Synergisms between microbial pathogens in plant disease complexes: a growing trend

Fungal Species Causing Canker and Wilt of Ficus carica and Evidence of Their Association by Bark Beetles in Italy

Field surveys conducted during 2021 and 2022 in Western Sicily, Italy, revealed the presence of common fig trees severely affected by trunk and crown root canker and bark cracking. Moreover, in conjunction with the symptomatic tissues, the same surveyed plants showed the presence of bark beetle holes and internal wood galleries. The predominant beetle Criphalus dilutus was previously reported attacking figs in Sicily. Phylogenetic analyses based on multilocus DNA data showed the presence of different fungal taxa associated with disease symptoms, including Botryosphaeria dothidea, Ceratocystis ficicola, Diaporthe foeniculina, Neocosmospora bostrycoides, N. perseae, and Neofusicoccum luteum. Pathogenicity tests conducted on potted fig plants showed that all the species were pathogenic to fig, with C. ficicola and Neocosmospora spp. as the most aggressive fungal species. Moreover, isolations conducted from the bodies of emerging adult insects recovered from disease samples confirmed the presence of C. ficicola and Neocosmospora spp., suggesting the potential involvement of C. dilutus in their dissemination.

Exploring the Phylogenetic Diversity of Botryosphaeriaceae and Diaporthe Species Causing Dieback and Shoot Blight of Blueberry in Serbia

Identifying the precise pathogens responsible for specific plant diseases is imperative for implementing targeted and efficient interventions and mitigating their spread. Dieback and shoot blight significantly diminish the lifespan and productivity of blueberries, yet the causative agents remain largely unidentified. To determine the identity and prevalence of the causal agents of branch dieback and shoot blight, we conducted multiyear and multisite sampling of diseased highbush blueberries (Vaccinium corymbosum cultivar Duke) in Serbia. Sixty-nine monosporic isolates were collected and characterized based on morphological, physiological features and multilocus phylogenetic analysis of internal transcribed spacer, β-tubulin, and translation elongation factor 1-α sequence data. Five species were identified as causal agents: Diaporthe eres (36 isolates), D. foeniculina (3 isolates), Neopestalotiopsis vaccinii (9 isolates), Neopestalotiopsis rosae (6 isolates), and Neofusicoccum parvum (15 isolates). The results of the pathogenicity tests performed with the 23 representative isolates confirmed the role of these species as primary pathogens in causing dieback and shoot blight of blueberry, with Neofusicoccum parvum being the most aggressive and D. eres the least. Our study underscores the diversity of genera and species of ascomycetes capable of causing blueberry dieback and shoot blight. Furthermore, our findings indicate that the agents responsible for the disease in Serbia differ from those identified in other regions worldwide.

Fungal Diseases in Yerba Mate: Status and Management Strategies

Yerba mate (Ilex paraguariensis St. Hil.), with its health benefits and socioeconomic significance, plays a crucial role in Argentina and other South American countries like Brazil and Paraguay. Its cultivation in the Province of Misiones (Argentina) supports various sectors, contributes to regional development, and provides employment opportunities. However, the transition from extractive practices to monoculture, accompanied with increased demand, has led to phytosanitary challenges. Imbalanced native microbiota, disease development, and pathogen dispersion have become prevalent issues. Understanding the known pathogens associated with yerba mate plants is crucial for developing effective agricultural strategies. The primary objective of this study is to synthesise current knowledge on prevalent fungal diseases in yerba mate cultivation, as well as to provide agricultural management recommendations for effective disease control. Fungal diseases can cause significant damage to different parts of the plant, resulting in economic losses. The proximity of neighbouring plantations to yerba mate crops may contribute to the cross-contamination of pathogens, emphasizing the need for comprehensive epidemiology and accurate diagnosis. Multiple fungal genera have been reported to cause pathologies in yerba mate. Among the fungi causing foliar diseases are Ceratobasidium niltonsouzanum, Cylindrocladium spathulatum, Pseudocercospora mate, Asterina sphaerelloides, Colletotrichum gloeosporioides aff var. yerbae, and Phyllosticta sp. Caulinary diseases are caused by Alternaria sp., Phoma sp., Colletotrichum sp., and Ceratocystis fimbriata. Regarding root rot, the genera Rhizoctonia sp., Pythium sp., Fusarium sp., and Rosellinia sp. have been reported. Proper crop management practices and monitoring are essential for effective disease control. To reduce reliance on chemical compounds, the use of biocontrol agents like Trichoderma sp. has shown promise in regulating phytopathogenic fungi populations. Continued research is vital to preserve the yerba mate industry and ensure its long-term viability while minimizing environmental impact.

New reports of pathogen spectrum associated with bulb rot and their interactions during the development of rot in tulip

Bulb rot, a highly damaging disease of tulip plants, has hindered their profitable cultivation worldwide. This rot occurs in both field and storage conditions posing significant challenges. While this disease has been attributed to a range of pathogens, previous investigations have solely examined it within the framework of a single-pathogen disease model. Our study took a different approach and identified four pathogens associated with the disease: Fusarium solani, Penicillium chrysogenum, Botrytis tulipae, and Aspergillus niger. The primary objective of our research was to examine the impact of co-infections on the overall virulence dynamics of these pathogens. Through co-inoculation experiments on potato dextrose agar, we delineated three primary interaction patterns: antibiosis, deadlock, and merging. In vitro trials involving individual pathogen inoculations on tulip bulbs revealed that B. tulipae,was the most virulent and induced complete bulb decay. Nonetheless, when these pathogens were simultaneously introduced in various combinations, outcomes ranged from partial bulb decay to elongated rotting periods. This indicated a notable degree of antagonistic behaviour among the pathogens. While synergistic interactions were evident in a few combinations, antagonism overwhelmingly prevailed. The complex interplay of these pathogens during co-infection led to a noticeable change in the overall severity of the disease. This underscores the significance of pathogen-pathogen interactions in the realm of plant pathology, opening new insights for understanding and managing tulip bulb rot.

Development of a Multiplex PCR Assay for the Detection of Tomato Wilt Caused by Coinfection of Fusarium brachygibbosum, Fusarium oxysporum, and Ralstonia solanacearum Based on Comparative Genomics

Tomato is consumed worldwide as fresh or processed food products. However, soilborne diseases of tomato plants caused by coinfection of various pathogens result in great economic losses to the tomato industry. It is difficult to accurately identify and diagnose soilborne diseases of tomato plants caused by pathogen complexes. In this study, we investigated field diseases of tomato plants by pathogen isolation and molecular identification and found that tomato wilt was caused by coinfection of Fusarium brachygibbosum, F. oxysporum, and Ralstonia solanacearum. Therefore, developing a method for simultaneous detection of DNA from F. brachygibbosum, F. oxysporum, and R. solanacearum is of great importance to efficiently and accurately monitor disease development at different growth stages of tomato plants. In this study, we performed a comparative genomic analysis of F. brachygibbosum, F. oxysporum, and R. solanacearum and determined the primer sets for simultaneous detection of DNA from these target pathogens. Then, we tested the reagent and condition parameters of multiplex PCR, including primers, dNTP and Mg2+ concentrations, and annealing temperatures, to determine the optimal parameters of a multiplex PCR system. We evaluated the specificity, sensitivity, and stability of the multiplex PCR system based on the optimized reaction conditions. The multiplex PCR system can specifically identify 13 target pathogens from 57 different fungal and bacterial pathogens, at the lower detection limit of the three target pathogens at concentrations of 100 pg/μl. In addition, we can accurately identify the three pathogens in tomato plants using the optimized multiplex PCR method. These results demonstrated that the multiplex PCR method developed in this study can simultaneously detect DNA from F. brachygibbosum, F. oxysporum, and R. solanacearum in a single PCR system to accurately identify and diagnose the pathogen causing tomato wilt.

Unveiling Dominant Fungal Pathogens Associated with Root Rot of Hybrid Bermudagrass Based on Culture Dependent and Independent Methods

Hybrid bermudagrass (Cynodon dactylon × C. transvaalensis) is widely used as turf in southern and transition zones of China. From June to September in 2022, an unknown disease was consistently observed on hybrid bermudagrass in different regions of Nanjing, China, that exhibited distinct symptoms of leaf necrosis, severe root rot, and circular or irregular necrotic patches with 20- to 300-cm diameters. In this study, culture-independent and -dependent methods were used to elucidate the dominant fungal pathogens associated with the disease. Basidiomycota and Marasmiellus were shown to be the dominant phyla (51.96 to 70.60%) and genera (50.09 to 69.84%) in the symptomatic samples. A total of 128 fungal strains were isolated from symptomatic root tissues, and 40 strains representing the largest proportion (31.25%) were identified as Marasmiellus mesosporus based on the morphological characteristics, phylogenetic analysis of the ITS and LSU rDNA region, and pathogenicity testing. Temperature sensitivity tests revealed that M. mesosporus grew well at high temperatures (growth rate of 13.74 mm/day at 36°C). To our knowledge, this is the first report of M. mesosporus causing root rot disease on hybrid bermudagrass during hot summer months. The study will have important implications for the management of the disease.

Phylogenomic analyses and comparative genomics of Pseudomonas syringae associated with almond (Prunus dulcis) in California

We sequenced and comprehensively analysed the genomic architecture of 98 fluorescent pseudomonads isolated from different symptomatic and asymptomatic tissues of almond and a few other Prunus spp. Phylogenomic analyses, genome mining, field pathogenicity tests, and in vitro ice nucleation and antibiotic sensitivity tests were integrated to improve knowledge of the biology and management of bacterial blast and bacterial canker of almond. We identified Pseudomonas syringae pv. syringae, P. cerasi, and P. viridiflava as almond canker pathogens. P. syringae pv. syringae caused both canker and foliar (blast) symptoms. In contrast, P. cerasi and P. viridiflava only caused cankers, and P. viridiflava appeared to be a weak pathogen of almond. Isolates belonging to P. syringae pv. syringae were the most frequently isolated among the pathogenic species/pathovars, composing 75% of all pathogenic isolates. P. cerasi and P. viridiflava isolates composed 8.3 and 16.7% of the pathogenic isolates, respectively. Laboratory leaf infiltration bioassays produced results distinct from experiments in the field with both P. cerasi and P. syringae pv. syringae, causing significant necrosis and browning of detached leaves, whereas P. viridiflava conferred moderate effects. Genome mining revealed the absence of key epiphytic fitness-related genes in P. cerasi and P. viridiflava genomic sequences, which could explain the contrasting field and laboratory bioassay results. P. syringae pv. syringae and P. cerasi isolates harboured the ice nucleation protein, which correlated with the ice nucleation phenotype. Results of sensitivity tests to copper and kasugamycin showed a strong linkage to putative resistance genes. Isolates harbouring the ctpV gene showed resistance to copper up to 600 μg/ml. In contrast, isolates without the ctpV gene could not grow on nutrient agar amended with 200 μg/ml copper, suggesting ctpV can be used to phenotype copper resistance. All isolates were sensitive to kasugamycin at the label-recommended rate of 100μg/ml.

Diversity of Strains in the Pseudomonas syringae Complex Causing Bacterial Stem Blight of Alfalfa (Medicago sativa) in the United States

Alfalfa growers in the Intermountain West of the United States have recently seen an increased incidence in bacterial stem blight (BSB), which can result in significant herbage yield losses from the first harvest. BSB has been attributed to Pseudomonas syringae pv. syringae and P. viridiflava; however, little is known about the genetic diversity and pathogenicity of these bacteria or their interaction with alfalfa plants. Here, we present a comprehensive phylogenetic and phenotypic analysis of P. syringae and P. viridiflava strains causing BSB on alfalfa. A multilocus sequence analysis found that they grouped exclusively with P. syringae PG2b and P. viridiflava PG7a. Alfalfa symptoms caused by both bacterial groups were indistinguishable, although there was a large range in mean disease scores for individual strains. Overall, PG2b strains incited significantly greater disease scores than those caused by PG7a strains. Inoculated plants showed browning in the xylem and collapse of epidermal and pith parenchyma cells. Inoculation with a mixture of PG2b and PG7a strains did not result in synergistic activity. The populations of PG2b and PG7a strains were genetically diverse within their clades and did not group by location or haplotype. The PG2b strains had genes for production of the phytotoxin coronatine, which is unusual in PG2b strains. The results indicate that both pathogens are well established on alfalfa across a wide geographic range and that a recent introduction or evolution of more aggressive strains as the basis for emergence of the disease is unlikely.

Metagenomic insight to apprehend the fungal communities associated with leaf blight of Welsh onion in Taiwan

Plants are associated with a large diversity of microbes, and these complex plant-associated microbial communities are critical for plant health. Welsh onion (Allium fistulosum L.) is one of the key and oldest vegetable crops cultivated in Taiwan. The leaf of the Welsh onion is one of the famous spices in Taiwanese cuisine, thus, it is crucial to control foliar diseases. In recent years, Welsh onion cultivation in Taiwan has been severely threatened by the occurrence of leaf blight disease, greatly affecting their yield and quality. However, the overall picture of microbiota associated with the Welsh onion plant is still not clear as most of the recent etiological investigations were heavily based on the isolation of microorganisms from diseased plants. Therefore, studying the diversity of fungal communities associated with the leaf blight symptoms of Welsh onion may provide information regarding key taxa possibly involved in the disease. Therefore, this investigation was mainly designed to understand the major fungal communities associated with leaf blight to identify key taxa potentially involved in the disease and further evaluate any shifts in both phyllosphere and rhizosphere mycobiome assembly due to foliar pathogen infection by amplicon sequencing targeting the Internal Transcribed Spacer (ITS) 1 region of the rRNA. The alpha and beta-diversity analyses were used to compare the fungal communities and significant fungal groups were recognized based on linear discriminant analyses. Based on the results of relative abundance data and co-occurrence networks in symptomatic plants we revealed that the leaf blight of Welsh onion in Sanxing, is a disease complex mainly involving Stemphylium and Colletotrichum taxa. In addition, genera such as Aspergillus, Athelia and Colletotrichum were abundantly found associated with the symptomatic rhizosphere. Alpha-diversity in some fields indicated a significant increase in species richness in the symptomatic phyllosphere compared to the asymptomatic phyllosphere. These results will broaden our knowledge of pathogens of Welsh onion associated with leaf blight symptoms and will assist in developing effective disease management strategies to control the progress of the disease.

Use of manganese oxide nanoparticle (MnO2 NPs) and Pseudomonas putida for the management of wilt disease complex of carrot

Wilt disease complex of carrot is caused by Ralstonia solancearum and Meloidogyne incognita and is responsible for considerable yield loss. Manganese oxide nanoparticle (MnO2 NPs) and Pseudomonas putida were used alone and in combination for the management of wilt disease complex. In vitro, MnO2 NPs 0.10 g.L-l caused 49.36% reduction in hatching and 14.23% mortality of second stage juveniles (J2) of M. incognita while paper disc dipped in MnO2 NPs suspension caused 0.51 mm inhibition zone around R. solanacearum in nutrient agar medium. Inoculation of P. putida to plants with pathogens caused a similar increase in plant growth, chlorophyll and carotenoid contents as caused by foliar spray with 0.10 g.L-1 MnO2 NPs. Use of P. putida with NPs foliar spray to plants with pathogens caused a greater increase in plant growth, chlorophyll and carotenoid contents than with P. putida or NPs foliar spray. Inoculation of M. incognita/R. solanacearum/M. incognita plus R. solanacearum/P. putida/MnO2 NPs and MnO2 NPs plus P. putida caused increase in proline contents. Root colonization by P. putida was reduced in plants with test pathogens. Foliar application of MnO2 NPs and P. putida reduce wilt disease indices. Galling and populations of M. incognita was also reduced in plants co-inoculated with R. solanacearum. The greatest reduction in nematode populations and galling was observed in plants with NPs spray together with P. putida. Principal component analysis demonstrated a clear influence of NPS and P. putida and their combination on various studied parameters in diseased plants.

Disentangling the effects of terroir, season, and vintage on the grapevine fungal pathobiome

The composition, diversity and dynamics of microbial communities associated with grapevines may be influenced by various environmental factors, including terroir, vintage, and season. Among these factors, terroir stands out as a unique possible determinant of the pathobiome, the community of plant-associated pathogens. This study employed high-throughput molecular techniques, including metabarcoding and network analysis, to investigate the compositional dynamics of grapevine fungal pathobiome across three microhabitats (soil, woody tissue, and bark) using the Furmint cultivar. Samples were collected during late winter and late summer in 2020 and 2021, across three distinct terroirs in Hungary's Tokaj wine region. Of the 123 plant pathogenic genera found, Diplodia, Phaeomoniella, and Fusarium displayed the highest richness in bark, wood, and soil, respectively. Both richness and abundance exhibited significant disparities across microhabitats, with plant pathogenic fungi known to cause grapevine trunk diseases (GTDs) demonstrating highest richness and abundance in wood and bark samples, and non-GTD pathogens prevailed soil. Abundance and richness, however, followed distinct patterns Terroir accounted for a substantial portion of the variance in fungal community composition, ranging from 14.46 to 24.67%. Season and vintage also contributed to the variation, explaining 1.84 to 2.98% and 3.67 to 6.39% of the variance, respectively. Notably, significant compositional differences in fungi between healthy and diseased grapevines were only identified in wood and bark samples. Cooccurrence networks analysis, using both unweighted and weighted metrics, revealed intricate relationships among pathogenic fungal genera. This involved mostly positive associations, potentially suggesting synergism, and a few negative relationships, potentially suggesting antagonistic interactions. In essence, the observed differences among terroirs may stem from environmental filtering due to varied edaphic and mesoclimatic conditions. Temporal weather and vine management practices could explain seasonal and vintage fungal dynamics. This study provides insights into the compositional dynamics of grapevine fungal pathobiome across different microhabitats, terroirs, seasons, and health statuses. The findings emphasize the importance of considering network-based approaches in studying microbial communities and have implications for developing improved viticultural plant health strategies.

Influence of Co-occurring Weakly Pathogenic Bacterial Species on Bacterial Spot Disease Dynamics on Tomato

Mixed infections caused by multiple pathogenic and weakly pathogenic strains inhabiting the same host plants are common in nature and may modify pathogen dynamics. However, traditional plant pathogen studies have mostly focused on the binary interaction between a single host and a single pathogen. In this study, we have looked beyond this binary interaction and evaluated the impact of coinfection on disease dynamics on tomato using the bacterial spot pathogen Xanthomonas perforans (Xp), the co-occurring weakly pathogenic strain of X. arboricola (Xa), and the co-occurring potential weak pathogenic strain of Pseudomonas capsici (Pc). Time-series coinfection experiments monitoring disease severity and within-host population dynamics revealed higher disease severity in coinfection by three species compared with infection by Xp alone. However, coinfection by dual species, Xp and Pc, or Xa resulted in lower disease severity compared with Xp alone. Thus, coinfection outcomes depend on interacting species. Weak pathogens could exploit Xp to colonize the host plant as indicated by their higher populations in coinfection. However, Xp population dynamics were dependent on the coinfecting partner. While resource competition might be a possible explanation for lower Xp population in dual coinfection, interaction of Pc with the host was found to influence Xp population. Interestingly, Xp population was higher in the presence of three-species interaction compared with Xp and Xa coinfection, suggesting potential modulation of cooperative interactions among Xp and Xa in three-species coinfection rather than competitive interactions. Humidity played a significant role in population dynamics of the three species. Overall, this study highlighted the importance of coinfection dynamics in studying plant disease outbreaks.

A deep learning model for predicting risks of crop pests and diseases from sequential environmental data

Crop pests reduce productivity, so managing them through early detection and prevention is essential. Data from various modalities are being used to predict crop diseases by applying machine learning methodology. In particular, because growth environment data is relatively easy to obtain, many attempts are made to predict pests and diseases using it. In this paper, we propose a model that predicts diseases through previous growth environment information of crops, including air temperature, relative humidity, dew point, and CO2 concentration, using deep learning techniques. Using large-scale public data on crops of strawberry, pepper, grape, tomato, and paprika, we showed the model can predict the risk score of crop pests and diseases. It showed high predictive performance with an average AUROC of 0.917, and based on the predicted results, it can help prevent pests or post-processing. This environmental data-based crop disease prediction model and learning framework are expected to be universally applicable to various facilities and crops for disease/pest prevention.

Location and timing govern tripartite interactions of fungal phytopathogens and host in the stem canker species complex

BACKGROUND

Leptosphaeria maculans "brassicae" (Lmb) and Leptosphaeria biglobosa "brassicae" (Lbb) make up a species complex involved in the stem canker (blackleg) disease of rapeseed (Brassica napus). They coinfect rapeseed together, from the early stage of infection on leaves to the final necrotic stage at the stem base, and both perform sexual crossings on plant residues. L. biglobosa is suggested to be a potential biocontrol agent against Lmb, but there has been no mechanistic investigation of the different types of interactions that may occur between the plant and the two fungal species.

RESULTS

We investigated the bi- or tripartite interaction mechanisms by (i) confronting Lmb and Lbb in culture conditions or during cotyledon infection, with different timing and/or spore concentration regimes, (ii) performing RNA-Seq experiments in vitro or on the kinetics of infection of cotyledons infected by Lmb and/or Lbb to evaluate the transcriptomic activity and the plant response when both fungal species are inoculated together. Lbb infection of B. napus cotyledons was typical of a necrotrophic behavior, with a very early setup of one pathogenicity program and very limited colonization of tissues. This contrasted with the complex succession of pathogenicity programs of the hemibiotroph Lmb. During simultaneous co-infection by both species, Lmb was strongly impacted in its growth and transcriptomic dynamics both in vitro and in planta, while Lbb was unaffected by the presence of Lmb. However, the drastic inhibition of Lmb growth by Lbb was ineffective in the case of delayed inoculation with Lbb or a lower amount of spores of Lbb compared to Lmb.

CONCLUSIONS

Our data suggest that Lmb growth inhibition by Lbb is the result of a combination of factors that may include competition for trophic resources, the generation by Lbb of an environment unsuitable for the lifecycle of Lmb or/and the effect on Lmb of plant defense responses induced by Lbb. It indicates that growth inhibition occurs in very specific conditions (i.e., co-inoculation at the same place of an equal amount of inoculum) that are unlikely to occur in the field where their coexistence does not prevent any species from completing their life cycle.

Xylella fastidiosa subsp. pauca, Neofusicoccum spp. and the Decline of Olive Trees in Salento (Apulia, Italy): Comparison of Symptoms, Possible Interactions, Certainties and Doubts

Xylella fastidiosa subsp. pauca (XFP), Neofusicoccum mediterraneum, N. stellenboschiana and other fungi have been found in olive groves of Salento (Apulia, Italy) that show symptoms of severe decline. XFP is well known to be the cause of olive quick decline syndrome (OQDS). It has also been assessed that Neofusicoccum spp. causes a distinct disease syndrome, namely, branch and twig dieback (BTD). All these phytopathogens incite severe symptoms that can compromise the viability of large canopy sectors or the whole tree. However, their specific symptoms are not easily distinguished, especially during the final stages of the disease when branches are definitively desiccated. By contrast, they can be differentiated during the initial phases of the infection when some facets of the diseases are typical, especially wood discoloration, incited solely by fungi. Here, we describe the typical symptomatological features of OQDS and BTD that can be observed in the field and that have been confirmed by Koch postulate experiments. Similar symptoms, caused by some abiotic adverse conditions and even by additional biotic factors, are also described. Thus, this review aims at: (i) raising the awareness that declining olive trees in Salento do not have to be linked a priori to XFP; (ii) defining the guidelines for a correct symptomatic diagnosis to orient proper laboratory analyses, which is crucial for the application of effective control measures. The possibility that bacterium and fungi could act as a polyspecies and in conjunction with predisposing abiotic stresses is also widely discussed.

Climate change impacts on plant pathogens, food security and paths forward

Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems.

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Fusarium-produced vitamin B6 promotes the evasion of soybean resistance by Phytophthora sojae

Plants can be infected by multiple pathogens concurrently in natural systems. However, pathogen-pathogen interactions have rarely been studied. In addition to the oomycete Phytophthora sojae, fungi such as Fusarium spp. also cause soybean root rot. In a 3-year field investigation, we discovered that P. sojae and Fusarium spp. frequently coexisted in diseased soybean roots. Out of 336 P. sojae-soybean-Fusarium combinations, more than 80% aggravated disease. Different Fusarium species all enhanced P. sojae infection when co-inoculated on soybean. Treatment with Fusarium secreted non-proteinaceous metabolites had an effect equal to the direct pathogen co-inoculation. By screening a Fusarium graminearum mutant library, we identified Fusarium promoting factor of Phytophthora sojae infection 1 (Fpp1), encoding a zinc alcohol dehydrogenase. Fpp1 is functionally conserved in Fusarium and contributes to metabolite-mediated infection promotion, in which vitamin B6 (VB6) produced by Fusarium is key. Transcriptional and functional analyses revealed that Fpp1 regulates two VB6 metabolism genes, and VB6 suppresses expression of soybean disease resistance-related genes. These results reveal that co-infection with Fusarium promotes loss of P. sojae resistance in soybean, information that will inform the sustainable use of disease-resistant crop varieties and provide new strategies to control soybean root rot.

What Can Be Learned by a Synoptic Review of Plant Disease Epidemics and Outbreaks Published in 2021?

A synoptic review of plant disease epidemics and outbreaks was made using two complementary approaches. The first approach involved reviewing scientific literature published in 2021, in which quantitative data related to new plant disease epidemics or outbreaks were obtained via surveys or similar methodologies. The second approach involved retrieving new records added in 2021 to the CABI Distribution Database, which contains over a million global geographic records of organisms from over 50,000 species. The literature review retrieved 186 articles, describing studies in 62 categories (pathogen species/species complexes) across more than 40 host species on six continents. Pathogen species with more than five articles were Bursaphelenchus xylophilus, 'Candidatus Liberibacter asiaticus', cassava mosaic viruses, citrus tristeza virus, Erwinia amylovora, Fusarium spp. complexes, F. oxysporum f. sp. cubense, Magnaporthe oryzae, maize lethal necrosis co-infecting viruses, Meloidogyne spp. complexes, Pseudomonas syringae pvs., Puccinia striiformis f. sp. tritici, Xylella fastidiosa, and Zymoseptoria tritici. Automated searches of the CABI Distribution Database identified 617 distribution records new in 2021 of 283 plant pathogens. A further manual review of these records confirmed 15 pathogens reported in new locations: apple hammerhead viroid, apple rubbery wood viruses, Aphelenchoides besseyi, Biscogniauxia mediterranea, 'Ca. Liberibacter asiaticus', citrus tristeza virus, Colletotrichum siamense, cucurbit chlorotic yellows virus, Erwinia rhapontici, Erysiphe corylacearum, F. oxysporum f. sp. cubense Tropical race 4, Globodera rostochiensis, Nothophoma quercina, potato spindle tuber viroid, and tomato brown rugose fruit virus. Of these, four pathogens had at least 25% of all records reported in 2021. We assessed two of these pathogens-tomato brown rugose fruit virus and cucurbit chlorotic yellows virus-to be actively emerging in/spreading to new locations. Although three important pathogens-'Ca. Liberibacter asiaticus', citrus tristeza virus, and F. oxysporum f. sp. cubense-were represented in the results of both our literature review and our interrogation of the CABI Distribution Database, in general, our dual approaches revealed distinct sets of plant disease outbreaks and new records, with little overlap. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Tobamovirus infection aggravates gray mold disease caused by Botrytis cinerea by manipulating the salicylic acid pathway in tomato

Botrytis cinerea is the causative agent of gray mold disease, and infects more than 1400 plant species, including important crop plants. In tomato, B. cinerea causes severe damage in greenhouses and post-harvest storage and transport. Plant viruses of the Tobamovirus genus cause significant damage to various crop species. In recent years, the tobamovirus tomato brown rugose fruit virus (ToBRFV) has significantly affected the global tomato industry. Most studies of plant-microbe interactions focus on the interaction between the plant host and a single pathogen, however, in agricultural or natural environments, plants are routinely exposed to multiple pathogens. Here, we examined how preceding tobamovirus infection affects the response of tomato to subsequent infection by B. cinerea. We found that infection with the tobamoviruses tomato mosaic virus (ToMV) or ToBRFV resulted in increased susceptibility to B. cinerea. Analysis of the immune response of tobamovirus-infected plants revealed hyper-accumulation of endogenous salicylic acid (SA), upregulation of SA-responsive transcripts, and activation of SA-mediated immunity. Deficiency in SA biosynthesis decreased tobamovirus-mediated susceptibility to B. cinerea, while exogenous application of SA enhanced B. cinerea symptoms. These results suggest that tobamovirus-mediated accumulation of SA increases the plants' susceptibility to B. cinerea, and provide evidence for a new risk caused by tobamovirus infection in agriculture.

Rapid defense mechanism suppression during viral- oomycete disease complex formation

Combined infection of the host plant with pathogens involving different parasitic lifestyles may result in synergistic effects that intensify disease symptoms. Understanding the molecular dynamics during concurrent infection provides essential insight into the host response. The transcriptomic pattern of cucumber plants infected with a necrotrophic pathogen, Pythium spinosum, and a biotrophic pathogen, Cucumber green mottle mosaic virus (CGMMV) was studied at different time points, under regimes of single and co-infection. Analysis of CGMMV infection alone revealed a mild influence on host gene expression at the stem base, while the infection by P. spinosum is associated with drastic changes in gene expression. Comparing P. spinosum as a single infecting pathogen with a later co-infection by CGMMV revealed a rapid host response as early as 24 hours post-CGMMV inoculation with a sharp downregulation of genes related to the host defense mechanism against the necrotrophic pathogen. Suppression of the defense mechanism of co-infected plants was followed by severe stress, including 30% plants mortality and an increase of the P. spinosum hyphae. The first evidence of defense recovery against the necrotrophic pathogen only occurred 13 days post-viral infection. These results support the hypothesis that the viral infection of the Pythium pre-infected plants subverted the host defense system and changed the equilibrium obtained with P. spinosum. It also implies a time window in which the plants are most susceptible to P. spinosum after CGMMV infection.

Impact of Enniatin and Deoxynivalenol Co-Occurrence on Plant, Microbial, Insect, Animal and Human Systems: Current Knowledge and Future Perspectives

Fusarium mycotoxins commonly contaminate agricultural products resulting in a serious threat to both animal and human health. The co-occurrence of different mycotoxins in the same cereal field is very common, so the risks as well as the functional and ecological effects of mycotoxins cannot always be predicted by focusing only on the effect of the single contaminants. Enniatins (ENNs) are among the most frequently detected emerging mycotoxins, while deoxynivalenol (DON) is probably the most common contaminant of cereal grains worldwide. The purpose of this review is to provide an overview of the simultaneous exposure to these mycotoxins, with emphasis on the combined effects in multiple organisms. Our literature analysis shows that just a few studies on ENN-DON toxicity are available, suggesting the complexity of mycotoxin interactions, which include synergistic, antagonistic, and additive effects. Both ENNs and DON modulate drug efflux transporters, therefore this specific ability deserves to be explored to better understand their complex biological role. Additionally, future studies should investigate the interaction mechanisms of mycotoxin co-occurrence on different model organisms, using concentrations closer to real exposures.

Deciphering plant health status: The link between secondary metabolites, fungal community and disease incidence in olive tree

Plant-associated microorganisms are increasingly recognized to play key roles in host health. Among several strategies, associated microorganisms can promote the production of specific metabolites by their hosts. However, there is still a huge gap in the understanding of such mechanisms in plant-microorganism interaction. Here, we want to determine whether different levels of olive leaf spot (OLS) disease incidence were related to differences in the composition of fungal and secondary metabolites (i.e. phenolic and volatile compounds) in leaves from olive tree cultivars with contrasting OLS susceptibilities (ranging from tolerant to highly susceptible). Accordingly, leaves with three levels of OLS incidence from both cultivars were used to assess epiphytic and endophytic fungal communities, by barcoding of cultivable isolates, as well as to evaluate leaf phenolic and volatile composition. Fungal and metabolite compositions variations were detected according to the level of disease incidence. Changes were particularly noticed for OLS-tolerant cultivars, opposing to OLS-susceptible cultivars, suggesting that disease development is linked, not only to leaf fungal and metabolite composition, but also to host genotype. A set of metabolites/fungi that can act as predictive biomarkers of plant tolerance/susceptibility to OLS disease were identified. The metabolites α-farnesene and p-cymene, and the fungi Fusarium sp. and Alternaria sp. were more related to disease incidence, while Pyronema domesticum was related to the absence of disease symptoms. Cultivar susceptibility to OLS disease is then suggested to be driven by fungi, volatile and phenolic host leaves composition, and above all to plant-fungus interaction. A deeper understanding of these complex interactions may unravel plant defensive responses.

Cooperative virulence via the collective action of secreted pathogen effectors

Although virulence is typically attributed to single pathogenic strains, here we investigated whether effectors secreted by a population of non-virulent strains could function as public goods to enable the emergence of collective virulence. We disaggregated the 36 type III effectors of the phytopathogenic bacterium Pseudomonas syringae strain PtoDC3000 into a 'metaclone' of 36 coisogenic strains, each carrying a single effector in an effectorless background. Each coisogenic strain was individually unfit, but the metaclone was collectively as virulent as the wild-type strain on Arabidopsis thaliana, suggesting that effectors can drive the emergence of cooperation-based virulence through their public action. We show that independently evolved effector suits can equally drive this cooperative behaviour by transferring the effector alleles native to the strain PmaES4326 into the conspecific but divergent strain PtoDC3000. Finally, we transferred the disaggregated PtoDC3000 effector arsenal into Pseudomonas fluorescens and show that their cooperative action was sufficient to convert this rhizosphere-inhabiting beneficial bacterium into a phyllosphere pathogen. These results emphasize the importance of microbial community interactions and expand the ecological scale at which disease may be attributed.

Surveillance of Landraces' Seed Health in South Italy and New Evidence on Crop Diseases

During the last three years, more than 300 landraces belonging to different plant species have been the main focus of an Italian valorization research project (AgroBiodiversità Campana, ABC) aiming at analyzing, recovering, preserving, and collecting local biodiversity. In this context, phytosanitary investigation plays a key role in identifying potential threats to the preservation of healthy seeds in gene banks and the successful cultivation of landraces. The surveillance carried out in this study, in addition to highlighting the expected presence of common species-specific pathogens such as Ascochyta pisi in peas, Ascochyta fabae in broad beans, and Macrophomina phaseolina, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans in beans, pointed to the presence of novel microorganisms never detected before in the seeds of some hosts (Apiospora arundinis in common beans or Sclerotinia sclerotiorum and Stemphylium vesicarium in broad beans). These novel seedborne pathogens were fully characterized by (i) studying their morphology, (ii) identifying them by molecular methods, and (iii) studying their impact on adult crop plants. For the first time, this study provides key information about three novel seedborne pathogens that can be used to correctly diagnose their presence in seed lots, helping prevent the outbreaks of new diseases in the field.

Cryptochromes and UBP12/13 deubiquitinases antagonistically regulate DNA damage response in Arabidopsis

Cryptochromes (CRYs) are evolutionarily conserved blue-light receptors that evolved from bacterial photolyases that repair damaged DNA. Today, CRYs have lost their ability to repair damaged DNA; however, prior reports suggest that human CRYs can respond to DNA damage. Currently, the role of CRYs in the DNA damage response (DDR) is lacking, especially in plants. Therefore, we evaluated the role of plant CRYs in DDR along with UBP12/13 deubiquitinases, which interact with and regulate the CRY2 protein. We found that cry1cry2 was hypersensitive, while ubp12ubp13 was hyposensitive to UVC-induced DNA damage. Elevated UV-induced cyclobutane pyrimidine dimers (CPDs) and the lack of DNA repair protein RAD51 accumulation in cry1cry2 plants indicate that CRYs are required for DNA repair. On the contrary, CPD levels diminished and RAD51 protein levels elevated in plants lacking UBP12 and UBP13, indicating their role in DDR repression. Temporal transcriptomic analysis revealed that DDR-induced transcriptional responses were subdued in cry1cry2, but elevated in ubp12ubp13 compared to WT. Through transcriptional modeling of the time-course transcriptome, we found that genes quickly induced by UVC (15 min) are targets of CAMTA 1-3 transcription factors, which we found are required for DDR. This transcriptional regulation seems, however, diminished in the cry1cry2 mutant, indicating that CAMTAs are required for CRY2-mediated DDR. Furthermore, we observed enhanced CRY2-UBP13 interaction and formation of CRY2 nuclear speckles under UVC, suggesting that UVC activates CRY2 similarly to blue light. Together, our data reveal the temporal dynamics of the transcriptional events underlying UVC-induced genotoxicity and expand our knowledge of the role of CRY and UBP12/13 in DDR.

A biotroph sets the stage for a necrotroph to play: 'Candidatus Phytoplasma solani' infection of sugar beet facilitated Macrophomina phaseolina root rot

'Candidatus Phytoplasma solani' (stolbur phytoplasma) is associated with rubbery taproot disease (RTD) of sugar beet (Beta vulgaris L.), while Macrophomina phaseolina is considered the most important root rot pathogen of this plant in Serbia. The high prevalence of M. phaseolina root rot reported on sugar beet in Serbia, unmatched elsewhere in the world, coupled with the notorious tendency of RTD-affected sugar beet to rot, has prompted research into the relationship between the two diseases. This study investigates the correlation between the occurrence of sugar beet RTD and the presence of root rot fungal pathogens in a semi-field 'Ca. P. solani' transmission experiment with the cixiid vector Reptalus quinquecostatus (Dufour), in addition to naturally infected sugar beet in the open field. Our results showed that: (i) Reptalus quinquecostatus transmitted 'Ca. P. solani' to sugar beet which induced typical RTD root symptoms; (ii) Macrophomina phaseolina root rot was exclusively present in 'Ca. P. solani'-infected sugar beet in both the semi-field experiment and naturally infected sugar beet; and that (iii) even under environmental conditions favorable to the pathogen, M. phaseolina did not infect sugar beet, unless the plants had been previously infected with phytoplasma.

Soil chemistry and fungal communities are associated with dieback in an Endangered Australian shrub

BACKGROUND AND AIMS

Field surveys across known populations of the Endangered Persoonia hirsuta (Proteaceae) in 2019 suggested the soil environment may be associated with dieback in this species. To explore how characteristics of the soil environment (e.g., pathogens, nutrients, soil microbes) relate to dieback, a soil bioassay (Experiment 1) was conducted using field soils from two dieback effected P. hirsuta populations. Additionally, a nitrogen addition experiment (Experiment 2) was conducted to explore how the addition of soil nitrogen impacts dieback.

METHODS

The field soils were baited for pathogens, and soil physiochemical and microbial community characteristics were assessed and related to dieback among plants in the field and nursery-grown plants inoculated with the same field soils. Roots from inoculated plants were harvested to confirm the presence of soil pathogens and root-associated endophytes. Using these isolates, a dual culture antagonism assay was performed to examine competition among these microbes and identify candidate pathogens or pathogen antagonists.

RESULTS

Dieback among plants in the field and Experiment 1 was associated with soil physiochemical properties (nitrogen and potassium), and soil microbes were identified as significant indicators of healthy and dieback-affected plants. Plants in Experiment 2 exhibited greater dieback when treated with elevated nitrogen. Additionally, post-harvest culturing identified fungi and other soil pathogens, some of which exhibited antagonistic behavior.

CONCLUSION

This study identified candidate fungi and soil physiochemical properties associated with observed dieback and dieback resistance in an Endangered shrub and provides groundwork for further exploring what drives dieback and how it can be managed to promote the conservation of wild populations.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11104-022-05724-7.

A Novel Seimatosporium and Other Sporocadaceae Species Associated with Grapevine Trunk Diseases in Cyprus

Besides well-known grapevine trunk disease (GTD)-related pathogens, there is an increased interest in wood-colonizing fungi that infect grapevines. During 2017-2018, a survey was conducted in Cyprus and wood samples were collected from vines exhibiting typical GTD symptoms. Based on morphological and multilocus phylogenetic analyses (ITS, LSU, bt2, tef1-a), four species in the Sporocadaceae family were described and typified; two in the genus of Seimatosporium: Seim. cyprium sp. nov. and Seim. vitis-viniferae and two in Sporocadus: Spo. kurdistanicus and Spo. rosigena. The teleomorph of Seim. cyprium sp. nov. was also described. Pathogenicity trials with representative isolates of each species were performed on woody stems of two-year-old potted grapevines for 12 months under field conditions. All isolates were pathogenic, causing dark brown to black vascular discoloration, extending upward and downward from the inoculation point. Sporocadus isolates were significantly more aggressive than Seimatosporium with lesion lengths ranging from 9.24 to 6.90 and 4.13 to 4.00 cm, respectively. Successful re-isolations were also evident for all species and isolates. Seim. cyprium sp. nov. is a newly described species, while Spo. kurdistanicus and Spo. rosigena are reported for the first time in Europe on Vitis vinifera, suggesting the potential role of Sporocadaceae in the GTDs complex.

Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources

Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.

Identity and Pathogenicity of Fungi Associated with Root, Crown, and Vascular Symptoms Related to Winter Squash Yield Decline

Winter squash (Cucurbita maxima cultivar Golden Delicious) produced in Oregon's Willamette Valley for edible seed production has experienced significant yield losses because of a soilborne disease. The symptoms associated with this disease problem include root rot, crown rot, and vascular discoloration in the stems, leading to a severe late season wilt and plant collapse. Through field surveys, Fusarium oxysporum, F. solani, F. culmorum-like fungi, Plectosphaerella cucumerina, and Setophoma terrestris were identified to be associated with diseased tissues, and each produced symptoms of root rot, crown rot, or stem discoloration in preliminary pathogenicity trials. In this study, 219 isolates of these species were characterized by molecular identity analyses using BLAST of the internal transcribed spacer and translation elongation factor 1 alpha genomic regions and by pathogenicity testing in outdoor, large-container trials. Molecular identity analyses confirmed the identity of isolates at 99 to 100% similarity to reference isolates in the database. In pathogenicity experiments, F. solani produced the most severe symptoms, followed by F. culmorum-like fungi, F. oxysporum, P. cucumerina, and S. terrestris. Some treatments of mixed-species inoculum produced symptom severity greater than what was expected from individual species. In particular, the mixture of F. culmorum-like fungi, F. oxysporum, and P. cucumerina and the mixture of F. culmorum-like fungi, F. solani, and S. terrestris had symptom ratings as high as that of F. solani by itself. Results indicate that this soilborne disease is caused primarily by Fusarium solani, but interactions between the complex of F. solani, F. culmorum-like fungi, F. oxysporum, and P. cucumerina can exacerbate disease severity.

How bacteria overcome flagellin pattern recognition in plants

Efficient plant immune responses depend on the ability to recognise an invading microbe. The 22-amino acids in the N-terminal domain and the 28-amino acids in the central region of the bacterial flagellin, called flg22 and flgII-28, respectively, are important elicitors of plant immunity. Plant immunity is activated after flg22 or flgII-28 recognition by the plant transmembrane receptors FLS2 or FLS3, respectively. There is strong selective pressure on many plant pathogenic and endophytic bacteria to overcome flagellin-triggered immunity. Here we provide an overview of recent developments in our understanding of the evasion and suppression of flagellin pattern recognition by plant-associated bacteria.

Metagenomic Assessment Unravels Fungal Microbiota Associated to Grapevine Trunk Diseases

Grapevine trunk diseases (GTDs) are among the most important problems that affect the longevity and productivity of vineyards in all the major growing regions of the world. They are slow-progression diseases caused by several wood-inhabiting fungi with similar life cycles and epidemiology. The simultaneous presence of multiple trunk pathogens in a single plant together with the inconsistent GTDs symptoms expression, their isolation in asymptomatic plants, and the absence of effective treatments make these diseases extremely complex to identify and eradicate. Aiming to gain a better knowledge of GTDs and search sustainable alternatives to limit their development, the present work studied the fungal community structure associated with GTDs symptomatic and asymptomatic grapevines, following a metagenomic approach. Two important cultivars from the Alentejo region with different levels of susceptibility to GTDs were selected, namely, ‘Alicante Bouschet’ and ‘Trincadeira’. Deep sequencing of fungal-directed ITS1 amplicon led to the detection of 258 taxa, including 10 fungi previously described as responsible for GTDs. Symptomatic plants exhibited a lower abundance of GTDs-associated fungi, although with significantly higher diversity of those pathogens. Our results demonstrated that trunk diseases symptoms are intensified by a set of multiple GTDs-associated fungi on the same plant. The composition of fungal endophytic communities was significantly different according to the symptomatology and it was not affected by the cultivar. This study opens new perspectives in the study of GTDs-associated fungi and their relation to the symptomatology in grapevines.

Epichloë Endophyte-Promoted Seed Pathogen Increases Host Grass Resistance Against Insect Herbivory

Plants host taxonomically and functionally complex communities of microbes. However, ecological studies on plant-microbe interactions rarely address the role of multiple co-occurring plant-associated microbes. Here, we contend that plant-associated microbes interact with each other and can have joint consequences for higher trophic levels. In this study we recorded the occurrence of the plant seed pathogenic fungus Claviceps purpurea and aphids (Sitobion sp.) on an established field experiment with red fescue (Festuca rubra) plants symbiotic to a seed transmitted endophytic fungus Epichloë festucae (E+) or non-symbiotic (E-). Both fungi are known to produce animal-toxic alkaloids. The study was conducted in a semi-natural setting, where E+ and E- plants from different origins (Spain and Northern Finland) were planted in a randomized design in a fenced common garden at Kevo Subarctic Research Station in Northern Finland. The results reveal that 45% of E+ plants were infected with Claviceps compared to 31% of E- plants. Uninfected plants had 4.5 times more aphids than Claviceps infected plants. By contrast, aphid infestation was unaffected by Epichloë symbiosis. Claviceps alkaloid concentrations correlated with a decrease in aphid numbers, which indicates their insect deterring features. These results show that plant mutualistic fungi can increase the infection probability of a pathogenic fungus, which then becomes beneficial to the plant by controlling herbivorous insects. Our study highlights the complexity and context dependency of species-species and multi-trophic interactions, thus challenging the labeling of species as plant mutualists or pathogens.

Pseudomonas viridiflava: An internal outsider of the Pseudomonas syringae species complex

Pseudomonas viridiflava is a gram-negative pseudomonad that is phylogenetically placed within the Pseudomonas syringae species complex. P. viridiflava has a wide host range and causes a variety of symptoms in different plant parts, including stems, leaves, and blossoms. Outside of its role as a pathogen, P. viridiflava also exists as an endophyte, epiphyte, and saprophyte. Increased reports of P. viridiflava causing disease on new hosts in recent years coincide with increased research on its genetic variability, virulence, phylogenetics, and phenotypes. There is high variation in its core genome, virulence factors, and phenotypic characteristics. The main virulence factors of this pathogen include the enzyme pectate lyase and virulence genes encoded within one or two pathogenicity islands. The delineation of P. viridiflava in the P. syringae complex has been investigated using several molecular approaches. P. viridiflava comprises its own species, within the complex. While seemingly an outsider to the complex as a whole due to differences in the core genome and virulence genes, low average nucleotide identity to other of P. syringae complex members, and some phenotypic traits, it remains as part of the complex. Defining phylogenetic, phenotypic, and genomic characteristics of P. viridiflava in comparison to other P. syringae members is important to understanding this pathogen and for the development of disease resistance and management practices.

TAXONOMY

Kingdom Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Family Pseudomonadaceae; Genus Pseudomonas; Species Pseudomonas syringae species complex, Genomospecies 6, Phylogroup 7 and 8.

MICROBIOLOGICAL PROPERTIES

Gram-negative, fluorescent, aerobic, motile, rod-shaped, oxidase negative, arginine dihydrolase negative, levan production negative (or positive), potato rot positive (or negative), tobacco hypersensitivity positive.

GENOME

There are two complete genomes, five chromosome-level genomes, and 1,540 genomes composed of multiple scaffolds of P. viridiflava available in the National Center for Biotechnology Information Genome database. The median total length of these assemblies is 5,975,050 bp, the median number of protein coding genes is 5,208, and the median G + C content is 59.3%.

DISEASE SYMPTOMS

P. viridiflava causes a variety of disease symptoms, including spots, streaks, necrosis, rots, and more in above- and below-ground plant parts on at least 50 hosts.

EPIDEMIOLOGY

There have been several significant disease outbreaks on field and horticultural crops caused by P. viridiflava since the turn of the century. P. viridiflava has been reported as a pathogen, epiphyte, endophyte, and saprophyte. This species has been isolated from a variety of environmental sources, including asymptomatic wild plants, snow, epilithic biofilms, and icepacks.

Isolation, Characterization, and Genomic Investigation of a Phytopathogenic Strain of Stenotrophomonas maltophilia

Stenotrophomonas maltophilia is ubiquitous in diverse environmental habitats. It merits significant concern because of its increasing incidence of nosocomial and community-acquired infection in immunocompromised patients and multiple drug resistance. It is rarely reported as a phytopathogen except in causing white stripe disease of rice in India and postharvest fruit rot of Lanzhou lily. For this study, Dickeya zeae and S. maltophilia strains were simultaneously isolated from soft rot leaves of Clivia miniata in Guangzhou, China, and were both demonstrated to be pathogenic to the host. Compared with the D. zeae strains, S. maltophilia strains propagated faster for greater growth in lysogeny broth medium and produced no cellulases or polygalacturonases, but did produce more proteases and fewer extracellular polysaccharides. Furthermore, S. maltophilia strains swam and swarmed dramatically less on semisolid media, but formed a great many more biofilms. Both D. zeae and S. maltophilia strains isolated from clivia caused rot symptoms on other monocot hosts, but not on dicots. Similar to previously reported S. maltophilia strains isolated from other sources, the strain JZL8 survived under many antibiotic stresses. The complete genome sequence of S. maltophilia strain JZL8 consists of a chromosome of 4,635,432 bp without a plasmid. Pan-genome analysis of JZL8 and 180 other S. maltophilia strains identified 50 genes that are unique to JZL8, seven of which implicate JZL8 as the potential pathogen contributor in plants. JZL8 also contains three copies of Type I Secretion System machinery; this is likely responsible for its greater production of proteases. Findings from this study extend our knowledge on the host range of S. maltophilia and provide insight into the phenotypic and genetic features underlying the plant pathogenicity of JZL8.

The Mycorrizal Status in Vineyards Affected by Esca

In this work we analyzed the relationship among native arbuscular mycorrhizal fungi (AMF) and vine roots affected by esca, a serious grapevine trunk disease. The AMF symbiosis was analyzed on the roots of neighboring plants (symptomatic and asymptomatic to esca) in 14 sites of three vineyards in Marche region (central–eastern Italy). The AMF colonization intensity, identified by non-vital staining, showed higher value in all esca symptomatic plants (ranging from 24.6% to 61.3%) than neighboring asymptomatic plants (from 17.4% to 57.6%). The same trend of Glomeromycota phylum abundance was detected by analyzing fungal operational taxonomic units (OTUs) linked to the AMF community, obtained by amplicon high throughput analysis of ITS 1 region. Overall, the highest amount of OTUs was detected on roots from symptomatic plants (0.42%), compared to asymptomatic roots (0.29%). Specific primer pairs for native Rhizophagus irregularis and Funneliformis mosseae AMF species, were designed in 28S rRNA and large subunit (LSU) ribosomal RNA, respectively, and droplet digital PCR protocol for absolute quantification was set up. A higher number of DNA copies of both fungal species were detected more frequently in symptomatic than asymptomatic vines. Our study suggests a relationship between esca and native AMF in grapevine. These results underline the importance of native rhizosphere microbial communities for a better knowledge of grapevine esca disease.

Untangling the Pea Root Rot Complex Reveals Microbial Markers for Plant Health

Plant health is recognised as a key element to ensure global food security. While plant breeding has substantially improved crop resistance against individual pathogens, it showed limited success for diseases caused by the interaction of multiple pathogens such as root rot in pea (Pisum sativum L.). To untangle the causal agents of the pea root rot complex and determine the role of the plant genotype in shaping its own detrimental or beneficial microbiome, fungal and oomycete root rot pathogens, as well as previously identified beneficials, i.e., arbuscular mycorrhizal fungi (AMF) and Clonostachys rosea, were qPCR quantified in diseased roots of eight differently resistant pea genotypes grown in four agricultural soils under controlled conditions. We found that soil and pea genotype significantly determined the microbial compositions in diseased pea roots. Despite significant genotype x soil interactions and distinct soil-dependent pathogen complexes, our data revealed key microbial taxa that were associated with plant fitness. Our study indicates the potential of fungal and oomycete markers for plant health and serves as a precedent for other complex plant pathosystems. Such microbial markers can be used to complement plant phenotype- and genotype-based selection strategies to improve disease resistance in one of the world's most important pulse crops of the world.

Co-Infections by Fusarium circinatum and Phytophthora spp. on Pinus radiata: Complex Phenotypic and Molecular Interactions

This study investigated the complex phenotypic and genetic response of Monterey pine (Pinus radiata) seedlings to co-infections by F. circinatum, the causal agent of pine pitch canker disease, and the oomycetes Phytophthora xcambivora and P. parvispora. Monterey pine seedlings were wound-inoculated with each single pathogen and with the combinations F. circinatum/P. xcambivora and F. circinatum/P. parvispora. Initially, seedlings inoculated only with F. circinatum showed less severe symptoms than seedlings co-inoculated or inoculated only with P. xcambivora or P. parvispora. However, 30 days post-inoculation (dpi), all inoculated seedlings, including those inoculated only with F. circinatum, showed severe symptoms with no significant differences among treatments. The transcriptomic profiles of three genes encoding pathogenesis-related proteins, i.e., chitinase (PR3), thaumatin-like protein (PR5), phenylalanine ammonia-lyase (PAL), and the pyruvate decarboxylase (PDC)-encoding gene were analyzed at various time intervals after inoculation. In seedlings inoculated with single pathogens, F. circinatum stimulated the up-regulation of all genes, while between the two oomycetes, only P. xcambivora induced significant up-regulations. In seedlings co-inoculated with F. circinatum and P.xcambivora or P. parvispora none of the genes showed a significant over-expression 4 dpi. In contrast, at 11 dpi, significant up-regulation was observed for PR5 in the combination F. circinatum/P.xcambivora and PDC in the combination F. circinatum/P. parvispora, thus suggesting a possible synergism of multiple infections in triggering this plant defense mechanism.

Distribution of the potential pathogenic Alternaria on plant leaves determines foliar fungal communities around the disease spot

Plant leaves are colonized by a remarkably diverse fungal microbiome, which contributes to host plant growth and health. However, responses of foliar fungal community to phytopathogen invasion and measures of the fungal community taken to resist or assist pathogens remain elusive. By utilizing high-throughput sequencing of internal transcribed spacer (ITS) amplicons, we studied the relationships between the foliar fungal community around the disease spot and the pathogen of brown spot disease. The pathogenic Alternaria was found to follow a dramatically decreased trend from the disease spot to its surrounding fungal communities, whose community structure also diverged substantially away from the disease spot community. With the increase of pathogenic Alternaria, diversity indexes, including Shannon, Pielou and Simpson, showed a trend of increasing first and then decreasing. Total network links and the average path distance exhibited strong negative and positive correlations with Alternaria, respectively. Five keystone members showed direct interactions with pathogenic Alternaria. Members of Botryosphaeria, Paraphoma and Plectosphaerella might act as key 'pathogen facilitators' to increase the severity and development of brown spot disease, while Pleospora and Ochrocladosporium might be important 'pathogen antagonists' to suppress the expansion of pathogenic Alternaria. Our study provides new insights in developing new strategies for leaf disease prediction or prevention.

Harnessing Eco-Evolutionary Dynamics of Xanthomonads on Tomato and Pepper to Tackle New Problems of an Old Disease

Bacterial spot is an endemic seedborne disease responsible for recurring outbreaks on tomato and pepper around the world. The disease is caused by four diverse species, Xanthomonas gardneri, Xanthomonas euvesicatoria, Xanthomonas perforans, and Xanthomonas vesicatoria. There are no commercially available disease-resistant tomato varieties, and the disease is managed by chemical/biological control options, although these have not reduced the incidence of outbreaks. The disease on peppers is managed by disease-resistant cultivars that are effective against X. euvesicatoria but not X. gardneri. A significant shift in composition and prevalence of different species and races of the pathogen has occurred over the past century. Here, I attempt to review ecological and evolutionary processes associated with the population dynamics leading to disease emergence and spread. The goal of this review is to integrate the knowledge on population genomics and molecular plant-microbe interactions for this pathosystem to tailor disease management strategies.

R. Patiranage D, Johansen K, Schmöckel SM, Bertero D, Oakey H, Colque-Little C, Afzal I, Raubach S, Miller N, Streich J, Amby DB, Emrani N, Warmington M, Mousa MAA, Wu D, Jacobson D, Andreasen C, Jung C, Murphy K, Bazile D, Tester M. Quinoa Phenotyping Methodologies: An International Consensus

Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher-throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally.

The rice foot rot pathogen Dickeya zeae alters the in-field plant microbiome

Studies on bacterial plant diseases have thus far been focused on the single bacterial species causing the disease, with very little attention given to the many other microorganisms present in the microbiome. This study intends to use pathobiome analysis of the rice foot rot disease, caused by Dickeya zeae, as a case study to investigate the effects of this bacterial pathogen to the total resident microbiome and to highlight possible interactions between the pathogen and the members of the community involved in the disease process. The microbiome of asymptomatic and the pathobiome of foot‐rot symptomatic field‐grown rice plants over two growing periods and belonging to two rice cultivars were determined via 16S rRNA gene amplicon sequencing. Results showed that the presence of D. zeae is associated with an alteration of the resident bacterial community in terms of species composition, abundance and richness, leading to the formation of microbial consortia linked to the disease state. Several bacterial species were significantly co‐presented with the pathogen in the two growing periods suggesting that they could be involved in the disease process. Besides, culture‐dependent isolation and in planta inoculation studies of a bacterial member of the pathobiome, identified as positive correlated with the pathogen in our in silico analysis, indicated that it benefits from the presence of D. zeae. A similar microbiome/pathobiome experiment was also performed in a symptomatically different rice disease evidencing that not all plant diseases have the same consequence/relationship with the plant microbiome. This study moves away from a pathogen‐focused stance and goes towards a more ecological perception considering the effect of the entire microbial community which could be involved in the pathogenesis, persistence, transmission and evolution of plant pathogens.

Role of Yeasts in the Cranberry Fruit Rot Disease Complex

Cranberry fruit rot (CFR) is an economically important disease caused by at least 10 species of filamentous fungi. Despite the application of fungicides, incidence of CFR is sometimes high, raising the possibility of a role for microbes other than fungi in the CFR complex. Isolation of microbes from rotten berries on culture media that favor either bacteria or yeasts resulted in mucoid colonies from <15% of dry-harvested rotten berries but up to 60% of wet-harvested berries. The mucoid colonies were identified as yeasts, primarily in the family Saccharomycetaceae. Inoculation of sound berries with three yeasts, Hanseniaspora uvarum, Pichia fermentans, and Pichia terricola, resulted in significantly higher incidence and severity of rot symptoms compared with mock-inoculated controls; these yeasts were recovered from inoculated berries, providing evidence of their pathogenicity. The minimum concentrations of azoxystrobin, chlorothalonil, and prothioconazole that resulted in 80% inhibition of growth compared with untreated controls (MIC80) were determined for a subset of yeasts. In general, MIC80s were higher for azoxystrobin and prothioconazole (usually >64 µg/ml) than for chlorothalonil (usually ≤1 µg/ml). To complement culture-dependent studies, DNA was isolated from wet- and dry-harvested rotten berries, and fungi were identified to the level of family by high-throughput sequencing of the fungal internal transcribed spacer region. There were no fungal families consistently detected among samples by one method (culturing or high-throughput sequencing) and missed by the other that have not previously been reported in cranberry; however, some fungal families were found to be more abundant by one method versus the other. Harvest method (wet or dry) had a significant effect on the composition of fungal communities of rotten berries (P < 0.001), and operational taxonomic units representing the Saccharomycetaceae were more abundant in wet- than dry-harvested berries. Taken together, the results suggest that some yeasts are pathogenic to cranberry and may be especially relevant in wet-harvested berries.

Enterobacter asburiae and Pantoea ananatis Causing Rice Bacterial Blight in China

Rice bacterial blight is a devastating bacterial disease threatening rice yield all over the world and Xanthomonas oryzae pv. oryzae is traditionally believed to be the pathogen. In recent years, we have received diseased rice samples with symptoms of blighted leaves from Sichuan and Guangdong provinces, China. Pathogen isolation and classification identified two different enterobacteria as the causal agents, namely Enterobacter asburiae and Pantoea ananatis. Among them, E. asburiae was isolated from samples of both provinces, and P. ananatis was only isolated from the Sichuan samples. Different from rice foot rot pathogen Dickeya zeae EC1 and rice bacterial blight pathogen X. oryzae pv. oryzae PXO99A, strains SC1, RG1, and SC7 produced rare cell wall degrading enzymes (CWDEs) but more extrapolysaccharides (EPS). E. asburiae strains SC1 and RG1 produced bacteriostatic substances while P. ananatis strain SC7 produced none. Pathogenicity tests indicated that all of them infected monocotyledonous rice and banana seedlings, but not dicotyledonous potato, radish, or cabbage. Moreover, strain RG1 was most virulent, while strains SC1 and SC7 were similarly virulent on rice leaves, even though strain SC1 propagated significantly faster in rice leaf tissues than strain SC7. This study firstly discovered E. asburiae as a new pathogen of rice bacterial blight, and in some cases, P. ananatis could be a companion pathogen. Analysis on production of virulence factors suggested that both pathogens probably employ a different mechanism to infect hosts other than using cell wall degrading enzymes to break through host cell walls.

Virulence and community dynamics of fungal species with vertical and horizontal transmission on a plant with multiple infections

The virulence evolution of multiple infections of parasites from the same species has been modeled widely in evolution theory. However, experimental studies on this topic remain scarce, particularly regarding multiple infections by different parasite species. Here, we characterized the virulence and community dynamics of fungal pathogens on the invasive plant Ageratina adenophora to verify the predictions made by the model. We observed that A. adenophora was highly susceptible to diverse foliar pathogens with mixed vertical and horizontal transmission within leaf spots. The transmission mode mainly determined the pathogen community structure at the leaf spot level. Over time, the pathogen community within a leaf spot showed decreased Shannon diversity; moreover, the vertically transmitted pathogens exhibited decreased virulence to the host A. adenophora, but the horizontally transmitted pathogens exhibited increased virulence to the host. Our results demonstrate that the predictions of classical models for the virulence evolution of multiple infections are still valid in a complex realistic environment and highlight the impact of transmission mode on disease epidemics of foliar fungal pathogens. We also propose that seedborne fungi play an important role in structuring the foliar pathogen community from multiple infections within a leaf spot.

A growing number of examples indicate that many plant diseases are caused by multiple taxa of microbes. Therefore, how virulence evolves in the context of multiple infections by different species with both vertical and horizontal transmission modes represents an important area of pathogen ecology and evolution, but there is a lack of experimental study. Here, we employ a naturally occurring host-parasite system, the invasive plant Ageratina adenophora and its foliar pathogens, to verify that theoretical predictions of classical models for virulence evolution are still valid in a complex realistic environment, i.e., the transmission mode determines the dynamics of the virulence and pathogen community under multiple infections. Moreover, we propose that seedborne fungi are important in structuring the foliar pathogen community consisting of multiple infections within a leaf spot. Our findings provide valuable information for understanding how multiple infections affect the key components, i.e., the virulence evolution and pathogen community dynamics, of host-pathogen interactions in the field.

Novel Disease Host Resistances in the World Core Collection of Trifolium subterraneum

Glasshouse and field investigations of the phenotypic expressions of resistance of a 97-member World Core Collection of subterranean clover (Trifolium subterraneum) collected from its native Mediterranean habitat and representing approximately 80% of the total genetic diversity within the known 10,000 accessions of the species against the most important damping-off and root rot (Phytophthora clandestina, and Pythium irregulare) and foliar (Kabatiella caulivora, Uromyces trifolii-repentis, and Erysiphe trifoliorum) pathogens were performed. An additional 28 diverse cultivars were also included. Associations of these genotypes among 18 disease parameters and 17 morphological traits, and among these disease parameters and 24 climatic and eco-geographic variables from their collection sites, were examined. Many genotypes showed strong phenotypic expression of novel host disease resistance against one or more pathogens, enabling their potential deployment as disease-resistant parents in subterranean clover breeding programs. These new sources of resistance enable future "pyramiding" of different resistance genes to improve resistance against these pathogens. Of particular value were genotypes with multiple disease-resistance across soilborne and/or foliar diseases, because many of these pathogens co-occur. All diseases had some parameters significantly correlated with one or more morphological traits and with one or more sites of origin variables. In particular, there were significant negative correlations between damping-off (i.e., germination) and 8 of the 17 morphological characters. The outcomes of these studies provide crucial information to subterranean clover breeding programs, enabling them to simultaneously select genotypes with multiple resistance to co-occurring soilborne and foliar diseases and desirable traits to offer renewed hope for re-establishing a more productive subterranean clover livestock feedbase despite multiple diseases prevailing widely.

Presence of the Weakly Pathogenic Fusarium poae in the Fusarium Head Blight Disease Complex Hampers Biocontrol and Chemical Control of the Virulent Fusarium graminearum Pathogen

Fusarium head blight (FHB) in wheat (Triticum aestivum L.) is caused by a consortium of mutually interacting Fusarium species. In the field, the weakly pathogenic F. poae often thrives on the infection sites of the virulent F. graminearum. In this ecological context, we investigated the efficacy of chemical and biocontrol agents against F. graminearum in wheat ears. For this purpose, one fungicide comprising prothioconazole + spiroxamine and two bacterial biocontrol strains, Streptomyces rimosus LMG 19352 and Rhodococcus sp. R-43120 were tested for their efficacy to reduce FHB symptoms and mycotoxin (deoxynivalenol, DON) production by F. graminearum in presence or absence of F. poae. Results showed that the fungicide and both actinobacterial strains reduced FHB symptoms and concomitant DON levels in wheat ears inoculated with F. graminearum. Where Streptomyces rimosus appeared to have direct antagonistic effects, Rhodococcus and the fungicide mediated suppression of F. graminearum was linked to the archetypal salicylic acid and jasmonic acid defense pathways that involve the activation of LOX1, LOX2 and ICS. Remarkably, this chemical- and biocontrol efficacy was significantly reduced when F. poae was co-inoculated with F. graminearum. This reduced efficacy was linked to a suppression of the plant's intrinsic defense system and increased levels of DON. In conclusion, our study shows that control strategies against the virulent F. graminearum in the disease complex causing FHB are hampered by the presence of the weakly pathogenic F. poae. This study provides generic insights in the complexity of control strategies against plant diseases caused by multiple pathogens.

Interaction between Dickeya dianthicola and Pectobacterium parmentieri in Potato Infection under Field Conditions

Dickeya and Pectobacterium spp. both cause blackleg and soft rot of potato, which can be a yield-reducing factor to potato production. The purpose of this study was to examine the interaction between these two bacterial genera causing potato infection, and subsequent disease development and yield responses under field conditions. Analysis of 883 potato samples collected in Northeastern USA using polymerase chain reaction determined that Dickeya dianthicola and P. parmentieri were found in 38.1% and 53.3% of all samples, respectively, and that 20.6% of samples contained both D. dianthicola and P. parmentieri. To further investigate the relationship between the two bacterial species and their interaction, field trials were established. Potato seed pieces of “Russet Burbank”, “Lamoka”, and “Atlantic” were inoculated with bacterial suspension of D. dianthicola at 10⁷ colony-forming unite (CFU)/mL using a vacuum infiltration method, air dried, and then planted in the field. Two-year results showed that there was a high correlation (p < 0.01) between yield loss and percent of inoculated seed pieces. In a secondary field trial conducted in 2018 and 2019, seed pieces of potato “Shepody”, “Lamoka” and “Atlantic” were inoculated with D. dianthicola, P. parmentieri, or mixture of both species, and then planted. In 2019, disease severity index, as measured by the most sensitive variety “Lamoka”, was 16.2 with D. dianthicola inoculation, 10.4 with P. parmentieri, 25.4 with inoculation with both bacteria. Two-year data had a similar trend. Thus, D. dianthicola was more virulent than P. parmentieri, but the co-inoculation of the two species resulted in increased disease severity compared to single-species inoculation with either pathogen.

Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale

BACKGROUND

The plant microbiome plays a vital role in determining host health and productivity. However, we lack real-world comparative understanding of the factors which shape assembly of its diverse biota, and crucially relationships between microbiota composition and plant health. Here we investigated landscape scale rhizosphere microbial assembly processes in oilseed rape (OSR), the UK's third most cultivated crop by area and the world's third largest source of vegetable oil, which suffers from yield decline associated with the frequency it is grown in rotations. By including 37 conventional farmers' fields with varying OSR rotation frequencies, we present an innovative approach to identify microbial signatures characteristic of microbiomes which are beneficial and harmful to the host.

RESULTS

We show that OSR yield decline is linked to rotation frequency in real-world agricultural systems. We demonstrate fundamental differences in the environmental and agronomic drivers of protist, bacterial and fungal communities between root, rhizosphere soil and bulk soil compartments. We further discovered that the assembly of fungi, but neither bacteria nor protists, was influenced by OSR rotation frequency. However, there were individual abundant bacterial OTUs that correlated with either yield or rotation frequency. A variety of fungal and protist pathogens were detected in roots and rhizosphere soil of OSR, and several increased relative abundance in root or rhizosphere compartments as OSR rotation frequency increased. Importantly, the relative abundance of the fungal pathogen Olpidium brassicae both increased with short rotations and was significantly associated with low yield. In contrast, the root endophyte Tetracladium spp. showed the reverse associations with both rotation frequency and yield to O. brassicae, suggesting that they are signatures of a microbiome which benefits the host. We also identified a variety of novel protist and fungal clades which are highly connected within the microbiome and could play a role in determining microbiome composition.

CONCLUSIONS

We show that at the landscape scale, OSR crop yield is governed by interplay between complex communities of both pathogens and beneficial biota which is modulated by rotation frequency. Our comprehensive study has identified signatures of dysbiosis within the OSR microbiome, grown in real-world agricultural systems, which could be used in strategies to promote crop yield. Video abstract.