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For decades, Xanthomonas vasicola pv. musacearum (Xvm) has been an economically important bacterial pathogen on enset in Ethiopia. Since 2001, Xvm has also been responsible for significant losses to banana crops in several East and Central African countries, with devastating consequences for smallholder farmers. Understanding the genetic diversity within Xvm populations is essential for the smart design of transnationally reasoned, durable, and effective management practices. Previous studies have revealed limited genetic diversity in Xvm, with East African isolates from banana each falling into one of two closely related clades previously designated as sublineages SL 1 and SL 2, the former of which had also been detected on banana and enset in Ethiopia. Given the presumed origin of Xvm in Ethiopia, we hypothesized that both clades might be found in that country, along with additional genotypes not seen in Central and East African bananas. Genotyping of 97 isolates and whole‐genome sequencing of 15 isolates revealed not only the presence of SL 2 in Ethiopia, but additional diversity beyond SL 1 and SL 2 in four new clades. Moreover, SL 2 was detected in the Democratic Republic of Congo, where previously SL 1 was the only clade reported. These results demonstrate a greater range of genetic diversity among Xvm isolates than previously reported, especially in Ethiopia, and further support the hypothesis that the East/Central Africa xanthomonas wilt epidemic has been caused by a restricted set of genotypes drawn from a highly diverse pathogen pool in Ethiopia.\ud \ud

Public awareness of the rising importance of allergies and other respiratory diseases has led to increased scientific effort to accurately and rapidly monitor and predict pollen, fungal spores and other bioaerosols in our atmosphere. An important driving force for the increased social and scientific concern is the realisation that climate change will increasingly have an impact on worldwide bioaerosol distributions and subsequent human health. In this review we examine new developments in monitoring of atmospheric pollen as well as observation and source-orientated modelling techniques. The results of a Scopus® search for scientific publications conducted with the terms ‘Pollen allergy’ and ‘Pollen forecast’ included in the title, abstract or keywords show that the number of such articles published has increased year on year. The 12 most important allergenic pollen taxa in Europe as defined by COST Action ES0603 were ranked in terms of the most ‘popular’ for model-based forecasting and for forecasting method used. Betula, Poaceae and Ambrosia are the most forecast taxa. Traditional regression and phenological models (including temperature sum and chilling models) are the most used modelling methods, but it is notable that there are a large number of new modelling techniques being explored. In particular, it appears that Machine Learning techniques have become more popular and led to better results than more traditional observation-orientated models such as regression and time-series analyses.

Questions: The floristic distinctiveness of ancient woodland relative to recent woodland is commonly measured by Ancient Woodland Indicator (AWI) species richness. However, focusing on a pre-defined subset of species means that wider community-level differences may be overlooked. Can ancient semi-natural, ancient replanted, and recent woodland herb layer communities be distinguished by alpha, beta, and gamma diversity? How are any differences partitioned across AWI and non-AWI species communities? \ud Location: Cotswolds, South-West UK.\ud Methods: To quantify AWI and non-AWI responses to stand history in ancient semi-natural, ancient replanted, and recent woodland, we conducted floristic surveys of 45 sites. Using a modelling approach, we tested the relative and additive contribution of alpha scale AWI and non-AWI species richness to woodland distinctiveness. Ordination was applied to analyse beta species composition distinctiveness, and multilevel pattern analysis was used to examine which species were significant contributors to gamma scale richness differences.\ud Results: AWI species richness models significantly distinguished ancient semi-natural woodland from both ancient replanted and recent woodland at the alpha scale. For the classification of ancient semi-natural woodland and recent woodland, the hierarchical inclusion of non-AWI alpha richness resulted in a superior and more significant model. AWI gamma richness was numerically similar for all three woodland categories, whereas non-AWI was more varied. AWI and non-AWI species composition showed significant beta diversity differences among all woodland types, with six species being significant drivers of differences.\ud Conclusions: Our results have revealed previously undetected complexity in the contributions of AWI and non-AWI species to floristic distinctiveness of ancient woodland. In addition to traditional AWI species, the non-AWI assemblage also exhibited a sensitivity to habitat continuity that: (a) adds weight to the argument that ancient woodland is floristically distinct from recent woodland; and (b) provides a useful measure of success for ancient replanted woodland restoration.

The key selective pressure shaping the morphology of samaras is seen as enhancing primary wind‐borne dispersal from the parent plant to the ground. However, the consequences of the samara wing of primarily wind‐dispersed tree species for post‐dispersal processes has not been well studied. We explored whether the presence of this wing in Acer pseudoplatanus either deters or promotes predation after dispersal, either by increasing the time and energy required to predate the seed or by increasing the seed's visibility to predators. We found that wing‐removed fruits were preferred, suggesting that the presence of samaras makes seed handling more expensive for granivores. Further, we found that fewer seeds were consumed from treatments that contained the most winged seeds, thus there was no evidence of the samaras making seed finding easier for granivores. We conclude that the presence of the wing may offer an anti‐predatory benefit as well as aiding primary dispersal. Postprint

3,6-anhydro-α-L-galactose (L-AHG) is one of the main monosaccharide constituents of red macroalgae. In the recently discovered bacterial L-AHG catabolic pathway, L-AHG is first oxidized by a NAD(P)+-dependent dehydrogenase (AHGD), which is a key step of this pathway. However, the catalytic mechanism(s) of AHGDs is still unclear. Here, we identified and characterized an AHGD from marine bacterium Vibrio variabilis JCM 19239 (VvAHGD). The NADP+-dependent VvAHGD could efficiently oxidize L-AHG. Phylogenetic analysis suggested that VvAHGD and its homologs represent a new aldehyde dehydrogenase (ALDH) family with different substrate preferences from reported ALDH families, named the L-AHGDH family. To explain the catalytic mechanism of VvAHGD, we solved the structures of VvAHGD in the apo form and complex with NADP+ and modeled its structure with L-AHG. Based on structural, mutational, and biochemical analyses, the cofactor channel and the substrate channel of VvAHGD are identified, and the key residues involved in the binding of NADP+ and L-AHG and the catalysis are revealed. VvAHGD performs catalysis by controlling the consecutive connection and interruption of the cofactor channel and the substrate channel via the conformational changes of its two catalytic residues Cys282 and Glu248. Comparative analyses of structures and enzyme kinetics revealed that differences in the substrate channels (in shape, size, electrostatic surface, and residue composition) lead to the different substrate preferences of VvAHGD from other ALDHs. This study on VvAHGD sheds light on the diversified catalytic mechanisms and evolution of NAD(P)+-dependent ALDHs.\ud \ud

Algae is an informal term used to describe a broad group of simple organisms from the plant kingdom. The organisms included within this grouping are aquatic photosynthetic biota with an extensive range of life habits and forms. These organisms range from micron‐sized unicellular forms to giant seaweeds and kelps, which can grow to several metres long. Both benthic and planktonic modes of life are known and display a wide variety of life cycles.

Although several bacterial lignin-oxidising enzymes have been discovered in recent years, it is not yet clear whether different lignin-degrading bacteria use similar mechanisms for lignin oxidation and degradation of lignin fragments. Genome sequences of 13 bacterial lignin-oxidising bacteria, including new genome sequences for Microbacterium phyllosphaerae and Agrobacterium sp., were analysed for the presence of lignin-oxidising enzymes and aromatic degradation gene clusters that could be used to metabolise the products of lignin degradation. Ten bacterial genomes contain DyP-type peroxidases, and ten bacterial strains contain putative multi-copper oxidases (MCOs), both known to have activity for lignin oxidation. Only one strain lacks both MCOs and DyP-type peroxidase genes. Eleven bacterial genomes contain aromatic degradation gene clusters, of which ten contain the central β-ketoadipate pathway, with variable numbers and types of degradation clusters for other aromatic substrates. Hence, there appear to be diverse metabolic strategies used for lignin oxidation in bacteria, while the β-ketoadipate pathway appears to be the most common route for aromatic metabolism in lignin-degrading bacteria.

The timing of the germination of seeds is highly responsive to inputs from the environment. Temperature plays a key role in the control of germination, with low temperatures acting to stimulate this developmental transition in many species. InArabidopsis, extensive gene expression changes have been reported at the whole seed level in response to cold, while much less is known about their spatial distribution across the diverse cell types of the embryo. In this study we examined the spatiotemporal patterns of promoter activity and protein abundance for key gibberellic acid (GA) and abscisic acid (ABA) factors which regulate the decision to germinate both during a time course of germination and in response to cold. Low temperature stimulated the spatial relocalization of these factors to the vasculature. The response of these seeds to dormancy-breaking stratification treatments therefore stimulates the distribution of both positive (GA) and negatively acting (ABA) components to this same cell type. This altered spatial pattern persisted following the transfer of seeds to 22°C, as well as after their rehydration, indicating that this alteration is persistent. These observations suggest that the vasculature plays a role in the low temperature-mediated stimulation of germination in this species, while novel cell types are recruited to promote germination in response to stratification.

Floral plantings are promoted to foster ecological intensification of agriculture through provisioning of ecosystem services. However, a comprehensive assessment of the effectiveness of different floral plantings, their characteristics and consequences for crop yield is lacking. Here we quantified the impacts of flower strips and hedgerows on pest control (18 studies) and pollination services (17 studies) in adjacent crops in North America, Europe and New Zealand. Flower strips, but not hedgerows, enhanced pest control services in adjacent fields by 16% on average. However, effects on crop pollination and yield were more variable. Our synthesis identifies several important drivers of variability in effectiveness of plantings: pollination services declined exponentially with distance from plantings, and perennial and older flower strips with higher flowering plant diversity enhanced pollination more effectively. These findings provide promising pathways to optimise floral plantings to more effectively contribute to ecosystem service delivery and ecological intensification of agriculture in the future., Our quantitative synthesis of the impacts of floral plantings on pest control, crop pollination and yield reveals that flower strips, but not hedgerows, enhanced pest control services in adjacent fields by 16% on average, while effects on crop pollination and yield were more variable. Our synthesis identifies several important drivers of this variability in effectiveness of plantings: pollination services declined exponentially with distance from plantings, and perennial and older flower strips with higher flowering plant diversity enhanced pollination more effectively, with important implications for the the design and implementation of these measures to effectively promote ecological intensification of agriculture in the future

Erwinia mallotivora, the causal agent of papaya dieback disease, is a devastating pathogen that has caused a tremendous decrease in Malaysian papaya export and affected papaya crops in neighbouring countries. A few studies on bacterial species capable of suppressing E. mallotivora have been reported, but the availability of antagonistic fungi remains unknown. In this study, mycelial suspensions from five rhizospheric Trichoderma isolates of Malaysian origin were found to exhibit notable antagonisms against E. mallotivora during co-cultivation. We further characterised three isolates, Trichoderma koningiopsis UKM-M-UW RA5, UKM-M-UW RA6, and UKM-M-UW RA3a, that showed significant growth inhibition zones on plate-based inhibition assays. A study of the genomes of the three strains through a combination of Oxford nanopore and Illumina sequencing technologies highlighted potential secondary metabolite pathways that might underpin their antimicrobial properties. Based on these findings, the fungal isolates are proven to be useful as potential biological control agents against E. mallotivora, and the genomic data opens possibilities to further explore the underlying molecular mechanisms behind their antimicrobial activity, with potential synthetic biology applications.

The natural auxin indole-3-acetic acid (IAA) is a key regulator of many aspects of plant growth and development. Synthetic auxin herbicides such as 2,4-D mimic the effects of IAA by inducing strong auxinic-signaling responses in plants. To determine the mechanism of 2,4-D resistance in a Sisymbrium orientale (Indian hedge mustard) weed population, we performed a transcriptome analysis of 2,4-D-resistant (R) and -susceptible (S) genotypes that revealed an in-frame 27-nucleotide deletion removing nine amino acids in the degron tail (DT) of the auxin coreceptor Aux/IAA2 (SoIAA2). The deletion allele cosegregated with 2,4-D resistance in recombinant inbred lines. Further, this deletion was also detected in several 2,4-D-resistant field populations of this species. Arabidopsis transgenic lines expressing the SoIAA2 mutant allele were resistant to 2,4-D and dicamba. The IAA2-DT deletion reduced binding to TIR1 in vitro with both natural and synthetic auxins, causing reduced association and increased dissociation rates. This mechanism of synthetic auxin herbicide resistance assigns an in planta function to the DT region of this Aux/IAA coreceptor for its role in synthetic auxin binding kinetics and reveals a potential biotechnological approach to produce synthetic auxin-resistant crops using gene-editing.\ud \ud

The development of enzymatic routes toward amide and carboxylic acid bond formation in bioactive molecular scaffolds using aqueous conditions is a major challenge for biopharmaceutical and fine chemical industrial sectors. We report biocatalytic and kinetic characterization of two indole-3-acetamide (IAM) pathway enzymes, tryptophan-2-monooxygenase (iaaM) and indole-3-acetamide hydrolase (iaaH), present in plant microbiomes that produce indole-3-acetic acid (IAA). In this pathway, tryptophan is converted to indole-3-acetamide by the monooxygenase activity of iaaM, followed by its hydrolysis to form carboxylic acid by iaaH enzyme. Since IAA or auxin is an essential natural plant hormone and an important synthon for fine chemicals, the developed monooxygenase-based bioconversion route has a wider scope compared to currently available synthetic and biocatalytic methods to produce synthetic auxins and a range of amides and carboxylic acids for agrochemical and pharmaceutical applications. To display this, one-pot multienzyme biosynthetic cascades for preparative-scale production of IAA derivatives were performed by incorporating tryptophan synthase and tryptophan halogenase enzymes. We also report the creation of an efficient de novo biosynthesis for IAA and its derivatives from glucose or indoles via a reconstructed IAM pathway in Escherichia coli.

Great potential exists to harness plant traits at the root-soil interface, mainly rhizodeposition and root hairs, to 'build' soils with better structure that can trap more carbon and resources, resist climate stresses, and promote a healthy microbiome. These traits appear to have been preserved in modern crop varieties, but scope exists to improve them further because they vary considerably between genotypes and respond to environmental conditions. From emerging evidence, rhizodeposition can act as a disperser, aggregator, and/or hydrogel in soil, and root hairs expand rhizosheath size. Future research should explore impacts of selecting these traits on plants and soils concurrently, expanding from model plants to commercial genotypes, and observing whether impacts currently limited to glasshouse studies occur in the field.

The rhizosphere microbiome is a major determinant of plant health, which can interact with the host directly and indirectly to promote or suppress productivity. Oil palm is one of the world’s most important crops, constituting over a third of global vegetable oil production. Currently there is little understanding of the oil palm microbiome and its contribution to plant health and productivity, with existing knowledge based almost entirely on culture dependent studies. We investigated the diversity and composition of the oil palm fungal microbiome in the bulk soil, rhizosphere soil, and roots of 2-, 18-, and 35-year old plantations in Selangor, Malaysia. The fungal community showed substantial variation between the plantations, accounting for 19.7% of community composition, with compartment (root, rhizosphere soil, and bulk soil), and soil properties (pH, C, N, and P) contributing 6.5 and 7.2% of community variation, respectively. Rhizosphere soil and roots supported distinct communities compared to the bulk soil, with significant enrichment of Agaricomycetes, Glomeromycetes, and Lecanoromycetes in roots. Several putative plant pathogens were abundant in roots in all the plantations, including taxa related to Prospodicola mexicana and Pleurostoma sp. The mycorrhizal status and dependency of oil palm has yet to be established, and using 18S rRNA primers we found considerable between-site variation in Glomeromycotinian community composition, accounting for 31.2% of variation. There was evidence for the selection of Glomeromycotinian communities in oil palm roots in the older plantations but compartment had a weak effect on community composition, accounting for 3.9% of variation, while soil variables accounted for 9% of community variation. While diverse Mucoromycotinian fungi were detected, they showed very low abundance and diversity within roots compared to bulk soil, and were not closely related to taxa which have been linked to fine root endophyte mycorrhizal morphology. Many of the fungal sequences showed low similarity to established genera, indicating the presence of substantial novel diversity with significance for plant health within the oil palm microbiome.

The long-term preservation of fungi has been carried out using several different methods, depending on resources and laboratory. Isolates have been deposited in culture collections for preservation and storage for periods of many years. Despite the widespread use of preservation regimes, little attention has been paid to the poststorage stability of the physiological and genetic characters of strains. The loss of viability of a biological control agent or the failure of an isolate to produce a secondary metabolite pivotal in the production of drugs or food could result in substantial economic loss for the manufacturing organisation. In this investigation the effects of five preservation protocols on fungal characters were assessed: continual sub-culture, lyophilisation, storage in water, storage at -20��C and cryopreservation in liquid nitrogen The physiology and genetic stability of three species of economically important fungi (Metarhizium anisopliae, Fusarium oxysporum and Serpula lacrymans) were examined by analysis of culture characteristics, secondary metabolite profiling, extracellular enzyme tests and PCR fingerprinting over a two-year testing period. It was found that preservation regime can influence the resultant characters of the test fungi. Radial growth rate and conidial production was changed from the original isolates after preservation and storage. Secondary metabolite profiles from all of the test fungi were susceptible to change by the preservation protocols assessed. Production of some metabolites was lost, whereas others remained stable after preservation and storage. Extracellular enzyme production was also affected in a similar way. For example, some replicates of an isolate of Metarhizium anisopliae lost ~-galactosidase activity after one year of preservation. Genetic stability was also compromised is some isolates. Polymorphisms were detected after PCR fingerprinting with a micro-satellite primer in replicates of two isolates of Metarhizium anisopliae that had been stored for one and two years by cryopreservation and lyophilisation and in two replicates of an isolate of Fusarium oxysporum maintained by continual sub-culture for sixteen weeks. The results indicate that response to preservation and storage is species- and strain-specific. Therefore, there is a need to develop new and existing preservation regimes with emphasis on strain-specific criteria. Scientists should preserve their important isolates by more than one preservation method to protect organisms from the stresses encountered during preservation and storage.

To meet the ever-increasing global food demand, the food production rate needs to be increased significantly in the near future. Speed breeding is considered as a promising agricultural technology solution to achieve the zero-hunger vision as specified in the United Nations Sustainable Development Goal 2. In speed breeding, the photoperiod of the artificial light has been manipulated to enhance crop productivity. In particular, regulating the photoperiod of different light qualities rather than solely white light can further improve speed breading. However, identifying the optimal light quality and the associated photoperiod simultaneously remains a challenging open problem due to complex interactions between multiple photoreceptors and proteins controlling plant growth. To tackle this, we develop a first comprehensive model describing the profound effect of multiple light qualities with different photoperiods on plant growth (i.e. hypocotyl growth). The model predicts that hypocotyls elongated more under red light compared to both red and blue light. Drawing similar findings from previous related studies, we propose that this might result from the competitive binding of red and blue light receptors, primarily Phytochrome B (phyB) and Cryptochrome 1 (cry1) for the core photomorphogenic regulator, CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). This prediction is validated through an experimental study on Arabidopsis thaliana. Our work proposes a potential molecular mechanism underlying plant growth under different light qualities and ultimately suggests an optimal breeding protocol that takes into account light quality.

Globally, agricultural land-use negatively affects soil biota that contribute to ecosystem functions such as nutrient cycling, yet arbuscular mycorrhizal fungi (AMF) are promoted as essential components of agroecosystems. Arbuscular mycorrhizal fungi include Glomeromycotinian AMF (G-AMF) and the arbuscule-producing fine root endophytes, recently re-classified into the Endogonales order within Mucoromycotina. The correct classification of Mucoromycotinian AMF (M-AMF) and the availability of new molecular tools can guide research to better the understanding of their diversity and ecology. To investigate the impact on G-AMF and M-AMF of agricultural land-use at a continental scale, we sampled DNA from paired farm and native sites across 10 Australian biomes. Glomeromycotinian AMF were present in both native and farm sites in all biomes. Putative M-AMF were favoured by farm sites, rare or absent in native sites, and almost entirely absent in tropical biomes. Temperature, rainfall, and soil pH were strong drivers of richness and community composition of both groups, and plant richness was an important mediator. Both fungal groups occupy different, but overlapping, ecological niches, with M-AMF thriving in temperate agricultural landscapes. Our findings invite exploration of the origin and spread of M-AMF and continued efforts to resolve the phylogeny of this newly reclassified group of AMF.

UB is funded by a Royal Society University Research Fellowship (UF150138) and Anne-Kristin Lenz is supported by a Royal Society Enhancement Award (RGF/EA/180059) held by UB. Water shedding from leaves is a complex process depending on multiple leaf traits interacting with rain, wind and air humidity, and with the entire plant and surrounding vegetation. Here, we synthesise the current knowledge of the physics of water shedding with implications for plant physiology and ecology. We argue that the drop retention angle is a more meaningful parameter to characterise the water shedding capacity of leaves than the commonly measured static contact angle. The understanding of the mechanics of water shedding is largely derived from laboratory experiments on artificial rather than natural surfaces, often on individual aspects such as surface wettability or drop impacts. In contrast, field studies attempting to identify the adaptive value of leaf traits linked to water shedding are largely correlative in nature, with inconclusive results. We make a strong case for taking the hypothesis-driven experimental approach of biomechanical lab studies into a real-world field setting to gain a comprehensive understanding of leaf water shedding in a whole-plant ecological and evolutionary context. Publisher PDF

Trees associating with different mycorrhizas often differ in their effects on litter decomposition, nutrient cycling, soil organic matter (SOM) dynamics, and plant-soil interactions. For example, due to differences between arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) tree leaf and root traits, ECM-associated soil has lower rates of C and N cycling and lower N availability than AM-associated soil. These observations suggest that many groups of nonmycorrhizal fungi should be affected by the mycorrhizal associations of dominant trees through controls on nutrient availability. To test this overarching hypothesis, we explored the influence of predominant forest mycorrhizal type and mineral N availability on soil fungal communities using next-generation amplicon sequencing. Soils from four temperate hardwood forests in southern Indiana, United States, were studied; three forests formed a natural gradient of mycorrhizal dominance (100% AM tree basal area to 100% ECM basal area), while the fourth forest contained a factorial experiment testing long-term N addition in both dominant mycorrhizal types. We found that overall fungal diversity, as well as the diversity and relative abundance of plant pathogenic and saprotrophic fungi, increased with greater AM tree dominance. Additionally, tree community mycorrhizal associations explained more variation in fungal community composition than abiotic variables, including soil depth, SOM content, nitrification rate, and mineral N availability. Our findings suggest that tree mycorrhizal associations may be good predictors of the diversity, composition, and functional potential of soil fungal communities in temperate hardwood forests. These observations help explain differing biogeochemistry and community dynamics found in forest stands dominated by differing mycorrhizal types. IMPORTANCE Our work explores how differing mycorrhizal associations of temperate hardwood trees (i.e., arbuscular [AM] versus ectomycorrhizal [ECM] associations) affect soil fungal communities by altering the diversity and relative abundance of saprotrophic and plant-pathogenic fungi along natural gradients of mycorrhizal dominance. Because temperate hardwood forests are predicted to become more AM dominant with climate change, studies examining soil communities along mycorrhizal gradients are necessary to understand how these global changes may alter future soil fungal communities and their functional potential. Ours, along with other recent studies, identify possible global trends in the frequency of specific fungal functional groups responsible for nutrient cycling and plant-soil interactions as they relate to mycorrhizal associations.

Five potato varieties were studied using an electronic nose with nine MOS sensors. Parameters measured included carbohydrate content, sugar level, and the toughness of the potatoes. Routine tests were carried out while the signals for each potato were measured, simultaneously, using an electronic nose. The signals obtained indicated the concentration of various chemical components. In addition to support vector machines (SVMs that were used for the classification of the samples, chemometric methods, such as the partial least squares regression (PLSR) method, the principal component regression (PCR) method, and the multiple linear regression (MLR) method, were used to create separate regression models for sugar and carbohydrates. The predictive power of the regression models was characterized by a coefficient of determination (R2), a root-mean-square error of prediction (RMSEP), and offsets. PLSR was able to accurately model the relationship between the smells of different types of potatoes, sugar, and carbohydrates. The highest and lowest accuracy of models for predicting sugar and carbohydrates was related to Marfona potatoes and Sprite cultivar potatoes. In general, in all cultivars, the accuracy in predicting the amount of carbohydrates was somewhat better than the accuracy in predicting the amount of sugar. Moreover, the linear function had 100% accuracy for training and validation in the C-SVM method for classification of five potato groups. The electronic nose could be used as a fast and non-destructive method for detecting different potato varieties. Researchers in the food industry will find this method extremely useful in selecting the desired product and samples.

Conophytum N.E.Br. (Aizoaceae) is a genus of dwarf succulent plants endemic to western South Africa and southern Namibia. It is highly diverse, with 106 constituent species and is considered a model genus for the Succulent Karoo Biome, an arid region with uniquely high desiccation-tolerant (succulent) plant diversity, based on its variety of distribution types and growth forms. The aim of this project was twofold: to provide a clearer understanding of the patterns and drivers of speciation in the genus, and to identify conservation strategies that maximise the likely survival of these species, based on spatial ecological analyses of their current distributions. The biodiversity of the Succulent Karoo biome is increasingly vulnerable to a multitude of threats, mostly as a consequence of growing levels of human activity. The current and future conservation of Conophytum is dependent on evidence-based interventions that, in particular, help mitigate the effects of a changing climate and illegal collecting. First, an updated phylogeny was produced providing the foundation to many of the analyses undertaken in this thesis, beginning with an assessment of the drivers of diversification. For the first time, nuclear gene regions and sequences from almost all species in the genus (102 of 106) were included in the development of phylogenetic hypotheses. From there, a selection of 12 pertinent characters was mapped over the phylogeny and phylogenetic signal was calculated in a univariate and multivariate manner. This, along with correlations in character evolution, was used to infer potential drivers of diversification. Nocturnal flowering was found to characterise certain clades and was correlated with pollen type D and flower structure A2, suggesting an influence of pollinator specialisation on evolution, while windowed leaves characterised one particularly large, strongly supported clade in the phylogeny, and, through correlated evolution with other traits such as the presence of bladder cells, suggested a key influence of the abiotic environment in this clade���s formation. This abiotic influence on speciation was further investigated using spatial environmental data to determine differences in the abiotic preferences of individual Conophytum species and five large, strongly supported clades in the phylogeny. Geological, topographical and climatic variables were mapped onto the phylogeny, while differences in clade and species��� environmental preferences were assessed. Associations between environmental variables and the evolution of certain traits were also analysed. Variation in precipitation/moisture, elevation and slope were identified as key drivers of diversification in the genus, with niche divergence prevalent in driving speciation. Additionally, some clades were characterised by both nocturnal flowering and certain leaf traits (e.g. very long trichomes, sunken stomata), suggesting a possible interaction between biotic and abiotic diversification drivers. These interactions were analysed mainly by calculating correlations between nocturnal flowering and abiotic variables. Nocturnal flowering was strongly correlated with a lower mean annual temperature, suggesting a possible climatic influence on pollinator assemblages potentially driving a greater likelihood of species in cooler locations to be nocturnally moth pollinated. After gaining a greater understanding of what drove diversity in Conophytum, attention switched to the vulnerability of this diversity to future changes in climate by projecting range change responses using species distribution models (SDMs). These analyses focused on the more broadly distributed species (a minimum of 20 occurrence points) to facilitate the building of statistically robust models, comparing climate change vulnerability at both the species- and clade-levels. For four of the five clades, and for the genus as a whole, range size reduction was prevalent, with a range contraction from the north occurring as conditions in the north of the genus��� range become unsuitable through lower winter rainfall and increased temperatures, while the more mesic southern reaches of South Africa remain unsuitable for Conophytum inhabitation. One clade, however, characterised by bladder cells and windowed leaves which give constituent species better adaptation to hotter conditions, may include some species that benefit from predicted future climate conditions. Two new regions were prioritised based on these projections for future protection, as these successfully cover the areas of high current and future diversity in the genus, along with protecting separate clades and thereby maintaining phylogenetic diversity. As SDMs excluded narrow endemics in the genus because of the low numbers of occurrence points available, a final assessment on the abiotic environmental preferences and trait associations of narrow endemic Conophytum species was performed to better understand their ecology and to aid their conservation. These taxa make up a sizable proportion of species in the genus (~33%) and are some of the most vulnerable Conophytum species through their small range and population sizes. This assessment demonstrated a preference of these species for more high-stress environments (steeper slopes, higher elevation and low moisture) compared to broadly distributed species, and identified that these taxa are predominantly diurnal flowering, although this was likely to be because narrow endemic distribution overlaps strongly with diurnal wasp pollinators. This study also identified an important region for the conservation of narrow endemics and these ecological findings will assist prioritising regions for protection or translocation. The findings of this project shed light on the evolution of Conophytum and its vulnerability to anthropogenic impacts and provide an improved basis for understanding of the genus��� ecology and biogeography. Based on these findings, Conophytum can now act as an ideal model genus for the Succulent Karoo, a uniquely biodiverse arid hotspot. An improved understanding of the evolution and vulnerability of Conophytum provides important evidence for drivers of rapid speciation in a region known for its diversifications and, perhaps even more importantly, highlights threats and important conservation strategies for the Succulent Karoo in an uncertain future.

The phytohormone auxin, indole-3-acetic acid (IAA), plays a prominent role in plant development. Auxin homeostasis is coordinately regulated by auxin synthesis, transport, and inactivation; however, the physiological contribution of auxin inactivation to auxin homeostasis has not been determined. The GH3 IAA–amino acid conjugating enzymes play a central role in auxin inactivation. Chemical inhibition of GH3 proteins in planta is challenging because the inhibition of these enzymes leads to IAA overaccumulation that rapidly induces GH3 expression. Here, we report the characterization of a potent GH3 inhibitor, kakeimide, that selectively targets IAA-conjugating GH3 proteins. Chemical knockdown of the auxin inactivation pathway demonstrates that auxin turnover is very rapid (about 10 min) and indicates that both auxin biosynthesis and inactivation dynamically regulate auxin homeostasis.

Observations of animals in the wild can result in the discovery of plants for human medicinal purposes. In this context, our closest relatives, the great apes, are of particular interest. The Euphorbiaceae Manniophyton fulvum possesses both phytochemical and biomechanical properties. Its use in the genus Pan (P. troglodytes; P. paniscus) is thought to be based on its mechanical properties promoting the egestion of intestinal parasites, but additional observations from different habitats where the behavior is performed may shed more light on its true purpose. To improve our understanding of what triggers this behavior, we investigated M. fulvum consumption in wild bonobos at LuiKotale, Democratic Republic of the Congo between December 2018 and July 2020. Specifically, we tested the hypothesis that M. fulvum ingestion is related to gastro-intestinal parasite expulsion. Of 649 focal follows of 37 individuals from two habituated communities, consumption of M. fulvum was observed on 111 days (N = 507), independent of seasons, environmental factors and the plant's availability. A total of 588 fecal samples were assessed for the presence/absence of gastro-intestinal parasites. We found strongyle eggs in 2.89% of samples and their presence was not associated with the ingestion of M. fulvum or environmental conditions. We discuss the importance of seasonality in the life cycle of strongyle species that may influence the pattern of M. fulvum consumption observed at LuiKotale. Our data open additional perspectives concerning behavioral parameters such as the existence of a cultural component when comparing ingestion behavior between communities. published

Polyclonal antisera were raised against the fungi Neurospora crassa and Paxillusinvolutus, respectively. These antisera were used in the development of an ELISA for subsequent use in monoclonal antibody (MAb) screens. Fungal cell walls were chosen as the most suitable immunogen for in situ ecological studies. Hyphal walls were isolated and bound to a poly-/-lysine coated ELISA plate. Both antisera showed cross-reactions with other species of fungi. These reactions were not diminished by pre-absorption of the antisera with cell walls from species of fungi which react with the antiserum. The ELISA was then used in the production of specific MAbs raised against fungal cell wall antigens. Hybridoma supernatants were screened following fusions of spleen cells from immunised mice and Sp2.0 myeloma cells. A successful immunisation protocol was established using fungal cell walls, and a titre of tailbleed plasma used to determine whether a mouse would be used for fusion. Four MAb cell lines were established (S4D1, S3B3, S1E5 and Pax-1).Of these MAbs, three were derived from mice immunised with cell walls of N. crassa and the fourth from a mouse immunised with the cell walls of P. involutus. In immunofluorescence studies the three MAbs raised against N. crassa recognised epitopes which show different patterns of distribution at the cell surface of N. crassa. MAb S4D1 recognises an epitope which is present on the surface of both conidia and hyphae; MAb S3B3 an epitope seen only at the end of conidia or in the septal region of hyphae and conidial chains; and S1E5 an epitope present on the surface of hyphae, but not mature conidia. MAb Pax-1, raised against P. involutus, reacts with cell wall fragments of P.involutus and reacts with N. crassa conidia in a similar way to S3B3 in immunofluorescence studies, i.e. with septa and the ends of conidia. The MAbs S3B3 and Pax-1 are, however, differentiated by their reaction with P. involutus, Pax-1 reacts with P. involutus, but S3B3 does not.S4D1 reacted with an epitope found in a-1,3 glucan fractions from different fungi. The surface distribution of this epitope varies across a taxonomic spectrum. It is found on the surface of both conidia and hyphae of N. crassa and Aspergillus nidulans, but only on the basidiospore surface of Amanita muscaria. Conversely it appears on the hyphae but not the conidia of Penicillium chry’sogenum. Immunogold studies revealed that the epitope was present throughout the wall of N. crassa. In quantification studies, S4D1 showed a linear relationship between the reaction of the MAb with its epitope, recorded as absorbance in an ELISA, and cell wall biomass (freeze-dried weight).S3B3 and Pax-1 also reacted with other fungi. Pax-1 cross-reacted with all fungi tested except for a member of the Zygomycotina. The nature of the epitopes of these two MAbs was not determined, nor was that of S1E5. Immunogold studies revealed that epitopes of these three MAbs were not present at the surface in all the morphological forms of N. crassa, but that they were present in inner layers of these walls. For example, the epitope of Pax-1 is found in a discrete layer next to the plasma membrane of N. crassa cells but not at the surface, except in the septal region. The epitope of Pax-1 is not chitin. The MAbs produced did not show species-specificity. The specific reaction of the MAbs with their epitopes enabled the localisation of the epitopes at the cell surface of fungi and their distribution throughout the wall of N. crassa to be studied. The distribution of the epitopes within the walls of hyphae and conidia has been schematically represented.

Terrestrial gastropods are highly pestiferous and pose a significant global threat to sustainable agriculture, horticulture and floriculture. Current control methods rely on metaldehyde formulated bait pellets. However, metaldehyde can harm non target organisms and cause environmental pollution. Metaldehyde is also due to be banned for use in the UK by 2022. A viable alternative is the gastropod parasitic nematode Phasmarhabditis hermaphrodita, which has been formulated into a biological control agent (Nemaslug®) by BASF Agricultural Specialities. However, the same strain of P. hermaphrodita (DMG0001) has been produced in an artificial environment for over 25 years and research suggests this strain is losing beneficial traits (e.g. virulence and host finding) and failing to provide protection against slug damage. The primary aim of this thesis was to use a collection of wild isolated Phas marhabditis species (P. hermaphrodita, P. neopapillosa and P. californica) to investigate whether they are more virulent than the commercial strain of P. hermaphrodita (DMG0001) to the pestiferous slug Deroceras invadens and the snail Cornu aspersum in laboratory experiments. Host feeding inhibition, numbers of nematode dauers produced on gastropod cadavers and natural variation in chemotaxis behaviour were also investigated. Additionally, the impact of virulent strains on beneficial non- target organisms and the mechanism of host behavioural manipulation were explored. Multiple wild strains were found to perform better than the commercial strain in regards to virulence, feeding inhibition, proliferation on cadavers and locating host cues. This research has demonstrated that other members of the Phasmarhabditis genus can be utilised as safe and effective biological control agents. This thesis presents which Phasmarhabditis species show the most potential for pathogenic ability and host seeking. Results obtained from this work have resulted the production of a new slug biocontrol product by BASF, utilising P. californica.

Balance indices that quantify the symmetry of branching events and the compactness of trees are widely used to compare evolutionary processes or tree-generating algorithms. Yet, existing indices are not defined for all rooted trees, are unreliable for comparing trees with different numbers of leaves, and are sensitive to the presence or absence of rare types. The contributions of this article are twofold. First, we define a new class of robust, universal tree balance indices. These indices take a form similar to Colless’ index but can account for population sizes, are defined for trees with any degree distribution, and enable meaningful comparison of trees with different numbers of leaves. Second, we show that for bifurcating and all other full m-ary cladograms (in which every internal node has the same out-degree), one such Colless-like index is equivalent to the normalized reciprocal of Sackin’s index. Hence, we both unify and generalize the two most popular existing tree balance indices. Our indices are intrinsically normalized and can be computed in linear time. We conclude that these more widely applicable indices have the potential to supersede those in current use. [Cancer; clone tree; Colless index; Sackin index; species tree; tree balance.]

Pre-processing is a crucial step in analyzing spectra from Fourier transform infrared (FTIR) spectroscopy because it can reduce unwanted noise and enhance system performance. Here, we present the results of pre-processing technique optimization to facilitate the detection of pepper yellow leaf curl virus (PYLCV)-infected chilli plants using FTIR spectroscopy. Optimization of a range of pre-processing techniques was undertaken, namely baseline correction, normalization (standard normal variate, vector, and min–max), and de-noising (Savitzky-Golay (SG) smoothing, 1st and 2 derivatives). The pre-processing was applied to the mid-infrared spectral range (4000 – 400 cm−1) and the biofingerprint region (1800 – 900 cm−1) then the discrete wavelet transform (DWT) was used for dimension reduction. The pre-processed data were then used as an input for classification using a multilayer perceptron neural network, a support vector machine, and linear discriminant analysis. The pre-processing method with the highest classification model accuracy was selected for the further use in the processing. It was seen that only the SG 1st derivative method applied to both wavenumber ranges could produce 100% accuracy. This result was supported by principal component analysis clustering. Thus, we have demonstrated that by using the right pre-processing technique, classification success can be increased, and the process simplified by optimization and minimization of the technique used.

Research Funding National Natural Science Foundation of China. Grant Numbers: 31872923, 31371922. Scottish Government Rural and Environmental Science and Analytical Services Division. Plant-parasitic nematodes need to deliver effectors that suppress host immunity for successful parasitism. We have characterized a novel isochorismatase effector from the root-knot nematode Meloidogyne incognita, named Mi-ISC-1. The Mi-isc-1 gene is expressed in the subventral oesophageal glands and is up-regulated in parasitic-stage juveniles. Tobacco rattle virus-induced gene silencing targeting Mi-isc-1 attenuated M. incognita parasitism. Enzyme activity assays confirmed that Mi-ISC-1 can catalyse hydrolysis of isochorismate into 2,3-dihydro-2,3-dihydroxybenzoate in vitro. Although Mi-ISC-1 lacks a classical signal peptide for secretion at its N-terminus, a yeast invertase secretion assay showed that this protein can be secreted from eukaryotic cells. However, the subcellular localization and plasmolysis assay revealed that the unconventional secretory signal present on the Mi-ISC-1 is not recognized by the plant secretory pathway and that the effector was localized within the cytoplasm of plant cells, but not apoplast, when transiently expressed in Nicotiana benthamiana leaves by agroinfiltration. Ectopic expression of Mi-ISC-1 in N. benthamiana reduced expression of the PR1 gene and levels of salicylic acid (SA), and promoted infection by Phytophthora capsici. The cytoplasmic localization of Mi-ISC-1 is required for its function. Moreover, Mi-ISC-1 suppresses the production of SA following the reconstitution of the de novo SA biosynthesis via the isochorismate pathway in the cytoplasm of N. benthamiana leaves. These results demonstrate that M. incognita deploys a functional isochorismatase that suppresses SA-mediated plant defences by disrupting the isochorismate synthase pathway for SA biosynthesis to promote parasitism. Publisher PDF

Colletotrichum gloeosporioides is the causal agent of anthracnose disease of mangoes. Infection occurs when humidity is high and rain-dispersed spores germinate and form an appressorium on immature mangoes. The infection then becomes quiescent until the fruit is harvested. On ripe fruit infection is visible as black, sunken lesions on the surface. At the pre-harvest stage, the disease is controlled with the application of a range of fungicides, and at the post-harvest stage by hot benomyl treatment. The extensive use of benomyl, both pre- and post-harvest, has resulted in the occurrence of isolates of C. gloeosporioides resistant to this fungicide. To devise an alternative strategy of disease control, the potential for biological control of anthracnose has been investigated. Potential microbial antagonists of C. gloeosporioides were isolated from blossom, leaves and fruit of mango, and screened using a series of assay techniques. In total 650 microorganisms, including bacteria, yeasts and filamentous fungi, were isolated and tested for their inhibition of growth of C. gloeosporioides on malt extract agar. Of these 650 isolates, 121 inhibited the fungus and were further tested on their ability to inhibit spore germination in vitro. Of these, 45 isolates, all bacteria and yeasts, were inoculated onto mangoes, which were artificially inoculated with C. gloeosporioides, and assessed for their potential to reduce the development of anthracnose lesions. A further selection was made, and 7 isolates were chosen to be used in a semi-commercial trial in the Philippines. This final screening procedure yielded two potential candidates for field trials, isolate 204 (identified as Bacillus cereus) and isolate 558 (identified as Pseudomonas fiuorescens). A field trial involving pre-harvest application of the biological control agent, was conducted using isolate 558. This isolate was chosen for this purpose since in in vitro experiments it significantly reduced germination of C. gloeosporioides spores. In the field trial 558 was applied in combination with nutrients and compared to treatments which had received no treatment or which had received conventional fungicide (benomyl) application. On spraying, high numbers of 558 were recorded on the leaf surface, but no reduction in post-harvest development of disease was observed. Failure of disease control was attributed to rapid death of the bacterium on the phylloplane. In post-harvest trials, isolates 204 and 558 were both tested in combination with different application methods, including the addition of sticker, peptone, fruit wax or a sucrose polyester. Application of 204 did not reduce disease development. Application of 558, however, did significantly reduce anthracnose development compared to the control fruit. No additional benefit was achieved by incorporating the bacteria in peptone, fruit wax or sucrose polyester. The mode of action of isolate 558 was investigated in detail. There was no evidence for parasitism taking place, or the production of volatile compounds, in the suppression of disease development. No antibiotic compounds were detected, but isolate 558 did produce a siderophore. A sharp increase in pH was also observed in culture media in which 558 was grown. Disease control may result from a combination of these two factors.

Leaf blotch caused by Alternaria spp. is a common disease in apple-producing regions. The disease is usually associated with one phylogenetic species and one species complex, Alternaria alternata and the Alternaria arborescens species complex (A. arborescens SC), respectively. Both taxa may include the Alternaria apple pathotype, a quarantine or regulated pathogen in several countries. The apple pathotype is characterized by the production of a host-selective toxin (HST) which is involved in pathogenicity towards the apple. A cluster of genes located on conditionally dispensable chromosomes (CDCs) is involved in the production of this HST (namely AMT in the case of the apple pathotype). Since 2016, leaf blotch and premature tree defoliation attributed to Alternaria spp. have been observed in apple-producing regions of central and south-eastern France. Our study aimed to identify the Alternaria species involved in apple tree defoliation and assess the presence of the apple pathotype in French orchards. From 2016 to 2018, 166 isolates were collected and identified by multi-locus sequence typing (MLST). This analysis revealed that all these French isolates belonged to either the A. arborescens SC or A. alternata. Specific PCR detection targeting three genes located on the CDC did not indicate the presence of the apple pathotype in France. Pathogenicity was assessed under laboratory conditions on detached leaves of Golden Delicious and Gala apple cultivars for a representative subset of 28 Alternaria isolates. All the tested isolates were pathogenic on detached leaves of cultivars Golden Delicious and Gala, but no differences were observed between the pathogenicity levels of A. arborescens SC and A. alternata. However, the results of our pathogenicity test suggest that cultivar Golden Delicious is more susceptible than Gala to Alternaria leaf blotch. Implications in the detection of the Alternaria apple pathotype and the taxonomic assignment of Alternaria isolates involved in Alternaria leaf blotch are discussed.

Turnip yellows virus (TuYV) is aphid-transmitted and causes considerable yield losses in oilseed rape (OSR, Brassica napus, genome: AACC) and vegetable brassicas. Insecticide control of the aphid vector is limited due to insecticide resistance and the banning of the most effective active ingredients in the EU. There is only one source of TuYV resistance in current commercial OSR varieties, which has been mapped to a single dominant quantitative trait locus (QTL) on chromosome A04. We report the identification, characterisation, and mapping of TuYV resistance in the diploid progenitor species of OSR, Brassica rapa (genome: AA), and Brassica oleracea (genome: CC). Phenotyping of F1 populations, produced from within-species crosses between resistant and susceptible individuals, revealed the resistances were quantitative and partially dominant. QTL mapping of segregating backcross populations showed that the B. rapa resistance was controlled by at least two additive QTLs, one on chromosome A02 and the other on chromosome A06. Together, they explained 40.3% of the phenotypic variation. In B. oleracea, a single QTL on chromosome C05 explained 22.1% of the phenotypic variation. The TuYV resistance QTLs detected in this study are different from those in the extant commercial resistant varieties. To exploit these resistances, an allotetraploid (genome: AACC) plant line was resynthesised from the interspecific cross between the TuYV-resistant B. rapa and B. oleracea lines. Flow cytometry confirmed that plantlets regenerated from the interspecific cross had both A and C genomes and were mixoploid. To stabilise ploidy, a fertile plantlet was self-pollinated to produce seed that had the desired resynthesised, allotetraploid genome AACC. Phenotyping of the resynthesised plants confirmed their resistance to TuYV. Genotyping with resistance-linked markers identified during the mapping in the progenitors confirmed the presence of all TuYV resistance QTLs from B. rapa and B. oleracea. This is the first report of TuYV resistance mapped in the Brassica C genome and of an allotetraploid AACC line possessing dual resistance to TuYV originating from both of its progenitors. The introgression into OSR can now be accelerated, utilising marker-assisted selection, and this may reduce selection pressure for TuYV isolates that are able to overcome existing sources of resistance to TuYV.

Background Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bacteria and phytoplankton. Polar oceans, which represent about one fifth of Earth’s surface, contribute significantly to the global oceanic DMS sea-air flux. However, a global overview of DMS and DMSP cycling in polar oceans is still lacking and the key genes and the microbial assemblages involved in DMSP/DMS transformation remain to be fully unveiled. Results Here, we systematically investigated the biogeographic traits of 16 key microbial enzymes involved in DMS/DMSP cycling in 60 metagenomic samples from polar waters, together with 174 metagenome and 151 metatranscriptomes from non-polar Tara Ocean dataset. Our analyses suggest that intense DMS/DMSP cycling occurs in the polar oceans. DMSP demethylase (DmdA), DMSP lyases (DddD, DddP, and DddK), and trimethylamine monooxygenase (Tmm, which oxidizes DMS to dimethylsulfoxide) were the most prevalent bacterial genes involved in global DMS/DMSP cycling. Alphaproteobacteria (Pelagibacterales) and Gammaproteobacteria appear to play prominent roles in DMS/DMSP cycling in polar oceans. The phenomenon that multiple DMS/DMSP cycling genes co-occurred in the same bacterial genome was also observed in metagenome assembled genomes (MAGs) from polar oceans. The microbial assemblages from the polar oceans were significantly correlated with water depth rather than geographic distance, suggesting the differences of habitats between surface and deep waters rather than dispersal limitation are the key factors shaping microbial assemblages involved in DMS/DMSP cycling in polar oceans. Conclusions Overall, this study provides a global overview of the biogeographic traits of known bacterial genes involved in DMS/DMSP cycling from the Arctic and Antarctic oceans, laying a solid foundation for further studies of DMS/DMSP cycling in polar ocean microbiome at the enzymatic, metabolic, and processual levels.

The extent of wildfires cannot be easily mapped using field-based methods in areas with complex topography, and in those areas the use of remote sensing is an alternative. This study first obtained images from the Sentinel-2 satellites for the period 2015–2020 with the objective of applying multi-temporal spectral indices to assess areas burned in wildfires and prescribed fires in the Margalla Hills of Pakistan using the Google Earth Engine (GEE). Using those images, the Normalized Difference Vegetation Index (NDVI) and the Normalized Burn Ratio (NBR), which are often used to assess the severity of fires, were calculated for wildfires and prescribed fires. For each satellite image, spectral indices values were extracted for the 5th, 20th, 40th, 60th, 80th and 95th percentiles of pixels of each burned area. Then, boxplots representing the distribution of these values were plotted for each satellite image to identify whether the regeneration time subsequent to a fire, also known as the burn scar, and the severity of the fire differed between the autumn and summer wildfires, and with prescribed fires. A statistical test revealed no differences for the regeneration time amongst the three categories of fires, but that the severity of summer wildfires was significantly different from that of prescribed fire, and this, for both indices. Second, SAR images were obtained from the Sentinel-1 mission for the same period as that of the optical imagery. A comparison of the response of 34 SAR variables with official data on wildfires and prescribed fires from the Capital Development Authority revealed that the 95th percentile of the Normalized Signal Ratio (NSR p_95) was found to be the best variable to detect fire events, although only 50% of the fires were correctly detected. Nonetheless, when the occurrence of fire events according to the SAR variable NSR p_95 was compared to that from the two spectral indices, the SAR variable was found to correctly identify 95% of fire events. The SAR variable NSR p_95 is thus a suitable alternative to spectral indices to monitor the progress of wildfires and assess their severity when there are limitations to the use of optical images due to cloud coverage or smoke, for instance.

Latex production from Hevea brasiliensis rubber tree is the second most important commodity in Malaysia, but this industry is threatened by the white root rot disease (WRD) caused by Rigidoporus microporus that leads to considerable latex yield loss and tree death. This study aimed to characterize and compare the virulence of five R. microporus isolates obtained from infected rubber trees located at different states in Malaysia. These isolates were subjected to morphological and molecular characterization for species confirmation and pathogenicity test for the determination of virulence level. BLAST search showed that the ITS sequences of all the pathogen isolates were 99% identical to R. microporus isolate SEG (accession number: MG199553) from Malaysia. The pathogenicity test of R. microporus isolates conducted in a nursery with 24 seedlings per isolate showed that isolate RL21 from Sarawak has developed the most severe above- and below-ground symptoms of WRD on the rubber clone RRIM600 as host. Six months after being infected with R. microporus, RL21 was evaluated with the highest average of disease severity index of 80.52% for above- and below-ground symptoms, followed by RL22 (68.65%), RL20 (66.04%), RL26 (54.38%), and RL25 (43.13%). The in vitro growth condition tests showed that isolate RL21 of R. microporus has optimum growth at 25–30 °C, with the preference of weakly acidic to neutral environments (pH 6–7). This study revealed that different virulence levels are possessed among different R. microporus isolates even though they were isolated from the same host species under the same climate region. Taken together, field evaluation through visual observation and laboratory assays have led to screening of the most virulent isolate. Determination of the most virulent isolate in the present study is vital and shall be taken into consideration for the selection of suitable pathogen isolate in the development of more effective control measures in combating tenacious R. microporus.

Phytoene is a colourless natural carotenoid that absorbs UV light and provides antioxidant and anti-inflammatory activities as well as protection against photodamage. It is therefore valued for its skin health and aesthetic benefits by the cosmetic industry, as well as by the health food sector. The halotolerant green microalga Dunaliella salina is one of the richest sources of natural carotenoids. We have previously investigated the over-production of phytoene in D. salina after cultivation with the well-characterised mitosis inhibitor, chlorpropham. In this study, 15 herbicides with different modes of action were tested for their potential to promote phytoene accumulation. All herbicides showed different levels of capabilities to support phytoene over-production in D. salina. Most significantly, the two mitosis inhibitors tested in this study, propyzamide and chlorpropham, showed similar capacities to support the over-production of phytoene by D. salina cultures as phytoene desaturase inhibitors. The cellular content of phytoene increased by over 10-fold within 48 h of treatment with the mitosis inhibitors compared to untreated cultures. Results indicate a general effect of mitosis inhibitors on phytoene accumulation in D. salina. Furthermore, red light was found to significantly enhance the phytoene yield when used in combination with effective inhibitor treatments. Red light can be applied to maximize the production of phytoene from D. salina.

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions. Introduction Results - Sequencing Depth and SNP Identification - Phylogeny and Population Clustering Distinguish Wild and Feral Populations - Species Tree and Admixture Inference Indicate Brassica cretica Is the Closest Living Wild Relative - Archaeological and Literary Evidence Point to a Late-Holocene Domestication - Late-Holocene Environmental Niche Modeling Highlights Wild Relatives’ Ranges Discussion - Multiple Lines of Evidence Support a Single Eastern Mediterranean Origin - The Role of Ferality in the Domestication of Brassica oleracea - Postdomestication Cultivar Relationships Materials and Methods - Taxon Sampling - RNA Isolation and Sequencing - Mapping and SNP Calling - Phylogenetic and Introgression Inference - Population Structure and Variation - Clustering Based on Expression Profiles - Environmental Niche Modeling

The DNA of all organisms is constantly damaged by physiological processes and environmental conditions. Upon persistent damage, plant growth and cell proliferation are reduced. Based on previous findings that RBR1, the only Arabidopsis homolog of the mammalian tumor suppressor gene retinoblastoma, plays a key role in the DNA damage response in plants, we unravel here the network of RBR1 interactors under DNA stress conditions. This led to the identification of homologs of every DREAM component in Arabidopsis, including previously not recognized homologs of LIN52. Interestingly, we also discovered NAC044, a mediator of DNA damage response in plants and close homolog of the major DNA damage regulator SOG1, to directly interact with RBR1 and the DREAM component LIN37B. Consistently, not only mutants in NAC044 but also the double mutant of the two LIN37 homologs and mutants for the DREAM component E2FB showed reduced sensitivities to DNA-damaging conditions. Our work indicates the existence of multiple DREAM complexes that work in conjunction with NAC044 to mediate growth arrest after DNA damage.

The focus of this research was to study the effect of combining nanofillers with different geometry and surface chemistry on the structure and properties of biopolymers as an alternative to traditional plastics. How the inclusion of 2D graphene oxide (GO) or reduced GO (rGO) combined with 1D sepiolite (SPT) or cellulose nanocrystals (CNCs) affect the structure and properties of chitosan and chitosan/carboxymethyl cellulose (CMC) materials was investigated. A 3D interconnected microstructure formed, composed of GO and SPT due to the strong interactions between these hydrophilic nanofillers. The chitosan/CMC/GO/SPT composite had the highest tensile strength (77.5 ± 1.2 MPa) and Young’s modulus (1925.9 ± 120.7 MPa). For the un-plasticised matrices, hydrophobic rGO nanosheets generally hindered the interaction of SPT or CNCs with the polysaccharides (chitosan and CMC) and consequently, composite properties were mainly determined by the rGO. However, for the chitosan matrix plasticised by 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), rGO + CNCs or rGO + SPT disrupted polymer chain interactions more effectively than the nanofillers when added alone and resulted in the chitosan being more plasticised, as shown by increased chain mobility, ductility, and surface hydrophilicity. For the [C2mim][OAc]-plasticised chitosan/CMC matrix, the advantages of including hybrid fillers, rGO + CNCs or rGO + SPT, were also obtained, resulting in higher thermal stability and surface hydrophobicity. Graphical Abstract

The wide host range of Xylella fastidiosa (Xf) indicates the existence of yet uncharacterized virulence mechanisms that help pathogens to overcome host defences. Various bioinformatics tools combined with prediction of the functions of putative virulence proteins are valuable approaches to study microbial pathogenicity. We collected a number of putative effectors from three Xf strains belonging to different subspecies: Temecula‐1 (subsp. fastidiosa), CoDiRO (subsp. pauca), and Ann‐1 (subsp. sandyi). We designed an in planta Agrobacterium‐based expression system that drives the expressed proteins to the cell apoplast, in order to investigate their ability to activate defence in Nicotiana model plants. Multiple Xf proteins differentially elicited cell death‐like phenotypes in different Nicotiana species. These proteins are members of different enzymatic groups: (a) hydrolases/hydrolase inhibitors, (b) serine proteases, and (c) metal transferases. We also classified the Xf proteins according to their sequential and structural similarities via the I‐TASSER online tool. Interestingly, we identified similar proteins that were able to differentially elicit cell death in different cultivars of the same species. Our findings provide a basis for further studies on the mechanisms that underlie both defence activation in Xf resistant hosts and pathogen adaptation in susceptible hosts., We categorize 19 putative Xylella fastidiosa effectors based on structural similarity predictions and we report nine of them with cell death‐inducing ability when driven in the leaf apoplast of various model Nicotiana species.

Aphids severely affect crop production by transmitting many plant viruses. Viruses are obligate intracellular pathogens that mostly depend on vectors for their transmission and survival. A majority of economically important plant viruses are transmitted by aphids. They transmit viruses either persistently (circulative or non-circulative) or non-persistently. Plant virus transmission by insects is a process that has evolved over time and is strongly influenced by insect morphological features and biology. Over the past century, a large body of research has provided detailed knowledge of the molecular processes underlying virus-vector interactions. In this review, we discuss how aphid biology and morphology can affect plant virus transmission. © 2021 Society of Chemical Industry.

37 p.-6 fig.-2 tab.-1 graph. abst., In order to better understand bacterial depolymerization of lignin, a new analytical approach was proposed using Pseudomonas putida KT2440 as delignifying bacterium and Escherichia coli as non-delignifying control. Two different types of lignins, technical Kraft lignin and synthetic dehydrogenopolymer (DHP), were submitted to a bioconversion kinetic study over 7 days. The concomitant analysis of the supernatant acid-precipitable lignin fraction and water-soluble extractives by high-performance size-exclusion chromatography (HPSEC) and gas chromatography – mass spectrometry (GC–MS) highlighted the specific action of P. putida towards these substrates, with the transitory formation of phenolic metabolites (dihydroferulic acid for Kraft lignins and dimers for DHP) and the prevention of Kraft lignin self-assemblying. In both cases lignin apparent depolymerization followed by repolymerization was observed. The analysis of the bacterial pellets indicated the time-increasing content of lignins associated to bacterial cells, which could account for the apparent structural changes observed with E. coli in the supernatant., This work was supported by ADEME [N° 1401C0066] and by the European Commission [ERA-IB-14-055] in the framework of the LIGBIO project. The IJPB benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS). Research in TDHB's group was supported by BBSRC grant BB/M025772/1.

Aims The effects of combinatorial stress on lipid production in Phanerochaete chrysosporium remain understudied. This species of white-rot fungi was cultivated on solid-state media while under variable levels of known abiotic and biotic stressors to establish the effect upon fungal oil profiles. Methods and results Environmental stressors induced upon the fungus included the following: temperature, nutrient limitation and interspecies competition to assess impact upon oil profiles. Fatty acid type and its concentration were determined using analytical methods of gas chromatography and mass spectrometry. Growth rate under stress was established using high-performance liquid chromatography with ergosterol as the biomarker. Fungi grown on solid-state agar were able to simultaneously produce short- and long-chain fatty acids which appeared to be influenced by nutritional composition as well as temperature. Addition of nitrogen supplements increased the growth rate, but lipid dynamics remained unchanged. Introducing competition-induced stress had significantly altered the production of certain fatty acids beyond that of the monoculture while under nutrient-limiting conditions. Linoleic acid concentrations, for example, increased from an average of 885 ng μl-1 at monoculture towards 13 820 ng μl-1 at co-culture, following 7 days of incubation. Conclusions Interspecies competition produced the most notable impact on lipid production for solid-state media cultivated fungi while the addition of nitrogen supplementation presented growth and lipid accumulation to be uncorrelated. Combinatorial stress therefore influences the yield of overall lipid production as well as the number of intermediate fatty acids produced, deriving similar oil profiles to the composition of vegetable and fish oils. Significance and impact of the study Fungal secondary metabolism remains highly sensitive following combinatorial stress. The outcome impacts the research towards optimizing fungal oil profiles for biomass and nutrition. Future investigations on fungal stress tolerance mechanisms need to address these environmental factors throughout the experimental design.

The oomycete Albugo candida causes white rust of Brassicaceae, including vegetable and oilseed crops, and wild relatives such as Arabidopsis thaliana. Novel White Rust Resistance (WRR) genes from Arabidopsis enable new insights into plant/parasite co-evolution. WRR4A from Arabidopsis accession Columbia (Col-0) provides resistance to many but not all white rust races, and encodes a nucleotide-binding, leucine-rich repeat immune receptor. Col-0 WRR4A resistance is broken by AcEx1, an isolate of A. candida. We identified an allele of WRR4A in Arabidopsis accession Øystese-0 (Oy-0) and other accessions that confers full resistance to AcEx1. WRR4A Oy-0 carries a C-terminal extension required for recognition of AcEx1, but reduces recognition of several effectors recognized by the WRR4A Col-0 allele. WRR4A Oy-0 confers full resistance to AcEx1 when expressed in the oilseed crop Camelina sativa.

Marine plastic pollution represents a key environmental concern. Whilst ecotoxicological data for plastic is increasingly available, its impact upon marine phytoplankton remains unclear. Owing to their predicted abundance in the marine environment and likely interactions with phytoplankton, here we focus on the smaller fraction of plastic particles (∼50 nm and ∼2 µm polystyrene spheres). Exposure of natural phytoplankton communities and laboratory cultures revealed that plastic exposure does not follow traditional trends in ecotoxicological research, since large phytoplankton appear particularly susceptible towards plastics exposure despite their higher surface-to-volume ratios. Cell declines appear driven by hetero-aggregation and co-sedimentation of cells with plastic particles, recorded visually and demonstrated using confocal microscopy. As a consequence, plastic exposure also caused disruption to photosynthetic functioning, as determined by both photosynthetic efficiency and high throughput proteomics. Negative effects upon phytoplankton are recorded at concentrations orders of magnitude above those estimated in the environment. Hence, it is likely that impacts of NPs and MPs are exacerbated at the high concentrations typically used in ecotoxicological research (i.e., mg L-1).

The threat of Ganoderma boninense, the causal agent of basal stem rot disease, in the oil palm industry warrants finding an effective control for it. The weakest link in the disease management strategy is the unattended stumps/debris in the plantations. Hence, this study aimed to determine whether the selected phenolic compounds could control G. boninense in inoculated oil palm woodblocks and restrict wood biodegradation. Results indicated a significant reduction in the wood mass loss when treated with all the phenolic compounds. Surprisingly, syringic and vanillic acids behaved ambivalently, at a lower concentration, the wood mass loss was increased, but it decreased as the concentrations were increased. In all four phenolic compounds, the inhibition of mass loss was dependent on the concentration of the compounds. After 120 days, the mass loss was only 31%, with 63% relative degradation of lignin and cellulose, and 74% of hemicellulose and wood anatomy, including silica bodies, were intact in those woodblocks treated with 1 mM benzoic acid. This study emphasizes the physicochemical and anatomical changes occurring in the oil palm wood during G. boninense colonization, and suggests that treating oil palm stumps with benzoic acid could be a solution to reducing the G. boninense inoculum pressure during replantation in a sustainable manner.

Pepper yellow leaf curl virus (PYLCV) is a threat to chili plants and can significantly reduce yields. This study aimed as a pilot project to detect PYLCV by analyzing compounds emitted by chili plants using gas chromatography-mass spectrometry (GC-MS). The samples investigated in this research were PYLCV-infected and PYLCV-undetected chili plants taken from commercial chili fields. The infection status was validated by using a polymerase chain reaction (PCR) test. A headspace technique was used to extract the volatile organic compounds emitted by plants. The analysis of GC-MS results began with pre-processing, analyzing sample compound variability with a boxplot analysis, and sample classification by using a multivariate technique. Unsupervised multivariate technique principal component analysis (PCA) was performed to discover whether GC-MS could identify PYLCV-infected or not. The results showed that PYLCV-infected and PYLCV-undetected chili plants could be differentiated, with a total percent variance of the first three principal components reaching 91.32%, and successfully discriminated between PYLCV-infected and PYLCV-undetected chili plants. However, more comprehensive studies are needed to find the potential biomarkers of the infected plants.

Classifying species as ‘native’ or ‘alien’ carries prescriptive force in the valuation and management of ‘nature’. But the classification itself and its application are contested, raising philosophical and geographical questions about place, space, rights, identity and belonging. This paper discusses leading critiques of the native/alien paradigm, including its conceptual fluidity, dichotomous rigidity and ethical difficulties, as well as the incendiary charge of xenophobia. It argues that valorizing ‘native nature’ as inherently the ‘best nature’ is not only obsolete but impracticable in the Anthropocene, and that the preeminence of biogeographic origins should be replaced with a pragmatic focus on species’ behavior. Publisher PDF

Summary It is increasingly evident that plants interact with their outside world through the production of volatile organic compounds,1, 2, 3, 4, 5 but whether the volatiles have evolved to serve in plant defense is still a topic of considerable debate.3,6, 7, 8 Unharmed leaves constitutively release small amounts of volatiles, but when the leaves are damaged by herbivorous arthropods, they emit substantially more volatiles. These herbivore-induced plant volatiles (HIPVs) attract parasitoids and predators that kill insect herbivores,9, 10, 11, 12 and this can benefit the plants.13,14 As yet, however, there is no tangible evolutionary evidence that this tritrophic interplay contributes to the selection forces that have shaped the volatile emissions of plants.2,3,5, 6, 7, 8,15 With this in mind, we investigated the evolutionary changes in volatile emissions in invasive common ragwort and the respective defensive roles of its constitutive and inducible volatiles. This Eurasian plant has invaded other continents, where it evolved for many generations in the absence of specialized herbivores and their natural enemies. We found that, compared to native ragworts, invasive plants release higher levels of constitutive volatiles but considerably lower levels of herbivore-induced volatiles. As a consequence, invasive ragwort is more attractive to a specialist moth but avoided by an unadapted generalist moth. Importantly, conforming to the indirect defense hypothesis, a specialist parasitoid was much more attracted to caterpillar-damaged native ragwort, which was reflected in higher parasitism rates in a field trial. The evolution of foliar volatile emissions appears to be indeed driven by their direct and indirect roles in defenses against insects., Graphical abstract, Highlights • The evolution of invasive plants can provide insight into the function of volatiles • Invasive ragwort releases more constitutive but fewer inducible volatiles • The invader is more attractive to a specialist herbivore but less to its parasitoid • The evolution of volatiles from invasive ragwort supports their defensive function, Lin et al. compare constitutive and herbivore-induced volatiles emitted by ragwort plants from native and invasive areas. The observed differences and the corresponding behavioral responses of a specialist and a generalist herbivore as well as of a parasitic wasp support the hypothesis that volatiles evolved as plant defenses.

Climate change impacts on the structure and function of ecosystems will worsen public health issues like allergic diseases. Birch trees (Betula spp.) are important sources of aeroallergens in Central and Northern Europe. Birches are vulnerable to climate change as these trees are sensitive to increased temperatures and summer droughts. This study aims to examine the effect of climate change on airborne birch pollen concentrations in Central Europe using Bavaria in Southern Germany as a case study. Pollen data from 28 monitoring stations in Bavaria were used in this study, with time series of up 30 years long. An integrative approach was used to model airborne birch pollen concentrations taking into account drivers influencing birch tree abundance and birch pollen production and projections made according to different climate change and socio-economic scenarios. Birch tree abundance is projected to decrease in parts of Bavaria at different rates, depending on the climate scenario, particularly in current centres of the species distribution. Climate change is expected to result in initial increases in pollen load but, due to the reduction in birch trees, the amount of airborne birch pollen will decrease at lower altitudes. Conversely, higher altitude areas will experience expansions in birch tree distribution and subsequent increases in airborne birch pollen in the future. Even considering restrictions for migration rates, increases in pollen load are likely in Southwestern areas, where positive trends have already been detected during the last three decades. Integrating models for the distribution and abundance of pollen sources and the drivers that control birch pollen production allowed us to model airborne birch pollen concentrations in the future. The magnitude of changes depends on location and climate change scenario.\ud \ud Supporting Information

The gram-positive pathogenic bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial canker disease in tomato, affecting crop yield and fruit quality. To understand how tomato plants respond, the dynamic expression profile of host genes was analyzed upon Cmm infection. Symptoms of bacterial canker became evident from the third day. As the disease progressed, the bacterial population increased in planta, reaching the highest level at six days and remained constant till the twelfth day post inoculation. These two time points were selected for transcriptomics. A progressive down-regulation of key genes encoding for components of the photosynthetic apparatus was observed. Two temporally separated defense responses were observed, which were to an extent interdependent. During the primary response, genes of the phenylpropanoid pathway were diverted towards the synthesis of monolignols away from S-lignin. In dicots, lignin polymers mainly consist of G- and S-units, playing an important role in defense. The twist towards G-lignin enrichment is consistent with previous findings, highlighting a response to generate an early protective barrier and to achieve a tight interplay between lignin recomposition and the primary defense response mechanism. Upon progression of Cmm infection, the temporal deactivation of phenylpropanoids coincided with the upregulation of genes that belong in a secondary response mechanism, supporting an elegant reprogramming of the host transcriptome to establish a robust defense apparatus and suppress pathogen invasion. This high-throughput analysis reveals a dynamic reorganization of plant defense mechanisms upon bacterial infection to implement an array of barriers preventing pathogen invasion and spread.