Worse Comes to Worst: Bananas and Panama Disease--When Plant and Pathogen Clones Meet

Climate change effects on Black Sigatoka disease of banana

Climate change has significantly altered species distributions in the wild and has the potential to affect the interactions between pests and diseases and their human, animal and plant hosts. While several studies have projected changes in disease distributions in the future, responses to historical climate change are poorly understood. Such analyses are required to dissect the relative contributions of climate change, host availability and dispersal to the emergence of pests and diseases. Here, we model the influence of climate change on the most damaging disease of a major tropical food plant, Black Sigatoka disease of banana. Black Sigatoka emerged from Asia in the late twentieth Century and has recently completed its invasion of Latin American and Caribbean banana-growing areas. We parametrize an infection model with published experimental data and drive the model with hourly microclimate data from a global climate reanalysis dataset. We define infection risk as the sum of the number of modelled hourly spore cohorts that infect a leaf over a time interval. The model shows that infection risk has increased by a median of 44.2% across banana-growing areas of Latin America and the Caribbean since the 1960s, due to increasing canopy wetness and improving temperature conditions for the pathogen. Thus, while increasing banana production and global trade have probably facilitated Black Sigatoka establishment and spread, climate change has made the region increasingly conducive for plant infection.

This article is part of the theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes’. This issue is linked with the subsequent theme issue ‘Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control’.

Bioinformatic Detection of Positive Selection Pressure in Plant Pathogens: The Neutral Theory of Molecular Sequence Evolution in Action

The genomes of plant pathogenic fungi and oomycetes are often exposed to strong positive selection pressure. During speciation, shifts in host range and preference can lead to major adaptive changes. Furthermore, evolution of total host resistance to most isolates can force rapid evolutionary changes in host-specific pathogens. Crop pathogens are subjected to particularly intense selective pressures from monocultures and fungicides. Detection of the footprints of positive selection in plant pathogen genomes is a worthwhile endeavor as it aids understanding of the fundamental biology of these important organisms. There are two main classes of test for detection of positively selected alleles. Tests based on the ratio of non-synonymous to synonymous substitutions per site detect the footprints of multiple fixation events between divergent lineages. Thus, they are well-suited to the study of ancient adaptation events spanning speciations. On the other hand, tests that scan genomes for local fluctuations in allelic diversity within populations are suitable for detection of recent positive selection in populations. In this review, I briefly describe some of the more widely used tests of positive selection and the theory underlying them. I then discuss various examples of their application to plant pathogen genomes, emphasizing the types of genes that are associated with signatures of positive selection. I conclude with a discussion of the practicality of such tests for identification of pathogen genes of interest and the important features of pathogen ecology that must be taken into account for accurate interpretation.

Label free proteomics and systematic analysis of secretome reveals effector candidates regulated by SGE1 and FTF1 in the plant pathogen Fusarium oxysporum f. sp. cubense tropical race 4

BACKGROUND

Phytopathogens secreted effectors during host colonization to suppress or trigger plant immunity. Identification of new effectors is one of the research focuses in recent years. There is only a limited knowledge about effectors of Fusarium oxysporum f. sp. Cubense tropical race 4 (Foc TR4), the causal agent of wilt disease in Cavendish banana.

RESULTS

Two transcription factors, SGE1 and FTF1, were constitutively over-expressed in Foc TR4 to partially mimic the in-planta state. Secreted proteins with high purity were prepared through a two-round extraction method. Then the secretome were analyzed via label free proteomics method. A total of 919 non-redundant proteins were detected, of which 74 proteins were predicted to be effector candidates. Among these candidates, 29 were up-regulated and 13 down-regulated in the strain over-expressing SGE1 and FTF1, 8 were up-regulated and 4 down-regulated in either SGE1 or FTF1 over expression strain.

CONCLUSIONS

Through label free proteomics analysis, a series of effector candidates were identified in secretome of Foc TR4. Our work put a foundation for functional research of these effectors.

Detecting Banana Plantations in the Wet Tropics, Australia, Using Aerial Photography and U-Net

Bananas are the world’s most popular fruit and an important staple food source. Recent outbreaks of Panama TR4 disease are threatening the global banana industry, which is worth an estimated $8 billion. Current methods to map land uses are time- and resource-intensive and result in delays in the timely release of data. We have used existing land use mapping to train a U-Net neural network to detect banana plantations in the Wet Tropics of Queensland, Australia, using high-resolution aerial photography. Accuracy assessments, based on a stratified random sample of points, revealed the classification achieves a user’s accuracy of 98% and a producer’s accuracy of 96%. This is more accurate compared to existing (manual) methods, which achieved a user’s and producer’s accuracy of 86% and 92% respectively. Using a neural network is substantially more efficient than manual methods and can inform a more rapid respond to existing and new biosecurity threats. The method is robust and repeatable and has potential for mapping other commodities and land uses which is the focus of future work.

Recognition of Banana Fusarium Wilt Based on UAV Remote Sensing

Fusarium wilt (Panama disease) of banana currently threatens banana production areas worldwide. Timely monitoring of Fusarium wilt disease is important for the disease treatment and adjustment of banana planting methods. The objective of this study was to establish a method for identifying the banana regions infested or not infested with Fusarium wilt disease using unmanned aerial vehicle (UAV)-based multispectral imagery. Two experiments were conducted in this study. In experiment 1, 120 sample plots were surveyed, of which 75% were used as modeling dataset for model fitting and the remaining were used as validation dataset 1 (VD1) for validation. In experiment 2, 35 sample plots were surveyed, which were used as validation dataset 2 (VD2) for model validation. An UAV equipped with a five band multispectral camera was used to capture the multispectral imagery. Eight vegetation indices (VIs) related to pigment absorption and plant growth changes were chosen for determining the biophysical and biochemical characteristics of the plants. The binary logistic regression (BLR) method was used to assess the spatial relationships between the VIs and the plants infested or not infested with Fusarium wilt. The results showed that the banana Fusarium wilt disease can be easily identified using the VIs including the green chlorophyll index (CIgreen), red-edge chlorophyll index (CIRE), normalized difference vegetation index (NDVI), and normalized difference red-edge index (NDRE). The fitting overall accuracies of the models were greater than 80%. Among the investigated VIs, the CIRE exhibited the best performance both for the VD1 (OA = 91.7%, Kappa = 0.83) and VD2 (OA = 80.0%, Kappa = 0.59). For the same type of VI, the VIs including a red-edge band obtained a better performance than that excluding a red-edge band. A simulation of imagery with different spatial resolutions (i.e., 0.5-m, 1-m, 2-m, 5-m, and 10-m resolutions) showed that good identification accuracy of Fusarium wilt was obtained when the resolution was higher than 2 m. As the resolution decreased, the identification accuracy of Fusarium wilt showed a decreasing trend. The findings indicate that UAV-based remote sensing with a red-edge band is suitable for identifying banana Fusarium wilt disease. The results of this study provide guidance for detecting the disease and crop planting adjustment.

Functional Analysis of MaWRKY24 in Transcriptional Activation of Autophagy-Related Gene 8f/g and Plant Disease Susceptibility to Soil-Borne Fusarium oxysporum f. sp. cubense

WRKYs play important roles in plant development and stress responses. Although MaWRKYs have been comprehensively identified in the banana (Musa acuminata), their in vivo roles and direct targets remain elusive. In this study, a transcript profile analysis indicated the common regulation of MaWRKYs transcripts in response to fungal pathogen Fusarium oxysporum f. sp. cubense (Foc). Among these MaWRKYs, MaWRKY24 was chosen for further analysis due to its higher expression in response to Foc. The specific nucleus subcellular location and transcription activated activity on W-box indicated that MaWRKY24 was a transcription factor. The correlation analysis of gene expression indicated that MaWRKYs were closely related to autophagy-associated genes (MaATG8s). Further analysis showed that MaWRKY24 directly regulated the transcriptional level of MaATG8f/g through binding to W-box in their promoters, as evidenced by quantitative real-time Polymerase Chain Reaction (PCR), dual luciferase assay, and electrophoretic mobility shift assay. In addition, overexpression of MaWRKY24 and MaATG8f/g resulted in disease susceptibility to Foc, which might be related to the activation of autophagic activity. This study highlights the positive regulation of MaWRKY24 in transcriptional activation of autophagy-related gene 8f/g in the banana and their common roles in disease susceptibility to soil-borne Foc, indicating the effects of MaWRKY24 on autophagy and disease susceptibility.

Compositional homogeneity in the pathobiome of a new, slow-spreading coral disease

BACKGROUND

Coral reefs face unprecedented declines in diversity and cover, a development largely attributed to climate change-induced bleaching and subsequent disease outbreaks. Coral-associated microbiomes may strongly influence the fitness of their hosts and alter heat tolerance and disease susceptibility of coral colonies. Here, we describe a new coral disease found in Micronesia and present a detailed assessment of infection-driven changes in the coral microbiome.

RESULTS

Combining field monitoring and histological, microscopic and next-generation barcoding assessments, we demonstrate that the outbreak of the disease, named 'grey-patch disease', is associated with the establishment of cyanobacterial biofilm overgrowing coral tissue. The disease is characterised by slow progression rates, with coral tissue sometimes growing back over the GPD biofilm. Network analysis of the corals' microbiome highlighted the clustering of specific microbes which appeared to benefit from the onset of disease, resulting in the formation of 'infection clusters' in the microbiomes of apparently healthy corals.

CONCLUSIONS

Our results appear to be in contrast to the recently proposed Anna-Karenina principle, which states that disturbances (such as disease) trigger chaotic dynamics in microbial communities and increase β-diversity. Here, we show significantly higher community similarity (compositional homogeneity) in the pathobiome of diseased corals, compared to the microbiome associated with apparently healthy tissue. A possible explanation for this pattern is strong competition between the pathogenic community and those associated with the 'healthy' coral holobiont, homogenising the composition of the pathobiome. Further, one of our key findings is that multiple agents appear to be involved in degrading the corals' defences causing the onset of this disease. This supports recent findings indicating a need for a shift from the one-pathogen-one-disease paradigm to exploring the importance of multiple pathogenic players in any given disease.

Molecular analysis of somatic embryogenesis through proteomic approach and optimization of protocol in recalcitrant Musa spp

Somatic embryogenesis (SE) is a complex stress related process regulated by numerous biological factors. SE is mainly applicable to mass propagation and genetic improvement of plants through gene transfer technology and induced mutations. In banana, SE is highly genome dependent as the efficiency varies with cultivars. To understand the molecular mechanism of SE, a proteomics approach was carried out to identify proteins expressed during embryogenic calli (EC) induction, regeneration and germination of somatic embryos in the banana cultivar cv. Rasthali (AAB). In total, 70 spots were differentially expressed in various developmental stages of SE, of which 16 were uniquely expressed and 17 were highly abundant in EC compared to non-embryogenic calli and explants. Also, four spots were uniquely expressed in germinating somatic embryos. The functional annotation of identified proteins revealed that calcium signaling along with stress and endogenous hormones related proteins played a vital role in EC induction and germination of somatic embryos. Thus, based on this outcome, the callus induction media was modified and tested in five cultivars. Among them, cultivars Grand Naine (AAA), Monthan (ABB) and Ney Poovan (AB) showed a better response in tryptophan added media, whereas Red Banana (AAA) and Karpuravalli (ABB) showed maximum EC induction in kinetin and CaCl₂ supplemented media respectively. Simultaneously, germination media were modified to induce proteins responsible for germination. In cv. Rasthali, media supplemented with 10 mM CaCl₂ showed a maximum increase in germination (51.79%) over control plants. Thus, the present study revealed that media modification based on proteomic analysis can induce SE in recalcitrant cultivars and also enhance germination in cultivars amenable for SE.

Fungal clones win the battle, but recombination wins the war

Clonal reproduction is common in fungi and fungal-like organisms during epidemics and invasion events. The success of clonal fungi shaped systems for their classification and some pathogens are tacitly treated as asexual. We argue that genetic recombination driven by sexual reproduction must be a starting hypothesis when dealing with fungi for two reasons: (1) Clones eventually crash because they lack adaptability; and (2) fungi find a way to exchange genetic material through recombination, whether sexual, parasexual, or hybridisation. Successful clones may prevail over space and time, but they are the product of recombination and the next successful clone will inevitably appear. Fungal pathogen populations are dynamic rather than static, and they need genetic recombination to adapt to a changing environment.

Plant-Pathogen Warfare under Changing Climate Conditions

Global environmental changes caused by natural and human activities have accelerated in the past 200 years. The increase in greenhouse gases is predicted to continue to raise global temperature and change water availability in the 21^st century. In this Review, we explore the profound effect the environment has on plant diseases - a susceptible host will not be infected by a virulent pathogen if the environmental conditions are not conducive for disease. The change in CO₂ concentrations, temperature, and water availability can have positive, neutral, or negative effects on disease development, as each disease may respond differently to these variations. However, the concept of disease optima could potentially apply to all pathosystems. Plant resistance pathways, including pattern-triggered immunity to effector-triggered immunity, RNA interference, and defense hormone networks, are all affected by environmental factors. On the pathogen side, virulence mechanisms, such as the production of toxins and virulence proteins, as well as pathogen reproduction and survival are influenced by temperature and humidity. For practical reasons, most laboratory investigations into plant-pathogen interactions at the molecular level focus on well-established pathosystems and use a few static environmental conditions that capture only a fraction of the dynamic plant-pathogen-environment interactions that occur in nature. There is great need for future research to increasingly use dynamic environmental conditions in order to fully understand the multidimensional nature of plant-pathogen interactions and produce disease-resistant crop plants that are resilient to climate change.

Climate change impacts on banana yields around the world

Nutritional diversity is a key element of food security^1-3. However, research on the effects of climate change on food security has, thus far, focussed on the major food grains^4-8, while the response of other crops, particularly those that play an important role in the developing world, are poorly understood. Bananas are a staple food and a major export commodity for many tropical nations⁹. Here we show that for 27 countries - accounting for 86% of global dessert banana production - a changing climate since 1961 has increased yields by an average of 1.37 T.ha^-1. Past gains have been largely ubiquitous across the countries assessed and African producers will continue to see yield increases into the future. However, global yield gains could be dampened or disappear in the future, reducing to 0.59 T.ha^-1and 0.19 T.ha^-1by 2050 under the RCP 4.5 and 8.5 climate scenarios, respectively, driven by declining yields amongst the largest producers and exporters. By quantifying climate-driven and technology-driven influences on yield, we also identify countries at risk from climate change and those capable of mitigating its effects, or capitalising on its benefits.

Comparative analysis uncovers the limitations of current molecular detection methods for Fusarium oxysporum f. sp. cubense race 4 strains

Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4) is threatening banana production worldwide. Despite quarantine efforts, the pathogen continues to spread; thus, early diagnosis plays an essential role for the proper execution of contingency plans. Here, we assess the accuracy of four PCR-based molecular methods described in the literature for the identification and detection of race 4 strains, including Subtropical (Foc STR4) and Tropical Race 4 causing Fusarium wilt of banana. We screened a total of 302 isolates using these four markers, and performed phylogenetic analyses, Vegetative Compatibility Group (VCG) testing, sequence comparison, and pathogenicity tests for selected isolates. Our results show that three out of the four markers tested are not reliable for identification of Foc STR4 and TR4, as DNA from isolates from Ecuador, pathogenic and nonpathogenic to banana, obtained from different banana cultivars, displayed cross-reaction with these methods; that is, false positives can occur during the diagnostic process for race 4. Phylogenetic analyses, VCG testing, sequence comparison, and pathogenicity tests suggest the presence of non-target F. oxysporum isolates that share genomic regions with pathogenic strains but lack true pathogenicity to banana. The findings of this work are of foremost importance for international regulatory agencies performing surveillance tests in pathogen-free areas using the current diagnostic methods. We suggest the use of a genetic locus possibly related to virulence, previously identified by T-DNA, and amplified with primers W2987F/ W2987R, for diagnosis of Foc TR4 as the most reliable alternative. We urge the adoption of a more holistic view in the study of F. oxysporum as a plant pathogen that considers the biology and diversity of the species for the development of better diagnostic tools.

Identification of Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) responsive miRNAs in banana root

The fungus, Fusarium oxysporum f. sp. cubense (Foc), is the causal agent of Fusarium wilt disease, which is the most serious disease affecting the whole banana industry. Although extensive studies have characterized many Foc-responsive genes in banana, the molecular mechanisms on microRNA level underlying both banana defense and Foc pathogenesis are not yet fully understood. In this study, we aimed to reveal the role of miRNA during banana-Foc TR4 interactions. Illumina sequencing was used to reveal the changes in small RNAome profiles in roots of Foc TR4-inoculated ‘Tianbaojiao’ banana (Musa acuminata cv. Tianbaojiao) in the early stages (i.e. 5 h, 10 h and 25 h post Foc TR4 inoculation, respectively). The expression of some differentially expressed (DE) miRNAs and their predicted target genes was studied by using quantitative real time PCR (qRT-PCR). Totally, 254 known miRNAs from 31 miRNA families and 28 novel miRNAs were identified. Differential expression analysis identified 84, 77 and 74 DE miRNAs at the three respective Foc TR4 infection time points compared with control healthy banana (CK). GO and KEGG analysis revealed that most of the predicted target genes of DE miRNAs (DET) were implicated in peroxisome, fatty acid metabolism, auxin-activated signaling pathway, sulfur metabolism, lignin metabolism and so on, and many known stress responsive genes were identified to be DETs. Moreover, expected inverse correlations were confirmed between some miRNA and their corresponding target genes by using qRT-PCR analysis. Our study revealed that miRNA play important regulatory roles during the banana-Foc TR4 interaction by regulating peroxidase, fatty acid metabolism, auxin signaling, sulfur metabolism, lignin metabolism related genes and many known stress responsive genes.

High-Quality Draft Genome Sequence of the Causal Agent of the Current Panama Disease Epidemic

We present a high-quality draft genome assembly for Fusarium oxysporum f. sp. cubense tropical race 4 (Fusarium odoratissimum), assembled from PacBio reads and consisting of 15 contigs with a total assembly size of 48.59 Mb. This strain appears to belong to vegetative compatibility group complex 01213/16.

We present a high-quality draft genome assembly for Fusarium oxysporum f. sp. cubense tropical race 4 (Fusarium odoratissimum), assembled from PacBio reads and consisting of 15 contigs with a total assembly size of 48.59 Mb. This strain appears to belong to vegetative compatibility group complex 01213/16.

Coordination as Management Response to the Spread of a Global Plant Disease: A Case Study in a Major Philippine Banana Production Area

An integrative management approach to the spread and emergence of global plant diseases, such as the soil-borne fungus Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), entails a combination of technical measures and the responsiveness and awareness of area-specific constellations supporting conditions conducive to interactions and coordination among organizations and actors with different resources and diverse interests. Responses to banana diseases are mostly studied through technical and epidemiological lenses and reflect a bias to the export industry. Some authors, however, indicate that cross-sector collaboration is crucial in responding to a disease outbreak. Earlier studies on the outbreak of diseases and natural disasters suggest that shared cognition and effective partnerships increased the success rate of response. Hence, it is important not to focus exclusively on the impacts of a pathogen at farm or field level and to shift attention to how tasks and knowledge are coordinated and shared. This paper aims to detect whether and how the emergence of Foc TR4 is a driver of coordination. The case study focuses on the interactions between a variety of banana producers and among a range of public and private actors in southern Philippines. The analysis identifies distinct forms of coordination emerging in the context of three organizational fields responding to Foc TR4, which underlie shared capacity to handle and understand the spread of a global plant disease. The research is based on qualitative key informant interviews and document analysis and on observations of instructive events in 2014-2017. Analysis of the composition and actions developed in three organizational fields leads to distinguishing three theory-driven forms of coordination: rule-based, cognition-based, and skill-based. The combination of these three forms constitutes the possibility of a collaborative community, which conditions the implementation of an integrative management approach to mitigate Foc TR4.

An Improved Phenotyping Protocol for Panama Disease in Banana

Fusarium oxysporum (Fo) belongs to a group of soil-borne hyphomycetes that are taxonomically collated in the Fusarium oxysporum Species Complex (FOSC). Hitherto, those infecting bananas were placed in the forma specialis cubense (Foc). Recently, however, these genetically different Foc lineages were recognized as new Fusarium spp. placed in the Fusarium of Banana Complex (FOBC). A member of this complex F. odoratissimum II-5 that uniquely comprises the so-called Tropical Race 4 (TR4), is a major problem sweeping through production zones of Cavendish banana in several regions of the world. Because of this, there is an urgent need for a phenotyping method that allows the screening for resistance to TR4 of large numbers of banana genotypes. Most Fusarium species produce three types of spores: macroconidia, microconidia and the persistent chlamydospores that can contaminate soils for many years. Inoculum production has been an important bottleneck for efficient phenotyping due to the low or variable number of conidia and the elaborate laboratory procedures requiring specific infrastructure. Here, we report a rapid, simple and high-yielding spore production method for nine F. oxysporum formae speciales as well as the biocontrol species Fo47 and Fo618-12. For Fusarium spp. causing Fusarium wilt or Panama disease of banana, we used the protocol for four species comprising the recognized physiological races, including Tropical Race 4 (TR4). We subsequently tested the produced inoculum in comparative inoculation trials on banana plants to evaluate their efficiency. All assays resulted in typical symptoms within 10 weeks; significant differences in final disease ratings were observed, depending on inoculum concentration. Pouring inoculum directly onto banana plants showed the most consistent and reproducible results, as expressed in external wilting, internal discoloration and determined by real-time PCR assays on entire rhizomes. Moreover, this method allows the inoculation of 250 plants per hour by one individual thereby facilitating the phenotyping of large mutant and breeding populations.

Many unreported crop pests and pathogens are probably already present

Invasive species threaten global biodiversity, food security and ecosystem function. Such incursions present challenges to agriculture where invasive species cause significant crop damage and require major economic investment to control production losses. Pest risk analysis (PRA) is key to prioritize agricultural biosecurity efforts, but is hampered by incomplete knowledge of current crop pest and pathogen distributions. Here, we develop predictive models of current pest distributions and test these models using new observations at subnational resolution. We apply generalized linear models (GLM) to estimate presence probabilities for 1,739 crop pests in the CABI pest distribution database. We test model predictions for 100 unobserved pest occurrences in the People's Republic of China (PRC), against observations of these pests abstracted from the Chinese literature. This resource has hitherto been omitted from databases on global pest distributions. Finally, we predict occurrences of all unobserved pests globally. Presence probability increases with host presence, presence in neighbouring regions, per capita GDP and global prevalence. Presence probability decreases with mean distance from coast and known host number per pest. The models are good predictors of pest presence in provinces of the PRC, with area under the ROC curve (AUC) values of 0.75-0.76. Large numbers of currently unobserved, but probably present pests (defined here as unreported pests with a predicted presence probability >0.75), are predicted in China, India, southern Brazil and some countries of the former USSR. We show that GLMs can predict presences of pseudoabsent pests at subnational resolution. The Chinese literature has been largely inaccessible to Western academia but contains important information that can support PRA. Prior studies have often assumed that unreported pests in a global distribution database represent a true absence. Our analysis provides a method for quantifying pseudoabsences to enable improved PRA and species distribution modelling.

Many unreported crop pests and pathogens are probably already present

Invasive species threaten global biodiversity, food security and ecosystem function. Such incursions present challenges to agriculture where invasive species cause significant crop damage and require major economic investment to control production losses. Pest risk analysis (PRA) is key to prioritize agricultural biosecurity efforts, but is hampered by incomplete knowledge of current crop pest and pathogen distributions. Here, we develop predictive models of current pest distributions and test these models using new observations at subnational resolution. We apply generalized linear models (GLM) to estimate presence probabilities for 1,739 crop pests in the CABI pest distribution database. We test model predictions for 100 unobserved pest occurrences in the People's Republic of China (PRC), against observations of these pests abstracted from the Chinese literature. This resource has hitherto been omitted from databases on global pest distributions. Finally, we predict occurrences of all unobserved pests globally. Presence probability increases with host presence, presence in neighbouring regions, per capita GDP and global prevalence. Presence probability decreases with mean distance from coast and known host number per pest. The models are good predictors of pest presence in provinces of the PRC, with area under the ROC curve (AUC) values of 0.75-0.76. Large numbers of currently unobserved, but probably present pests (defined here as unreported pests with a predicted presence probability >0.75), are predicted in China, India, southern Brazil and some countries of the former USSR. We show that GLMs can predict presences of pseudoabsent pests at subnational resolution. The Chinese literature has been largely inaccessible to Western academia but contains important information that can support PRA. Prior studies have often assumed that unreported pests in a global distribution database represent a true absence. Our analysis provides a method for quantifying pseudoabsences to enable improved PRA and species distribution modelling.

The photoactivity of natural products - An overlooked potential of phytomedicines?

BACKGROUND

Photoactivity, though known for centuries, is only recently shifting back into focus as a treatment option against cancer and microbial infections. The external factor light is the ingenious key-component of this therapy: Since light activates the drug locally, a high level of selectivity is reached and side effects are avoided. The first reported photoactive medicines were plant extracts. Synthetic entities (so-called photosensitizers PSs), however, paved the route towards the clinical approval of the so-called photodynamic therapy (PDT), and thus natural PSs took a backseat in the past.

HYPOTHESIS

Many isolated bioactive phytochemicals hold a hidden photoactive potential, which is overlooked due to the reduced common awareness of photoactivity.

METHODS

A systematic review of reported natural PSs and their supposed medicinal application was conducted by employing PubMed, Scifinder, and Web of Science. The identified photoactive natural products were compiled including information about their natural sources, their photoyield, and their pharmacological application. Furthermore, the common chemical scaffolds of natural PS are shown to enable the reader to recognize potentially overlooked natural PSs.

RESULTS

The literature review revealed over 100 natural PS, excluding porphyrins. The PSs were classified according to their scaffold. Thereby it was shown that some PS-scaffolds were analyzed in a detailed way, while other classes were only scarcely investigated, which leaves space for future discoveries. In addition, the literature revealed that many PSs are phytoalexins, thus the selection of the starting material significantly matters in order to find new PSs.

CONCLUSION

Photoactive principles are ubiquitous and can be found in various plant extracts. With the increasing availability of light-irradiation setups for the identification of photoactive natural products, we anticipate the discovery of many new natural PSs in the near future. With the accumulation of chemically diverse PSs, PDT itself might finally reach its clinical breakthrough as a promising alternative treatment against multi-resistant microbes and cancer types.

Molecular Diagnostics of Banana Fusarium Wilt Targeting Secreted-in-Xylem Genes

Fusarium wilt is currently spreading in banana growing regions around the world leading to substantial losses. The disease is caused by the fungus Fusarium oxysporum f. sp. cubense (Foc), which is further classified into distinct races according to the banana varieties that they infect. Cavendish banana is resistant to Foc race 1, to which the popular Gros Michel subgroup succumbed last century. Cavendish effectively saved the banana industry, and became the most cultivated commercial subgroup worldwide. However, Foc tropical race 4 (TR4) subsequently emerged in Southeast Asia, causing significant yield losses due to its high level of aggressiveness to cultivars of Cavendish, and other commonly grown cultivars. Preventing further spread is crucially important in the absence of effective control methods or resistant market-acceptable banana cultivars. Implementation of quarantine and containment measures depends on early detection of the pathogen through reliable diagnostics. In this study, we tested the hypothesis that secreted in xylem (SIX) genes, which currently comprise the only known family of effectors in F. oxysporum, contain polymorphisms to allow the design of molecular diagnostic assays that distinguish races and relevant VCGs of Foc. We present specific and reproducible diagnostic assays based on conventional PCR targeting SIX genes, using as templates DNA extracted from pure Foc cultures. Sets of primers specifically amplify regions of: SIX6 in Foc race 1, SIX1 gene in TR4, SIX8 in subtropical race 4, SIX9/SIX10 in Foc VCG 0121, and SIX13 in Foc VCG 0122. These assays include simplex and duplex PCRs, with additional restriction digestion steps applied to amplification products of genes SIX1 and SIX13. Assay validations were conducted to a high international standard including the use of 250 Fusarium spp. isolates representing 16 distinct Fusarium species, 59 isolates of F. oxysporum, and 21 different vegetative compatibility groups (VCGs). Tested parameters included inter and intraspecific analytical specificity, sensitivity, robustness, repeatability, and reproducibility. The resulting suite of assays is able to reliably and accurately detect R1, STR4, and TR4 as well as two VCGs (0121 and 0122) causing Fusarium wilt in bananas.

Lime and ammonium carbonate fumigation coupled with bio-organic fertilizer application steered banana rhizosphere to assemble a unique microbiome against Panama disease

Microbiome plays a key role in determining soil suppressiveness against invading pathogens. Our previous study revealed that microbial community of bulk soil could be manipulated by lime and ammonium bicarbonate fumigation followed by biofertilizer application. However, the assembly of microbial community suppressive to banana Panama disease in the rhizosphere is still unclear. In this study, we used high-throughput sequencing and quantitative PCR to explore the assembly of rhizosphere microbiome associated with banana Panama disease suppression in a two-seasonal pot experiment. We found biofertilizer applied to lime and ammonium bicarbonate fumigated soil significantly (P < 0.05) reduced the abundance of rhizosphere Fusarium oxysporum compared to biofertilizer applied to non-fumigated soil. Principal coordinate analysis revealed that biofertilizer applied to lime and ammonium bicarbonate fumigated soil re-shaped the rhizosphere bacterial community composition by increasing the phylogenetic relatedness, and stimulating indigenous microbes, for example, Gemmatimonas, Sphingomonas, Pseudomonas, Lysobacter and Bacillus. Co-occurrence analysis revealed that potential species involved in disease suppression were more interrelated in disease-suppressive soils. Taken together, lime and ammonium bicarbonate fumigation followed by biofertilizer application could induce banana rhizosphere to assemble beneficial microbes dominated consortia to suppress banana Panama disease.

Metabolite profiling characterises chemotypes of Musa diploids and triploids at juvenile and pre-flowering growth stages

Bananas (Musa spp.) are consumed worldwide as dessert and cooking types. Edible banana varieties are for the most part seedless and sterile and therefore vegetatively propagated. This confers difficulties for breeding approaches against pressing biotic and abiotic threats and for the nutritional enhancement of banana pulp. A panel of banana accessions, representative of the diversity of wild and cultivated bananas, was analysed to assess the range of chemotypes available globally. The focus of this assessment was banana leaves at two growth stages (juvenile and pre-flowering), to see when during the plant growth metabolic differences can be established. The metabolic data corresponded to genomic trends reported in previous studies and demonstrated a link between metabolites/pathways and the genomes of M. acuminata and M. balbisiana. Furthermore, the vigour and resistance traits of M. balbisiana was connected to the phenolic composition and showed differences with the number of B genes in the hybrid accessions. Differences in the juvenile and pre-flowering data led to low correlation between the growth stages for prediction purposes.

New endemic Fusarium species hitch-hiking with pathogenic Fusarium strains causing Panama disease in small-holder banana plots in Indonesia

Fusarium species are well known for their abundance, diversity and cosmopolitan life style. Many members of the genus Fusarium are associated with plant hosts, either as plant pathogens, secondary invaders, saprotrophs, and/or endophytes. We previously studied the diversity of Fusarium species in the Fusarium oxysporum species complex (FOSC) associated with Fusarium wilt of banana in Indonesia. In that study, several Fusarium species not belonging to the FOSC were found to be associated with Fusarium wilt of banana. These Fusarium isolates belonged to three Fusarium species complexes, which included the Fusarium fujikuroi species complex (FFSC), Fusarium incarnatum-equiseti species complex (FIESC) and the Fusarium sambucinum species complex (FSSC). Using a multi-gene phylogeny that included partial fragments of the beta-tubulin (tub), calmodulin (cmdA), translation elongation factor 1-alpha (tef1), the internal transcribed spacer region of the rDNA (ITS), the large subunit of the rDNA (LSU), plus the RNA polymerase II large subunit (rpb1) and second largest subunit (rpb2) genes, we were able to identify and characterise several of these as new Fusarium species in the respective species complexes identified in this study.

Phylogeny and genetic diversity of the banana Fusarium wilt pathogen Fusarium oxysporum f. sp. cubense in the Indonesian centre of origin

Fusarium oxysporum f. sp. cubense (Foc), the causal agent of Fusarium wilt or Panama disease on banana, is one of the major constraints in banana production worldwide. Indonesia is the centre of origin for wild and cultivated bananas, which likely co-evolved with Foc. This study explored the widest possible genetic diversity of Foc by sampling across Indonesia at 34 geographically and environmentally different locations in 15 provinces at six islands. This resulted in a comprehensive collection of ∼200 isolates from 40 different local banana varieties. Isolates were identified and assessed using sequence analysis of the translation elongation factor-1alpha (tef1), the RNA polymerase II largest subunit (rpb1), and the RNA polymerase II second largest subunit (rpb2). Phylogenetic analyses of these genes allowed the identification of 180 isolates of Fusarium oxysporum f. sp. cubense (Foc), and 20 isolates of the Fusarium fujikuroi species complex (FFSC), the Fusarium incarnatum-equiseti species complex (FIESC), and the Fusarium sambucinum species complex (FSSC). Further analyses, incorporating a worldwide collection of Foc strains, revealed nine independent genetic lineages for Foc, and one novel clade in the Fusarium oxysporum species complex (FOSC). Selected isolates from each lineage were tested on the banana varieties Gros Michel and Cavendish to characterise their pathogenicity profiles. More than 65 % of the isolates were diagnosed as Tropical Race 4 (Foc-TR4) due to their pathogenicity to Cavendish banana, which supports the hypothesis that Foc-TR4 is of Indonesian origin. Nine independent genetic lineages for Foc are formally described in this study. This biodiversity has not been studied since the initial description of Foc in 1919. This study provides a detailed overview of the complexity of Fusarium wilt on banana and its diversity and distribution across Indonesia.

Handling Tensions between Natural and Utility Purpose of Farm Animals and Crop Plants

We analyze the extent to which humans respect farm animals and crop plants and whether humans provide them adequate care. Concerns are justified, since many farm animals and crop plants have become completely dependent on humans for their survival. We explore whether the concept of ‘telos’ can be useful. From a biocentric and ecocentric custodian position, an animal or a plant possesses a telos, a nature of its own and a natural, species-specific purpose, but also a telos through its destination imposed by humanity because of its usefulness and service to human beings. Based on both forms of telos farm animals and crop plants deserve respect and have a moral value. Both forms of telos seem to oppose each other: the more humans domesticate the animal or plant, the more it must sacrifice its ‘natural telos’ to serve its ‘utility telos’. Humans should enable the animal or the plant to realize its natural telos in harmony with its utility telos. Both forms of telos could be reconciled if humans fulfil their moral duty to support farm animals and crops in completing their production cycle in a respectful manner. We formulate some guidelines to operationalize, and give meaning to, the concept of telos.

The Epidemiology of Fusarium Wilt of Banana

Fusarium wilt of banana (also known as Panama disease) has been a problem in Australia since 1874. Race 1 of the pathogen (Fusarium oxysporum f. sp. cubense) is responsible for damage to 'Lady Finger' (AAB, Pome subgroup) and other less widely grown cultivars such as 'Ducasse' (Pisang Awak, ABB). Subtropical Race 4 (STR4) also affects these cultivars as well as Cavendish cultivars (AAA) in southern Queensland and northern New South Wales where cold temperature predisposition is involved. Tropical Race 4 (TR4) has led to the demise of the Cavendish industry in the Northern Territory, and its presence was confirmed in a North Queensland plantation in 2015, which warranted destruction of all banana plants on the property; as of this writing (April 2019), TR4 has spread to two adjacent properties. This review, which was commissioned by Biosecurity Queensland in response to the 2015 TR4 outbreak, considers the key epidemiological factors associated with the onset of a Fusarium wilt epidemic. Resistance to TR4, which is mediated by events following entry by the pathogen into the xylem, is not present in any commercially acceptable banana cultivar. Also, there is no effective chemical agent that can be used to manage the disease. Besides prevention, very early recognition and rapid containment of a disease outbreak are necessary to prevent epidemic development. A good understanding of the key factors responsible for disease development is required when devising practical protocols for the destruction of infected plants, treatment of surrounding infested soil, and reduction of inoculum in plant residues and soil.

A SIX1 homolog in Fusarium oxysporum f.sp. cubense tropical race 4 contributes to virulence towards Cavendish banana

The fungus Fusarium oxysporum f.sp. cubense (Focub) causes Fusarium wilt of banana. Focub strains are divided into races according to their host specificity, but which virulence factors underlie these interactions is currently unknown. In the F. oxysporum f.sp. lycopersici (Fol)-tomato system, small secreted fungal proteins, called Six proteins, were identified in the xylem sap of infected plants. The Fol Six1 protein contributes to virulence and has an avirulence function by activating the I-3 immune receptor of tomato. The Focub tropical race 4 (TR4) genome harbors three SIX1 homologs: SIX1a, b and c. In this study, the role of Focub-SIX1a in pathogenicity was evaluated since this homolog is present in not only TR4 but also in other races. A deletion mutant of the SIX1a gene from Focub TR4 strain II5 was generated (FocubΔSIX1a) and tested in planta. Mutants were found to be severely compromised in their virulence. Ectopic integration of the Focub-SIX1a gene in the FocubΔSIX1a strain restored virulence to wild type levels. We conclude that Focub-SIX1a is required for full virulence of Focub TR4 towards Cavendish banana.

The impact of Genetically Modified (GM) crops in modern agriculture: A review

Genetic modification in plants was first recorded 10,000 years ago in Southwest Asia where humans first bred plants through artificial selection and selective breeding. Since then, advancements in agriculture science and technology have brought about the current GM crop revolution. GM crops are promising to mitigate current and future problems in commercial agriculture, with proven case studies in Indian cotton and Australian canola. However, controversial studies such as the Monarch Butterfly study (1999) and the Séralini affair (2012) along with current problems linked to insect resistance and potential health risks have jeopardised its standing with the public and policymakers, even leading to full and partial bans in certain countries. Nevertheless, the current growth rate of the GM seed market at 9.83-10% CAGR along with promising research avenues in biofortification, precise DNA integration and stress tolerance have forecast it to bring productivity and prosperity to commercial agriculture.

Genome-Wide Detection of Genes Under Positive Selection in Worldwide Populations of the Barley Scald Pathogen

Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abiotic factors could lead to locally adapted pathogen populations. However, the genetic basis of local adaptation is poorly understood. Rhynchosporium commune, the pathogen causing barley scald disease, interacts at least partially in a gene-for-gene manner with its host. We analyzed global field populations of 125 R. commune isolates to identify candidate genes for local adaptation. Whole genome sequencing data showed that the pathogen is subdivided into three genetic clusters associated with distinct geographic and climatic regions. Using haplotype-based selection scans applied independently to each genetic cluster, we found strong evidence for selective sweeps throughout the genome. Comparisons of loci under selection among clusters revealed little overlap, suggesting that ecological differences associated with each cluster led to variable selection regimes. The strongest signals of selection were found predominantly in the two clusters composed of isolates from Central Europe and Ethiopia. The strongest selective sweep regions encoded protein functions related to biotic and abiotic stress responses. Selective sweep regions were enriched in genes encoding functions in cellular localization, protein transport activity, and DNA damage responses. In contrast to the prevailing view that a small number of gene-for-gene interactions govern plant pathogen evolution, our analyses suggest that the evolutionary trajectory is largely determined by spatially heterogeneous biotic and abiotic selection pressures.

MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data

Unraveling the genetic diversity held in genebanks on a large scale is underway, due to advances in Next-generation sequence (NGS) based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm from the global genepool based on a combination of passport, genotypic and phenotypic data. To facilitate this, a new generation of information systems is being designed to efficiently handle data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS), the database for global ex situ-held banana genetic resources, has been developed to address those needs in a user-friendly way. In developing MGIS, we selected a generic database schema (Chado), the robust content management system Drupal for the user interface, and Tripal, a set of Drupal modules which links the Chado schema to Drupal. MGIS allows germplasm collection examination, accession browsing, advanced search functions, and germplasm orders. Additionally, we developed unique graphical interfaces to compare accessions and to explore them based on their taxonomic information. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer has been implemented to facilitate the link with complementary databases like the Banana Genome Hub and the MusaBase breeding database.

Database URL:https://www.crop-diversity.org/mgis/

New Geographical Insights of the Latest Expansion of Fusarium oxysporum f.sp. cubense Tropical Race 4 Into the Greater Mekong Subregion

Banana is the most popular and most exported fruit and also a major food crop for millions of people around the world. Despite its importance and the presence of serious disease threats, research into this crop is limited. One of those is Panama disease or Fusarium wilt. In the previous century Fusarium wilt wiped out the "Gros Michel" based banana industry in Central America. The epidemic was eventually quenched by planting "Cavendish" bananas. However, 50 years ago the disease recurred, but now on "Cavendish" bananas. Since then the disease has spread across South-East Asia, to the Middle-East and the Indian subcontinent and leaped into Africa. Here, we report the presence of Fusarium oxysporum f.sp. cubense Tropical Race 4 (Foc TR4) in "Cavendish" plantations in Laos, Myanmar, and Vietnam. A combination of classical morphology, DNA sequencing, and phenotyping assays revealed a very close relationship between the Foc TR4 strains in the entire Greater Mekong Subregion (GMS), which is increasingly prone to intensive banana production. Analyses of single-nucleotide polymorphisms enabled us to initiate a phylogeography of Foc TR4 across three geographical areas-GMS, Indian subcontinent, and the Middle East revealing three distinct Foc TR4 sub-lineages. Collectively, our data place these new incursions in a broader agroecological context and underscore the need for awareness campaigns and the implementation of validated quarantine measures to prevent further international dissemination of Foc TR4.

Lipid and protein fingerprinting for Fusarium oxysporum f. sp. cubense strain-level classification

Banana is one of the most popular fruits in the world but has been substantially impaired by Panama disease in the last years. Fusarium oxysporum f. sp. cubense (Foc) is the causal agent and colonizes banana cultivars from many subgroups with different aggressiveness levels, often leading to plant death while compromising new crops in infested areas. This study has evaluated the ability of MALDI-MS protein and lipid fingerprinting to provide intraspecies classification of Foc isolates and to screen biomolecules related to host-pathogen relationship. The MS data, when inspected via partial least square discriminant analysis (PLS-DA), distinguished the isolates by aggressiveness as well as by specific location and host. Although both lipids and proteins show discriminating tendencies, these differences were more clearly perceived via the protein profiles. Considering that Cavendish cultivar is the more resistant option to endure Foc presence in the field, the lipids and proteins related to this subgroup might have an important role in pathogen adaptation. This study reports a new application of MALDI-MS for the analysis of a banana pathogen with intraspecies classification ability. Graphical abstract MALDI-MS classified Foc isolates by aggressiveness level on banana revealing the additional influence of location and host cultivar on the expression of lipids and proteins.

A method of determining where to target surveillance efforts in heterogeneous epidemiological systems

The spread of pathogens into new environments poses a considerable threat to human, animal, and plant health, and by extension, human and animal wellbeing, ecosystem function, and agricultural productivity, worldwide. Early detection through effective surveillance is a key strategy to reduce the risk of their establishment. Whilst it is well established that statistical and economic considerations are of vital importance when planning surveillance efforts, it is also important to consider epidemiological characteristics of the pathogen in question-including heterogeneities within the epidemiological system itself. One of the most pronounced realisations of this heterogeneity is seen in the case of vector-borne pathogens, which spread between 'hosts' and 'vectors'-with each group possessing distinct epidemiological characteristics. As a result, an important question when planning surveillance for emerging vector-borne pathogens is where to place sampling resources in order to detect the pathogen as early as possible. We answer this question by developing a statistical function which describes the probability distributions of the prevalences of infection at first detection in both hosts and vectors. We also show how this method can be adapted in order to maximise the probability of early detection of an emerging pathogen within imposed sample size and/or cost constraints, and demonstrate its application using two simple models of vector-borne citrus pathogens. Under the assumption of a linear cost function, we find that sampling costs are generally minimised when either hosts or vectors, but not both, are sampled.

Emerging Fungal Threats to Plants and Animals Challenge Agriculture and Ecosystem Resilience

While fungi can make positive contributions to ecosystems and agro-ecosystems, for example, in mycorrhizal associations, they can also have devastating impacts as pathogens of plants and animals. In undisturbed ecosystems, most such negative interactions will be limited through the coevolution of fungi with their hosts. In this article, we explore what happens when pathogenic fungi spread beyond their natural ecological range and become invasive on naïve hosts in new ecosystems. We will see that such invasive pathogens have been problematic to humans and their domesticated plant and animal species throughout history, and we will discuss some of the most pressing fungal threats of today.

Two new species of the Fusarium fujikuroi species complex isolated from the natural environment

Two new species in the Fusarium fujikuroi species complex (FFSC) are introduced. One of these, represented by strain CBS 454.97 was isolated from plant debris (Striga hermonthica) in the Sudan, while the second, represented by strains CBS 119850 and CBS 483.94, which originated from soil in Australia. Molecular analyses were performed including TEF1 spanning 576 bp region, 860 bp region of rPB2, and 500 bp BT2 region. Phylogenetic trees based on these regions showed that the two species are clearly distinct from all known taxa in the F. fujikuroi species complex. Based on phenotypic, physiological characters and molecular data, we introduce Fusarium sudanense and Fusarium terricola as novel species in the complex.

Development of a hydrolysis probe-based real-time assay for the detection of tropical strains of Fusarium oxysporum f. sp. cubense race 4

Fusarium oxysporum f. sp. cubense (Foc) is one of the most important threats to global banana production. Strategies to control the pathogen are lacking, with plant resistance offering the only long-term solution, if sources of resistance are available. Prevention of introduction of Foc into disease-free areas thus remains a key strategy to continue sustainable banana production. In recent years, strains of Foc affecting Cavendish bananas have destroyed plantations in a number of countries in Asia and in the Middle East, and one African country. One vegetative compatibility group (VCG), 01213/16, is considered the major threat to bananas in tropical and subtropical climatic conditions. However, other genetically related VCGs, such as 0121, may potentially jeopardize banana cultures if they were introduced into disease-free areas. To prevent the introduction of these VCGs into disease-free Cavendish banana-growing countries, a real-time PCR test was developed to accurately detect both VCGs. A previously described putative virulence gene was used to develop a specific combination of hydrolysis probe/primers for the detection of tropical Foc race 4 strains. The real-time PCR parameters were optimized by following a statistical approach relying on orthogonal arrays and the Taguchi method in an attempt to enhance sensitivity and ensure high specificity of the assay. This study also assessed critical performance criteria, such as repeatability, reproducibility, robustness, and specificity, with a large including set of 136 F. oxysporum isolates, including 73 Foc pathogenic strains representing 24 VCGs. The validation data demonstrated that the new assay could be used for regulatory testing applications on banana plant material and can contribute to preventing the introduction and spread of Foc strains affecting Cavendish bananas in the tropics.

Ecology of Fungal Plant Pathogens

Fungal plant pathogens are ubiquitous and highly diverse. Key to their success is high host density, which notably is the case in agroecosystems. Several hypotheses related to the effects of plant pathogens on plant diversity (the Janzen-Connell hypothesis, the dilution effect hypothesis) and the phenomenon of higher biomass in plant mixtures (i.e., overyielding) can all be explained by the quantitative interplay between host and pathogen density. In many agroecosystems, fungal plant pathogens cause great losses, since in monocultures diseased plants cannot be replaced by healthy plants. On the other hand, in natural ecosystems fungal plant pathogens shape the succession of vegetation and enhance the biodiversity of forests and grasslands. When pathogens are introduced into areas outside their natural range, they may behave differently, causing severe damage. Once introduced, changes may occur such as hybridization with other closely related pathogens or host shifts, host jumps, or horizontal gene transfer. Such changes can be hazardous for both agricultural and natural ecosystems.

Rapid emergence of pathogens in agro-ecosystems: global threats to agricultural sustainability and food security

Agricultural ecosystems are composed of genetically depauperate populations of crop plants grown at a high density and over large spatial scales, with the regional composition of crop species changing little from year to year. These environments are highly conducive for the emergence and dissemination of pathogens. The uniform host populations facilitate the specialization of pathogens to particular crop cultivars and allow the build-up of large population sizes. Population genetic and genomic studies have shed light on the evolutionary mechanisms underlying speciation processes, adaptive evolution and long-distance dispersal of highly damaging pathogens in agro-ecosystems. These studies document the speed with which pathogens evolve to overcome crop resistance genes and pesticides. They also show that crop pathogens can be disseminated very quickly across and among continents through human activities. In this review, we discuss how the peculiar architecture of agro-ecosystems facilitates pathogen emergence, evolution and dispersal. We present four example pathosystems that illustrate both pathogen specialization and pathogen speciation, including different time frames for emergence and different mechanisms underlying the emergence process. Lastly, we argue for a re-design of agro-ecosystems that embraces the concept of dynamic diversity to improve their resilience to pathogens. This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

Global food and fibre security threatened by current inefficiencies in fungal identification

Fungal pathogens severely impact global food and fibre crop security. Fungal species that cause plant diseases have mostly been recognized based on their morphology. In general, morphological descriptions remain disconnected from crucially important knowledge such as mating types, host specificity, life cycle stages and population structures. The majority of current fungal species descriptions lack even the most basic genetic data that could address at least some of these issues. Such information is essential for accurate fungal identifications, to link critical metadata and to understand the real and potential impact of fungal pathogens on production and natural ecosystems. Because international trade in plant products and introduction of pathogens to new areas is likely to continue, the manner in which fungal pathogens are identified should urgently be reconsidered. The technologies that would provide appropriate information for biosecurity and quarantine already exist, yet the scientific community and the regulatory authorities are slow to embrace them. International agreements are urgently needed to enforce new guidelines for describing plant pathogenic fungi (including key DNA information), to ensure availability of relevant data and to modernize the phytosanitary systems that must deal with the risks relating to trade-associated plant pathogens.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

Recent advances on Candida albicans biology and virulence

Candida albicans is an important human fungal pathogen, in terms of both its clinical significance and its use as an experimental model for scientific investigation. Although this opportunistic pathogen is a natural component of the human flora, it can cause life-threatening infections in immunosuppressed patients. There are currently a limited number of antifungal molecules and drug targets, and increasing resistance to the front-line therapeutics, demonstrating a clear need for new antifungal drugs. Understanding the biology of this pathogen is an important prerequisite for identifying new drug targets for antifungal therapeutics. In this review, we highlight some recent developments that help us to understand how virulence traits are regulated at the molecular level, in addition to technical advances that improve the ability of genome editing in C. albicans.

Fungal and Oomycete Diseases of Tropical Tree Fruit Crops

The tropics produce a range of fruit from tree crops that cannot be grown in colder climates. Bananas, mangos, several nuts, spices, coffee, and cacao are widely traded and much sought after around the world. However, the sustainable production of these tropical tree fruit crops faces significant challenges. Among these, losses due to pests and diseases play a large part in reducing yields, quality, and profitability. Using bananas and cacao as key examples, we outline some of the reasons fungal and oomycete diseases cause such significant losses to tropical tree crops. Cultivation of monocultures derived from limited genetic diversity, environmental conditions conducive for disease development, high levels of disease incidence and severity, a lack of disease resistance in planting materials, shortages of labor, and inadequate infrastructure and investment pose significant challenges, especially for smallholder producers. The expansion of travel and trade has given rise to emerging infectious plant diseases that add further insecurity and pressure. We conclude that holistic actions are needed on multiple fronts to address the growing problem of disease in tropical fruit tree crops.

Effector profiles distinguish formae speciales of Fusarium oxysporum

Formae speciales (ff.spp.) of the fungus Fusarium oxysporum are often polyphyletic within the species complex, making it impossible to identify them on the basis of conserved genes. However, sequences that determine host-specific pathogenicity may be expected to be similar between strains within the same forma specialis. Whole genome sequencing was performed on strains from five different ff.spp. (cucumerinum, niveum, melonis, radicis-cucumerinum and lycopersici). In each genome, genes for putative effectors were identified based on small size, secretion signal, and vicinity to a "miniature impala" transposable element. The candidate effector genes of all genomes were collected and the presence/absence patterns in each individual genome were clustered. Members of the same forma specialis turned out to group together, with cucurbit-infecting strains forming a supercluster separate from other ff.spp. Moreover, strains from different clonal lineages within the same forma specialis harbour identical effector gene sequences, supporting horizontal transfer of genetic material. These data offer new insight into the genetic basis of host specificity in the F. oxysporum species complex and show that (putative) effectors can be used to predict host specificity in F. oxysporum.