Root Pathogens Research Articles

Pathocomplex of root rot of apple tree in nurseries and young orchards of the South of Russia

Root rot poses a serious threat to the main fruit crop domestic apple in nurseries and young orchards. Obtaining healthy planting material, free from root pathogens and root rot, is an especially priority task in conditions of intensive production. In the process of analyzing the affected plants from nurseries and young orchards at four sampling points, pathogens of apple root rot from 11 genera were identified and 431 isolates were extracted. The most common causative agents of apple root rot seedlings in the entire studied sample were species of the genus Fusarium spp. Soil micromycetes such as Rhizoctonia spp., Cladosporium spp., Cylinrocarpon spp., and oomycetes from the genus Pythium were rare. The composition and occurrence of species were heterogeneous at different points in the studied region. Phomopsis mali (Schulzer & Sacc.) Died., Cytospora spp., Alternaria alternate (Fr.) Keissl., and Aspergillus niger Tiegh. have been associated with root rot of seedlings and young apple trees.

Mass reproduction of Polygraphus proximus Blandford in fir forests of Siberia infected with root and stem pathogens: monitoring, patterns, biological control

Mass reproduction of Polygraphus proximus Blandford in fir forests of Siberia infected with root and stem pathogens: monitoring, patterns, biological control

Bio-control potentiality of Penicillium multicolor Grig.-Man. and Porad., against important root pathogens

Bio-control potentiality of Penicillium multicolor Grig.-Man. and Porad., against important root pathogens

Suppression of clubroot (Plasmodiophora brassicae) development in Brassica campestris sp. chinensis L. via exogenous inoculation of Piriformospora indica

The aim of the current study is to contribute to the basic understanding of Piriformosporaindica–Brassica campestris sp. chinensis interactions and to assess its impact on clubroot. This study revealed that P. indica, plant-root-colonizing fungus of Basidiomycetes, is capable to reduce the formation of clubroot in B. campestris sp. chinensis which is extremely susceptible to the root pathogen Plasmodiophora brassicae. Roots of the P. brassicae-infected plant were colonized with P. indica, as demonstrated by staining technique and microscopy. Like that, enhanced biomass was observed in P. indica co-inoculated plants by comparing with plants grown without P. indica as well as the plants infected with the pathogen only. Co-inoculation of the plant with both P. indica and P. brassicae reduced gall formation up to 61.60% by comparing plants infected with only P. brassicae as shown by the disease index. Higher level of flavonoids was also observed in P. indica inoculated plants which contribute to enhancing the plant immune system. Thus, a hypothesis was proposed that P. brassicae development in B. campestris sp. chinensis plants could be delayed with the inoculation of P. indica. Expression of P. brassicae genes which were differentially expressed during disease development was monitored using quantitative polymerase chain reaction and was corroborated with delayed pathogen development. The results suggest that P. indica and perhaps other beneficial endosymbionts could be an effective tool for the management of clubroot infection.

Editing of an effector gene promoter sequence impacts plant-Phytophthora interaction.

Pathogen avirulence (Avr) effectors interplay with corresponding plant resistance (R) proteins and activate robust plant immune responses. Although the expression pattern of Avr genes has been tied to their functions for a long time, it is still not clear how Avr gene expression patterns impact plant-microbe interactions. Here, we selected PsAvr3b, which shows a typical effector gene expression pattern from a soybean root pathogen Phytophthora sojae. To modulate gene expression, we engineered PsAvr3b promoter sequences by in situ substitution with promoter sequences from Actin (constitutive expression), PsXEG1 (early expression), and PsNLP1 (later expression) using the CRISPR/Cas9. PsAvr3b driven by different promoters resulted in distinct expression levels across all the tested infection time points. Importantly, those mutants with low PsAvr3b expression successfully colonized soybean plants carrying the cognate R gene Rps3b. To dissect the difference in plant responses to the PsAvr3b expression level, we conducted RNA-sequencing of different infection samples at 24 h postinfection and found soybean immune genes, including a few previously unknown genes that are associated with resistance. Our study highlights that fine-tuning in Avr gene expression impacts the compatibility of plant disease and provides clues to improve crop resistance in disease control management.

Structure and ecological function of the soil microbiome affecting plant-soil feedbacks in the presence of a soil-borne pathogen.

SummaryInteractions between plants and soil microbes are important for plant growth and resistance. Through plant–soil‐feedbacks, growth of a plant is influenced by the previous plant that was growing in the same soil. We performed a plant–soil feedback study with 37 grass, forb and legume species, to condition the soil and then tested the effects of plant‐induced changes in soil microbiomes on the growth of the commercially important cut‐flower Chrysanthemum in presence and absence of a pathogen. We analysed the fungal and bacterial communities in these soils using next‐generation sequencing and examined their relationship with plant growth in inoculated soils with or without the root pathogen, Pythium ultimum. We show that a large part of the soil microbiome is plant species‐specific while a smaller part is conserved at the plant family level. We further identified clusters of plant species creating plant growth promoting microbiomes that suppress concomitantly plant pathogens. Especially soil inocula with higher relative abundances of arbuscular mycorrhizal fungi caused positive effects on the Chrysanthemum growth when exposed to the pathogen. We conclude that plants differ greatly in how they influence the soil microbiome and that plant growth and protection against pathogens is associated with a complex soil microbial community.

The Conifer Root and Stem Rot Pathogen (Heterobasidion parviporum): Effectome Analysis and Roles in Interspecific Fungal Interactions.

Heterobasidion parviporum Niemelä & Korhonen is an economically important basidiomycete, causing root and stem rot disease of Norway spruce (Picea abies (L.) Karst) in Northern Europe. The H. parviporum genome encodes numerous small secreted proteins, which might be of importance for interacting with mycorrhiza symbionts, endophytes, and other saprotrophs. We hypothesized that small secreted proteins from H. parviporum (HpSSPs) are involved in interspecific fungal interaction. To identify HpSSP-coding genes potentially involved, we screened the H. parviporum effectome and compared their transcriptomic profiles during fungal development and in planta tree infection. We further conducted phylogenetic analysis, and identified a subset of hypothetical proteins with nonpredicted domain or unknown function as HpSSPs candidates for further characterization. The HpSSPs candidates were selected based on high-quality sequence, cysteine residue frequency, protein size, and in planta expression. We subsequently explored their roles during in vitro interaction in paired cultures of H. parviporum with ectomycorrhizal Cortinarius gentilis, endophytic Phialocephala sphaeroides, saprotrophs (Mycena sp., Phlebiopsis gigantea, and Phanerochaete chrysosporium), respectively. The transcriptomic profile revealed that a large proportion of effector candidates was either barely expressed or highly expressed under all growth conditions. In vitro dual-culture test showed that P. sphaeroides and C. gentilis were overgrown by H. parviporum. The barrage zone formation or no physical contact observed in paired cultures with the saprotrophs suggest they had either combative interaction or antibiosis effect with H. parviporum. Several HpSSPs individuals were up- or downregulated during the nonself interactions. The results of HpSSPs gene expression patterns provide additional insights into the diverse roles of SSPs in tree infection and interspecific fungal interactions.

Connection the Rhizomicrobiome and Plant MAPK Gene Expression Response to Pathogenic Fusarium oxysporum in Wild and Cultivated Soybean.

Little known the connections between soybeans mitogen-activated protein kinase (MAPK) gene expression and the rhizomicrobiome upon invasion of the root pathogen Fusarium oxysporum. To address this lack of knowledge, we assessed the rhizomicrobiome and root transcriptome sequencing of wild and cultivated soybean during the invasion of F. oxysporum. Results indicated F. oxysporum infection enriched Bradyrhizobium spp. and Glomus spp. and induced the expression of more MAPKs in the wild soybean than cultivated soybean. MAPK gene expression was positively correlated with Pseudomonadaceae but negatively correlated with Sphingomonadaceae and Glomeraceae in both cultivated and wild soybean. Specifically, correlation profiles revealed that Pseudomonadaceae was especially correlated with the induced expression of GmMAKKK13-2 (Glyma.14G195300) and GmMAPK3-2 (Glyma.12G073000) in wild and cultivated soybean during F. oxysporum invasion. Main fungal group Glomeraceae was positively correlated with GmMAPKKK14-1 (Glyma.18G060900) and negatively correlated with GmRaf6-4 (Glyma.02G215300) in the wild soybean response to pathogen infection; while there were positive correlations between Hypocreaceae and GmMAPK3-2 (Glyma.12G073000) and between Glomeraceae and GmRaf49-3 (Glyma.06G055300) in the wild soybean response, these correlations were strongly negative in the response of cultivated soybean to F. oxysporum. Taken together, MAPKs correlated with different rhizomicrobiomes indicating the host plant modulated by the host self-immune systems in response to F. oxysporum.

Isolasi dan Identifikasi Endomikoriza pada Perakaran Tanaman Jagung (Zea mays L.) Dataran Sedang serta Perbanyakannya pada Tingkat Kadar Air Tanah Berbeda

Isolation and Identification of Endomycorrhizal on Corn Root (Zea mays L.) at Medium Plain and its Propagation at Different Soil Water Level. Endomycorrhizal has several benefits that can increase the absorption of water and nutrients, protect plants from root pathogens and toxic elements, play a role in the improvement of soil structure, and increase the solubility of nutrients. The purpose of this research is to find out the types endomycorrhizal contained in the corn roots at medium plains in Gianyar Regency, and the influence of different soil water level to endomycorrhizal ability to reproduce spores. This research was conducted from September 2017 to February 2018. The method of the research includes exploration, isolation, identification, propagation of spores endomycorrhizal, and soil samples analysis. Isolation and identification result found 2 genus of spores endomycorrhizal that was Glomus and Acaulospora, with various spore amount and the level of infection endomycorrhizal was very high with percentage of 83.33-86.67%. Spores propagation test results showed that the highest percentage enhacement of spores endomycorrhizal amount was found in the third soil sampling location in soil water level of 40% field capacity treatment with percentage of 551.85%. The level of endomycorrhizal infections at the roots of all treatment of soil sampling location and soil water level were very high with percentage of 100%.

Jasmonate-Induced Defense Mechanisms in the Belowground Antagonistic Interaction Between Pythium arrhenomanes and Meloidogyne graminicola in Rice.

Next to their essential roles in plant growth and development, phytohormones play a central role in plant immunity against pathogens. In this study we studied the previously reported antagonism between the plant-pathogenic oomycete Pythium arrhenomanes and the root-knot nematode Meloidogyne graminicola, two root pathogens that co-occur in aerobic rice fields. In this manuscript, we investigated if the antagonism is related to imbalances in plant hormone levels, which could be involved in activation of plant defense. Hormone measurements and gene expression analyses showed that the jasmonate (JA) pathway is induced early upon P. arrhenomanes infection. Exogenous application of methyl-jasmonate (MeJA) on the plant confirmed that JA is needed for basal defense against both P. arrhenomanes and M. graminicola in rice. Whereas M. graminicola suppresses root JA levels to increase host susceptibility, Pythium inoculation boosts JA in a manner that prohibits JA repression by the nematode in double-inoculated plants. Exogenous MeJA supply phenocopied the defense-inducing capacity of Pythium against the root-knot nematode, whereas the antagonism was weakened in JA-insensitive mutants. Transcriptome analysis confirmed upregulation of JA biosynthesis and signaling genes upon P. arrhenomanes infection, and additionally revealed induction of genes involved in biosynthesis of diterpenoid phytoalexins, consistent with strong activation of the gene encoding the JA-inducible transcriptional regulator DITERPENOID PHYTOALEXIN FACTOR. Altogether, the here-reported data indicate an important role for JA-induced defense mechanisms in this antagonistic interaction. Next to that, our results provide evidence for induced expression of genes encoding ERF83, and related PR proteins, as well as auxin depletion in P. arrhenomanes infected rice roots, which potentially further contribute to the reduced nematode susceptibility seen in double-infected plants.

At the root of the problem.

This study identifies a role for members of the endophytic root microbiome and their functional traits in plant protection from the fungal root pathogen Rhizoctonia solani.

Mycorrhiza induced tolerance in Cucumis sativus against root rot caused by Pythium ultimum depends on fungal species in the arbuscular mycorrhizal symbiosis

Biocontrol traits of arbuscular mycorrhizal fungi (AMF) against root pathogens are well known, but information on biocontrol mode of action and biocontrol efficiency of AMF species are limited.In this study, we investigated the influence of three AMF on root rot in Cucumis sativus caused by Pythium ultimum. Plants were grown in symbiosis with the AMF Funelliformis mosseae, Rhizophagus irregularis, Claroideoglomus claroideum or left uninoculated, and 14 days after sowing half of the plants were inoculated with P. ultimum. Plants were harvested 14, 21 and 28 days after sowing and analyzed for dry weights, AMF colonization and P. ultimum infection. The results showed three scenarios of biological control by the AM symbioses: AM with F. mosseae fully counteracted the plant growth depression caused by the pathogen; R. irregularis AM resulted in plant growth depression, but counteracted plant growth depression by the pathogen; AM symbiosis with C. claroideum caused plant growth depression and had no biological control effect against P. ultimum.Overall, the study showed biocontrol features of AMF in terms of tolerance induction though depending on species of AMF. Such differential traits of AMF should be considered when developing biocontrol strategies against root rot in cucumber.

Fosetyl-aluminium injection controls root rot disease affecting Quercus suber in southern Spain

In Spain, natural and managed cork oak woodlands are severely affected by decline caused by the root rot oomycetes Phytophthora cinnamomi and Pythium spiculum. The need for environmental-friendly disease management makes the use of resistance inducers a suitable option. As the use of phosphite is prohibited in Spain, trunk injections of fosetyl-aluminium were tested in a seminatural cork oak woodland (dehesa). Sixty cork oaks in three different defoliation classes (asymptomatic, slight, and moderate defoliation) were selected for fosetyl- aluminium or control (water) trunk injections, and periodically checked for defoliation and presence of both pathogens in roots and rhizosphere soil. Three years after treatments, fosetyl-aluminium injection significantly decreased defoliation in treated cork oaks in comparison with water-injected controls, regardless of the initial defoliation class considered. Changes in inoculum density in the rhizosphere or presence of the two pathogens in roots were not significantly dependent on treatment. However, a trend to a lower presence of pathogens in roots of treated oaks was observed with increasing soil inoculum densities. Fosetyl-aluminium, a phosphonate fungicide registered in the European Union, was experimentally proved to protect cork oaks against root rot caused by P. cinnamomi and Py. spiculum, even exhibiting a therapeutic effect on preexisting infections. This effective measure can therefore be used to fight against this highly destructive disease in seminatural woodlands and in protected natural ecosystems.

Towards biocontrol of ophiostomatoid fungi by plant growth-promoting rhizobacteria

ABSTRACTOphiostomatoid fungi, Leptographium terebrantis and Grosmannia huntii, are among the most important agents of wood blue stain and root disease of Pinus species. A number of physical, chemical, and cultural strategies adopted to minimise the impact of these fungi are of limited success. Biological control of tree diseases with plant growth-promoting rhizobacteria (PGPR) is attractive given that they provide an alternative and supplement to synthetic chemicals without negative impact on the environment. While a significant number of studies have shown the ability of PGPR to control pathogens of agricultural plants, studies to understand the activity of PGPR against ophiostomatoid fungal pathogens of conifers is still lacking. To understand the utility of PGPR in treating blue stain in woods, twenty-seven Bacillus velezensis strains and single strains of Paenibacillus peoriae and B. altitudinis that had previously shown antibiosis against plant pathogens from six different genera were tested for in vitro antibiosis against L. terebrantis and G. huntii. To understand the efficacy of PGPR in controlling root-disease, Bacillus pumilus SE-34 and INR7, and Serratia marcescens (90–166), previously reported to have efficacy against a root pathogen in conifer, were tested for their capacity to induce resistance of P. taeda to these fungi. All PGPR strains inhibited the growth of L. terebrantis and G. huntii in vitro. In a second experiment, specific PGPR treatment resulted in increased seedling dry matter biomass and reduction of diseased tissue. The results demonstrate tested PGPR strains may have potential as biocontrol agents to the tested ophiostomatoid fungi.

The Current Survey of Indigenous Arbuscular Mycorrhizal Fungi of Wheat (Triticum aestivum) in Benghazi’s Coastal Plain

Rhizospheres of crop plants are complexes of chemical and microbial interactions. Of importance, arbuscular mycorrhizal fungi (AMF) are beneficial microorgansims associated with roughly eighty-percent of terrestrial land plants. In this mutualistic symbiosis, the fungus receives the photosynthetic product (sugar) fixed from its host by photosynthesis. In return, the host plant gains a plethora of benefits from the fungus such as enhanced nutrient uptakes, protection against both biotic (soil-borne root pathogens, insect attack) and abiotic (drought, heavy metal pollution, and soil salinity) stresses. Taxonomically, AMF belong to a new erected phylum called Glomeromycota. The field study was conducted in a farm owned and supervised by The Great Man-Made Project in February 2019. The present study was performed to determine the presence or the absence of AMF in a field cultivated with wheat crops (Triticum aestivum, L.) during the vegetative stage, and also to investigate soil physiochemical properties effect on AMF colonization. Results showed that colonization of wheat plant roots were significantly low. The result clearly implies that high-input fertilizers viz., phosphorus fertilization, and agricultural practices such as intensive tillage drastically reduced AMF colonization.

Does Inoculation with Arbuscular Mycorrhizal Fungi Reduce Trunk Disease in Grapevine Rootstocks?

Ilyonectria is a weak pathogen known for causing black foot disease in young vines, infecting roots and vascular tissues at the basal end of the rootstock and restricting the movement of water and nutrients. This negatively impacts vine establishment during transplant into the vineyard. Arbuscular mycorrhizal (AM) fungi are symbiotic fungi that associate with most plants and have been shown to mitigate the infection and effect of pathogens. This greenhouse study was designed to determine if the mycorrhizal fungi could mitigate Ilyonectria infection and whether this was dependent on inoculation timing. ‘Riparia gloire’ grapevine rootstocks (Vitis riparia) were infected with Ilyonectria either after AM fungi, at the same time as AM fungi, or to roots that were not inoculated by AM fungi. We measured the abundance using specific markers for both the pathogen and AM fungi. Colonization by AM fungi did not suppress Ilyonectria, but instead increased the abundance of Ilyonectria. Further, mycorrhizal rootstocks did not have enhanced growth effects on physiological parameters when compared to non-mycorrhizal rootstocks. These findings stand in contrast to the general perception that AM fungi provide protection against root pathogens.

Common and unique rhizosphere microbial communities of wheat and canola in a semiarid Mediterranean environment

In wheat (Triticum aestivum L.)-based cropping systems, rotation crops often provide a yield benefit to the following wheat crop. This has been documented for legume crops and canola (Brassica napus L.). In the present study, we examined bacterial and fungal communities in the rhizosphere of wheat and canola at six paired locations on fall and spring sampling dates using high-throughput sequencing of marker genes (bacterial 16S rRNA gene and fungal internal transcribed spacers). Soil type was the primary driver of both fungal and bacterial communities, with the communities of locations geographically closest, and with the same soil type, clustering together. Season (fall vs spring sampling) had the next strongest effect, followed by the crop species. Differences between the wheat and canola were more evident in the spring than in the fall. However, in contrast, bacterial and fungal species richness and diversity were not related to location or season, and instead were consistently higher in the rhizosphere of canola compared to wheat. Many bacterial groups were shared across both crop species, especially Janthinobacterium and Kaistobacter. Bacterial communities of wheat in the fall were dominated by Actinomycetes and Acidobacteria. But in the spring, these communities shifted to fast growing bacterial copiotrophs, including Pseudomonas, Janthinobacterium, Flavobacterium, Oxalobacteraceae, and Sphingobacteriaceae. Saprotrophic fungi such as Ulocladium, Mortierella, Cryptoccocus, Chaetomium, Penicillium and Trichoderma were also common to, and equally abundant in, the rhizosphere of both crops. Potential wheat root pathogens such as Thanatephorus (Rhizoctonia) Ceratobasidium, Oculimacula, Typhula, and Microdochium were more abundant in the wheat rhizosphere compared to canola. In conclusion, most of the communities of fungi and bacteria are not “host specific” but colonize the roots of both wheat and canola with differing relative abundance dependent on the season. A much smaller group of taxa were unique to the specific crop. This work provides novel insight into changes in crop rhizosphere communities when canola is introduced into dryland monoculture wheat cropping systems.

Streptomyces griseocarneus R132 controls phytopathogens and promotes growth of pepper (Capsicum annuum)

Endophytic actinomycetes are important for the prospection of biologically active compounds and the development of biotechnological processes in agriculture for the biological control of plant diseases and phytopathogens. Eleven endophytic actinobacteria species isolated from Paullinia cupana were screened for in vitro antibiosis against five phytopathogens and control of anthracnose in pepper (Capsicum annuum) fruits. Cultures of the most active actinobacteria were fractionated with methanol and ethyl acetate, and the anthracnose control capacity of the resulting extracts was evaluated. Actinobacteria-mediated growth promotion and control of root pathogens in pepper plants were evaluated in a greenhouse. Streptomyces griseocarneus R132 (i) inhibited the growth of phytopathogens the most strongly, ranging from 57.24 ± 4.54% (Fusarium oxysporum 46.7) to 73.93 ± 3.71% (Botryosphaeria dothidea CFMAC3); (ii) markedly controlled the development of anthracnose symptoms caused by Colletotrichum gloeosporioides MPU99 in pepper fruits and plants; and (iii) promoted growth of pepper plants, increasing 42% of shoot dry mass. Actinobacteria extracts effectively controlled the anthracnose symptoms and reduced the lesion size by 30% in pepper fruits. Streptomyces griseocarneus R132 is a promising tool for the biological control of both pre- and post-harvest plant pathogens and growth promotion in pepper.

Biocontrol effects of Penicillium griseofulvum against monkshood (Aconitum carmichaelii Debx.) root diseases caused by Sclerotium rolfsiii and Fusarium spp.

The aims of this study were to investigate the biocontrol effects of Penicillium griseofulvum strain CF3 and its mechanisms against soil-borne root pathogens (Fusarium oxysporum and Sclerotium rolfsii) of the medical plant Aconitum carmichaelii Debx. The effects of P. griseofulvum strain CF3 were evaluated with regard to the hyphal growth of S. rolfsii and F. oxysporum, the sclerotial formation and germination of S. rolfsii and its expression of sclerotia-formation-related genes. A field experiment was conducted to explore how strain CF3 controls the severity of soil-borne diseases, promotes the growth of A. carmichaelii plants and mediates shifts in the culturable rhizosphere microbial populations. The results showed that treatment with a cell-free culture filtrate of strain CF3 considerably inhibited the hyphal growth of both S. rolfsii and F. oxysporum, in addition to limiting the sclerotial formation and germination of S. rolfsii. Three genes related to sclerotial formation (ArsclR, ArnsdD1 and ArnsdD2) were predicted in S. rolfsii and their expression was found suppressed by the CF3 treatment. Field application of the CF3 biocontrol agent in a powder form (1·9×1010 conidia per gram of substrate) reduced soil-borne disease severity by 15·0%. The shoot and root growth of A. carmichaelii plants was promoted by 61·6 and 83·1% respectively, as the biocontrol strain massively colonized the rhizosphere soil. The CF3 treatment also markedly reduced the density of some known species harmful to plants while increasing the density of some beneficial species in the rhizosphere soil. Genes related to sclerotia formation of S. rolfsii are predicted for the first time and their expression patterns in the presence of P. griseofulvum strain CF3 are evaluated. This comprehensive study provides a candidate fungal biocontrol strain and reveals its potential mechanisms against S. rolfsii and F. oxysporum in A. carmichaelii plants.

Interactions between dark septate endophytes, ectomycorrhizal fungi and root pathogens in vitro.

Dark septate endophytes (DSEs) are widely distributed worldwide and can promote plant growth. Therefore, they are considered potentially important plant allies, especially in stressful environments. Previous studies have reported that DSEs cohabit roots with other microorganisms such as ectomycorrhizal (ECM), endophytic and pathogenic fungi/oomycetes. However, interactions between different DSE species have not yet been reported, and studies on the interactions between DSEs and other fungi are scarce. Using a simple and reproducible pairwise growth assay in vitro, we studied the synergistic/antagonistic interactions between eight DSEs, two ECM fungi and three root pathogens. Most of the DSE/DSE outcomes were neutral. Interestingly, we identified several DSE strains acting in synergy with other strains, as well as strains that could potentially act as biocontrol agents. Notably, three metal-tolerant DSE strains, namely, Cadophora sp., Leptodontidium sp. and Phialophora mustea, could decrease the growth of the root phytopathogens Pythium intermedium, Phytophthora citricola and Heterobasidion annosum. The present data are discussed in the general context of the use of fungal consortia as inocula in the tree-based phytomanagement of marginal lands.