Small subunit ribosomal DNA-based phylogenetic analysis of foliar nematodes (Aphelenchoides spp.) and their quantitative detection in complex DNA backgrounds

Molecular and Morphological Characteristics of a Novel Cyst Nematode in the Rhizosphere of Artemisia lavandulaefolia DC. in Gansu Province, Northwest China

Cyst nematodes are obligate parasitic nematodes found in the fields of many cultivated crops. These nematodes, which have great economic importance, pose a threat to food security, though they are frequently ignored or misdiagnosed as pests because of covert parasitism. A cyst nematode population parasitizing on Artemisia lavandulaefolia DC., one of the traditional Chinese medicines was collected in Gansu Province. The species was diagnosed using integrative taxonomy and molecular approaches. The cyst population is spherical or lemon-shaped, light brown or dark brown in color, with a long neck and a protruding vulval cone. The stylet of the second-stage juvenile is strong, and the front end of the ball at the base of the stylet is concave; the median bulb and excretory pore are prominent; the tail is blunt and circular, and the transparent tail is usually shorter than the stylet. A phylogenetic analysis was carried out using the internal transcribed spacer (ITS) and 28S genes of ribosomal DNA, which further confirmed the presence of Cactodera chenopodiae. According to our literature review, this is the first report on C. chenopodiae in Compositae. By following this research, we can better understand the challenges posed by A. lavandulaefolia DC. and develop effective strategies for managing its spread and impacts. This will help to protect vulnerable ecosystems and ensure the sustainability of agricultural and forestry activities in affected areas.

Characterisation of Nematoda and Digenea in selected Australian freshwater snails

Freshwater snails are integral to local ecosystems as a primary food source for various vertebrate species, thereby contributing significantly to ecological food webs. However, their role as intermediate hosts also makes them pivotal in the transmission of parasites. In Australia, research on freshwater snails has predominantly focused on their role as intermediate hosts for livestock parasites, while there has been limited exploration of the impact of these parasites on snail health and population dynamics. The aim of this study was to determine parasitic infection in freshwater snails. This study was conducted in the south-eastern region of Australia, in 2022. A total of 163 freshwater snails from four different species were collected and examined in the Murrumbidgee catchment area in the southeastern part of Australia during the Southern Hemisphere summer and autumn months (February to May). The species included Isidorella hainesii, Glyptophysa novaehollandica, Bullastra lessoni (endemic species), and Physella acuta (an introduced species). Through the analysis of sequence data from the various regions of the nuclear ribosomal DNA, we determined that the Digenea species in this study belonged to three distinct species, including Choanocotyle hobbsi, Petasiger sp. and an unidentified species belonging to Plagiorchioidea. Additionally, analysis of the sequences from Nematoda found in this study, revealed they could be categorized into two separate taxa, including Krefftascaris sp. and an unidentified nematode closely associated with plant and soil nematodes. This research holds significant implications for the future understanding and conservation of Australian freshwater ecosystems. Most parasites found in the present study complete their life cycle in snails and turtles. As many of freshwater snail and turtle species in Australia are endemic and face population threats, exploring the potential adverse impacts of parasitic infections on snail and turtle health, is crucial for advancing our understanding of these ecosystems and also paving the way for future research and conservation efforts. While none of the native snail species in the present study have been listed as endangered or threatened, this may simply be attributed to the absence of regular population surveys.

Morphological and Molecular Analysis of Two Mycophagous Nematodes, Aphelenchoides bicaudatus and A. rutgersi (Nematoda: Aphelenchoididae) from Florida Strawberry

From 2016 to 2021, nematode surveys in Florida strawberry fields revealed several species of foliar nematodes (Aphelenchoides spp.). Aphelenchoides besseyi sensu stricto was detected only in 2016 and 2017 on photosynthetic strawberry leaves/buds, but other not well characterized populations of Aphelenchoides sp. were found on declining/dessicated leaves. Morphological analyses showed that these samples of Aphelenchoides sp. consisted of A. bicaudatus, a species detected in Florida for the first time, and A. rutgersi, a species previously reported in Florida from the citrus rhizosphere. These two species differed from A. besseyi in the shape of their tail terminus: bifurcate in A. bicaudatus; mucronate with a ventral thin mucro in A. rutgersi; and stellate in A. besseyi. One population each of these species was used for morphological and molecular analyses after being reared on Monilinia fructicola. Body and tail length differences were observed among Florida A. bicaudatus and other populations from the Far East and South Africa. Phylogenetic analyses of the rRNA gene sequences showed that Florida A. bicaudatus grouped with those of species from South Korea, Taiwan, and the Netherlands and several other populations listed as Aphelenchoides sp. from Brazil, Costa Rica, and Japan, which were considered as representatives of A. bicaudatus in this study. Similarly, sequences of Florida A. rutgersi grouped with those from environmental samples in Japan and North Carolina, which were listed as Aphelenchoides sp. and were considered as representatives of A. rutgersi in this study. Photosynthetic strawberry leaf samples were free from both A. bicaudatus and A. rutgersi, indicating that these two species did not damage strawberry. They were associated with desiccated leaves and/or propagative stolons, usually infected by fungi, confirming that they are mycetophagous under field conditions in this study. Results of soybean leaf inoculation on moist filter paper containing A. bicaudatus specimens showed that this species could become phytophagous under artificial conditions. Nematodes penetrated the leaf epidermis and migrated into the mesophyll causing leaf tissue discoloration/necrosis, which remained localized within the infested area. Soybean leaf damage was almost negligible, and no nematode reproduction was observed in the inoculated soybean areas.

Rapid Detection of the Strawberry Foliar Nematode Aphelenchoides fragariae Using Recombinase Polymerase Amplification Assay with Lateral Flow Dipsticks

Rapid and reliable diagnostic methods for plant-parasitic nematodes are critical for facilitating the selection of effective control measures. A diagnostic recombinase polymerase amplification (RPA) assay for Aphelenchoides fragariae using a TwistAmp® Basic Kit (TwistDx, Cambridge, UK) and AmplifyRP® Acceler8® Discovery Kit (Agdia, Elkhart, IN, USA) combined with lateral flow dipsticks (LF) has been developed. In this study, a LF-RPA assay was designed that targets the ITS rRNA gene of A. fragariae. This assay enables the specific detection of A. fragariae from crude nematode extracts without a DNA extraction step, and from DNA extracts of plant tissues infected with this nematode species. The LF-RPA assay showed reliable detection within 18-25 min with a sensitivity of 0.03 nematode per reaction tube for crude nematode extracts or 0.3 nematode per reaction tube using plant DNA extracts from 0.1 g of fresh leaves. The LF-RPA assay was developed and validated with a wide range of nematode and plant samples. Aphelenchoides fragariae was identified from seed samples in California. The LF-RPA assay has great potential for nematode diagnostics in the laboratory with minimal available equipment.

Description of Aphelenchoides persicus sp. n. (Nematoda: Aphelenchoididae) from Iran

During a survey on the soil nematodes, a population of the genus Aphelenchoides was collected around the rhizosphere of persimmon in Guilan Province, Iran. The morphological and molecular characters confirmed the new species, namely A. persicus sp. n. The new species is characterized by a female body length (699-1068 μm), lip region offset from the rest of the body by a slight constriction, lateral fields with six incisures, stylet 12-13.5 μm long, with a clear basal swelling, excretory pore ca 1.5 metacorpal length posterior to base of the metacorpus, post uterine sac elongate, about 4-7 times than the vulval body diameter; conical female tail with a single centrally located mucron with tiny projection close to the tail tip, male body length (663-908 μm), and spicule well developed with rounded condylus, blunt conical rostrum, and a hook-like tip of dorsal limb. The new species belongs to the Group 2 category of Aphelenchoides species and was similar to seven known species with six lateral field incisures, including A. allius, A. chinensis, A. meghalayensis, A. nechaleos, A. paranechaleos, A. parasexlineatus, and A. sexlineatus. The molecular phylogeny based on 28S rDNA revealed that the new species stands close to A. hamospiculatus (MN931591; MN931592) and two unidentified Aphelenchoides (KY769057; LC583315). The measurements, line illustrations, LM photographs, and phylogenetic analysis are given for the new species.

The Fight against Plant-Parasitic Nematodes: Current Status of Bacterial and Fungal Biocontrol Agents

Plant-parasitic nematodes (PPNs) are among the most notorious and underrated threats to food security and plant health worldwide, compromising crop yields and causing billions of dollars of losses annually. Chemical control strategies rely heavily on synthetic chemical nematicides to reduce PPN population densities, but their use is being progressively restricted due to environmental and human health concerns, so alternative control methods are urgently needed. Here, we review the potential of bacterial and fungal agents to suppress the most important PPNs, namely Aphelenchoides besseyi, Bursaphelenchus xylophilus, Ditylenchus dipsaci, Globodera spp., Heterodera spp., Meloidogyne spp., Nacobbus aberrans, Pratylenchus spp., Radopholus similis, Rotylenchulus reniformis, and Xiphinema index.

CRISPR/Cas12a Coupled With Recombinase Polymerase Amplification for Sensitive and Specific Detection of Aphelenchoides besseyi

Aphelenchoides besseyi (A. besseyi), a seed-borne parasitic nematode, is the causal agent of rice white tip disease (RWTD), which may result in a drastic loss of rice yield. Seed treatments are currently considered to be the most effective means of preventing the spread of RWTD. Therefore, the rapid, highly specific, and accurate detection of A. besseyi from rice seeds is crucial for the surveillance, prevention, and control of RWTD. Here, we describe a novel detection assay that combines recombinase polymerase amplification (RPA) and CRISPR/Cas12a to detect A. besseyi (termed RPA-Cas12a-Ab), with a low limit of detection (LOD) of 1 copy/μl of plasmid or 1:10⁷ diluted DNA extracted from individual nematodes. To improve the user-friendliness, lateral flow strip assay (LFA) was adopted to visualize the detection result. The LOD of the RPA-Cas12a-Ab LFA assay was 1,000 copies/μl plasmid or 1:10 diluted DNA extracted from individual nematodes. The assay developed in this study was able to identify A. besseyi in 45 min with high accuracy and sensitivity without cross reaction with three closely related non-A. besseyi species. Thus, RPA-Cas12a-Ab is a rapid, sensitive, and specific detection system that requires no sophisticated equipment and shows promise for on-site surveillance of A. besseyi.

Taxonomy and Identification of Principal Foliar Nematode Species (Aphelenchoides and Litylenchus)

Nematodes are Earth's most numerous multicellular animals and include species that feed on bacteria, fungi, plants, insects, and animals. Foliar nematodes are mostly pathogens of ornamental crops in greenhouses, nurseries, forest trees, and field crops. Nematode identification has traditionally relied on morphological and anatomical characters using light microscopy and, in some cases, scanning electron microscopy (SEM). This review focuses on morphometrical and brief molecular details and key characteristics of some of the most widely distributed and economically important foliar nematodes that can aid in their identification. Aphelenchoides genus includes some of the most widely distributed nematodes that can cause crop damages and losses to agricultural, horticultural, and forestry crops. Morphological details of the most common species of Aphelenchoides (A. besseyi, A. bicaudatus, A. fragariae, A. ritzemabosi) are given with brief molecular details, including distribution, identification, conclusion, and future directions, as well as an updated list of the nominal species with its synonyms. Litylenchus is a relatively new genus described in 2011 and includes two species and one subspecies. Species included in the Litylenchus are important emerging foliar pathogens parasitizing trees and bushes, especially beech trees in the United States of America. Brief morphological details of all Litylenchus species are provided.

Identification and Characterization of a Fatty Acid- and Retinoid-Binding Protein Gene (Ar-far-1) from the Chrysanthemum Foliar Nematode, Aphelenchoides ritzemabosi

The chrysanthemum foliar nematode (CFN), Aphelenchoides ritzemabosi, is a migratory, plant-parasitic nematode that is widely distributed and infects the aboveground parts of many plants. The fatty acid- and retinoid-binding proteins (FAR) are nematode-specific proteins that are involved in the development, reproduction, and infection of nematodes and are secreted into the tissues to disrupt the plant defense reaction. In this study, we obtained the full-length sequence of the FAR gene (Ar-far-1) from CFN, which is 727 bp and includes a 546 bp ORF that encodes 181 amino acids. Ar-FAR-1 from CFN has the highest sequence similarity to Ab-FAR-1 from A. besseyi, and they are located within the same branch of the phylogenetic tree. Fluorescence-based ligand-binding analysis confirmed that recombinant Ar-FAR-1 was bound to fatty acids and retinol. Ar-far-1 mRNA was expressed in the muscle layer, intestine, female genital system, and egg of CFN, and more highly expressed in females than in males among the four developmental stages of CFN. We demonstrated that the reproduction number and infection capacity of CFN decreased significantly when Ar-far-1 was effectively silenced by in vitro RNAi. Ar-far-1 plays an important role in the development, reproduction, infectivity, and pathogenesis of CFN and may be used as an effective target gene for the control of CFN. The results provide meaningful data about the parasitic and pathogenic genes of CFN to study the interaction mechanism between plant-parasitic nematodes and hosts.

Development of a Species-Specific PCR for Detection and Quantification of Meloidogyne hapla in Soil Using the 16D10 Root-Knot Nematode Effector Gene

The Northern root-knot nematode (Meloidogyne hapla) is an important soilborne pathogen of numerous agricultural crops in temperate regions. Accurate detection and quantification is vital to supporting informed pest management decisions. However, traditional methods of manual nematode extraction and morphology-based identification are time-consuming and require highly specialized training. Molecular methods may expand the diagnostician's toolkit beyond those methods that rely on this disappearing specialized skillset. However, molecular assays targeting the internal transcribed spacer region may lead to inaccurate results because of intraspecific variability. The Meloidogyne spp. effector gene 16D10 was assessed as a target for a SYBR Green I quantitative PCR (qPCR) assay for detection and quantification of M. hapla. M. hapla-specific qPCR primers were developed and evaluated for specificity against five M. hapla isolates and 14 other plant-parasitic nematodes. A standard curve was generated by relating the quantification cycle (Cq) to the log of M. hapla population densities artificially introduced into soil. The influence of soil inhibitors on quantitative amplification was assessed by generating a dilution series from DNA extracted from pure nematode cultures and inoculated soil. Extracts from soil produced significantly higher Cq values than those produced from pure culture extracts. The utility of the qPCR was evaluated using soil samples collected from three naturally infested potato fields, resulting in a significant positive relationship between populations estimated using qPCR and populations derived from manual counting. The qPCR developed in this study provides a useful method for detecting and quantifying M. hapla in soil and demonstrates the utility of effector genes in plant-parasitic nematode diagnostics. The ability to use effector genes as targets for qPCR and other molecular detection and quantification methods may open additional avenues of novel research and support development of improved species-level diagnostics.

A Rapid Diagnostic for Detection of Aphelenchoides besseyi and A. fujianensis Based on Real-Time PCR

Aphelenchoides besseyi and A. fujianensis have been frequently found in mixed populations associated with forage grass seed in Brazil. The morphological similarity between both species has previously led A. fujianensis to be erroneously identified as A. besseyi. A. besseyi is a quarantine pest in many countries that import Brazilian forage seed; however, there is no current evidence suggesting that A. fujianensis is a plant-parasitic species. Two real-time polymerase chain reaction (qPCR) diagnostics were developed to detect each species and an operational envelope was established. A set of primers and hydrolysis probes for each species was designed targeting the large subunit (LSU) region. To assess their specificity, primers and probes sets were tested with samples of nontarget Aphelenchoides and Paraphelenchus sp. also frequently associated with forage seed. Experiments using dilutions of purified plasmid standards underpinned the sensitivity of the qPCR assays, which detected as few as 10 copies of target nematode ribosomal DNA. Thus, the developed diagnostics were sufficiently sensitive to detect DNA extracted from a fragment of a single target nematode. There was a positive correlation between copy number of the target species and nematode abundance, suggesting the potential of this method for quantification. Evidence of intra-individual variability among cloned sequences of the LSU region in a single A. besseyi population is also reported.

Molecular and morphological characterisation of Aphelenchoides kheirii n. sp. (Nematoda: Aphelenchoididae) isolated from Pinus nigra in north-western Iran

Aphelenchoides kheirii n. sp. was isolated during a survey of nematodes associated with bark samples of pine trees (Pinus nigra) in West Azerbaijan province, north-western Iran. The new species has a body length of 500 (448-520) μm in the female and 442 (402-480) μm in the male. The cuticle is weakly annulated with four lateral lines and the lip region is offset. The stylet is 10.4 (10-11) μm long with small basal swellings and the excretory pore located immediately posterior to base of metacorpus; hemizonid invisible. The post-vulval uterine sac length 37.7 (28-45) μm. Spicules are relatively short (18-20 μm in dorsal limb) and the end of the dorsal limb clearly curved ventrally like a hook. The male tail has usual three pairs of caudal papillae (2 + 2 + 2) and a well-developed mucron. The female tail is conical, terminating in a complicated step-like projection, usually with many tiny nodular protuberances. The new species belongs to the Group 2 category of Aphelenchoides species sensu Shahina in which ten known species among Groups 2 and 4 sensu Shahina, namely: A. arcticus, A. blastophthorus, A. fuchsi, A. parasaprophilus, A. paraxui, A. xui, A. dactylocercus, A. gynotylurus, A. iranicus and A. saprophilus are the most similar species. Phylogenetic analysis based on small subunit (SSU) and partial large subunit (LSU) sequences of rRNA supported the morphological results.

Description of Aphelenchoides giblindavisi n. sp. (Nematoda: Aphelenchoididae), and Proposal for a New Combination

One new and one known species of the genus Aphelenchoides from Iran are studied. Aphelenchoides giblindavisi n. sp. is mainly characterized by having five lines in the lateral fields at mid-body, and a single mucro with several tiny nodular protuberances, giving a warty appearance to it, as revealed by detailed scanning electron microscopic (SEM) studies. The new species is further characterized by having a body length of 546 to 795 μm in females and 523 to 679 μm in males, rounded lip region separated from the rest body by a shallow depression, 10 to 11 μm long stylet with small basal swellings, its conus shorter than the shaft ( m  = 36-43), 52 to 69 µm long postvulval uterine sac (PUS), males with 16 to 18 μm long arcuate spicules, and three pairs of caudal papillae. The new species was morphologically compared with two species of the genus having five lines in the lateral fields namely A. paramonovi and A. shamimi and species having a warty-surfaced mucro at tail end and similar morphometric data ranges. The morphological features and morphometrics of the second studied species, A. helicus , agreed well with the data given for the type population. However, detailed study of fresh females revealed it has three drop-shaped stylet knobs and long PUS, making it typologically similar to the genus Robustodorus , meriting its taxonomic revision, i.e., transferring to it. In molecular phylogenetic analyses using partial small and large subunit ribosomal RNA gene (SSU and LSU rDNA) sequences, the new species formed a clade with A. heidelbergi in both SSU and LSU D2-D3 trees. The species A. helicus , however, clustered inside a well-supported clade of the genus Robustodorus in both trees, corroborating its newly proposed taxonomic placement as Robustodorus helicus n. comb.

Description of Aphelenchoides macrospica n. sp. (Nematoda: Aphelenchoididae) from Northwestern Iran

Aphelenchoides macrospica n. sp. is described and illustrated from the West Azerbayjan province, northwestern Iran. The new species is characterized by its body length of 807 to 963 μm (males) and 792 to 1,094 μm (females), offset cephalic region, lateral fields with four incisures, long stylet with 15 to 16 μm length, and excretory pore situated opposite or behind the nerve ring. Pharyngeal glands overlapping intestine dorsally and extending for 90 to 121 μm, tail terminus mucronate in both sexes. Vagina directed anteriad, and spicules are relatively large (27-32 μm) with well-developed broadly rounded apex and condylus. The new species comes close to seven known species of the genus namely A. arcticus, A. blastophthorus, A. haguei, A. huntensis, A. lucknowensis, A. parasaprophilus, and A. xui, but it differs from them by the body size, stylet length, size of spicules, and length of postvulval uterine sac. The results of phylogenetic analyses based on sequences of D2-D3 expansion region of 28S and 18S rDNA, confirmed its status as a new species.

Signatures of adaptation to plant parasitism in nematode genomes

Plant-parasitic nematodes cause considerable damage to global agriculture. The ability to parasitize plants is a derived character that appears to have independently emerged several times in the phylum Nematoda. Morphological convergence to feeding style has been observed, but whether this is emergent from molecular convergence is less obvious. To address this, we assess whether genomic signatures can be associated with plant parasitism by nematodes. In this review, we report genomic features and characteristics that appear to be common in plant-parasitic nematodes while absent or rare in animal parasites, predators or free-living species. Candidate horizontal acquisitions of parasitism genes have systematically been found in all plant-parasitic species investigated at the sequence level. Presence of peptides that mimic plant hormones also appears to be a trait of plant-parasitic species. Annotations of the few genomes of plant-parasitic nematodes available to date have revealed a set of apparently species-specific genes on every occasion. Effector genes, important for parasitism are frequently found among those species-specific genes, indicating poor overlap. Overall, nematodes appear to have developed convergent genomic solutions to adapt to plant parasitism.

Aphelenchoides eldaricus n. sp. (Nematoda: Aphelenchoididae) isolated from Pinus eldarica in western Iran

Aphelenchoides eldaricusn. sp. is described and illustrated from wood and bark samples of a dead Mondell pine in Kermanshah Province, western Iran. The new species has a body length of 597 (507-700) μm (females) and 662 (636-695) μm (males). The cuticle is weakly annulated with three lateral lines and the lip region is offset. The stylet is 9.6 (9-10) μm long with small basal swellings and the excretory pore is locatedcaone body diam. posterior to the metacorpus valve. The spicules are large with the dorsal limb 40 (38-42) μm long with a prominent rostrum and rounded apex. The female tail is conical, tapering gradually to an acute terminus with a simple ventral mucron. The male tail bears six (2 + 2 + 2) caudal papillae and a well-developed mucron. The new species belongs to the Group 2 category ofAphelenchoidesspecies and is close to four known species, namelyA. cibolensis,A. indicus,A. rutgersiandA. sacchari. Molecular analyses of the partial 18S and the D2-D3 expansion segments of the 28S rRNA gene confirmed its morphological status as a new species.

Aphelenchoides salixae n. sp. (Nematoda: Aphelenchoididae) isolated from Salix alba in western Iran

Aphelenchoides salixaen. sp. was isolated from wood and bark samples of a dead willow in Kermanshah Province, western Iran. The nematodes were collected directly from wood samples and were successfully reared onBotrytis cinerea. The new species has a body length of 567 (507-620) μm (females) and 382 or 400 μm (males). The cuticle is weakly annulated with four lateral lines. Lip region offset. The stylet is 9.5 (9-10) μm long with small basal swellings. The excretory pore is locatedcaone body diam. posterior to the metacorpus valve. The spicules are short with the dorsal limb 14 or 15 μm long (n = 2), apex and rostrum rounded and only slight offset. The female tail is cylindrical with a broadly rounded terminus. The male tail is conical, bearing six (2 + 2 + 2) caudal papillae with a hamate mucron at terminus. The new species belongs to the Group 1 category ofAphelenchoidesspecies and is close to seven known species, namely:A. capsuloplanus,A. confusus,A. limberi,A. obtusicaudatus,A. obtusus,A. orientalisandA. rotundicaudatus. Molecular analyses of the partial 18S, D2-D3 expansion segments of the 28S rRNA genes and internal transcribed spacer (ITS) supported it as a new species and that the new species is closest toA.besseyi,A. fujianensisandA. ritzemabosiin dendrograms inferred using 18S and 28S D2-D3 genes.

Molecular and Morphological Characterization of Aphelenchoides fuchsi sp. n. (Nematoda: Aphelenchoididae) Isolated from Pinus eldarica in Western Iran

Aphelenchoides fuchsi sp. n. is described and illustrated from bark and wood samples of a weakened Mondell pine in Kermanshah Province, western Iran. The new species has body length of 332 to 400 µm (females) and 365 to 395 µm (males). Lip region set off from body contour. The cuticle is weakly annulated, and there are four lines in the lateral field. The stylet is 8 to 10 μm long and has small basal swellings. The excretory pore is located ca one body diam. posterior to metacorpus valve or 51 to 62 μm from the head. The postuterine sac well developed (60-90 µm). Spicules are relatively short (15-16 μm in dorsal limb) with apex and rostrum rounded, well developed, and the end of the dorsal limb clearly curved ventrad like a hook. The male tail has usual three pairs of caudal papillae (2+2+2) and a well-developed mucro. The female tail is conical, terminating in a complicated step-like projection, usually with many tiny nodular protuberances. The new species belongs to the Group 2 sensu Shahina, category of Aphelenchoides species. Phylogenetic analysis based on small subunit (SSU) and partial large subunit (LSU) sequences of rRNA supported the morphological results.

Aphelenchoides iranicus n. sp. (Nematoda: Aphelenchoididae) from West Azerbaijan province, Iran

Aphelenchoidesiranicusn. sp. is described and illustrated from bark samples of an oak tree (Quercussp.) in West Azerbaijan province, north-western Iran. The new species is characterised by body length of 350 (330-383) μm in females and 343 (323-370) μm in males, lip region set off from body contour, lateral fields with three lines, stylet 8 (7-9) μm long with small basal swellings, excretory pore 59 (56-62) μm from anterior end, hemizonid invisible, pharyngeal glands overlapping intestine dorsally and extending for 48 (41-54) μm, female tail subcylindrical with many tiny finger-like appendages at the tip, and male with aphelenchoid type spicules 17.6 (17-18) μm long. The new species comes close to nine known species of the genus namely:A. brevicaudatus,A. cibolensis,A. conimucronatus,A. editocaputis,A. montanus,A. pusillus,A. rarus,A. sphaerocephalusandA. vaughani, but differs from them by the number of incisures in the lateral field, shape of tail mucron, stylet length, size of spicules and length of post-vulval uterine sac. Additionally, this species is characterised molecularly and phylogenetically by sequences of the D2-D3 expansion segments of the 28S and partial 18S rRNA genes that are unique in relation to the sequences deposited in GenBank.

Morphological and molecular characterisation of Aphelenchoides besseyi and A. fujianensis (Nematoda: Aphelenchoididae) from rice and forage grass seeds in Brazil

Morphologically similarAphelenchoidesspp. populations extracted from rice and forage grass seeds from different geographical regions in Brazil were morphologically and molecularly characterised. Overall, the populations studied separated into two groups based on morphological and phylogenetic analyses, referred to herein as ‘Group-rice’ and ‘Group-forage’. Bayesian phylogenetic analyses of SSU, LSU and mtCOI regions strongly supported the presence of two dichotomous groups with Group-rice and Group-forage populations genetically similar toA. besseyiandA. fujianensis, respectively. This study reports the presence of a morphologically similar species toA. besseyiassociated with seeds of grasses, but genetically distinct based on three genomic regions, which our results strongly suggest to beA. fujianensis, this being a new geographical record for Brazil. Additional information regarding spicule morphology of maleA. besseyiis also reported.

Development and Validation of LNA-Based Quantitative Real-Time PCR Assays for Detection and Identification of the Root-Knot Nematode Meloidogyne enterolobii in Complex DNA Backgrounds

Meloidogyne enterolobii is a quarantine root-knot nematode posing a major threat to agricultural production systems worldwide. It attacks many host plants, including important agricultural crops, ornamentals, and trees. M. enterolobii is a highly virulent and pathogenic root-knot nematode species, able to reproduce on plants resistant to other Meloidogyne spp. Significant crop damage has been reported in Asia, South America, Africa, the United States, France, and greenhouses in Switzerland. To identify potential introduction pathways and ensure appropriate phytosanitary measures and management strategies, accurate detection and identification tools are needed. Therefore, two real-time quantitative polymerase chain reaction (PCR) assays based on the second intergenic spacer region of the ribosomal DNA cistron and the cytochrome oxidase c subunit I (COI) gene using locked nucleic acid probes were developed and validated for fast and reliable detection and identification of M. enterolobii. Analytical specificity was confirmed with 16 M. enterolobii populations, 16 populations of eight closely related Meloidogyne spp., and four species from other nematode genera. Optimizing and testing the assays on two real-time PCR platforms revealed an analytical sensitivity of one juvenile in a background of 1,000 nematodes and the intended limit of detection of one juvenile per 100 ml of soil. Both assays performed equally well, with the COI-based assay showing a slightly better performance concerning detection of M. enterolobii target DNA in complex DNA backgrounds.

Evolution of plant parasitism in the phylum Nematoda

Within the species-rich and trophically diverse phylum Nematoda, at least four independent major lineages of plant parasites have evolved, and in at least one of these major lineages plant parasitism arose independently multiple times. Ribosomal DNA data, sequence information from nematode-produced, plant cell wall-modifying enzymes, and the morphology and origin of the style(t), a protrusible piercing device used to penetrate the plant cell wall, all suggest that facultative and obligate plant parasites originate from fungivorous ancestors. Data on the nature and diversification of plant cell wall-modifying enzymes point at multiple horizontal gene transfer events from soil bacteria to bacterivorous nematodes resulting in several distinct lineages of fungal or oomycete-feeding nematodes. Ribosomal DNA frameworks with sequence data from more than 2,700 nematode taxa combined with detailed morphological information allow for explicit hypotheses on the origin of agronomically important plant parasites, such as root-knot, cyst, and lesion nematodes.

Morphological and molecular studies on Aphelenchoides arachidis Bos, 1977 (Tylenchina: Aphelenchoididae) from groundnuts in South Africa

Aphelenchoides arachidisis reported for the first time from South Africa and for the fourth time outside Nigeria. TheA. arachidis-infested pods from South Africa showed the following symptoms: small seeds with the testa wrinkled and darker in colour than that of non-infested seeds; the pods showed dark lesions and some seeds within the pods showed early germination. Differences between the two South African and the Nigerian populations ofA. arachidisinclude more lateral lines in some specimens (2-4vs2) and, on average, longer post-uterine sac length (extending for 74 (41-96) and 62 (33-82)vsabout 50% of vulva to anus distance). Scanning electron micrographs of this species are presented for the first time. The ITS regions of ribosomal DNA were amplified, sequenced, aligned and compared with other sequences ofAphelenchoidesspecies. Two pathogenic fungi,Thielaviopsis basicolaandNeocosmospora vasinfecta, were also isolated from this material.

Phylogenetic analysis of entomoparasitic nematodes, potential control agents of flea populations in natural foci of plague

Entomoparasitic nematodes are natural control agents for many insect pests, including fleas that transmit Yersinia pestis, a causative agent of plague, in the natural foci of this extremely dangerous zoonosis. We examined the flea samples from the Volga-Ural natural focus of plague for their infestation with nematodes. Among the six flea species feeding on different rodent hosts (Citellus pygmaeus, Microtus socialis, and Allactaga major), the rate of infestation varied from 0 to 21%. The propagation rate of parasitic nematodes in the haemocoel of infected fleas was very high; in some cases, we observed up to 1,000 juveniles per flea specimen. Our study of morphology, life cycle, and rDNA sequences of these parasites revealed that they belong to three distinct species differing in the host specificity. On SSU and LSU rRNA phylogenies, these species representing three genera (Rubzovinema, Psyllotylenchus, and Spilotylenchus), constitute a monophyletic group close to Allantonema and Parasitylenchus, the type genera of the families Allantonematidae and Parasitylenchidae (Nematoda: Tylenchida). We discuss the SSU-ITS1-5.8S-LSU rDNA phylogeny of the Tylenchida with a special emphasis on the suborder Hexatylina.

Description of Aphelenchoides stellatus n. sp. (Nematoda: Aphelenchoididae) found in packaging wood from Japan

Aphelenchoides stellatusn. sp. is described and figured. The new species was isolated from packaging wood from Japan imported to Ningbo harbour, China. The new species has a body length of 485-533 μm (males) and 547-699 μm (females). The cuticle is weakly annulated and there are four lines in the lateral field. The stylet is 9-11 μm long and has small basal swellings. The excretory pore is located posterior to the nerve ring. Spicules smoothly curved, rose-thorn shaped. Apex and rostrum round, only slightly offset, dorsal limb 19-21 μm long. Male tail bearing six (2 + 2 + 2) caudal papillae. The female spermatheca is axial and oblong with round sperm present in multiple rows. Both male and female tail pegs have 3-4 processes, appearing star-like under SEM. The new species belongs to the Group 3 category ofAphelenchoidesspecies. Phylogenetic analyses based on full length ITS and 28S D2/D3 region of rDNA confirmed its morphological status as a new species.

Description of Aphelenchoides rotundicaudatus n. sp. (Nematoda: Aphelenchoididae) found in packaging wood from South Korea

Aphelenchoides rotundicaudatus n. sp. was isolated from packaging wood from South Korea imported to Ningbo harbour, China. Specimens were collected directly from wood samples using the Baermann method. Multiplication on Botryotinia fuckeliana failed. The new species has a body length of 364-509 μm (males) and 371-493 μm (females). The cuticle is weakly annulated and there are four lines in the lateral field. The stylet is 8-9 μm long and has small basal swellings. The excretory pore is located ca one body diam. anterior to median bulb. Spicules are small (10-13 μm), apex and rostrum rounded and only slight offset. The male tail has six (2 + 2 + 2) caudal papillae. Both male and female tails are cylindrical with a broadly rounded terminus, often with a small region of thickened cuticle or a blunt peg ca 1 μm long, particularly in the female. The new species belongs to the Group 1 category of Aphelenchoides species. Phylogenetic analyses based on full length ITS, partial LSU and SSU of rDNA confirmed its status as a new species.

Characterisation of the transcriptome of Aphelenchoides besseyi and identification of a GHF 45 cellulase

While the majority of Aphelenchoides species are fungivorous, some species are plant parasites that have retained the ability to feed on fungi. Aphelenchoides besseyi is an important and widespread pathogen that causes ‘white tip’ disease on rice. This migratory endoparasitic nematode makes a significant contribution to the estimated $US 16 billion worth of damage caused by nematodes to rice crops. Here we describe a small-scale analysis of the transcriptome of A. besseyi. After sequencing, QC and assembly, approximately 5000 contigs were analysed. Bioinformatic analysis allowed 375 secreted proteins to be identified, including orthologues of proteins known to be secreted by other nematodes. One contig could encode an A. besseyi orthologue of a GHF45 cellulase, similar to those present in Bursaphelenchus xylophilus. No transcripts similar to GHF5 cellulases were present in this dataset.

Top 10 plant-parasitic nematodes in molecular plant pathology

The aim of this review was to undertake a survey of researchers working with plant-parasitic nematodes in order to determine a 'top 10' list of these pathogens based on scientific and economic importance. Any such list will not be definitive as economic importance will vary depending on the region of the world in which a researcher is based. However, care was taken to include researchers from as many parts of the world as possible when carrying out the survey. The top 10 list emerging from the survey is composed of: (1) root-knot nematodes (Meloidogyne spp.); (2) cyst nematodes (Heterodera and Globodera spp.); (3) root lesion nematodes (Pratylenchus spp.); (4) the burrowing nematode Radopholus similis; (5) Ditylenchus dipsaci; (6) the pine wilt nematode Bursaphelenchus xylophilus; (7) the reniform nematode Rotylenchulus reniformis; (8) Xiphinema index (the only virus vector nematode to make the list); (9) Nacobbus aberrans; and (10) Aphelenchoides besseyi. The biology of each nematode (or nematode group) is reviewed briefly.

SSU ribosomal DNA-based monitoring of nematode assemblages reveals distinct seasonal fluctuations within evolutionary heterogeneous feeding guilds

Soils are among the most complex, diverse and competitive habitats on Earth and soil biota are responsible for ecosystem services such as nutrient cycling, carbon sequestration and remediation of freshwater. The extreme biodiversity prohibits the making of a full inventory of soil life. Hence, an appropriate indicator group should be selected to determine the biological condition of soil systems. Due to their ubiquity and the diverse responses to abiotic and biotic changes, nematodes are suitable indicators for environmental monitoring. However, the time-consuming microscopic analysis of nematode communities has limited the scale at which this indicator group is used. In an attempt to circumvent this problem, a quantitative PCR-based tool for the detection of a consistent part of the soil nematofauna was developed based on a phylum-wide molecular framework consisting of 2,400 full-length SSU rDNA sequences. Taxon-specific primers were designed and tested for specificity. Furthermore, relationships were determined between the quantitative PCR output and numbers of target nematodes. As a first field test for this DNA sequence signature-based approach, seasonal fluctuations of nematode assemblages under open canopy (one field) and closed canopy (one forest) were monitored. Fifteen taxa from four feeding guilds (covering ∼ 65% of the free-living nematode biodiversity at higher taxonomical level) were detected at two trophic levels. These four feeding guilds are composed of taxa that developed independently by parallel evolution and we detected ecologically interpretable patterns for free-living nematodes belonging to the lower trophic level of soil food webs. Our results show temporal fluctuations, which can be even opposite within taxa belonging to the same guild. This research on nematode assemblages revealed ecological information about the soil food web that had been partly overlooked.