Decomposition of cellulose strips in relation to climate,litterfall nitrogen,phosphorus and C/N ratio in natural boreal forests

Isolates of Alternaria alternata, Botrytis cinerea, Fusarium oxysporum, Penicillium sp., Rhizoctonia solani, Stemphylium sp., Thielaviopsis basicola, and Verticillium dahliae were cultured on potato–dextrose agar (PDA), barley-sand and alfalfa-sand substrates in petri-dish or in column microcosms. N-mineralization by fungi and fungal-feeding nematodes in combination or fungi alone was assessed. Numbers of Aphelenchus avenae or Aphelenchoides composticola supported by the fungi were measured every 7 days. Times for full colonization of the substrates by fungi ranged from 5 to 15 days. Rhizoctonia solani and B. cinerea on PDA supported the largest A. avenae and A. composticola populations, respectively. Penicillium sp. was a nonhost for A. composticola and A. avenae. Rhizoctonia solani, B. cinerea, V. dahliae, and F. oxysporum supported significantly more nematodes than the other four fungal species. The ranked order of fungi based on the amount of N mineralized in columns free of nematodes was A. alternata (with a rate of 0.052 μg N/g-sand per day), Stemphylium sp., V. dahliae, T. basicola, B. cinerea, F. oxysporum, R. solani, and Penicillium sp. (with a rate of 0.0045 μg N/g-sand perday). The presence of A. avenae resulted in significant increases in mineral N, compared to nematode-free columns colonized by F. oxysporum, R. solani, and T. basicola alone. The presence of A. composticola resulted in significant increases in mineral N, compared to nematode-free columns colonized by A. alternata, B. cinerea, F. oxysporum, and R. solani alone. There was more mineral N incolumns in the presence of A. composticola than A. avenae in most cases. This revised version was published online in August 2006 with corrections to the Cover Date.     

Effect of temperature on growth and nitrogen mineralization of fungi and fungal-feeding nematodes

Dish and column microcosms containing alfalfa-sand medium were established to determine effect of temperature on growth and N mineralization ability of two fungi (Rhizoctonia solaniand Botrytis cinerea) and two nematodes (Aphelenchus avenaeand Aphelenchoides composticola). The microcosms were incubated at 15, 20, 25 and 29 °C for 21 days. In the dish microcosms, hyphal growth rates of both fungal species increased with temperature in the range of 15–25 °C. Above that temperature range, the growth rate of R. solani remained almost constant while that of B. cinereadecrease considerably. The population growth rate of A. avenae increased with temperature between 15 and 29 °C on colonies of R. solani and B. cinerea in dish microcosms. The growth rate of A. composticola also increased in the range of 15–25 °C but decreased greatly beyond that temperature range independent of the fungal species as food source. Inorganic N (NH₄ ⁺ + NO₃ ^–) was collected from each column microcosm by leaching every 3 days. In the columns containing R. solani, there was a significant effect of temperature on the amount of N detected in the fungus+A avenaeor A. composticolabut not in the fungus alone columns. The total amount of N was greatest at 29 °C for A. avenaeand at 20 °C for A. composticola columns, concurrent with the population growth rates of the nematodes. In the columns containing B. cinerea, the effect of temperature on the amount of inorganic N was not significant in either the fungus alone or fungus+nematode columns, although the population growth rates of the both nematode species were highest at 20 °C. For B. cinerea, the N amount across temperatures was the same or larger for the fungus alone as for the fungus+nematode columns. In general, the contribution of fungal-feeding nematodes to N mineralization was small in any combinations of fungus and nematode species at any temperature. Similarity in C/N ratio of the fungal and nematode biomass, organic substrate C/N ratios too low for measurable increase in net mineralization by the nematodes and small reproduction of the nematodes in the column microcosms were probable contributory factors.     

Evaluation of five sugar beet varieties for root-knot nematode and root-rot fungal infection

Survey results during 2010–2011 season revealed that the Meloidogyne spp., Helico–tylenchus spp. and Tylenchorhynchus spp. were the common plant parasitic nematodes in the rhizospheres of sugar beet in El-Behera, El-Fayoum and Beni Sueif Governorates. Aspergillus spp., Aspergillus niger, Fusarium spp., Penicillium spp., Penicillium chrysogenum, Penicillium citrinum, Rhizoctonia spp., Rhizopus nigricans, Trichoderma spp. and others were also the common fungi in the same rhizospheres. The rhizosphere of El-Behera Governorate was highly infected with Meloidogyne spp., Fusarium spp. and Rhizoctonia spp., compared to the rhizospheres of El-Fayoum and Beni Sueif, respectively. Evaluation of five of sugar beet cultivars, viz. Chems, Dema-Poly, DS 9001, Manila and Ras-Poly to infection, with Meloidogyne incognita (root-knot nematode), Fusarium solani and Rhizoctonia solani (root rot disease) was carried out under naturally field infection condition in the Nubariya region, Behera Governorate during 2011–2012 season. Host susceptibility rating revealed that the varieties of Ras-Poly, DS 9001 and Manila can be considered as susceptible, while the varieties of Dema-Poly and Chems can be considered as highly susceptible. Pathological results showed that the varieties of Dema-Poly and Ras-Poly were highly infected with F. solani, while not infected with R. solani. The varieties of DS 9001, Manila and Chems were moderately infected with the two pathogens.     

Association of Nematodes and Dogwood Cankers

Dogwood canker is a serious production problem of unknown etiology. From May 1985 through April 1989, cankers from 290 flowering dogwood trees in 15 separate nurseries were sampled for nematodes. Seventy-three percent (213) of the cankers contained nematodes. Panagrolaimus rigidus (Schneider) Thorne (115/290) and Aphelenchoides spp. (91/290) were the most frequently collected taxa. Panagrolaimus rigidus was reared on 2% water agar with unidentified bacteria as the food source. Aphelenchoides spp. were reared in antibiotic-amended agar culture with the fungus Glomerella cingulata (Stoneman) Spauld. &Schrenk as a food source. Repeated attempts to culture Aphelenchoides spp. on dogwood callus tissue were unsuccessful. Artificially created stem wounds inoculated with combinations of Aphelenchoides spp. and P. rigidus callused completely in 60 days with no indication of canker development. Very low numbers of nematodes were recovered from inoculated trees, but P. rigidus and one Aphelenchoides sp. were efficient dispersers and occurred in treatments other than those in which they were inoculated.     

Widespread Distribution of Fungivorus Aphelenchoides spp. in Blight Cankers on American Chestnut Trees

Previously we showed in laboratory studies that the fungivorus nematode, Aphelenchoides hylurgi, was attracted to and fed upon the chestnut blight fungus, Cryphonectria parasitica, from American chestnut bark cankers and was a carrier of biocontrol, white hypovirulent C. parasitica strains. In the present field study, we recovered Aphelenchoides spp. in almost all (97.0 %) of 133 blight canker tissue assays (three 5-g samples each) from four eastern states. High mean population densities (227 to 474 nematodes per 5 g tissue) of Aphelenchoides spp. were recovered from cankers in Virginia, West Virginia, and Tennessee but not from New Hampshire (mean = 75 nematodes per 5 g tissue). Overall, most canker assays yielded population densities less than 200 nematodes per 5 g tissue. All of 12 very small or young cankers yielded a few to many Aphelenchoides spp. Regression analysis indicated greatest recovery of Aphelenchoides spp. occurred in the month of May (r = 0.94). The results indicate that Aphelenchoides spp. appear to be widespread in blight cankers on American chestnut trees and could play a role in biocontrol of chestnut blight.     

Impact of biocontrol agents in combination with Prosopis juliflora (Swartz) DC. in controlling the root-infecting fungi of leguminous crops

Biocontrol agents, viz., Rhizobium meliloti, Pseudomonas aeruginosa, Aspergillus niger and Trichoderma harzianum, are used as seed dressing and soil is amended with Prsosopis juliflora (Swartz) DC. plant parts like stem, leaves and flower at 1% w/w for the control of root-rot fungi. All antagonists suppressed the infection of root-rot fungi viz., Fusarium spp., Rhizoctonia solani and Macrophomina phaseolina whereas the infection of R. solani and M. phaseolina was controlled when cowpea (Vigna unguiculata L.) and mungbean (Vigna radiata L.) seeds were treated with P. aeruginosa and T. harzianum and the soil was amended with P. juliflora leaves’ powder at 1% w/w. However, germination of both the crops was observed in all treatments. Growth parameters like shoot and root length, shoot and root weight, and leaf area significantly increased in all the treatments as compared to the control parameters. P. aeruginosa and T. harzianum in combination with soil amendment with P. juliflora plant parts at 1% w/w were the most effective for the control of root-rot fungi of leguminous plants.     

An integrated approach to managing Rhizoctonia solani on maize in marginal soils: field studies

Abstract

A study was conducted over two seasons in a marginal soil with an acid saturation of 54%. A plant growth promoting rhizobacterium, Bacillus megaterium, a commercial biocontrol agent, Trichoderma harzianum Strain kd (Eco-T^®), and soluble potassium silicate were used in this study. The objective was to control maize yield reduction caused by Rhizoctonia solani AG2 root rot isolated from infected maize. R. solani reduced maize yields significantly by 34% in the first season. However, the losses decreased in the second season from 34% to 10%. In the first season, combination of T. harzianum, B. megaterium and potassium silicate increased maize yields by 130%. The highest yield in the presence of R. solani was treatments with T. harzianum (216%) followed by T. harzianum plus potassium silicate (214%) and lastly T. harzianum plus B. megaterium (178%). However, in the second season, T. harzianum plus potassium silicate treatment resulted in the highest yields.     

Effects of microbivore species composition and basal resource enrichment on trophic-level biomasses in an experimental microbial-based soil food web

Previous theoretical and empirical evidence suggests that species composition within trophic levels may profoundly affect the response of trophic-level biomasses to enhanced basal resources. To test whether species composition of microbivorous nematodes has such an effect in microbial-based soil food webs, I created three microcosm food webs, consisting of bacteria, fungi, bacterial-feeding nematodes (Acrobeloides tricornus, Caenorhabditis elegans), fungal-feeding nematodes (Aphelenchus avenae, Aphelenchoides sp.) and a predatory nematode (Prionchulus punctatus). The food webs differed in species composition at the second trophic level: food web A included A. tricornus and Aph. avenae, food web B included C. elegans and Aphelenchoides sp., and food web AB included all four species. I increased basal resources by adding glucose to half of the replicates of each food web, and sampled microcosms destructively four times during a 22-week experiment to estimate the biomass of organisms at each trophic level. Microbivore species composition significantly affected bacterivore and fungivore biomass but not bacterial, fungal or predator biomass. Greatest bacterivore and fungivore biomass was found in food web A, intermediate biomass in food web AB, and smallest biomass in food web B. Basal resource addition increased the biomass of microbes and microbivores but did not affect predator biomass. Importantly, microbivore species composition did not significantly modify the effect of additional resources on trophic-level biomasses. The presence of a competitor reduced the biomass of A. tricornus and Aph. avenae, in that the biomass of these species was less in food web AB than in food web A, whereas the biomass of C. elegans and Aphelenchoides sp. was not affected by their potential competitors. The biomass of Aph. avenae increased with additional resources in the absence of the competitor only, while the biomass of A. tricornus and Aphelenchoides sp. increased also in the presence of their competitors. The results imply that microbivore species composition may determine the second-level biomass in simple microbe-nematode food webs, but may not significantly affect biomass at other levels or modify the response of trophic-level biomasses to enhanced basal resources. The study also shows that even if the role of predation in a food web is diminished, the positive response of organisms to increased resource availability may still be hindered by competition. Received: 22 June 1998 / Accepted: 28 August 1998     

Potential Biofumigation Effects of Brassica oleracea var. caulorapa on Growth of Fungi

Biofumigation, as an environment‐friendly alternative to methyl bromide is gaining attention in sustainable agricultural production systems. Based on the biofumigation suppression of growth of three soil‐borne filamentous fungi (Fusarium sp., F. oxysporum and P. aphanidermatum), Brassica oleracea var. caulorapa was selected from eight Brassica and other plant species as a potential material for the purpose. Powdered tissues of plants were confined to individual Petri dishes without physical contact with each of the following 28 fungal isolates from 16 hosts: 13 Fusarium spp., two Verticillium dahliae, two Ceratocystis fimbriata, Bipolaris sorokiniana, Gaeumannomyces graminis, Ceratobasidium cornigerum, Rhizotonia cerealis, Phytophthora parasitica, Phytophthora capsici, Botrytis cinerea, two Rhizoctonia solani, Sclerotinia sclerotiorum and Magnaporthe grisea. The level of suppression of growth 7 days after inoculation varied. Based on growth suppression, the 28 isolates were grouped into three clusters by Fuzzy clustering: Cluster I contains F. proliferatum with 20.5% suppression, Cluster II composed of 15 isolates, Fusarium sp., two V. dahliae, two C. fimbriata, B. sorokiniana, C. cornigerum, two R. solani, R. cerealis, S. sclerotiorum, P. parasitica and M. grisea, with 75.2–100% suppression and Cluster III consisted of 12 isolates; five F. oxysporum, F. solani, F. azysporum, F. moniliforme, F. graminearum, F. verticillioides, G. graminis, P. capsici with 40.7–66.2% suppression. Ceratobasidium fimbriata and V. dahliae were more sensitive to biofumigation than S. sclerotiorum and F. culmorum when different amounts of ground powder were used. One gram of powder could suppress the growth of the former two up to 68.6% and 68.7%, but the growth suppression in the latter two by 12.7% and 24.0%, respectively. These results indicated that the amount of plant tissue to be used should be considered depending on target pathogen species. The swollen root of B. oleracea var. botrytis appeared a better material than the leaf for achieving suppression of growth in pathogenic fungi.     

Identification and Pathogenicity of Rhizoctonia spp. Causing Wirestem of Betula nigra in China

During July 2004, wirestem was frequently observed on the seedlings of Betula nigra at Dehong district in Yunnan Province, China. Isolates of Rhizoctonia spp. consistently obtained from their diseased leaves, roots and stems were identified as belonging to binucleate Rhizoctonia anastomosis groups (AG) AG‐P and AG‐R, and R. solani AG‐I IB and AG‐4 HG‐I, based on cultural characteristics, nuclear staining, anastomisis reaction and analysis of their ITS rDNA region. The percentage of recovery of AG‐P, AG‐1, AG‐R and AG‐4 was 48%, 39%, 8% and 3%, respectively. This is the first report of wirestem of red birch cause by binucleate Rhizoctonia AG‐P and AG‐R, and R. solani AG‐1 IB and AG‐4 HG‐I in China.     

Rhizoctonia spp. Causing Root and Hypocotyl Rot in Phaseolus vulgaris in Cuba

Sixty isolates of Rhizoctonia spp. were obtained from Cuban bean fields during the period 2004–2007. Isolates were characterized with different techniques, including nuclei staining, pectic zymogram, PCR–RFLP analysis of the rDNA–ITS region and sequencing of the rDNA–ITS region. The majority of the isolates were identified as multinucleate Rhizoctonia solani isolates, representing two different anastomosis groups (AGs), AG 2‐2 WB and AG 4 HGI; the remaining isolates were binucleate Rhizoctonia isolates and belonged to AG F and AG A. AG 4 HGI isolates were equally distributed in all soil types; AG 2‐2 isolates were more frequently isolated from cambisols, whereas AG F isolates were related to calcisols. Pathogenicity experiments in vitro and in the greenhouse, revealed that binucleate isolates only caused root rot, whereas R. solani isolates were able to cause root rot and hypocotyl rot. Furthermore, differences in virulence level were observed between R. solani and binucleate isolates and among different AGs. Isolates of R. solani AG 4 HGI and R. solani AG 2‐2 WB were the most aggressive, binucleate isolates of AG F were intermediate aggressive, whereas a binucleate isolate of AG A was weakly aggressive. In contrast with other reports about R. solani in bean, web blight symptoms were never observed during this study.     

Antagonistic assessment of Trichoderma spp. by producing volatile and non-volatile compounds against different fungal pathogens

Trichoderma spp. are well-known biological agents that have significant antagonistic activity against several plant pathogenic fungi. In the present study, Trichoderma spp. were tested in vitro for their antagonistic activity against different spp. of Fusarium and Alternaria viz. Alternaria alternata, A. brassicae, A. solani, Fusarium oxysporum and F. solani using dual plate assay and by the production of volatile and non-volatile compounds. The results obtained revealed that Trichoderma harzianum and T. viride effectively inhibited the growth and spore production of different spp. of Fusarium and Alternaria. The highest growth inhibition was found in A. alternata 62.50% and 60.00% by non-volatile compounds of T. harzianum and T. viride, respectively. Similarly, the volatile compounds inhibit the maximum growth of A. alternata 40.00% and 35.00% by T. harzianum and T. viride, respectively. Volatile and non-volatile compounds of Trichoderma spp. were analysed by GC-MS technique and the properties of distinguished compounds showed antifungal, antimicrobial and antibiotic activities. Volatile compounds of T. harzianum and T. viride showed highest percent abundance for glacial acetic acid (45.32%) and propyl-benzene (41.75%), respectively. In case of non-volatile compounds, T. harzianum and T. viride showed D-Glucose, 6-O-α-D-galactopyranosyl- (38.45%) and 17-Octadecynoic acid (36.23%), respectively. The results of present study confirmed that T. harzianum can be used as a promising biological control agent against Alternaria and Fusarium spp. that cause diseases in various vegetables and crops.     

Biological Control of Soil Pests by Mixed Application of Entomopathogenic and Fungivorous Nematodes

In greenhouse experiments, massive application of the fungivorous nematode, Aphelenchus avenae, in summer at 26-33 C (1 x l0⁵ nematodes/500 cm³ autoclaved soil) or in autumn at 18-23 C (5 x 10⁴ nematodes/500 cm³ autoclaved soil) suppressed pre-emergence damping-off of cucumber seedlings due to Rhizoctonia solani AG-4 by 67% or 87%, respectively. Application of 2 x l0⁵ A. avenae to sterilized soil infested with R. solani caused leafminer-like symptom on the cotyledons, which did not occur in mixed inoculations with the entomopathogenic nematode, Steinernema carpocapsae. When 1 x 10⁶ A. avenae were applied 3 days before inoculation with 100 Meloidogyne incognita juveniles, gall numbers on tomato roots were reduced to 50% of controls. Gall numbers also were suppressed by S. carpocapsae (str. All). Reduction in gall numbers was no greater with mixed application of A. avenae and S. carpocapsae than with application of single species, even though twice the number of nematodes were added in the former case. These nematodes were positively attracted to tomato root tips. Aphelenchus avenae suppressed infection of the turnip moth, Agrotis segetum, but not the common cutworm, Spodoptera litura, by S. carpocapsae.     

Plant parasitic nematodes associated with ornamental plant Pseuderanthemum atropurpureum in Aligarh district of western Uttar Pradesh

A survey was conducted to determine the nematodes associated with the soil, substratum and roots of the ornamental plant, Pseuderanthemum atropurpureum, grown in the Aligarh district of western Uttar Pradesh, India. Ten genera of plant parasitic nematodes, viz. Meloidogyne spp., Helicotylenchus sp., Hemicriconemoides sp., Hoplolaimus sp., Xiphinema sp., Pratylenchus sp., Trichodorus sp., Tylenchorhynchus sp., Aphelenchoides sp. and Rotylenchus sp., were isolated from 345 soil samples collected from 15 different localities. Our study indicates that among the 10 genera of the plant parasitic nematodes, Meloidogyne spp. was widely spread in all the examined localities of Aligarh district, except at Khair. It was observed that the population density and diversity of nematodes in all the soil samples was not uniform. Meloidogyne spp. showed the highest absolute frequency and relative frequency followed by Helicotylenchus sp., Hemicriconemoides sp., Xiphinema sp., Hoplolaimus sp., Pratylenchus sp., Trichodorus sp., Tylenchorhynchus sp., Aphelenchoides sp. and Rotylenchus sp. Since no records are available in the literature related to the association of root-knot nematode in P. atropurpureum, it is worthy to note that this study may be considered as a new hope towards further study of the interaction between the root-knot nematode and ornamental plant P. atropurpureum if any.     

Morphological,molecular and biological characterization of Esteya vermicola,a nematophagous fungus isolated from intercepted wood packing materials exported from Brazil

The nematophagous fungus Esteya vermicola, strain NKF 13222, was purified from an isolate of Bursaphelenchus rainulfi which was intercepted from wood packaging materials originating in Brazil and arriving at Tianjin port in China. The fungus produced two types of conidiogenous cells and conidia, each with different germination modes. More lunate adhesive conidia than bacilloid conidia were produced on nutrient-poor water agar medium. Morphological comparisons revealed the NKF 13222 strain closely resembled the Taiwan strain E. vermicola (ATCC 74485) previously isolated from the pinewood nematode B. xylophilus. Phylogenetic analysis of the β-tubulin and elongation factor 1-α genes indicated that the NKF 13222 grouped with other strains of E. vermicola including the Taiwan strain. This was the first record of E. vermicola from B. rainulfi in South America. Infection tests demonstrated that NKF 13222 was more infective to aphelenchid than tylenchid nematodes and that only lunate adhesive conidia were infectious. The results suggest that the fungus might be a pathogen of plant parasitic nematodes with a broad distribution and provide new information for the potential biocontrol of plant diseases caused by B. xylophilus, Aphelenchoides spp. and Ditylenchus destructor.     

The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant-parasitic nematodes

Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the family Aphelenchoididae capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7–47.4 Mb and are among the smallest in clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is one of the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus. Our results comprehensively improve the understanding of HGT in nematodes.     

Endophytic fungus Piriformospora indica induced systemic resistance against rice sheath blight via affecting hydrogen peroxide and antioxidants

In this study, the effect of endophytic fungus Piriformospora indica on Rhizoctonia solani AG1-IA, causal agent of sheath blight disease, was investigated. In addition, plant defence responses activated in P. indica-inoculated rice plants were analysed. Two-week-old seedlings were inoculated by dipping their roots in P. indica chlamydospore suspension and transferred to pots containing sterilized soil. After two weeks, the seedlings pre-inoculated with P. indica were inoculated with R. solani. Statistical analysis of biological indicators showed that application of P. indica increased both fresh and dry weight of rice shoots and roots, compared to those of uninoculated healthy controls and the samples only inoculated with R. solani. Accumulation of hydrogen peroxide (H₂O₂) and activity of antioxidants such as superoxide dismutase (SOD) and guaiacol peroxidase (GPX) in plants inoculated with P. indica, R. solani, and P. indica-R. solani were investigated. The obtained results revealed that P. indica not only increased the plant biomass, but also delayed the infection process of R. solani and decreased sheath blight severity. Decreased severity of the disease was associated with decreased levels of H₂O₂ and increased SOD activity. Considering the necessity of reducing fungicide application, using P. indica in seedling bed before transplantation to the field could be a novel and effective method to increase rice production and decrease sheath blight progress.     

Measuring abundance,diversity and parasitic ability in two populations of the nematophagous fungus Pochonia chlamydosporia var. chlamydosporia

Abundance, genetic diversity and parasitic ability in the facultative nematode parasite Pochonia chlamydosporia var. chlamydosporia were compared in soils from two sites in Portugal under long-term tomato cultivation where root-knot nematodes (Meloidogyne sp.) were present. Fungal abundance assessed by selective agar or real-time quantitative PCR with specific primers was similar in both soils. PCR fingerprinting of isolates with ERIC primers indicated that the dominant P. c. var. chlamydosporia biotypes (profiles A and B) in both soils were very closely related, although a second biotype (profile C) was detected in one soil. When tomato plants infected with M. incognita were grown in the two soils, only profiles A and B were recovered from eggs. Primers based on polymorphisms in vcp1 demonstrated that isolates with profiles A and B were likely to prefer root-knot nematodes, whereas profile C preferred cyst nematodes. In the soil containing profiles A, B and C, egg parasitism by P. chlamydosporia was estimated at 1% using water agar plates with antibiotics but fewer than 0.2% of M. incognita eggs were shown to be infected with P. c. var. chlamydosporia when using species-specific β-tubulin-PCR primers. In contrast, the soil containing only profile B showed 22% egg parasitism on water agar plates and more than 2.5% of eggs were confirmed as P. c. var. chlamydosporia by species-specific β-tubulin-PCR primers. The results, which reveal limited diversity within the fungus at the two sites, are discussed in relation to biological control of plant-parasitic nematodes.     

In situ and in vitro suppressive effect of agricultural composts and their water extracts on some phytopathogenic fungi

In situ and in vitro experiments were carried out to determine the effect of various composts (leafy fruit compost (LFC), garden compost (GC), and crops compost (CC)) and their water extract on Pythium debaryanum, Fusarium oxysporum f.sp. lycopersici, Sclerotium bataticola. Compost water extract (CWE) of LFC, GC, and CC were found to contain Bacillus spp., Micrococcus spp., Staphylococcus spp. and Corynebacterium spp., and the fungi Aspergillus spp., Rhizopus spp., and Drechslera spp., and various Actinomycetes. In situ results indicated considerable decrease in fungal growth around the unautoclaved compost especially in the case of S. bataticola and F. oxysporum f.sp. lycopersici, compared to the autoclaved compost. In vitro tests showed that concentration of CWE at 5, 10 and 15% (v/v) suppressed the hyphal growth of S. bataticola by 83% using 5% CC and by 94.4% using 5% LFC or 10% GC, and F. oxysporum f.sp. lycopersici by 94.4% using either composts. CWE of GC decreased fungal dry weight of F. oxysporum f.sp. lycopersici by 97.7%, P. debaryanum by 92.8%, and S. bataticola by 84.4%; CC decreased F. oxysporum f.sp. lycopersici by 94%, P. debaryanum by 86.2%, and S. bataticola by 63.3%, while CWE of LFC was the least effective against the tested fungi. CWE produced clear inhibition zones against all the tested fungi. Microflora found in CWE have an important role in suppressing the growth of tested fungi. CWE contained neither antibiotics nor siderophores. The presence of protease, chitinase, lipase and -1,3 glucanase (lysogenic enzymes) in CWE indicates a possible role in fungal degradation.     

Improving the Genome Annotation of Rhizoctonia solani Using Proteogenomics

Background Rhizoctonia solani is a pathogenic fungus that causes serious diseases in many crops, including rice, wheat, and soybeans. In crop production, it is very important to understand the pathogenicity of this fungus, which is still elusive. It might be helpful to comprehensively understand its genomic information using different genome annotation strategies.MethodsAiming to improve the genome annotation of R. solani, we performed a proteogenomic study based on the existing data. Based on our study, a total of 1060 newly identified genes, 36 revised genes, 139 single amino acid variants (SAAVs), 8 alternative splicing genes, and diverse post-translational modifications (PTMs) events were identified in R. solani AG3. Further functional annotation on these 1060 newly identified genes was performed through homology analysis with its 5 closest relative fungi.ResultsBased on this, 2 novel candidate pathogenic genes, which might be associated with pathogen-host interaction, were discovered. In addition, in order to increase the reliability and novelty of the newly identified genes in R. solani AG3, 1060 newly identified genes were compared with the newly published available R. solani genome sequences of AG1, AG2, AG4, AG5, AG6, and AG8. There are 490 homologous sequences. We combined the proteogenomic results with the genome alignment results and finally identified 570 novel genes in R. solani.ConclusionThese findings extended R. solani genome annotation and provided a wealth of resources for research on R. solani.