Profiling Nematode Communities in Unmanaged Flowerbed and Agricultural Field Soils in Japan by DNA Barcode Sequencing

Soil nematodes play crucial roles in the soil food web and are a suitable indicator for assessing soil environments and ecosystems. Previous nematode community analyses based on nematode morphology classification have been shown to be useful for assessing various soil environments. Here we have conducted DNA barcode analysis for soil nematode community analyses in Japanese soils. We isolated nematodes from two different environmental soils of an unmanaged flowerbed and an agricultural field using the improved flotation-sieving method. Small subunit (SSU) rDNA fragments were directly amplified from each of 68 (flowerbed samples) and 48 (field samples) isolated nematodes to determine the nucleotide sequence. Sixteen and thirteen operational taxonomic units (OTUs) were obtained by multiple sequence alignment from the flowerbed and agricultural field nematodes, respectively. All 29 SSU rDNA-derived OTUs (rOTUs) were further mapped onto a phylogenetic tree with 107 known nematode species. Interestingly, the two nematode communities examined were clearly distinct from each other in terms of trophic groups: Animal predators and plant feeders were markedly abundant in the flowerbed soils, in contrast, bacterial feeders were dominantly observed in the agricultural field soils. The data from the flowerbed nematodes suggests a possible food web among two different trophic nematode groups and plants (weeds) in the closed soil environment. Finally, DNA sequences derived from the mitochondrial cytochrome oxidase c subunit 1 (COI) gene were determined as a DNA barcode from 43 agricultural field soil nematodes. These nematodes were assigned to 13 rDNA-derived OTUs, but in the COI gene analysis were assigned to 23 COI gene-derived OTUs (cOTUs), indicating that COI gene-based barcoding may provide higher taxonomic resolution than conventional SSU rDNA-barcoding in soil nematode community analysis.     

Nematode biomass and morphometric attributes as biological indicators of local environmental conditions in Arctic fjords

Kongsfjord and Hornsund are fjords located on the west coast of the island of Spitsbergen that differ in terms of hydrographical conditions and food source availability for benthic organisms. We studied the nematode communities of these two glacial fjords with respect to their morphometric attributes (body length, width, length/width ratio) and biomass (total and individual) to evaluate whether their differences reflect differences in hydrographical and biogeochemical conditions. Sediments collected from Kongsfjord, which contained enhanced marine organic material than sediments from Hornsund, supported nematode communities exhibiting higher biomass and morphological diversity. The roles that the biochemical properties of sediments and food availability play in structuring biological communities were reflected in the wider spectrum of length/width ratio (L/W) and size spectra, with biomass dominance in the higher weight-classes observed in Kongsfjord. In this respect, the appearance of short and plump nematodes in the Kongsfjord nematode assemblage (12% of all nematodes), characterised by a L/W ratio of <12, was striking. This morphotype, which is almost absent in the Hornsund fjord (4%), is considered to be an indicator of well-oxygenated sediments with favourable food sources and may further confirm that the organic material in the Kongsfjord sediments is of higher quality. Furthermore, the homogeneity of sediment composition suggests that the morphological landscape of nematode communities are not structured by granulometry per se, as has been suggested in other studies, but rather by other environmental factors that are indirectly connected with particle size. The results of the present study provide evidence that the morphometric characteristics of nematodes are suitable for detecting differences in sediments, particularly with regard to organic matter availability.     

Botanical nematicides in the mediterranean basin

Achieving food sufficiency in a sustainable manner is a major challenge for farmers, agro-industries, researchers and governments. Amongst agricultural pests supressing crops, root-knot nematodes (Meloidogyne spp.) represent possibly the world’s most damaging one, the control of which has been mainly based on chemical nematicides. In the recent years the environmental, food safety and animal welfare issues pose the need for alternative nematode control measures. Screening naturally occurring compounds in plants, involved in the complex chemical-mediated interactions between a plant and other organisms in its environment, can provide with innovative nematode control measures that can be safely used in integrated pest management programs. The Mediterranean Basin is an area where various soils and climatic conditions allow a vast plant biodiversity providing with chemical botanicals of significant nematicidal potency. This is a review on the Mediterranean botanicals that can control Meloidogyne spp.     

Host location success of root-feeding nematodes in patches that differ in size and quality: A belowground release-recapture experiment

Resource patch size and patch nutritional quality are both important factors influencing local densities of herbivores. The responses of herbivores to resource patch size have been mostly studied in aboveground plant–insect interactions, whereas belowground organisms have received little attention. We studied responses of different root-feeding nematode species associated with marram grass (Ammophila arenaria (L.) Link) to resource patch size and quality. Different nematode species were released in experimental mesocosms filled with dune sand in which we established marram grass patches of varying sizes. Half of the patches of small, medium and large size were fertilized to test if immigration probabilities of nematodes depended on patch quality. We tested the hypotheses that (1) nematodes should aggregate on larger patches and (2) colonization of patches would also depend on patch nutritional quality, with higher nematode recapture rates expected in fertilized patches. Two species (Helicotylenchus pseudorobustus, Hemicycliophora thornei) of the five released species were recaptured in the experiment. The fraction of nematodes immigrating into the rhizosphere of a plant patch increased with patch size (i.e. root biomass), which was in line with predictions of the Resource Concentration Hypothesis. When fractions were recalculated to represent recapture rates per liter of soil, recapture rates of nematodes did not differ among patch sizes, indicating that the increase in recapture rates was directly proportional to the increase in patch size. This suggests that the process through which nematodes located patches was not distinguishable from a random process where entering patches is based on random encounters with patch boundaries. In contrast to our expectation, fertilization had a strong negative effect on patch responses of both nematode species. Our study represents an approach that may be used to explore whether belowground biota behave in similar ways as aboveground biota, in order to determine how perceived differences in environments affect ecological interactions.     

The Surface Coat of Plant-Parasitic Nematodes: Chemical Composition,Origin, and Biological Role—A Review

Chemical composition, origin, and biological role of the surface coat (SC) of plant-parasitic nematodes are described and compared with those of animal-parasitic and free-living nematodes. The SC of the plant-parasitic nematodes is 5-30 nm thick and is characterized by a net negative charge. It consists, at least in part, of glycoproteins and proteins with various molecular weights, depending upon the nematode species. The lability of its components and the binding of human red blood cells to the surface of many tylenchid plant-parasitic nematodes, as well as the binding of several neoglycoproteins to the root-knot nematode Meloidogyne, suggest the presence of carbohydrate-recognition-domains for host plants and parasitic or predatory soil microorganisms (Pasteuria penetrans and Dactylaria spp., for example). These features may also assist in nematode adaptations to soil environments and to plant hosts with defense mechanisms that depend on reactions to nematode surfaces. Surface coat proteins can be species and race specific, a characteristic with promising diagnostic potential.     

Problems and Strategies Associated with Long-term Use of Nematode Resistant Cultivars

Plant-parasitic nematodes are obligate parasites, and planting cultivars that are highly resistant to these organisms places extensive selection pressure on the target species and affects nontarget nematodes as well. Problems encountered with long-term planting of cultivars resistant to nematodes include shifts in nematode races or species and the occurrence of multiple species of nematodes within the same field. These problems can be alleviated to some extent when crop management is used to lessen the selection pressure for change on the nematode populations. Race shifts within populations and possibly shifts between nematode species can be delayed by rotating susceptible cultivars and nonhost crops with resistant cultivars. Nematicides in conjunction with resistant cultivars may be used to limit damage by multiple species of nematodes. Some cultivars have resistance to multiple species of nematodes, but greatly increased research effort is needed in this area. More intensive plant breeding effort will be required to make nematode resistant cultivars competitive in quality and yield with more productive, susceptible cultivars.     

An overview of arbuscular mycorrhizal fungi–nematode interactions

Plant parasitic nematodes and arbuscular mycorrhizal fungi (AMF) share plant roots as a resource for food and space. The interest in AMF-nematode interactions lies in the possibility of enhanced resistance or tolerance of AMF-infected plants to nematodes, and the potential value of this for control of crop pests. Data collated from previous studies revealed a great diversity of AMF-nematode responses and we seek to generalise from these by evaluating and discussing interactions involving three groups of nematodes distinguished by their mode of parasitism: (i) ectoparasites; (ii) sedentary endoparasites; and (iii) migratory endoparasites. Based on proximity in tissue, we expected that the interactions between endoparasites and AMF would be stronger, i.e. more reciprocal effects of endoparasitic nematodes on AMF, than those between ectoparasites and AMF. Contrary to this hypothesis, we found that, relative to AMF-free plants, AMF-infected plants were damaged more by ectoparasites than by endoparasites. Of the sedentary endoparasites, numbers of root-knot nematodes were reduced more by mycorrhizal infection than were those of cyst nematodes. The reduction in nematode damage by AMF was not different for root-knot or cyst nematode infested plants. Migratory endoparasitic nematodes were the only group whose numbers were greater on AMF-infected plants. However, the experiments involving migratory nematodes were characterised by relatively high levels of AMF infection and little nematode damage compared to the other feeding types. The outcomes of the AMF-nematode interactions are determined by many factors during the interactions between organisms and their physical, physiological and temporal environments. Assessing effects by recording plant sizes and total nematode or AMF populations at the end of experiments gives very little information on the mechanisms of the interactions. It is time to stop doing studies of black boxes and time to start observing processes, directly by using microscopy and indirectly by application of molecular genetics.     

The Influence of Trichoderma harzianum on the Root-knot Fusarium Wilt Complex in Cotton

Wilt-susceptible cultivar ''Rowden'' cotton was inoculated wilh Meloidogyne incognita (N), Trichoderma harzianum (T), and Fusarium oxysporum f. sp. vasinfectum (F) alone and in all combinations in various time sequences. Plants inoculated with F alone or in combination with T did not develop wilt, Simultaneous inoculation of 7-day-old seedlings with all three organisms (NTF) produced earliest wilt. However, plants receiving nematodes at 7 days and Fusarium and Trichoderma at 2 or 4 weeks later (N-T-F, N-TF) developed the greatest wilt between 49-84 days after initial nematode inoculation. During the same period, Fusarium added 4 weeks after initial nematode inoculation (N-F) and Fusarium added 4 weeks after initial simultaneous inoculation of nematode and Trichoderma (NT-F) produced the least wilt. The addition of Fusarium inhibited nematode reproduction. Simultaneous inoculation with nematodes and Trichoderma (NT-) resulted in the greatest root gall development, whereas nematodes alone produced the greatest number of larvae. In comparison with noninoculated controls (CK), treatments involving all three organisms inhibited plant growth, plants inoculated with the nematode alone (N-) or with nematodes and Trichoderma (NT-) simultaneously had greatest root weight. Any treatment involving the nematode resulted in fewer bolls per plant and greater necrosis on roots than the noninoculated checks.     

Influence of bacterivorous nematodes on the decomposition of cordgrass

The influence of bacterivorous nematodes (Diplolaimelloides meyli, Diplolaimelloides oschei, Diplolaimella dievengatensis, Panagrolaimus paetzoldi) on the decomposition of a macrophyte (Spartina anglica) in an aquatic environment was investigated by using laboratory microcosm experiments. Several earlier studies have shown enhancement of the decomposition process in the presence of nematodes, but nematode species-specific effects were never tested. In this study four bacterivorous nematode species were applied separately to microcosms to investigate such species-specific influences.No stimulation of the decomposition process nor of the microbial community was observed in the presence of the nematodes, both were highest in the absence of nematodes. However, clear differences were found between nematode treatments. P. paetzoldi reached much higher numbers than the other species, causing a decrease in microbial activity, probably due to (over)grazing. Remarkably this low microbial activity did not result in a slow-down of the decomposition process compared to the other nematode treatments, raising the question whether P. paetzoldi might be able to directly assimilate detrital compounds. Other nematode species reached much lower densities, but nevertheless an influence on the decomposition process was observed. However, this experiment does not support the view that bacterivorous nematodes enhance decomposition rate.The experimental results show that in nematode communities the use of functional groups is inadequate for biodiversity studies. The four nematode species used in this study belong to the same functional group, but are clearly not functionally redundant since they all have a different influence on the cordgrass decomposition. This suggests that the relationship between nematode species diversity and ecosystem functioning may be idiosyncratic.     

Population Development and Influence of Bursaphelenchus xylophilus on Gliocladium virens

Gliocladium virens was isolated from slash pine trees symptomatic and asymptomatic for pine wilt disease with frequencies of 24% and 10%, respectively. Populations of Bursaphelenchus xylophilus, the nematode incitant of this disease, reproduced on this fungus and inhibited its growth. Growth inhibition of the fungus was characterized by an absence of sporulation and by the formation of chains of dark, thick-walled, chlamydospore-like cells. Population increase during a 12-day period following infestation of cultures of the fungus with 10,000 nematodes averaged 3-fold at 16 C, 9-fold at 20 C, and 24-fold at 24 C. In greenhouse studies, nematode recovery from slash pine seedlings coinoculated with both organisms was significantly greater than that obtained from seedlings inoculated with the nematode alone.     

Overview of organic amendments for management of plant-parasitic nematodes, with case studies from Florida

Organic amendments have been widely used for management of plant-parasitic nematodes. Relatively rapid declines in nematode population levels may occur when decomposing materials release toxic compounds, while longer-term effects might include increases in nematode antagonists. Improved crop nutrition and plant growth following amendment use may lead to tolerance of plant-parasitic nematodes. Results depend on a great variety of factors such as material used, processing/composting of material, application rate, test arena, crop rotation and agronomic practices, soil type, climate, and other environmental factors. Reasons for variable performance and interpretation of results from amendment studies are discussed. Case studies of amendments for nematode management are reviewed from Florida, where composts and crop residues are the most frequently used amendments. Plant growth was often improved by amendment application, free-living nematodes (especially bacterivores) were often stimulated, but suppression of plant-parasitic nematodes was inconsistent. Amendments were generally not as effective as soil fumigation with methyl bromide for managing root-knot nematodes (Meloidogyne spp.), and often population levels or galling of root-knot nematodes in amended plots did not differ from those in non-amended control plots. While amendments may improve plant growth and stimulate soil food webs, additional study and testing are needed before they could be used reliably for management of plant-parasitic nematodes under Florida conditions.     

On the potential of basing an ecological typology of aquatic sediments on the nematode fauna: An example from the River Rhine

In Dutch river sediments nematodes can occur in high numbers; azoic seediments are as yet unknown. In aseries of samples takenj from the river Rhine and its estuaries, nematode density varied from 5.000 to 1.7 million per square metre, and about 50 genera were identified. Anoxic conditions appear to have less influence on the nematode abundance than the presence of ammonia. Based on nematode genera, an ecological typology of aquatic soils would appear to be feasible. The use of nematodes in environmental studies is discussed.     

Quantitative Locomotion Study of Freely Swimming Micro-organisms Using Laser Diffraction

Soil and aquatic microscopic organisms live and behave in a complex three-dimensional environment. Most studies of microscopic organism behavior, in contrast, have been conducted using microscope-based approaches, which limit the movement and behavior to a narrow, nearly two-dimensional focal field.¹ We present a novel analytical approach that provides real-time analysis of freely swimming C. elegans in a cuvette without dependence on microscope-based equipment. This approach consists of tracking the temporal periodicity of diffraction patterns generated by directing laser light through the cuvette. We measure oscillation frequencies for freely swimming nematodes.Analysis of the far-field diffraction patterns reveals clues about the waveforms of the nematodes. Diffraction is the process of light bending around an object. In this case light is diffracted by the organisms. The light waves interfere and can form a diffraction pattern. A far-field, or Fraunhofer, diffraction pattern is formed if the screen-to-object distance is much larger than the diffracting object. In this case, the diffraction pattern can be calculated (modeled) using a Fourier transform.²C. elegans are free-living soil-dwelling nematodes that navigate in three dimensions. They move both on a solid matrix like soil or agar in a sinusoidal locomotory pattern called crawling and in liquid in a different pattern called swimming.³ The roles played by sensory information provided by mechanosensory, chemosensory, and thermosensory cells that govern plastic changes in locomotory patterns and switches in patterns are only beginning to be elucidated.⁴ We describe an optical approach to measuring nematode locomotion in three dimensions that does not require a microscope and will enable us to begin to explore the complexities of nematode locomotion under different conditions.     

Coprinus comatus Damages Nematode Cuticles Mechanically with Spiny Balls and Produces Potent Toxins To Immobilize Nematodes

We reported recently a unique fungal structure, called the spiny ball, on the vegetative hyphae of Coprinus comatus (O. F. Müll.:Fr.) Pers. Although some observations regarding the role of this structure were presented, its function remained largely unknown. In this study, we showed that purified (isolated and washed) spiny balls could immobilize and kill the free-living nematode Panagrellus redivivus Goodey highly efficiently. Scanning electron microscopy studies illustrated that the spiny structure damaged the nematode cuticle, suggesting the presence of a mechanical force during the process of nematode immobilization. Severe injuries on nematode cuticles caused the leakage of inner materials of the nematodes. When these structures were ground in liquid nitrogen, their killing efficacy against nematodes was lost, indicating that the shape and the complete structure of the spiny balls are indispensable for their function. However, extraction with organic solvents never lowered their activity against P. redivivus, and the extracts showed no obvious effect on the nematode. We also investigated whether C. comatus was able to produce toxins which would aid in the immobilization of nematodes. In total, we identified seven toxins from C. comatus that showed activity to immobilize the nematodes P. redivivus and Meloidogyne incognita (Kofoid et White) Chitwood. The chemical structures of these toxins were identified with nuclear magnetic resonance, mass spectrometry, infrared, and UV spectrum analysis. Two compounds were found to be novel. The toxins found in C. comatus are O-containing heterocyclic compounds.     

The relationship of potato yield with and without nematicide to density of potato cyst nematodes, lobodera rostochiensis and G. pallida

Trials relating response to nematicide to potato cyst nematode density were conducted initially in the West Midlands and later in other Regions. Thirteen trials, only three of which were within the intensive potato growing areas, conformed to a general pattern with yield losses being largely recouped by nematicide treatment. Five trials, four within the intensive areas, gave no correlation between potato yield and nematode density and an unpredictable response to nematicide. The control of the nematode appeared to be poorer in the latter trials but other factors affecting yield and nematode multiplication may have been involved. It is speculated the main factor might be interaction with fungal organisms e.g. Rhizoctonia or Verticillium. Evidence is presented to show that on several trials the nematicide has an effect other than by controlling potato cyst nematodes. Yield losses caused by potato cyst nematodes are more variable than previous work indicated, probably due to varietal, seasonal or environmental influences.     

Pineapple Nematode Research in Hawaii: Past,Present, and Future

The first written record of pineapple in Hawaii is from 1813. In 1901 commercial pineapple production started, and in 1924 the Experiment Station for pineapple research was established. Nematode-related problems were recognized in the early 1900s by N. A. Cobb. From 1920 to approximately 1945 nematode management in Hawaiian pineapple was based on fallowing and crop rotation. During the 1920s and 1930s G. H. Godfrey conducted research on pineapple nematode management. In the 1930s and 1940s M. B. Linford researched biological control and described several new species of nematodes including Rotylenchulus reniformis. In 1941 nematology and nematode management were advanced by Walter Carter''s discovery of the first economical soil fumigant for nematodes, D-D mixture. Subsequently, DBCP was discovered and developed at the Pineapple Research Institute (PRI). Since 1945 soil fumigation has been the main nematode management strategy in Hawaiian pineapple production. Recent research has focused on the development of the nonvolatile nematicides, their potential as systemic nematicides, and their application via drip irrigation. Current and future research addresses biological and cultural alternatives to nematicide-based nematode management.     

The Effect of Endophytic Fungi on Nematode Populations in Summer-dormant and Summer-active Tall Fescue

Summer-active (continental) and summer-dormant (Mediterranean) tall fescue morphotypes are each adapted to different environmental conditions. Endophyte presence provides plant parasitic nematode resistance, but not with all endophyte strains and cultivar combinations. This study sought to compare effects of four nematode genera on continental and Mediterranean cultivars infected with common toxic or novel endophyte strains. A 6-mon greenhouse study was conducted with continental cultivars, Kentucky 31 (common toxic) and Texoma MaxQ II (novel endophyte) and the Mediterranean cultivar Flecha MaxQ (novel endophyte). Endophyte-free plants of each cultivar were controls. Each cultivar × endophyte combination was randomly assigned to a control, low or high inoculation rate of a mixed nematode culture containing stunt nematodes (Tylenchorhynchus spp.), ring nematodes (Criconemella spp.), spiral nematodes (Helicotylenchus spp.), and lesion nematodes (Pratylenchus spp.). Endophyte infection had no effect on nematode population densities. The cultivar × endophyte interaction was significant. Population densities of stunt nematode, spiral nematode, and ring nematodes were higher for Flecha MaxQ than other cultivar × endophyte combinations. Novel endophyte infection enhances suitability of Flecha MaxQ as a nematode host.     

Fungal chitinases and their biological role in the antagonism onto nematode eggs. A review

Chitin, the most abundant aminopolysaccharide in nature, is a rigid and resistant structural component that contributes to the mechanical strength of chitin-containing organisms. Chemically, it is a linear cationic heteropolysaccharide composed of N-acetyl-D-glucosamine and D-glucosamine units. The enzymatic degradation of chitin is performed by a chitinolytic system with synergistic and consecutive action. Diverse organisms (containing chitin or not) produce a great variety of chitinolytic enzymes with different specificities and catalytic properties. Their physiological roles involve nutrition, parasitism, chitin recycling, morphogenesis, and/or defense. Microorganisms, as the main environmental chitin degraders, constitute a very important natural source of chitinolytic enzymes. Nowadays, the most used method for pest and plant diseases control is the utilization of chemical agents, causative of significant environmental pollution. Social concern has generated the search for alternative control systems (i.e., biological control), which contribute to the generation of sustainable agricultural development. Interactions among the different organisms are the natural bases of biological control. Interest in chitinolytic enzymes in the field of biological control has arisen due to their possible involvement in antagonistic activity against pathogenic chitin-containing organisms. The absence of chitin in plants and vertebrate animals allows the consideration of safe and selective “target” molecules for control of chitin-containing pathogenic organisms. Fungi show appropriate characteristics as potential biological control agents of insects, fungi, and nematodes due to the production of fungal enzymes with antagonistic action. The antagonistic interactions between fungi and plant nematode parasites are among the most studied experimental models because of the high economic relevance. Fungi which target nematodes are known as nematophagous fungi. The nematode egg is the only structural element where the presence of chitin has been demonstrated. In spite of being one of the most resistant biological structures, eggs are susceptible to being attacked by egg-parasitic fungi. A combination of physical and chemical phenomena result in their complete destruction. The contribution of fungal chitinases to the in vitro rupture of the eggshell confirms their role as a pathogenic factor. Chitinases have been produced by traditional fermentation methods, which have been improved by optimizing the culture conditions for industrial processes. Although wild-type microorganisms constitute an alternative source of chitinolytic enzymes, the advances in molecular biology are allowing the genetic transformation of fungi to obtain strains with high capability as biocontrol agents. Simultaneously, a better understanding of rhizosphere interactions, additional to the discovery of new molecular biology tools, will allow the choosing of better alternatives for the biological control of nematodes in order to achieve an integrated management of the soil ecosystem.     

Temporary Changes in Populations of Soil Organisms after Field Application of Entomopathogenic Nematodes

To assess the effect of an inundative release of entomopathogenic nematodes on soil organisms, population densities of soil-dwelling organisms were monitored before and after an application of an aqueous suspension of Heterorhabditis megidis to field plots in mown grassland (Exp. I) at a level of 0.38 million/m² and to plots (Exp. II) situated in a forested area, a grass sports field and an orchard at a level of 1.5 million/m². At the forested site, heat-killed H. megidis (1.5 million/m²) also were applied to two plots to compare the impact on soil organisms of a large introduction of living and dead nematodes. Post-treatment, temporary changes in natural population densities of several nematode genera and other organisms were detected in H. megidis-treated plots in both experiments. Temporary changes in the nematode trophic structure occurred in the percentages of nematode omnivores, herbivores and predators in both experiments. Evidence from all sites suggests that the changes were temporary and that the presence of decaying H. megidis following treatment contributed to nutrient enrichment of the soil and to direct and indirect effects on the nematode community.