the UKRI Biotechnology and Biological Sciences Research Council (BBSRC) grant number BB/T00875X/1 and by the Rural and Environment Science and Analytical Services Division of the Scottish Government at The James Hutton Institute and The University of St Andrews. Work on plant-parasitic nematodes at the University of Cambridge is supported by DEFRA licence 125034/359149/3 and funded by BBSRC grants BB/R011311/1, BB/N021908/1, and BB/S006397/1. Plant parasitic nematodes need to overcome the barrier presented by the plant cell wall in order to invade their host. A variety of plant cell wall degrading enzymes are present in endoparasitic nematodes including enzymes that degrade cellulose (beta 1,4 endoglucanases) and various pectin components. We describe the cloning and functional analysis of genes encoding GH53 arabinogalactan endo-1,4-beta-galactosidases from three related plant parasitic nematodes Globodera rostochiensis, Globodera pallida and Rotylenchulus reniformis. Phylogenetic and structural analyses strongly indicate that these genes have been acquired by horizontal gene transfer from bacteria. We show that the genes are expressed at invasive stages of the parasites in the secretory gland cells. We also demonstrate that the enzymes from these species are biochemically active, showing the expected hydrolytic enzymatic activity when galactan was used as a substrate. This work further demonstrates the importance of cell wall degradation to the success of the parasitic process and the extensive role that horizontal gene transfer has played in the evolution of plant parasitism by nematodes. Publisher PDF

Funding: This research was funded in part by the award of a Natural Environment Research Council (NERC) CASE research studentship to J.J.M. Background: Parapatric (or ‘budding’) speciation is increasingly recognised as an important phenomenon in plant evolution but its role in extreme (e.g. desert) environments is poorly documented. Aims: To test this speciation model in a hypothesised sister pair, the Southwest – North African disjunct Senecio flavus and its putative progenitor, the Namibian Desert endemic S. englerianus. Methods: Phylogenetic inferences were combined with niche divergence tests, morphometrics, and experimental-genetic approaches. We also evaluated the potential role of an African Dry Corridor (ADC) in promoting the hypothesised northward expansion of S. flavus (from Namibia), using palaeodistribution models. Results: Belonging to an isolated (potential ‘relict’) clade, the two morphologically distinct species showed pronounced niche divergence in Namibia and signs of digenic-epistatic hybrid incompatibility (based on F2 pollen fertility). The presence of ‘connate-fluked’ pappus hairs in S. flavus, likely increasing dispersal ability, is controlled by a single gene locus. Conclusions: Our results provide evidence for a possible (and rare) example of ‘budding’ speciation in which a wider-ranged derivative (S. flavus) originated at the periphery of a smaller-ranged progenitor (S. englerianus) in the Namib Desert region. The Southwest – North African disjunction of S. flavus could have been established by dispersal across intermediate ADC areas during periods of (Late) Pleistocene aridification. Publisher PDF

Funding: The work at University of Bonn was supported by the Federal Ministry of Education and Research, Germany (BMBF) (Grant 031A326B to FMWG) and by the German Research Foundation (DFG) (Grant SI1739/3–1 and SI1739/5-1 to S.S.). M.S.H. was supported by a fellowship from German Academic Exchange Service (DAAD; Grant 91525252)). The work at University of California Davis was supported by the National Science Foundation (NSF) (Grant IOS-1954929) and National Institute of Food and Agriculture (NIFA) (Grant 20-3994). Work on plant-parasitic nematodes at the University of Cambridge is supported by DEFRA license 125034/359149/3, and funded by BBSRC grants BB/R011311/1, BB/N021908/1, and BB/S006397/1. C.P. received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 882941. P.T. was supported by the University of St Andrews Bioinformatics Unit, funded by Wellcome Trust ISSF awards 105621/Z/14/Z and 204821/Z/16/Z. Work at Iowa State University was supported by Hatch and State of Iowa funds and a grant from the North Central Soybean Research Program. J.L.L.-T. was supported by an NWO domain Applied and Engineering Sciences VENI grant (14250) and a Wageningen University & Research Experimental Plant Sciences strategic funds grant. M.G.S. was supported by NWO domain Applied and Engineering Sciences VENI grant (17282). Plant-parasitic nematodes are a major threat to crop production in all agricultural systems. The scarcity of classical resistance genes highlights a pressing need to find new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality phased genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major parasitism stages. Analysis of the hologenome of the plant-nematode infection site identified metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that a highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is required for full pathogenicity. Knockout of either plant-encoded or now nematode-encoded steps in the pathway significantly reduces parasitic success. Our experiments establish a reference for cyst nematodes, further our understanding of the evolution of plant-parasitism by nematodes, and show that congruent differential expression of metabolic pathways in the infection hologenome represents a new way to find nematode susceptibility genes. The approach identifies genome-editing-amenable targets for future development of nematode-resistant crops. Publisher PDF

Differences in ethylene biosynthesis, and cyanide detoxification have been reported to be mechanisms of quinclorac resistance in Echinochloa crusgalli var. zelayensis. Resistant phenotypes could be a consequence of the altered endogenous IAA homeostasis induced by the herbicide. In this study we determined the IAA content and expression levels of auxin homeostasis-related genes in susceptible and resistant biotypes of E. crusgalli var. zelayensis after quinclorac treatment. The results showed that the IAA content of JNNX-S (susceptible biotype) was significantly higher than that of SSXB-R (resistant biotype) after treatment with 50 μM quinclorac. To better understand this rise in IAA, the expression profiles of seven genes (one for auxin synthesis, five for IAA conjugation, and one for IAA oxidation) and the biochemical activities of two oxidases involved in IAA homeostasis were measured. The expression of EcYUCCA10 was significantly higher in JNNX-S than in SSXB-R. The expression levels of the EcGH3s were significantly lower in JNNX-S than in SSXB-R. These expression profiles were consistent with the elevation of IAA levels in the susceptible biotype. In contrast, EcUGT and EcDAO were induced in each biotype, but a smaller increase was observed in SSXB-R than in JNNX-S. The enzymatic activities of IAA oxidases and peroxidases were higher in SSXB-R than in JNNX-S 24 h after treatment. It was inferred that altered expression of specific genes involved in IAA synthesis, conjugation, and oxidation resulted in less IAA being induced in the resistant biotype, resulting in a lower ethylene burst and the associated quinclorac resistance. These results suggest novel layers of complexity in the mechanism of quinclorac resistance.

Infections caused by Candida species are becoming seriously dangerous and difficult to cure due to their sophisticated mechanisms of resistance. The host organism defends itself from the invader, e.g., by increasing the concentration of metal ions. Therefore, there is a need to understand the overall mechanisms of metal homeostasis in Candida species. One of them is associated with AMT1, an important virulence factor derived from Candida glabrata, and another with MAC1, present in Candida albicans. Both of the proteins possess a homologous Cys/His-rich domain. In our studies, we have chosen two model peptides, L680 (Ac-10ACMECVRGHRSSSCKHHE27-NH2, MAC1, Candida albicans) and L681 (Ac-10ACDSCIKSHKAAQCEHNDR28-NH2, AMT1, Candida glabrata), to analyze and compare the properties of their complexes with Zn(II) and Cd(II). We studied the stoichiometry, thermodynamic stability, and spectroscopic parameters of the complexes in a wide pH range. When competing for the metal ion in the equimolar mixture of two ligands and Cd(II)/Zn(II), L680 forms more stable complexes with Cd(II) while L681 forms more stable complexes with Zn(II) in a wide pH range. Interestingly, a Glu residue was responsible for the additional stability of Cd(II)-L680. Despite a number of scientific reports suggesting Cd(II) as an efficient surrogate of Zn(II), we showed significant differences between the Zn(II) and Cd(II) complexes of the studied peptides.

Plants are resistant to most microbial species due to nonhost resistance (NHR), providing broad-spectrum and durable immunity. However, the molecular components contributing to NHR are poorly characterised. We address the question of whether failure of pathogen effectors to manipulate nonhost plants plays a critical role in NHR. RxLR (Arg-any amino acid-Leu-Arg) effectors from two oomycete pathogens, Phytophthora infestans and Hyaloperonospora arabidopsidis , enhanced pathogen infection when expressed in host plants ( Nicotiana benthamiana and Arabidopsis, respectively) but the same effectors performed poorly in distantly related nonhost pathosystems. Putative target proteins in the host plant potato were identified for 64 P . infestans RxLR effectors using yeast 2-hybrid (Y2H) screens. Candidate orthologues of these target proteins in the distantly related non-host plant Arabidopsis were identified and screened using matrix Y2H for interaction with RxLR effectors from both P . infestans and H . arabidopsidis . Few P . infestans effector-target protein interactions were conserved from potato to candidate Arabidopsis target orthologues (cAtOrths). However, there was an enrichment of H . arabidopsidis RxLR effectors interacting with cAtOrths. We expressed the cAtOrth AtPUB33, which unlike its potato orthologue did not interact with P . infestans effector PiSFI3, in potato and Nicotiana benthamiana. Expression of AtPUB33 significantly reduced P . infestans colonization in both host plants. Our results provide evidence that failure of pathogen effectors to interact with and/or correctly manipulate target proteins in distantly related non-host plants contributes to NHR. Moreover, exploiting this breakdown in effector-nonhost target interaction, transferring effector target orthologues from non-host to host plants is a strategy to reduce disease.

Background The genus Tetracladium De Wild. (Ascomycota) has been traditionally regarded as a group of Ingoldian fungi or aquatic hyphomycetes—a polyphyletic group of phylogenetically diverse fungi which grow on decaying leaves and plant litter in streams. Recent sequencing evidence has shown that Tetracladium spp. may also exist as root endophytes in terrestrial environments, and furthermore may have beneficial effects on the health and growth of their host. However, the diversity of Tetracladium spp. communities in terrestrial systems and the factors which shape their distribution are largely unknown. Results Using a fungal community internal transcribed spacer amplicon dataset from 37 UK Brassica napus fields we found that soils contained diverse Tetracladium spp., most of which represent previously uncharacterised clades. The two most abundant operational taxonomic units (OTUs), related to previously described aquatic T. furcatum and T. maxilliforme, were enriched in roots relative to bulk and rhizosphere soil. For both taxa, relative abundance in roots, but not rhizosphere or bulk soil was correlated with B. napus yield. The relative abundance of T. furcatum and T. maxilliforme OTUs across compartments showed very similar responses with respect to agricultural management practices and soil characteristics. The factors shaping the relative abundance of OTUs homologous to T. furcatum and T. maxilliforme OTUs in roots were assessed using linear regression and structural equation modelling. Relative abundance of T. maxilliforme and T. furcatum in roots increased with pH, concentrations of phosphorus, and increased rotation frequency of oilseed rape. It decreased with increased soil water content, concentrations of extractable phosphorus, chromium, and iron. Conclusions The genus Tetracladium as a root colonising endophyte is a diverse and widely distributed part of the oilseed rape microbiome that positively correlates to crop yield. The main drivers of its community composition are crop management practices and soil nutrients.

Advances in DNA sequencing technologies have drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Important ecological interactions being performed by microbes can be investigated by analyzing the extracellular protein fraction. Here, we combined a unique protein extraction method and an iterative bioinformatics pipeline to capture and identify extracellular proteins (metaexoproteomics) synthesized in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analyzed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1,885 plant, insect, and microbial proteins were identified across bulk and rhizosphere samples. Metaexoproteomics identified a significant shift in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This included stimulation of rhizosphere-specialized bacteria, such as Gammaproteobacteria, Betaproteobacteria, and Flavobacteriia, and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralization. Our metaproteomic assessment of the “active” plant microbiome at the field-scale demonstrates the importance of moving beyond metagenomics to determine ecologically important plant-microbe interactions underpinning plant health.\ud

Prunus armeniaca L. (Rosaceae)-syn. Amygdalus armeniaca (L.) Dumort., Armeniaca armeniaca (L.) Huth, Armeniaca vulgaris Lam is commonly known as the apricot tree. The plant is thought to originate from the northern, north-western, and north-eastern provinces of China, although some data show that it may also come from Korea or Japan. The apricot fruit is used medicinally to treat a variety of ailments, including use as an antipyretic, antiseptic, anti-inflammatory, emetic, and ophthalmic remedy. The Chinese and Korean pharmacopeias describe the apricot seed as an herbal medicinal product. Various parts of the apricot plant are used worldwide for their anticancer properties, either as a primary remedy in traditional medicine or as a complementary or alternative medicine. The purpose of this review was to provide comprehensive and up-to-date information on ethnobotanical data, bioactive phytochemicals, anticancer potential, pharmacological applications, and toxicology of the genus Prunus armeniaca, thus providing new perspectives on future research directions. Included data were obtained from online databases such as PubMed/Medline, Google Scholar, Science direct, and Wiley Online Library. Multiple anticancer mechanisms have been identified in in vitro and in vivo studies, the most important mechanisms being apoptosis, antiproliferation, and cytotoxicity. The anticancer properties are probably mediated by the contained bioactive compounds, which can activate various anticancer mechanisms and signaling pathways such as tumor suppressor proteins that reduce the proliferation of tumor cells. Other pharmacological properties resulting from the analysis of experimental studies include neuroprotective, cardioprotective, antioxidant, immunostimulatory, antihyperlipidemic, antibacterial, and antifungal effects. In addition, data were provided on the toxicity of amygdalin, a compound found in apricot kernel seeds, which limits the long-term use of complementary/alternative products derived from P. armeniaca. This updated review showed that bioactive compounds derived from P. armeniaca are promising compounds for future research due to their important pharmacological properties, especially anticancer. A detailed analysis of the chemical structure of these compounds and their cytotoxicity should be carried out in future research. In addition, translational pharmacological studies are required for the correct determination of pharmacologically active doses in humans.

Halauxifen-methyl is a new auxin herbicide developed by Corteva Agriscience (Wilmington, DE, USA). It has been suggested that ABF5 may be the target of halauxifen-methyl, as AFB5 mutants of Arabidopsis thaliana are resistant to halauxifen-methyl, which preferentially binds to AFB5. However, the mode of action of halauxifen-methyl has not yet been reported. Therefore, the aim of the present study was to reveal the mode of action of halauxifen-methyl by exploring its influence on indole-3-acetic acid (IAA) homeostasis and the biosynthesis of ethylene and Abscisic Acid (ABA) in Galium aparine. The results showed that halauxifen-methyl could disrupt the homeostasis of IAA and stimulate the overproduction of ethylene and ABA by inducing the overexpression of the 1-aminocyclopropane-1-carboxylate synthase (ACS) and 9-cis-epoxycarotenoid dioxygenase (NCED) genes involved in ethylene and ABA biosynthesis, finally leading to senescence and plant death.

The plcR gene, which encodes the pleiotropic transcriptional regulator of secreted proteins found in most members of the Bacillus cereus group, is truncated in all Bacillus anthracis isolates. The current dogma suggests this truncation was evolved to accommodate the acquisition of the anthrax toxin regulator, AtxA. However, the B. cereus-B. anthracis “cross-over” strain Bacillus cereus G9241, isolated from a Louisiana welder suffering from an anthrax-like infection, appears to contradict the proposed dogma as it encodes intact copies of both regulators. Here we report that when cultured at 25 °C, cell free B. cereus G9241 culture supernatants are cytotoxic and haemolytic to various eukaryotic cells in addition to insect haemocytes from Manduca sexta. However, this cytotoxic and haemolytic activity of the culture supernatant is lost when the bacteria are grown at 37 °C, behaving much like the supernatants generated by B. anthracis. Using a combination of genetic and proteomic approaches, we identified several PlcR-regulated toxins secreted at 25 °C. We demonstrate that a limiting step for the production of these virulence factors at 37 °C exists within the PlcR-PapR regulation circuit in strain G9241, giving rise to the temperature-dependent haemolytic and cytotoxic activity of the culture supernatants. Differential expression of the protease responsible in processing the PlcR quorum sensing activator PapR appears to be responsible for this phenotype. This study confirms that B. cereus G9241 is able to ‘switch’ between B. cereus and B. anthracis–like phenotypes in a temperature-dependent manner, potentially accommodating the activities of both PlcR and AtxA.

International audience; Fresh berries are a popular and important component of the human diet. The demand for high-quality berries and sustainable production methods is increasing globally, challenging breeders to develop modern berry cultivars that fulfill all desired characteristics. Since 1994, research projects have characterized genetic resources, developed modern tools for high-throughput screening, and published data in publicly available repositories. However, the key findings of different disciplines are rarely linked together and only a limited range of traits and genotypes has been investigated. The Horizon2020 project BreedingValue will address these challenges by studying a broader panel of strawberry, raspberry and blueberry genotypes in detail, in order to recover the lost genetic diversity that has limited the aroma and flavor intensity of recent cultivars. We will combine metabolic analysis with sensory panel tests and surveys to identify the key components of taste, flavor and aroma in berries across Europe, leading to a high-resolution map of quality requirements for future berry cultivars. Traits linked to berry yields and the effect of environmental stress will be investigated using modern image analysis methods and modeling. We will also use genetic analysis to determine the genetic basis of complex traits for the development and optimization of modern breeding technologies such as molecular marker arrays, genomic selection and genome wide association studies. Finally, the results, raw data and metadata will be made publicly available on the open platform Germinate in order to meet FAIR data principles and provide the basis for sustainable research in the future.

Water hyacinth (Pontederia crassipes, also known as Eichhornia crassipes) is a highly invasive aquatic macrophyte species, indigenous to Amazonia, Brazil and tropical South America. It was introduced to India in 1896 and has now become an environmental and social challenge throughout the country in community ponds, freshwater lakes, irrigation channels, rivers and most other surface waterbodies. Considering its large speed of propagation on the water surface under conducive conditions and the adverse impact the infesting weed has, constant monitoring is needed to aid civic bodies, governments and policy makers involved in remedial measures. The synoptic coverage provided by satellite imaging and other remote sensing practices make it convenient to find a solution using this type of data. While there is an established background for the practice of remote sensing in the detection of aquatic plants, the use of Synthetic Aperture Radar (SAR) has yet to be fully exploited in the detection of water hyacinth. This research focusses on detecting water hyacinth within Vembanad Lake, Kuttanad, India. Here, results show that the monitoring of water hyacinth has proven to be possible using Sentinel-1 SAR data. A quantitative analysis of detection performance is presented using traditional and state-of-the-art change detectors. Analysis of these more powerful detectors showed true positive detection ratings of ~95% with 0.1% false alarm, showing significantly greater positive detection ratings when compared to the more traditional detectors. We are therefore confident that water hyacinth can be monitored using SAR data provided the extent of the infestation is significantly larger than the resolution cell (bigger than a quarter of a hectare).

Polysaccharide methylation, especially that of pectin, is a common and important feature of land plant cell walls. Polysaccharide methylation takes place in the Golgi apparatus and therefore relies on the import of S-adenosyl methionine (SAM) from the cytosol into the Golgi. However, so far, no Golgi SAM transporter has been identified in plants. Here we studied major facilitator superfamily members in Arabidopsis that we identified as putative Golgi SAM transporters (GoSAMTs). Knockout of the two most highly expressed GoSAMTs led to a strong reduction in Golgi-synthesized polysaccharide methylation. Furthermore, solid-state NMR experiments revealed that reduced methylation changed cell wall polysaccharide conformations, interactions and mobilities. Notably, NMR revealed the existence of pectin 'egg-box' structures in intact cell walls and showed that their formation is enhanced by reduced methyl esterification. These changes in wall architecture were linked to substantial growth and developmental phenotypes. In particular, anisotropic growth was strongly impaired in the double mutant. The identification of putative transporters involved in import of SAM into the Golgi lumen in plants provides new insights into the paramount importance of polysaccharide methylation for plant cell wall structure and function.

BackgroundCarrot is a crop with a wide range of phenotypic and molecular diversity. Within cultivated carrots, the western gene pool comprises types characterized by different storage root morphology. First western carrot cultivars originated from broad-based populations. It was followed by intercrosses among plants representing early open-pollinated cultivars, combined with mass phenotypic selection for traits of interest. Selective breeding improved root uniformity and led to the development of a range of cultivars differing in root shape and size. Based on the root shape and the market use of cultivars, a dozen of market types have been distinguished. Despite their apparent phenotypic variability, several studies have suggested that western cultivated carrot germplasm was genetically non-structured.ResultsNinety-threeDcS-ILP markers and 2354 SNP markers were used to evaluate the structure of genetic diversity in the collection of 78 western type open-pollinated carrot cultivars, each represented by five plants. The mean percentage of polymorphic loci segregating within a cultivar varied from 31.18 to 89.25% forDcS-ILP markers and from 45.11 to 91.29% for SNP markers, revealing high levels of intra-cultivar heterogeneity, in contrast to its apparent phenotypic stability. Average inbreeding coefficient for all cultivars was negative for bothDcS-ILP and SNP, whereas the overall genetic differentiation across all market classes, as measured by FST, was comparable for both marker systems. ForDcS-ILPs 90–92% of total genetic variation could be attributed to the differences within the inferred clusters, whereas for SNPs the values ranged between 91 to 93%. Discriminant Analysis of Principal Components enabled the separation of eight groups cultivars depending mostly on their market type affiliation. Three groups of cultivars, i.e. Amsterdam, Chantenay and Imperator, were characterized by high homogeneity regardless of the marker system used for genotyping.ConclusionsBoth marker systems used in the study enabled detection of substantial variation among carrot plants of different market types, therefore can be used in germplasm characterization and analysis of genome relationships. The presented results likely reveal the actual genetic diversity structure within the western carrot gene pool and point at possible discrepancies within the cultivars’ passport data.

The complete mitogenome of Fusarium oxysporum f. sp. albedinis (FOA), the causal agent of the destructive fusarium wilt in date palm, is sequenced and assembled. The circular mitogenome of isolate Foa44 is 51,601 bp in length and contains 26 transfer RNA (tRNA) genes, one ribosomal RNA (rRNA), and 28 protein-coding genes. A mitogenome-based phylogenetic analysis of Fusarium revealed that FOA is congruent with previous nuclear-gene phylogenetic results.

Understanding the relationship between flowering patterns and pollen dispersal is important in climate change modelling, pollen forecasting, forestry and agriculture. Enhanced understanding of this connection can be gained through detailed spatial and temporal flowering observations on a population level, combined with modelling simulating the dynamics. Species with large distribution ranges, long flowering seasons, high pollen production and naturally large populations can be used to illustrate these dynamics. Revealing and simulating species-specific demographic and stochastic elements in the flowering process will likely be important in determining when pollen release is likely to happen in flowering plants. Spatial and temporal dynamics of eight populations of Dactylis glomerata were collected over the course of two years to determine high-resolution demographic elements. Stochastic elements were accounted for using Markov chain approaches in order to evaluate tiller-specific contribution to overall population dynamics. Tiller-specific developmental dynamics were evaluated using three different RV matrix correlation coefficients. We found that the demographic patterns in population development were the same for all populations with key phenological events differing only by a few days over the course of the seasons. Many tillers transitioned very quickly from non-flowering to full flowering, a process that can be replicated with Markov chain modelling. Our novel approach demonstrates the identification and quantification of stochastic elements in the flowering process of D. glomerata, an element likely to be found in many flowering plants. The stochastic modelling approach can be used to develop detailed pollen release models for Dactylis, other grass species and probably other flowering plants.

Light-to-heat conversion materials generate great interest due to their widespread applications, notable exemplars being solar energy harvesting and photoprotection. Another more recently identified potential application for such materials is in molecular heaters for agriculture, whose function is to protect crops from extreme cold weather and extend both the growing season and the geographic areas capable of supporting growth, all of which could help reduce food security challenges. To address this demand, a new series of phenolic-based barbituric absorbers of ultraviolet (UV) radiation has been designed and synthesised in a sustainable manner. The photophysics of these molecules has been studied in solution using femtosecond transient electronic and vibrational absorption spectroscopies, allied with computational simulations and their potential toxicity assessed by in silico studies. Following photoexcitation to the lowest singlet excited state, these barbituric absorbers repopulate the electronic ground state with high fidelity on an ultrafast time scale (within a few picoseconds). The energy relaxation pathway includes a twisted intramolecular charge-transfer state as the system evolves out of the Franck–Condon region, internal conversion to the ground electronic state, and subsequent vibrational cooling. These barbituric absorbers display promising light-to-heat conversion capabilities, are predicted to be non-toxic, and demand further study within neighbouring application-based fields., The synthesis and photophysical properties of phenolic barbiturics are reported. These molecules convert absorbed ultraviolet light to heat with high fidelity and may be suitable for inclusion in foliar sprays to boost crop protection and production.

Significance Maize is a global food staple with great economic and cultural importance. Archaeogenomic studies have revealed a process of protracted maize domestication and multiple waves of human-mediated dispersal in the Americas. Maize first arrived in South America as a partial domesticate, where the domestication syndrome became independently fixed and improved varieties developed away from the influence of wild gene flow. We demonstrate that hybrids of some of these improved varieties were likely reintroduced back to Central America. We hypothesize that this backflow of South American genetic material may have contributed to the development of a more productive staple, which was related to the growth and aggregation of human populations, and the formation of more complex social and political structures regionally., Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ∼9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7,000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but it has been unclear until now whether the deeply divergent maize lineages underwent any subsequent gene flow between these regions. Here we report ancient maize genomes (2,300–1,900 cal. BP) from El Gigante rock shelter, Honduras, that are closely related to ancient and modern maize from South America. Our findings suggest that the second wave of maize brought into South America hybridized with long-established landraces from the first wave, and that some of the resulting newly admixed lineages were then reintroduced to Central America. Direct radiocarbon dates and cob morphological data from the rock shelter suggest that more productive maize varieties developed between 4,300 and 2,500 cal. BP. We hypothesize that the influx of maize from South America into Central America may have been an important source of genetic diversity as maize was becoming a staple grain in Central and Mesoamerica.

Volatile nitrogen oxides (N2O, NO, NO2, HONO, …) can negatively impact climate, air quality, and human health. Using soils collected from temperate forests across the eastern United States, we show microbial communities involved in nitrogen (N) cycling are structured, in large part, by the composition of overstory trees, leading to predictable N‐cycling syndromes, with consequences for emissions of volatile nitrogen oxides to air. Trees associating with arbuscular mycorrhizal (AM) fungi promote soil microbial communities with higher N‐cycle potential and activity, relative to microbial communities in soils dominated by trees associating with ectomycorrhizal (ECM) fungi. Metagenomic analysis and gene expression studies reveal a 5 and 3.5 times greater estimated N‐cycle gene and transcript copy numbers, respectively, in AM relative to ECM soil. Furthermore, we observe a 60% linear decrease in volatile reactive nitrogen gas flux (NOy ≡ NO, NO2, HONO) as ECM tree abundance increases. Compared to oxic conditions, gas flux potential of N2O and NO increase significantly under anoxic conditions for AM soil (30‐ and 120‐fold increase), but not ECM soil—likely owing to small concentrations of available substrate (NO3‐) in ECM soil. Linear mixed effects modeling shows that ECM tree abundance, microbial process rates, and geographic location are primarily responsible for variation in peak potential NOy flux. Given that nearly all tree species associate with either AM or ECM fungi, our results indicate that the consequences of tree species shifts associated with global change may have predictable consequences for soil N cycling., Volatile nitrogen oxides can negatively impact climate, air quality, and human health. Using soils collected from temperate forests across the eastern United States, we show microbial communities involved in nitrogen (N) cycling are structured, in large part, by the composition of overstory trees, leading to predictable N cycling syndromes, with consequences for emissions of volatile nitrogen oxides to air. Trees associating with arbuscular mycorrhizal (AM) fungi promote soil microbial communities with higher N‐cycle potential and activity, relative to microbial communities in soils dominated by trees associating with ectomycorrhizal (ECM) fungi. Given that nearly all tree species associate with either AM or ECM fungi, our results indicate that the consequences of tree species shifts associated with global change may have predictable consequences for soil N cycling.

Deep learning-based methods have recently provided a means to rapidly and effectively extract various plant traits due to their powerful ability to depict a plant image across a variety of species and growth conditions. In this study, we focus on dealing with two fundamental tasks in plant phenotyping, i.e., plant segmentation and leaf counting, and propose a two-steam deep learning framework for segmenting plants and counting leaves with various size and shape from two-dimensional plant images. In the first stream, a multi-scale segmentation model using spatial pyramid is developed to extract leaves with different size and shape, where the fine-grained details of leaves are captured using deep feature extractor. In the second stream, a regression counting model is proposed to estimate the number of leaves without any pre-detection, where an auxiliary binary mask from segmentation stream is introduced to enhance the counting performance by effectively alleviating the influence of complex background. Extensive pot experiments are conducted CVPPP 2017 Leaf Counting Challenge dataset, which contains images of Arabidopsis and tobacco plants. The experimental results demonstrate that the proposed framework achieves a promising performance both in plant segmentation and leaf counting, providing a reference for the automatic analysis of plant phenotypes.

Exploring the Mid-Late Holocene interactions between ecological and climate variations in semi-arid areas such as Songnen grasslands (northeastern China) provide insights into how future vegetation changes and hydrological variations may have an impact on semi-arid ecosystems, in general. In this study, we present a high-resolution palaeoecological dataset covering the past 7300 years. For this purpose, a peat section has been sampled from the shore of Dabusu lake situated in the southwestern part of the Songnen grasslands. We use pollen analyses to reconstruct the regional and local vegetation dynamics, and measure TOC (total organic carbon) and the degree of peat humification to study changes in regional and local biomass. Diatom analysis, grain size analysis, and CaCO3 contents are used to assess the water-table fluctuations of the Dabusu peatlands. The results show that from 7300 to 6000 cal BP, Dabusu peatlands were characterized by grasslands, dominated by Poaceae plants and high-water level. From 6000 to 910 cal BP, forest-steppes and dry-steppes dominated in the region alternatively. The water level of Dabusu peatlands experienced relatively low levels following an earlier rapid decline around 6000–5100 cal BP. Then after a slight increase between 5100 and 4000 cal BP, it remained at a relatively low level until 910 cal BP. After 910 cal BP, steppe vegetation dominated in the region and the water level of Dabusu peatlands slightly rose. By comparing these features with regional climate change, we show that EASM circulations might be the main driving forces controlling the regional paleovegetation dynamics and hydrological variations. This outcome is critical for the understanding of the long-term interactions between vegetation, hydrology, and climate of mid-latitude semi-arid grasslands.

16 Pág., Turnip mosaic virus (TuMV) is an economically important virus infecting a broad range of arable and vegetable crops and many wild plant species. It is also of particular scientific interest as it has the broadest host range of any of the potyviruses, infects dicotyledonous and monocotyledonous plants, is transmitted by many (>89) aphid species and is the best adapted potyvirus to Arabidopsis thaliana. For these reasons it has been particularly well studied from many angles and is being exploited for biotechnological purposes. This review aims to consolidate the most recent advances in research on TuMV and will form the basis of an updated version on the Association of Applied Biologists (AAB) Description of Plant Viruses for TuMV.

Choline and glycine betaine (GBT) are utilized as osmolytes to counteract osmotic stress, but also constitute important nutrient sources for many marine microbes. Bacterial catabolism of these substrates can then lead to the production of climate active trace gases such as methylamine and methane. Using radiotracers, we investigated prokaryotic choline/GBT uptake and determined biotic and abiotic factors driving these processes in the Western English Channel, UK. Kinetic uptake parameters indicated high affinity (nM range) for both osmolytes and showed a seasonal pattern for choline uptake. Generalized linear modeling of uptake parameters suggested a significant influence of sea surface temperature and salinity on prokaryotic uptake of both osmolytes. The presence of diatoms significantly influenced prokaryotic choline/GBT uptake dynamics. Choline uptake was further related to the occurrence of Phaeocystis spp., which were highly abundant in the phytoplankton community during spring, and dinoflagellates abundance during summer. While Rhodobacteraceae were the most important bacterial drivers for prokaryotic choline uptake, prokaryotic GBT uptake was associated with various groups such as SAR11 (Pelagibacterales) and Gammaproteobacteria, suggesting a wider capacity for GBT catabolism than previously recognized. Furthermore, using a newly developed approach we determined the first available data for dissolved GBT concentrations in seawater and found both osmolytes to be at the sub-nanomolar range. Together, this study improves our understanding of the biogeochemical cycling of these environmentally important osmolytes and highlights how their cycles may be affected by a changing climate.\ud \ud

Open Access funding enabled and organized by Projekt DEAL. This research was funded by the University of St Andrews, Scotland. Bumble bees (Bombus; Hymenoptera) are crucial pollinators for many agricultural crops, but their numbers have declined - with climate change as a possible driver. Different aspects of local weather conditions can have substantial effects on bumble bees’ ability to forage. Here we made 501 observations of bumblebee workers on bramble flowers (Rubus fruticosus) to explore how the characteristic sizes of foragers active and their individual rate of movement between flowers were correlated with aspects of weather. Firstly, we found that increased ambient temperature is correlated to reduced activity in larger workers. Moreover, while higher humidity was linked to an increase in smaller workers, an increase in cloud cover led their numbers to decrease. Visitation rate and temperature showed a significant negative relationship whereas no other weather aspect affected visitation rate significantly. Our results suggest that predicted rises in ambient temperatures will adversely affect bumble bee foraging, and particularly so for larger-bodied workers. We anticipate that this study can be used as a foundation for longer-term and more detailed studies on bumble bee foraging and colony performance. Such work is vital to identify management measures to mitigate pollinator declines and preserve food security. Publisher PDF

Plants use complex gene regulatory mechanisms to overcome diverse environmental challenges. For instance, cold stress induces rapid and massive transcriptome changes via alternative\udsplicing (AS) to confer cold tolerance in plants. In mammals, mounting evidence suggests chromatin\udstructure can regulate co-transcriptional AS. Recent evidence also supports co-transcriptional regulation of AS in plants, but how dynamic changes in DNA methylation and the chromatin structure\udinfluence the AS process upon cold stress remains poorly understood. In this study, we used the DNA\udmethylation inhibitor 5-Aza-20\ud-Deoxycytidine (5-aza-dC) to investigate the role of stochastic variations in DNA methylation and nucleosome occupancy in modulating cold-induced AS, in Arabidopsis\udthaliana (Arabidopsis). Our results demonstrate that 5-aza-dC derived stochastic hypomethylation\udmodulates nucleosome occupancy and AS profiles of genes implicated in RNA metabolism, plant\udhormone signal transduction, and of cold-related genes in response to cold stress. We also demonstrate that cold-induced remodelling of DNA methylation regulates genes involved in amino acid\udmetabolism. Collectively, we demonstrate that sudden changes in DNA methylation via drug treatment can influence nucleosome occupancy levels and modulate AS in a temperature-dependent\udmanner to regulate plant metabolism and physiological stress adaptation.

Sugarcane (Saccharum spp.) is an important economic crop for both sugar and biomass, the yields of which are negatively affected by flowering. The molecular mechanisms controlling flowering in sugarcane are nevertheless poorly understood. RNA-seq data analysis and database searches have enabled a comprehensive description of the PEBP gene family in sugarcane. It is shown to consist of at least 13 FLOWERING LOCUS T (FT)-like genes, two MOTHER OF FT AND TFL (MFT)-like genes, and four TERMINAL FLOWER (TFL)-like genes. As expected, these genes all show very high homology to their corresponding genes in Sorghum, and also to FT-like, MFT-like, and TFL-like genes in maize, rice, and Arabidopsis. Functional analysis in Arabidopsis showed that the sugarcane ScFT3 gene can rescue the late flowering phenotype of the Arabidopsis ft-10 mutant, whereas ScFT5 cannot. High expression levels of ScFT3 in leaves of short day-induced sugarcane plants coincided with initial stages of floral induction in the shoot apical meristem as shown by histological analysis of meristem dissections. This suggests that ScFT3 is likely to play a role in floral induction in sugarcane; however, other sugarcane FT-like genes may also be involved in the flowering process.

Stinging nettles (Urtica spp.) have been used in a diverse range of traditional and historical medicines from around the world for the treatment of skin diseases, wounds, urinary disorders, respiratory diseases, bone and joint pain, anaemia and other circulatory problems, as well as in cosmetic preparations for skin and haircare. As part of an interdisciplinary exploration of nettle-based remedies, we performed a systematic review of published evidence for the antimicrobial activity of Urtica spp. extracts against bacteria and fungi that commonly cause skin, soft tissue and respiratory infections. We focussed on studies in which minimum inhibitory concentration (MIC) assays of U. dioica were conducted on the common bacterial opportunistic pathogens Escherichia coli , Pseudomonas aeruginosa , Klebsiella pneumoniae and Staphylococcus aureus . No studies used fresh leaves (all were dried prior to use), and no studies prepared nettles in weak acid (corresponding to vinegar) or in fats/oils, which are common combinations in historical and traditional preparations. We addressed this gap by conducting new antibacterial tests of extracts of fresh U. dioica leaves prepared in vinegar, butter or olive oil against P. aeruginosa and S. aureus . Our systematic review and additional experimental data leads us to conclude that there is no strong evidence for nettles containing molecules with clinically useful antimicrobial activity. It seems most likely that the utility of nettles in traditional topical preparations for wounds may simply be as a ‘safe’ absorbent medium for keeping antibacterial (vinegar) or emollient (oils) ingredients at the treatment site.

Cryopreservation of biological material is vital for existing and emerging biomedical and biotechnological research and related applications, but there remain significant challenges. Cryopreservation of cells in sub-milliliter volumes is difficult because they tend to deeply supercool, favoring lethal intracellular ice formation. Some tree pollens are known to produce polysaccharides capable of nucleating ice at warm sub-zero temperatures. Here we demonstrated that aqueous extractions from European hornbeam pollen (pollen washing water, PWW) increased ice nucleation temperatures in 96-well plates from ≈ − 13 °C to ≈ − 7 °C. Application of PWW to the cryopreservation of immortalized T-cells in 96-well plates resulted in an increase of post-thaw metabolic activity from 63.9% (95% CI [58.5 to 69.2%]) to 97.4% (95% CI [86.5 to 108.2%]) of unfrozen control. When applied to cryopreservation of immortalized lung carcinoma monolayers, PWW dramatically increased post-thaw metabolic activity, from 1.6% (95% CI [− 6.6 to 9.79%]) to 55.0% (95% CI [41.6 to 68.4%]). In contrast to other ice nucleating agents, PWW is soluble, sterile and has low cytotoxicity meaning it can be readily incorporated into existing cryopreservation procedures. As such, it can be regarded as a unique class of cryoprotectant which acts by inducing ice nucleation at warm temperatures.

Spinach RNA-mimicking GFP (S-RMG) has been successfully used to monitor cellular RNAs including microRNAs in bacterium, yeast, and human cells. However, S-RMG has not been established in plants. In this study, we found that like bacterial, yeast, and human cellular tRNAs, plant tRNAs such as tRNALys can protect and/or stabilize the Spinach RNA aptamer interaction with the fluorophore DFHBI enabling detectable levels of green fluorescence to be emitted. The tRNALys-Spinach-tRNALys, once delivered into “chloroplast-free” onion epidermal cells can emit strong green fluorescence in the presence of DFHBI. Our results demonstrate for the first time that Spinach-based RNA visualization has the potential for in vivo monitoring of RNAs in plant cells.

Accumulating evidence suggests that peptidoglycan, consistent with a bacterial cell wall, is synthesized around the chloroplasts of many photosynthetic eukaryotes, from glaucophyte algae to early-diverging land plants including pteridophyte ferns, but the biosynthetic pathway has not been demonstrated. Here, we employed mass spectrometry and enzymology in a two-fold approach to characterize the synthesis of peptidoglycan in chloroplasts of the moss Physcomitrium (Physcomitrella) patens. To drive the accumulation of peptidoglycan pathway intermediates, P. patens was cultured with the antibiotics fosfomycin, D-cycloserine, and carbenicillin, which inhibit key peptidoglycan pathway proteins in bacteria. Mass spectrometry of the trichloroacetic acid-extracted moss metabolome revealed elevated levels of five of the predicted intermediates from uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) through the uridine diphosphate N-acetylmuramic acid (UDP-MurNAc)-D,L-diaminopimelate (DAP)-pentapeptide. Most Gram-negative bacteria, including cyanobacteria, incorporate meso-diaminopimelic acid (D,L-DAP) into the third residue of the stem peptide of peptidoglycan, as opposed to L-lysine, typical of most Gram-positive bacteria. To establish the specificity of D,L-DAP incorporation into the P. patens precursors, we analyzed the recombinant protein UDP-N-acetylmuramoyl-L-alanyl-D-glutamate–2,6-diaminopimelate ligase (MurE) from both P. patens and the cyanobacterium Anabaena sp. (Nostoc sp. strain PCC 7120). Both ligases incorporated D,L-DAP in almost complete preference to L-Lys, consistent with the mass spectrophotometric data, with catalytic efficiencies similar to previously documented Gram-negative bacterial MurE ligases. We discuss how these data accord with the conservation of active site residues common to DL-DAP-incorporating bacterial MurE ligases and of the probability of a horizontal gene transfer event within the plant peptidoglycan pathway.

Strigolactones (SLs) are the most recently discovered phytohormones, and their roles in root architecture and metabolism are not fully understood. Here, we investigated four MORE AXILLARY GROWTH (MAX) SL mutants in Arabidopsis thaliana, max3-9, max4-1, max1-1 and max2-1, as well as the SL receptor mutant d14-1 and karrikin receptor mutant kai2-2. By characterising max2-1 and max4-1, we found that variation in SL biosynthesis modified multiple metabolic pathways in root tissue, including that of xyloglucan, triterpenoids, fatty acids and flavonoids. The transcription of key flavonoid biosynthetic genes, including TRANSPARENT TESTA4 (TT4) and TRANSPARENT TESTA5 (TT5) was downregulated in max2 roots and seedlings, indicating that the proposed MAX2 regulation of flavonoid biosynthesis has a widespread effect. We found an enrichment of BRI1-EMS-SUPPRESSOR 1 (BES1) targets amongst genes specifically altered in the max2 mutant, reflecting that the regulation of flavonoid biosynthesis likely occurs through the MAX2 degradation of BES1, a key brassinosteroid-related transcription factor. Finally, flavonoid accumulation decreased in max2-1 roots, supporting a role for MAX2 in regulating both SL and flavonoid biosynthesis.