Potential Plant Pathogens Research Articles

Plastic mulch film residues in agriculture: impact on soil suppressiveness, plant growth, and microbial communities.

Plastic mulch film residues have been accumulating in agricultural soils for decades, but so far, little is known about its consequences on soil microbial communities and functions. Here, we tested the effects of plastic residues of low-density polyethylene and biodegradable mulch films on soil suppressiveness and microbial community composition. We investigated how plastic residues in a Fusarium culmorum suppressive soil affect the level of disease suppressiveness, plant biomass, nutrient status, and microbial communities in rhizosphere using a controlled pot experiment. The addition of 1% plastic residues to the suppressive soil did not affect the level of suppression and the disease symptoms index. However, we did find that plant biomasses decreased, and that plant nutrient status changed in the presence of plastic residues. No significant changes in bacterial and fungal rhizosphere communities were observed. Nonetheless, bacterial and fungal communities closely attached to the plastisphere were very different from the rhizosphere communities with overrepresentation of potential plant pathogens. The plastisphere revealed a high abundance of specific bacterial phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) and fungal genera (Rhizoctonia and Arthrobotrys). Our work revealed new insights and raises emerging questions for further studies on the impact of microplastics on the agroecosystems.

Post-termination Effects of Cover Crop Monocultures and Mixtures on Soil Inorganic Nitrogen and Microbial Communities on Two Organic Farms in Illinois

Cover crops can continue to affect agricultural systems even after they have been terminated by influencing nitrogen dynamics and by altering soil microbial communities. These post-termination effects can influence soil fertility, weed pressure, and the dynamics of potential plant pathogens in the narrow window of time between cover crop termination and cash crop emergence. We evaluated the post-termination effects of 12 different spring-sown cover crop mixtures and monocultures on soil nitrogen and microbial communities on two different organic farms in Central Illinois (on Lawson silt loam soil) and Northern Illinois (on Virgil silt loam soil). In comparison to control plots with no cover crops, all cover crop treatments significantly reduced soil nitrate levels but increased the potentially mineralizable nitrogen pool following termination. Nitrate levels of cover crop plots approached those of controls after 2 and 4 weeks, respectively, but potentially mineralizable nitrogen levels in cover plots remained elevated for at least 4 weeks following termination. Monocultures of Brassica cover crops showed the greatest decrease in soil nitrate, while Brassicas and unplanted control plots containing high biomass of weeds showed the greatest increase in potentially mineralizable nitrogen in comparison to plant-free control plots. In contrast to their effect on soil nitrogen, cover crops had very limited impact on the composition of soil microbial communities. Overall microbial community composition varied across sites and years, and only soil fungi significantly responded to cover cropping treatments. Nevertheless, we found that some highly correlated groups of soil microbes showed significant responses to soil nitrate and to high plant biomass. Key members of these correlated groups included ammonia-oxidizing organisms and saprotrophic fungi. Our results suggest that cover crops may reduce the potential for springtime nitrogen leaching losses by retaining nitrogen in the soil organic pool, and they may also have impacts on the soil microbial community that are particularly relevant for nitrogen cycling and decomposition of plant residues.

Combination of Chitosan and Peppermint Essential Oil as Potential Active Coating Against Penicillium digitatum and Botrytis cinerea

This work evaluates the effect of antifungal agent based on chitosan (CS) or peppermint essential oil (PEO) treatment and their mixtures to control P. digitatum and B. cinerea, identified as the potential plant pathogens. The efficacy of each CS (0.6%) and PEO (0.1–0.6%) or in combination to inhibit spore germination is assessed. The distribution of PEO in the emulsion system is more pronounced along with the increase in the oil level. Either CS or PEO can inhibit the growth of spore and germ tube elongation effectively. The mixtures of CS and PEO exhibit a greater inhibitory action additively or synergistically according to the Abbott index value. Propidium iodide staining test confirms the loss of membrane integrity of spores in response to coating treatment. The combination treatment of CS/0.6% PEO and CS/0.5% PEO can be an effective alternative to inhibit the spore germination, respectively, for P. digitatum by 91.54% and B. cinerea by 100%. Application of the composite coatings obtained in this study can prove to be potential for primary packaging, particularly for fresh postharvest commodities.

High variation of fungal communities and associated potential plant pathogens induced by long-term addition of N fertilizers rather than P, K fertilizers: A case study in a Mollisol field

Nitrogen (N), phosphate (P), and potassium (K) are the three most important nutrients applied into agricultural soils, but the impacts of their single or combined application on soil fungal community structure and stability are still open questions. Using qPCR and Illumina Miseq sequencing, the variation of soil fungal communities in response to long-term addition of N, P, or K fertilization alone and their combinations in a Mollisol field was investigated in this study. In addition, the fungal community resistance indices and network structure were studied. Results showed that N fertilizations (N, NK, NP and NPK treatments) rather than P, K fertilizations (P, K and PK treatments) significantly increased fungal abundance, but decreased fungal diversity and shifted fungal community structures when compared to non-fertilization (NoF). Additionally, N fertilization treatments presented lower resistance of fungal communities to environment disturbances than those of P, K fertilization treatments. More numbers and higher abundances of changed fungal taxa at the genus and OTU levels were induced by N fertilizations rather than by addition of P, K fertilizers. In addition, N fertilizations induced a more changeable fungal network and complex pathogenic subnetwork with many positive interactions among responding plant pathogens (RP, the changeable plant pathogens induced by fertilizers addition compared to NoF) when compared to P, K fertilizations. These RP directly and negatively influenced fungal community resistance examined by structural equation modeling (SEM), which were indirectly detrimental to soybean yields. Our findings revealed that addition of N fertilizers significantly disturbed fungal communities and promoted pathogenic interactions, and provided insights into the optimization of fertilization strategies toward agricultural sustainability.

Rapid Molecular Diagnostics in the Field and Laboratory to Detect Plant Pathogen DNA in Potential Insect Vectors.

A variety of sensitive and specific molecular diagnostic assays has been described for detecting nucleic acids in biological samples that may harbor pathogens of interest. These methods include very rapid, isothermal nucleic acid amplification methods that can be deployed outside of the laboratory environment, such as loop-mediated isothermal DNA amplification (LAMP) and recombinase-polymerase amplification (RPA). However, all molecular diagnostic assays must be preceded by nucleic acid extraction from the biological samples of interest, which provides suitable template molecules for the assays. To exploit the features of the amplification assays and be utilized outside of the lab, these methods must be rapid and avoid the need for typical laboratory chemicals and equipment. We describe a protocol for the extraction of DNA from field-collected insects that can be implemented at the point of collection and used to detect the presence of DNA sequences from potential plant pathogens that may be vectored by the insects. This protocol provides template DNA that is suitable for PCR, LAMP, and RPA. The FTA PlantSaver card-based DNA extraction product was also confirmed to amplify the mitochondrial cytochrome oxidase 1 (CO1) universal barcode that could later be sequenced to identify any insect. Lastly, we provide an example using field-collected insects, Neokolla (Graphocephala) heiroglyphica, and demonstrate the detection of the plant pathogen Xylella fastidiosa in carrier insects using PCR, RPA, and LAMP.

Composition of the Microbiomes from Spinach Seeds Infested or Noninfested with Peronospora effusa or Verticillium dahliae

The worldwide distribution of plant seeds can disseminate beneficial and plant-pathogenic microorganisms. This phenomenon is of particular concern where seed production is geographically isolated from crop production, as is the case with spinach in the United States. We aimed to characterize the structure and function of spinach seed microbiomes in commercial spinach seed lots originating from Europe and New Zealand. The seed lots we analyzed were infested with Peronospora effusa and Verticillium dahliae, only infested with V. dahliae, or not infested with either of these pathogens. The microbial taxonomic composition and gene function (assessed by gene ontology [GO] terms) of spinach seeds were highly influenced by geographic origin and the status of pathogen infestation. Through taxonomic profiling, we found that potentially plant-beneficial bacterial genera such as Pseudomonas and Pantoea were the most abundant taxa both in infested and noninfested seeds, and Stenotrophomonas was observed in seed lots infested with P. effusa and V. dahliae. Many potential plant pathogens that are not known to be associated with spinach seed were also discovered by metagenomic analysis, including Sclerotinia sclerotiorum, Botrytis cinerea, Bipolaris sorokiniana, Fusarium pseudograminearum, Alternaria brassicae, A. solani, Parastagonospora nodorum, and Pyrenophora teres f. teres. Our analysis of the function of prokaryotic genes in de novo assembled metagenomes revealed distinct GO terms associated with the geographic origin of seed lots. This work provides an important first step toward identifying spinach seedborne microorganisms that could be utilized to improve plant health and plant pathogens that could be inadvertently carried to new locations.

Comparative Bacterial Metagenomics of Cnidoscolus aconitifolius (Mill.) I. M. Johnston and Other Leafy Vegetables

Aims: Vegetables provide a favourable habitat for diverse populations of microorganisms. Some vegetables, especially the ones used in salads are ready-to-eat food products and some phyllosphere bacteria might contribute to the prolonged presence of human food-borne pathogens in these vegetables.
 Methodology: Phyllosphere bacteria associated with Cnidoscolus aconitifolius were evaluated using a culture-independent approach, Illumina MiSeq platform of 16S rRNA gene sequencing and then compared with publicly available data obtained from Spinacia oleracea (spinach) and Lactuca sativa (lettuce) on GenBank.
 Results: The results from this study showed that the three vegetables harbor diverse bacterial organisms. Eighty-three (83) Operational Taxonomic Units (OTUs) assigned to five phyla were obtained from C. aconitifolius phyllosphere. The most predominant phyla across studied vegetables were: Proteobacteria (74.79%), Actinobacteria (8.69%) and Firmicutes (7.37%). Potential human pathogenic species such as Bacillus spp., Enterococcus spp., Staphylococcus spp., Klebsiella spp., and Pseudomonas spp. were also present in lettuce and spinach. Bacteria with potential for antibiotic production, anti-microbial and antibiotic resistant genes belong to the families Bacillaceae, Streptomycetaceae, Pseudomonaceae, Enterobacteriaceae, Staphylococcaceae, Enterococcaceae and Streptococcaceae. The most abundant taxa obtained from this study were Pseudomonas, Erwinia, Brachybacterium, Megasphaera, Janthinobacterium, Sphingomonas and Lactobacillus.
 Conclusion: Our result successfully determined the relative abundance of potential human and plant pathogens in the leafy vegetables and also showed the bacterial community structure in the studied vegetables.

Co-Occurrence of Viruses, Plant Pathogens, and Symbionts in an Underexplored Hemipteran Clade.

Interactions between insect symbionts and plant pathogens are dynamic and complex, sometimes involving direct antagonism or synergy and sometimes involving ecological and evolutionary leaps, as insect symbionts transmit through plant tissues or plant pathogens transition to become insect symbionts. Hemipterans such as aphids, whiteflies, psyllids, leafhoppers, and planthoppers are well-studied plant pests that host diverse symbionts and vector plant pathogens. The related hemipteran treehoppers (family Membracidae) are less well-studied but offer a potentially new and diverse array of symbionts and plant pathogenic interactions through their distinct woody plant hosts and ecological interactions with diverse tending hymenopteran taxa. To explore membracid symbiont–pathogen diversity and co-occurrence, this study performed shotgun metagenomic sequencing on 20 samples (16 species) of treehopper, and characterized putative symbionts and pathogens using a combination of rapid blast database searches and phylogenetic analysis of assembled scaffolds and correlation analysis. Among the 8.7 billion base pairs of scaffolds assembled were matches to 9 potential plant pathogens, 12 potential primary and secondary insect endosymbionts, numerous bacteriophages, and other viruses, entomopathogens, and fungi. Notable discoveries include a divergent Brenneria plant pathogen-like organism, several bee-like Bombella and Asaia strains, novel strains of Arsenophonus-like and Sodalis-like symbionts, Ralstonia sp. and Ralstonia-type phages, Serratia sp., and APSE-type phages and bracoviruses. There were several short Phytoplasma and Spiroplasma matches, but there was no indication of plant viruses in these data. Clusters of positively correlated microbes such as yeast-like symbionts and Ralstonia, viruses and Serratia, and APSE phage with parasitoid-type bracoviruses suggest directions for future analyses. Together, results indicate membracids offer a rich palette for future study of symbiont–plant pathogen interactions.

A combined catalog of non-pollen palynomorphs (NPPs) of fungal origin from soil and airborne samples of Uruguay

Here is presented a commented catalog of non-pollen palynomorphs (NPPs) of fungal origin, that arises from the articulation of research efforts in the disciplines of paleoecology and aerobiology. It includes the morphotypes recorded in projects carried out in the ‘campos’ region of Uruguay. The aim is to give a baseline resource for the identification of fungal NPPs, to encourage their inclusion in the forthcoming research in the Region. Surface soils were taken at 14 sites in the Department of Rocha, covering as much environmental variability as possible, while volumetric airborne samples were collected daily in the city of Montevideo, during 24 months. The soils were treated by standard palynological methods, considering all the microremains of known or suspected fungal origin. The airborne samples were observed fresh in the microscope. In topsoils, 157 different morphotypes were found, with 90 identified at some taxonomic level. Among the unknown types, 17 had been reported by other researchers and 50 were new reports. The most widespread types were Coniochaeta aff. ligniaria, Glomus sp., Sporormiella-type, Sordaria sp., and Cercophora-type, especially in grasslands and swamps, where most remains seem to come from coprophilous fungi. The morphotype assemblage found in soils under forested communities was different from that observed in open environments, with the prevalence of spores of anamorph stages of saprobic/parasitic fungi. In the air, 68 morphotypes were identified in a previous contribution, but pictures are shown for the first time here, together with descriptions. There were 24 types in common between topsoil and airborne samples, including spores of potential plant pathogens such as Nigrospora sp., Alternaria sp., and Stemphylium sp. and spores of coprophilous fungi, especially the Sporormiella-type. The most frequent types found in the air were conidia of plant pathogens, probably sourced in urban trees or periurban grasslands (Cladosporium sp., Alternaria sp., and Curvularia sp.). Since most NPPs have a wide or even cosmopolitan geographic distribution, the catalog presented here is of international interest.

Integrated analysis reveals an association between the rhizosphere microbiome and root rot of arecanut palm

The rhizosphere microbial community is crucial to plant health. Many studies have explored the association between the rhizosphere microbiome and plant disease. However, few studies have focused on root rot in arecanut palm, a disease causing devastating effects and thus resulting in economic losses that considerably affect the development of the arecanut industry. Here, rhizosphere samples were collected from both healthy arecanut palm plants and root-rotted arecanut palm plants, and the microbial communities were analyzed using high-throughput sequencing. The root-rotted samples exhibited distinct microbial community richness, diversity, and composition compared with the healthy samples, which was associated with pH according to the Mantel test. Identified potential plant pathogens, including Proteobacteria, Bacteroidetes, Chytridiomycota, and Mortierellomycota, were significantly enriched in the root-rotted samples. In contrast, potentially beneficial plant microbes, such as Acidobacteria and Gemmatimonadetes, were significantly depleted in the root-rotted samples. Co-occurrence networks were constructed to further identify microbial relationships in the root-rotted samples. These findings revealed ecological imbalance among beneficial bacteria in the root-rotted samples. The present study therefore provides an integrated view of the association between the microbial community and root rot in arecanut palm.

Accidental introduction of Candidatus Liberibacter europaeus into New Zealand via a weed biocontrol agent from the UK

The bacterium, Candidatus Liberibacter europaeus (Leu) was reported in New Zealand (NZ) in 2011 in Scotch broom, Cytisus scoparius Link, and its biocontrol agent, Arytainilla spartiophila Förster (Hemiptera: Psyllidae). The aim of the study was to investigate the pathway by which Leu arrived in NZ using a retrospective risk assessment of Leu being accidentally imported with the broom psyllids in the 1990s. We developed species-specific primers for Leu detection and carried out end-point and real-time PCR analyses for Leu in potential host plants and broom psyllids throughout NZ to test two hypotheses: 1) Leu was accidentally released in NZ in broom psyllids in 1993; or 2) Leu was present in NZ pre-1993, and maintained in cultivated plants via cuttings/grafting, or in wild Scotch broom populations via shared parasitic plants. There was strong evidence to support the arrival of Leu with broom psyllids in NZ. Firstly, methods used to import broom psyllids from the UK provided a likely pathway for inadvertent release of Leu, which at the time was unknown to science, into NZ. Secondly, Leu in NZ Scotch broom plants was significantly associated with the presence of broom psyllids, with Leu absent from plants at sites without psyllids. In contrast, there was no evidence suggesting Leu was present in NZ before the release of broom psyllids: Leu was not found in ornamental brooms or pears, Pyrus communis L. (a Leu host in Europe), and parasitic plants were too uncommon to maintain Leu in wild Scotch broom. In addition, Leu in UK Scotch broom and broom psyllids has a matching partial 16S sequence to NZ Leu. It remains uncertain whether Leu is pathogenic in Scotch broom, or symptomless as in pears. Unpredictable impacts of Ca. Liberibacter spp. in different plant species probably implies that psyllids considered as future weed biocontrol agents will need to be free of these potential plant pathogens. This accidental introduction of Candidatus Liberibacter europaeus into NZ via a weed biocontrol agent happened because detection methods for unculturable organisms were not developed at the time. Molecular characterisation of insect microbiomes could become an essential procedure for pre-release safety screening of biocontrol agents that are potential vectors of plant pathogens.

Conventional and conservation tillage practices affect soil microbial co-occurrence patterns and are associated with crop yields

A comprehensive understanding of the effects of tillage practices on soil microbial communities is fundamental to a better understanding of their roles in maintaining or improving the stability of agroecosystems. However, little is known regarding soil microbial co-occurrence patterns and their function in ecosystems shaped by long-term tillage practices. The goal of the present study was to investigate the impact of no-tillage (NT), reduced tillage (RT) and moldboard plow tillage (MP) practices on soil microbial interactions, central species and functional taxa as well as to investigate their associations with crop yields. The results showed that the average node degree was lower in the RT network than in the NT and MP networks of bulk and rhizosphere soils, indicating inefficient mutual effects among taxa and a more stable network structure induced by RT. Moldboard plow tillage resulted in the most fungal-fungal interactions (17.6%), while RT yielded the most bacterial-fungal interactions (32.3%) in the rhizosphere soils. The potential plant pathogens Fusarium were identified as hub node with most connections, and pathogen Sphingomonas and Clonostachys were found as central speices with those simultaneously termed as hub node and generalist in the MP network of rhizosphere soils. Intriguingly, these potential plant pathogens had negative correlations with crop yields in both bulk and rhizosphere soils, as determined by structural equation modeling (SEM). In contrast, RT might help to alleviate the ecological risks of the potential plant pathogens and increased the availability of soil nutrients mediated by central species, such as Nitrospira. These findings suggested RT as an optimal practice that could stabilize microbial network structure, alleviated the potential transmission of pathogens and finally enhance crop yields, providing a new perspective for tillage application in agroecosystems.

Potential Human and Plant Pathogenic Species in Airborne PM10 Samples and Relationships with Chemical Components and Meteorological Parameters

A preliminary local database of potential (opportunistic) airborne human and plant pathogenic and non-pathogenic species detected in PM10 samples collected in winter and spring is provided, in addition to their seasonal dependence and relationships with meteorological parameters and PM10 chemical species. The PM10 samples, collected at a Central Mediterranean coastal site, were analyzed by the 16S rRNA gene metabarcoding approach, and Spearman correlation coefficients and redundancy discriminant analysis tri-plots were used to investigate the main relationships. The screening of 1187 detected species allowed for the detection of 76 and 27 potential (opportunistic) human and plant pathogens, respectively. The bacterial structure of both pathogenic and non-pathogenic species varied from winter to spring and, consequently, the inter-species relationships among potential human pathogens, plant pathogens, and non-pathogenic species varied from winter to spring. Few non-pathogenic species and even fewer potential human pathogens were significantly correlated with meteorological parameters, according to the Spearman correlation coefficients. Conversely, several potential plant pathogens were strongly and positively correlated with temperature and wind speed and direction both in winter and in spring. The number of strong relationships between presumptive (human and plant) pathogens and non-pathogens, and meteorological parameters slightly increased from winter to spring. The sample chemical composition also varied from winter to spring. Some potential human and plant pathogens were correlated with chemicals mainly associated with marine aerosol and/or with soil dust, likely because terrestrial and aquatic environments were the main habitats of the detected bacterial species. The carrier role on the species seasonal variability was also investigated.

Drivers of richness and community composition of fungal endophytes of tree seeds.

Recent studies revealed a high diversity of fungal endophytes in traded tree seeds, including potential plant pathogens. The factors determining richness and composition of seed mycobiomes are poorly understood, but might be an important determinant for tree health. We assessed the relative impact of host identity, site, several site-specific environmental factors, and whether the host was sampled in its native or non-native distribution range, on the richness and composition of fungal seed endophytes of nine tree species across 15 sites in Europe and North America. Our results show that fungal richness was affected by host identity, but not by environmental variables or host distribution range. Fungal community composition was primarily driven by host identity, and to a lesser extent by environment. Around 25% of the 2147 amplicon sequence variants (ASVs) were generalists appearing on both continents and in both gymnosperms and angiosperms. Around 63% of the ASVs appeared in only gymnosperms or angiosperms, and 33% of the ASVs were associated with a single host species, while none were found in all tree species. Our results suggest that although seed trade might facilitate movements of fungi, their establishment and spread in the new environment might be limited by host availability.

Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat

Despite the large morphological and physiological changes that plants have undergone through domestication, little is known about their impact on their microbiome. Here we characterized rhizospheric bacterial and fungal communities as well as the abundance of N-cycling microbial guilds across thirty-nine accessions of tetraploid wheat, Triticum turgidum, from four domestication groups ranging from the wild subspecies to the semi dwarf elite cultivars. We identified several microbial phylotypes displaying significant variation in their relative abundance depending on the wheat domestication group with a stronger impact of domestication on fungi. The relative abundance of potential fungal plant pathogens belonging to the Sordariomycetes class decreased in domesticated compared to wild emmer while the opposite was found for members of the Glomeromycetes, which are obligate plant symbionts. The depletion of nitrifiers and of arbuscular mycorrhizal fungi in elite wheat cultivars compared to primitive domesticated forms suggests that the Green Revolution has decreased the coupling between plant and rhizosphere microbes that are potentially important for plant nutrient availability. Both plant diameter and fine root percentage exhibited the highest number of associations with microbial taxa, highlighting their putative role in shaping the rhizosphere microbiota during domestication. Aside from domestication, significant variation of bacterial and fungal community composition was found among accessions within each domestication group. In particular, the relative abundances of Ophiostomataceae and of Rhizobiales were strongly dependent on the host accession, with heritability estimates of ~ 27% and ~ 25%, indicating that there might be room for genetic improvement via introgression of ancestral plant rhizosphere-beneficial microbe associations.

First Inventory of Fungi in Symptomless and Symptomatic Chinese Mesona Indicates Phytopathological Threat.

Chinese mesona (Platostoma palustre) plays an important role as special crop in Southeast Asia and Taiwan for the production of herbal tea, grass jelly, and further processed food. In order to assess the potential threat of fungi to Chinese mesona, we surveyed isolates from symptomless plants in the area of mesona production, as well as from leaf spots of potted plants in a garden shop and a plantation in a botanical garden in Taiwan. From leaves, stems, and roots of 15 symptomless plants sampled at five collection events over two years, 154 isolates from 810 surface-sterilized plant fragments were obtained and identified based on DNA sequence data of the internal transcribed spacer region, and partially of the β-tubulin and histone H3 genes. The most common species belonged to the genera Cercospora, Colletotrichum, and Fusarium and were considered to be potential plant pathogens. Latent pathogenicity was confirmed by an infection experiment with an endophytic strain of Corynespora cassiicola. Observation of leaf spot disease associated with Cercospora kikuchii suggested pathogenicity of this fungus, which was also isolated as an endophyte from symptomless leaves. We hypothesize that the most common endophytic fungi are latent pathogens in the host and may cause plant disease when the host becomes weakened by senescence or changed cultivation condition. Leaf spots of plants in the botanical garden were associated with a species of Pseudocercospora, which was not found among the endophytic isolates and is newly described based on morphology and analysis of translation elongation factor 1 alpha gene sequences.

Intercropping with Potato-Onion Enhanced the Soil Microbial Diversity of Tomato.

Intercropping can achieve sustainable agricultural development by increasing plant diversity. In this study, we investigated the effects of tomato monoculture and tomato/potato-onion intercropping systems on tomato seedling growth and changes of soil microbial communities in greenhouse conditions. Results showed that the intercropping with potato-onion increased tomato seedling biomass. Compared with monoculture system, the alpha diversity of soil bacterial and fungal communities, beta diversity and abundance of bacterial community were increased in the intercropping system. Nevertheless, the beta-diversity and abundance of fungal community had no difference between the intercropping and monoculture systems. The relative abundances of some taxa (i.e., Acidobacteria-Subgroup-6, Arthrobacter, Bacillus, Pseudomonas) and several OTUs with the potential to promote plant growth were increased, while the relative abundances of some potential plant pathogens (i.e., Cladosporium) were decreased in the intercropping system. Redundancy analysis indicated that bacterial community structure was significantly influenced by soil organic carbon and pH, the fungal community structure was related to changes in soil organic carbon and available phosphorus. Overall, our results suggested that the tomato/potato-onion intercropping system altered soil microbial communities and improved the soil environment, which may be the main factor in promoting tomato growth.

The proportion of soil-borne pathogens increases with warming at the global scale

Understanding the present and future distribution of soil-borne plant pathogens is critical to supporting food and fibre production in a warmer world. Using data from a global field survey and a nine-year field experiment, we show that warmer temperatures increase the relative abundance of soil-borne potential fungal plant pathogens. Moreover, we provide a global atlas of these organisms along with future distribution projections under different climate change and land-use scenarios. These projections show an overall increase in the relative abundance of potential plant pathogens worldwide. This work advances our understanding of the global distribution of potential fungal plant pathogens and their sensitivity to ongoing climate and land-use changes, which is fundamental to reduce their incidence and impacts on terrestrial ecosystems globally. Plant pathogens threaten food security and ecosystem health. Projections of potential fungal plant pathogens under different warming and land-use scenarios indicate that warming temperatures under climate change will lead to increases in the relative abundance of such pathogens in most soils worldwide.

Exploring the Potential for Fungal Antagonism and Cell Wall Attack by Bacillus subtilis natto.

To develop more ecologically sustainable agricultural practices requires that we reduce our reliance on synthetic chemical pesticides for crop protection. This will likely involve optimized biocontrol approaches – the use of beneficial soil microbes to attack potential plant pathogens to protect plants from diseases. Many bacterial species, including strains of Bacillus subtilis, have been explored for their biocontrol properties, as they can control the growth of harmful fungi, often by disrupting the fungal cell wall. A strain that is not often considered for this particular application is Bacillus subtilis natto, primarily known for fermenting soybeans via cell wall degradation in the Japanese probiotic dish “natto.” Because deconstruction of the fungal cell wall is considered an important biocontrol trait, we were motivated to explore the possible anti-fungal properties of the B. subtilis natto strain. We show that B. subtilis natto can use complex fungal material as a carbon source for growth, and can effectively deconstruct fungal cell walls. We found degradation of fungal cell wall proteins, and showed that growth on a mix of peptides was very strong. We also found that intact fungal cell walls can induce the secretion of chitinases and proteases. Surprisingly, we could show that chitin, the bulk component of the fungal cell wall, does not permit successful growth of the natto strain or induce the secretion of chitinolytic enzymes, although these were produced during exposure to proteins or to complex fungal material. We have further shown that protease secretion is likely a constitutively enabled mechanism for nutrient scavenging by B. subtilis natto, as well as a potent tool for the degradation of fungal cell walls. Overall, our data highlight B. subtilis natto as a promising candidate for biocontrol products, with relevant behaviors that can be optimized by altering growth conditions. Whereas it is common for bacterial biocontrol products to be supplied with chitin or chitosan as a priming polysaccharide, our data indicate that this is not a useful approach with this particular bacterium, which should instead be supplied with either glucose or attenuated fungal material.

Fertility-related interplay between fungal guilds underlies plant richness-productivity relationships in natural grasslands.

The plant richness-productivity relationship is a central subject in ecology, yet the mechanisms behind this pattern remain debated. Soil fungi are closely associated with the dynamics of plant communities, however empirical evidence on how fungal communities integrate into the richness-productivity relationships of natural environments is lacking. We used Illumina high-throughput sequencing to identify rhizosphere fungal communities across a natural plant richness gradient at two sites with different fertility conditions, and related the subsequent information to plant richness and productivity to elucidate the role of fungal guilds in integrating the linkages of both plant components. Saprotrophs, mycorrhizal fungi and potential plant pathogens interacted differently between the sites, with saprotrophic and mycorrhizal fungal abundances being positively correlated at the high-nutrient site and abundances of mycorrhizal fungi and potential plant pathogens being negatively correlated at the low-nutrient site. The synergistic associations between these fungal guilds with plant richness and productivity operated in concert to promote positive richness-productivity relationships. Our findings provide empirical evidence for the importance of soil fungal guilds in integrating the linkages of plant richness and productivity, and suggest that future work incorporating soil fungal communities into richness-productivity relationships would advance our mechanistic understanding of their linkages.