Search

Microbial diversity of cultivated soil is the key resource for maintaining the functional capacity of agricultural and natural ecosystem. The research aimed to study the prevalence of soil fungi from the soils of rice and napier grass fields. Soil samples were collected from the fields of rice in flooded condition and napier grass in the upland condition at the University farm. Soil fungi were cultured on RB media through the serial dilution method. A total of 13 isolates were cultured, in which 11 from the soil collected from rice cultivated field and 2 from napier grass field. Seven out of 11 isolates collected from rice and 2 from napier grass were selected and identified through the morphological characters such as colony color, mycelium diameter, color and segmentaiton, spore size and color. Mycelium growths were examined on the PDA and RB media. Fungal isolates collected in this study were morphologically identified/ characterized as Aspergillus niger, A. flavus, A. terreus, A. carbonarius, A. nidulans, Alternaria sp., Penicillium and Talaromyces. Fungal species differed among the soils were discussed.

Summary Rice is an important agricultural crop in Vietnam. Nematodes are diverse in soil agroecosystems. However, little is known about their seasonal variation in extremely intensive rice cultivation in tropical regions. The objectives of this study were to investigate the seasonal variation and spatial distribution of the nematode community, and to assess its relationship with the soil chemical property and rice yield. Soils (0-10 cm and 10-20 cm deep) were collected at harvest in spring-summer (S-S), summer-autumn (S-A), and winter-spring (W-S) cultivation in 2017 and 2018. Plant-parasitic nematodes were the largest group and accounted for 47-80 and 79-92% of total nematode abundance in the topsoil and subsoil, respectively. Hirschmanniella was the most dominant taxon whose abundance in topsoil varied from 275-739 in W-S to 1010-1270 indiv. (100 g soil)−1 in the S-S season. Nematode assemblages differed between topsoil and subsoil, and those of topsoil had clear seasonal distribution patterns. Bacterivore nematodes were the predominant group of free-living nematodes, with increasing relative abundance in the topsoil of S-S (average 23.2% of total free-living nematodes) < S-A (average 41.9%) < W-S (average 57.3%). Furthermore, soil in the W-S season had the highest microbial activity in 2018. Soil pH, EC and abundance of Hirschmanniella spp. were significantly negatively related with rice yield. The present results suggest that the presence of Hirschmanniella spp. in soil may be involved in a reduction of rice yield in the triple rice system.

We surveyed diseases of sesame in 10 farmers’ fields at Nay Pyi Taw, Myanmar and did interviews 25 farmers for the occurrence of diseases and its impact on yield in Magway, the major sesame growing area in Myanmar. We found phyllody, charcoal rot (root and stem rot), Alternaria leaf blight, powdery mildew, and leaf curl, based on on-site symptoms and their microscopic observation in Nay Pyi Taw. The disease incidence ranged from 5% to 30% in phyllody, from 10% to 30% in charcoal rot (root and stem rot) and 10% to 40% in Alternaria blight, while leaf curl and powdery mildew were not observed abundantly. According to interviews conducted in Magway, 60% of the farmers suffered from phyllody disease symptoms, 80% from charcoal rot, 48% from Cercospora, 28% bacterial leaf spot and 24% diseases with the symptoms of leaf roll. Most farmers (84%) noticed combinations of diseases symptoms either phyllody or charcoal rot/black and stem rot or Cercospora leaf spot and/or bacterial leaf spot. Yield losses ranged from 5 to 50% by phyllody, from 10 to 75% by charcoal rot (root and stem rot), from 5 to 50% by Cercospora leaf spot, and 5% by bacterial leaf spot. Other abnormal symptoms such as discoloring of root, seedling death and leaf yellowing were also observed and the yield losses ranged from 5 to 50%.There were no significance relations between the actual yield and yield losses estimated by each disease. A half of farmers (54%) burnt the crop residues after harvest, while 45% directly buried them in their fields including plant parts infected with diseases. Although there was no difference in sesame yield between these two practices, the average yield was higher by 15% in farmers with the burnt practice. Only a few farmers applied fungicides. Potential constraints to cause yield reduction and necessary actions to increase sesame yield are discussed.

The Central Dry Zone (CDZ) of Myanmar is home to an estimated 12 million people, provides 35% of Myanmar's grain cropping, but is underdeveloped and food-insecure. We examined the cropping systems of the CDZ to understand the biophysical drivers of those systems, the need for change to improve productivity and sustainability, and how future research and extension might be framed to best serve the rural communities. Data were sourced from (i) published empirical studies and web-based documents produced by the Myanmar Government and international agencies and (ii) a face to face survey of 190 Central Dry Zone farmers. Our analysis indicates that CDZ cropping systems have low productivity which threatens sustainability and future production. Farmers practice traditional cultivation and remove crop residues to use as animal feed, which together deplete soil organic matter reserves and expose the soil to physical degradation. The soils are generally coarse-textured with low water retention, high leaching potential and nutritionally deficient. Nutrient inputs from farm-yard manure and mineral fertiliser are also low. As a consequence, crop nutrient deficiencies are widespread across the CDZ and a major productivity constraint. Mineral-fertiliser use is increasing however, but farmers are conscious of the need for high-quality advice on how best to use these inputs. A narrow range of crops is grown in the CDZ with ca. 80% of the land used to grow pulse and oilseed legumes and sesame and sunflower, but few cereals. The lack of crop diversity exposes farmers to market price fluctuations and the lack of balance between broadleaf and cereal crops results in disease and yield loss. Climate changes further threaten the sustainability and economic viability of grain cropping with increasing temperatures, more erratic rainfall and fewer but more intense rainfall events during the monsoon. Consequences are more floods and dry periods and increased risk of soil erosion. The imperative now is to transition the upland cropping of Myanmar's CDZ to embrace the basic elements of conservation agriculture, i.e. crop diversity, effective weed control, in situ retention of crop residues, optimised crop nutrition and minimal-to-zero soil disturbance, to sustainably increase crop water use-efficiency and system productivity.

Rice, pulses and oilseed crops are major exporting crops in Myanmar. Many plant-parasitic nematodes, such asMeloidogyne incognita,M. javanica,M. graminicola,Ditylenchus angustus,Hirschmanniella oryzae,Heterodera cajaniandPratylenchusspp., have been detected in these crops in different cropping patterns and are considered one of the reasons for their low yields. Previous surveys have shown potential impact to yield losses in the crops. This Forum article provides collective information on species of the major plant-parasitic nematodes, possible damage and available control measures to such economically important crops in Myanmar.

The rice root-knot nematode,Meloidogyne graminicola, and the rice root nematode,Hirschmanniella oryzae, are soil-borne pests causing damage to rice, and the pigeon pea cyst nematode,Heterodera cajani, is a pest to beans and sesame. Real-time PCR primers were designed for quantification. Relationships between the threshold cycle (Ct:y) values and number (no.) of nematodes inoculated () were:M. graminicola: ;H. oryzae: ; andH. cajani: .Meloidogyne graminicolaandH. oryzaewere detected in 25 and 38 out of 50 soils, collected from different fields in the lowland and central area of Myanmar, and their densities ranged from 1.0 to 4779 and from 0.4 to 787 (20 g soil)−1, respectively, whileH. cajaniwas detected only in two fields (3 and 268 (20 g soil)−1). The DNA-based method enables rapid and reliable quantification of the nematodes in soil.

Long-term intensive rice monoculture, triple rice cultivation (rice crops are cultivated three times per year) in the Mekong Delta, Vietnam, causes a reduction in topsoil quality. Rotating rice with an upland crop in a tropical paddy field may improve the soil physicochemical properties but effects on the soil nematode community are unknown. This study was conducted in a triple rice field to evaluate the responses of the nematode community to a crop rotation (the first rice in a year was replaced with sesame and soybean, and the second and third crops were rice) and to organic amendment. The experiment was based on a split-plot design with two factors that were crops (main factor, n = 3) and compost amendment (sub-factor, n = 3). The crops were rice, soybean, and sesame and the sub-factors were cow manure plus rice straw compost, sugarcane compost, and no amendment. Soil samples were taken at harvest of the first crops in topsoil (0–10 cm) and subsoil (10–20 cm) in 2017 and 2018. In 2018, the abundance of free-living nematodes (FLN), which were dominated by bacterivores and fungivores, was greater in upland crops, while that of plant-parasitic nematodes (PPN) was greater in paddy rice. In particular, the density of the most predominant PPN genus, Hirschmanniella, was lower in upland crops than in paddy rice. Cultivation of sesame also reduced the number of the second predominant PPN genus, Bitylenchus, resulted in an increase in the ratio of the free-living to plant-parasitic nematodes. The diversity evenness index (J), Shannon-Wiener (H′) and Hill's indices increased in upland crops compared to those in rice fields in 2018. Crop rotation with sesame or soybean in a paddy field enhanced abundance and biodiversity of FLN and suppressed PPN and thus can be proposed for agricultural sustainability.

A total of 12 soils collected from different agricultural fields, having different backgrounds of organic input, were evaluated for their suppressive potential against Meloidogyne incognita. Second-stage juveniles (J2) of M. incognita were inoculated into the soils and their survival was evaluated. The number of M. incognita J2 5 days after inoculation differed depending on soil and was significantly lower in two soils, suggesting higher suppressiveness against M. incognita in these soils. This was confirmed by an experiment using tomato as a test plant, in which the gall formation was significantly lower in the two soils than in other soils. To estimate the contribution of below-ground biota to the suppressiveness, numbers of nematodes (predator, omnivore, bacterivore and fungivore) and other soil fauna such as tardigrades and rotifers, were counted. Some soil chemical and biological properties were also measured. Results from multiple linear regression analysis suggested that the number of rotifers, microbial activity, soil pH and total C may be involved in the suppression. The relationship between the suppressiveness and soil chemical and biological parameters is discussed.

We have developed a direct quantification method using real-time PCR for various plant-parasitic nematodes. Firstly, specific primers were designed for the root-knot nematode Meloidogyne incognita, the root-lesion nematode Pratylenchus penetrans, the potato cyst nematode Globodera rostochiensis and the soybean cyst nematode Heterodera glycines. A DNA extraction method was then developed beginning with 20 g of soil, a relatively large amount of soil but a necessary amount in the consideration of heterogeneous distribution of nematodes in soil. To estimate the density of the target nematode in soil, calibration curves for each plant-parasitic nematode were obtained by inoculating different numbers of the target nematode and then extracting DNA from the soils. The detection limit was 4-5 nematodes (20 g soil)−1. This method was applied to nematode diagnostics. Soil sampling was done when transplanting of radish and sweet potato in fields was taking place, and the density of plant-parasitic nematodes was measured using both the Baermann funnel extraction method and real-time PCR methods. In some soils, P. penetrans and M. incognita were not found with the Baermann method but were detected with the real-time PCR method. At harvest, damage to crops was evaluated and its relationship with initial densities was investigated. The real-time PCR method more precisely predicted damage to radish and sweet potato by nematodes and was considered to be a powerful tool in the diagnosis of nematode diseases.

Multiplex real-time PCR assays were developed to quantify multiple species of Meloidogyne incognita, Pratylenchus penetrans, Globodera rostochiensis and Heterodera glycines in soil. The probes specific for P. penetrans and H. glycines are labelled with a fluorescence molecule, FAM, and those for M. incognita and G. rostochiensis with ROX. The primers and probes are species-specific to P. penetrans, but group-specific to the other species. DNA was extracted from suspensions containing each nematode and multiplex Cycleave® PCR assays were done for pairs of P. penetrans and M. incognita, P. penetrans and G. rostochiensis, or G. rostochiensis and H. glycines. The results revealed that the target nematode, except for H. glycines, was quantified in the presence of less than 100 times that of the other nematode (competitor), but underestimated in the presence of 1000 times the competitor. Such underestimation was solved by the use of SYBR Green I real time PCR assays targeting a single species. Multiplex PCR assay for P. penetrans and M. incognita was done using environmental DNA (eDNA) extracted from a soil naturally infested with the nematodes. Results quantified both species. Multiplex assay using eDNA may enable a sensitive and simultaneous detection of P. penetrans and M. incognita or P. penetrans and G. rostochiensis in soil although caution is needed in case the existing ratio is biased to one of the species.

A real-time PCR (quantitative PCR: qPCR)-based detection method of the root-knot nematode Meloidogyne incognita was developed for sandy soils, the major soil type in sweet potato cultivated fields in Tokushima prefecture, Japan. Different numbers (5, 20, 80, 200 and 500) of second-stage juveniles (J2) were artificially added into 20 g of an air-dried sandy soil not containing M. incognita. To make homogenous samples, soil was homogenised by two different ways (ground with either a mortar and pestle or ball mill) and then 0.5 g of the soil was used for DNA extraction. There was a strong negative correlation in each homogenisation method between the cycle threshold number (Ct) and inoculated numbers of M. incognita J2. The Ct values were consistently lower and their variations among replicates were smaller in the samples ground with ball mill, suggesting that grinding with ball mill may be suitable for the preparation of soil for DNA extraction. Sandy soils were collected from sweet potato fields in Tokushima prefecture at the transplanting and harvesting times. Damage to sweet potato caused by M. incognita was also evaluated in some of the fields. At the transplanting time, no M. incognita was extracted in all the soils by the Baermann funnel method, while detection in the qPCR method ranged from zero to 4 210 000 J2 equivalent (20 g soil)–1. Heavy damage was observed in fields with more than 500 equivalent M. incognita J2 (20 g soil)–1. By contrast, very few galls were observed in fields with fewer than four individuals (20 g soil)–1. At harvest, zero to >1000 individuals of M. incognita was counted by the Baermann method and there was a significant correlation in estimated numbers of M. incognita between the two methods. However, the estimated numbers were 15 times higher in the qPCR method than in the Baermann method. These results indicate that direct quantification of M. incognita based on the qPCR method might enable a sensitive diagnosis to predict damage by the nematode.

The primers PCN280f and NEPCN398r were designed for the quantitative detection of the potato-cyst nematode Globodera rostochiensis using real-time polymerase chain reaction (PCR). One, five, 50, 125 and 250 individuals of the second-stage juveniles (J2) of G. rostochiensis were mixed with various stages of vermiform Caenorhabditis elegans to make a total of 500 individuals and DNA was extracted from the nematode mixture. There was a significant correlation (r 2 = 0.9355, P

Pratylenchus penetrans causes damage to different vegetables such as radish, carrot, burdock, lettuce, butterbur, and strawberry (Chikaoka, 1983) and is considered as one of the most important nematode pests for Japanese agriculture. Because it is known that there is a significant correlation between the population density of P. penetrans in soil and degree of damage on the host (Chikaoka, 1983; Ohbayashi, 1989), reliable and rapid identification and counts of the causal agent is critically important for successful management of the nematode pest. Mandani et al. (2005) also emphasized that precise identification and knowledge about the density of nematodes in field soil are necessary to develop effective integrated pest control. However, identification of nematodes based on their morphological characteristics is sometimes difficult, especially for inexperienced nematologists. In addition, to detect a single P. penetrans individual in a sample with an abundant number of nematodes is tedious and time-consuming. Recently, characteristic 18S rDNA has been used as a biomarker to identify soil nematodes (Foucher and Wilson, 2002; Floyd et al., 2005; Bhadury et al., 2005; Madani et al., 2005; Jones et al., 2006). Specific primers are also reported for differentiating Pratylenchus spp. (Uehara et al., 1998; Waeyenberge et al., 2000) and these are useful to identify P. penetrans if DNA is extracted from individual nematodes as well as to estimate the presence of P. penetrans in a nematode community consisting of a variety of species. However, these primers are not suitable to quantify P. penetrans in a complex community. Thus, the purpose of this study was to develop a rapid and precise method for the detection and quantification of P. penetrans in a nematode community using real-time PCR.