An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding

Both-strand gene coding in a plastome-like mitogenome of an enoplid nematode

The phylum Nematoda remains very poorly sampled for mtDNA, with a strong bias toward parasitic, economically important or model species of the Chromadoria lineage. Most chromadorian mitogenomes share a specific order of genes encoded on one mtDNA strand. However, the few sequenced representatives of the Dorylaimia lineage exhibit a variable order of mtDNA genes encoded on both strands. While the ancestral arrangement of nematode mitogenome remains undefined, no evidence has been reported for Enoplia, the phylum's third early divergent major lineage. We describe the first mitogenome of an enoplian nematode, Campydora demonstrans, and contend that the complete 37-gene repertoire and both-strand gene encoding are ancestral states preserved in Enoplia and Dorylaimia versus the derived mitogenome arrangement in some Chromadoria. The C. demonstrans mitogenome is 17,018 bp in size and contains a noncoding perfect inverted repeat with 2013 bp-long arms, subdividing the mitogenome into two coding regions. This mtDNA arrangement is very rare among animals and instead resembles that of chloroplast genomes in land plants. Our report broadens mtDNA taxonomic sampling of the phylum Nematoda and adds support to the applicability of cox1 gene as a phylogenetic marker for establishing nematode relationships within higher taxa.

Integrative taxonomic study of mononchid nematodes from riparian habitats in Bulgaria. I. Genera Mononchus Bastian, 1865 and Coomansus Jairajpuri & Khan, 1977 with the description of Mononchuspseudoaquaticus sp. nov. and a key to the species of Mononchus

The species diversity of the genera Mononchus Bastian, 1865 and Coomansus Jairajpuri & Khan, 1977 was assessed in a study of the mononchid nematodes from a wide range of riparian habitats in Bulgaria. Four species were identified based on morphological and morphometric data: Coomansusparvus (de Man, 1880), Mononchustruncatus Bastian, 1865, Mononchuspseudoaquaticus sp. nov., and Mononchus sp. The first three species were characterised both morphologically and molecularly (18S and 28S rRNA gene sequences) and the integration of these data and phylogenetic analyses provided support for their distinct species status. This paper provides detailed descriptions, morphometric data for multiple species populations, drawings and photomicrographs, and the first taxonomically verified sequences for C.parvus (n = 6), M.truncatus (sensu stricto) (n = 4) and M.pseudoaquaticus sp. nov. (n = 3). Comparative sequence and phylogenetic analyses suggested that the utility of the 18S rRNA gene for species delimitation is rather limited at least for some species complexes within the genus Mononchus. At the generic and suprageneric level, the 18S and 28S rDNA phylogenies both recovered the three genera represented by two or more species (Mononchus, Mylonchulus, and Parkellus) as monophyletic with strong support, the Mononchidae as paraphyletic, the Anatonchidae as monophyletic, and there was no support for a sister-group relationship between Mylonchulus and Mononchus. A key to the species of Mononchus is provided to facilitate the identification of the currently recognised 31 species.

Sediment DNA metabarcoding and morphology provide complementary insight into macrofauna and meiobenthos response to environmental gradients in an Arctic glacial fjord

Arctic fjords ecosystems are highly dynamic, with organisms exposed to various natural stressors along with productivity clines driven by advection of water masses from shelves. The benthic response to these environmental clines has been extensively studied using traditional, morphology-based approaches mostly focusing on macroinvertebrates. In this study we analyse the effects of glacially mediated disturbance on the biodiversity of benthic macrofauna and meiobenthos (meiofauna and Foraminifera) in a Svalbard fjord by comparing morphology and eDNA metabarcoding. Three genetic markers targeting metazoans (COI), meiofauna (18S V1V2) and Foraminifera (18S 37f) were analyzed. Univariate measures of alpha diversity and multivariate compositional dissimilarities were calculated and tested for similarities in response to environmental gradients using correlation analysis. Our study showed different taxonomic composition of morphological and molecular datasets for both macrofauna and meiobenthos. Some taxonomic groups while abundant in metabarcoding data were almost absent in morphology-based inventory and vice versa. In general, species richness and diversity measures in macrofauna morphological data were higher than in metabarcoding, and similar for the meiofauna. Both methodological approaches showed different patterns of response to the glacially mediated disturbance for the macrofauna and the meiobenthos. Macrofauna showed an evident distinction in taxonomic composition and a dramatic cline in alpha diversity indices between the outer and inner parts of fjord, while the meiobenthos showed a gradual change and more subtle responses to environmental changes along the fjord axis. The two methods can be seen as complementing rather than replacing each other. Morphological approach provides more accurate inventory of larger size species and more reliable quantitative data, while metabarcoding allows identification of inconspicuous taxa that are overlooked in morphology-based studies. As different taxa may show different sensitivities to environmental changes, both methods shall be used to monitor marine biodiversity in Arctic ecosystems and its response to dramatically changing environmental conditions.

First report of Paracapillaria philippinensis infection in flowerhorn cichlid in India

The flowerhorn cichlid is a popular ornamental fish in many Asian countries. The present study reports the occurrence of Paracapillaria philippinensis (Chitwood et al., 1968), a parasitic nematode in flowerhorn cichlid (Cichlasoma sp.) from south India. The infected fish demonstrated clinical symptoms viz. dark coloration, poor appetite, lethargy, erratic swimming, and white stringy faeces. Microscopic observation of the intestinal content and faeces revealed the presence of adult worms, larvae, and unembryonated eggs. PCR amplification of eukaryotic 18S rRNA, P. philippinensis-specific SSU rRNA gene, and the subsequent sequence analysis confirmed the species identity as P. philippinensis. The generated sequences were submitted in the GenBank, NCBI, under the accession numbers, MK895507.1, MK895446.1, MW144993.1, and OR685675.1. This is the first scientific report of P. philippinensis in fish from India, and it confirms that the flowerhorn cichlid can act as a definitive host for P. philippinensis. This report alerts fish handlers and enthusiasts to undertake suitable precautionary measures while handling live flowerhorn cichlids to prevent possible transmission of P. Philippinensis, which has the potential to infect humans causing intestinal capillariasis.

First report of Rhabditis (Rhabditella) axei with the invasive palm borer Paysandisia archon

Rhabditis (Rhabditella) axei is a free-living, pseudoparasitic, necromenic, and parasitic nematode, depending on the host. This species feeds mainly on bacteria present in decaying organic matter, soil, and other substrates; however, in its parasitic form, it can colonize some species of snails. Moreover, the presence of R. axei has also been detected in birds and mammals, including humans. In 2021-2023, during monitoring of the palm borer Paysandisia archon in Central Italy, R. axei emerged from dead larvae of this alien invasive moth and was extracted from palm fibres of Trachycarpus fortunei in three independent sites. The nematode was identified by morphological and morphometric analyses. Molecular analyses using SSU and LSU gene fragments were used to confirm the identification and to perform Bayesian reconstruction of the phylogeny. Each sampling site showed a unique haplotype. Concerning the pathogenicity of this nematode against insects, the test performed on Galleria mellonella larvae did not show any entomopathogenic effect. This is the first time that R. axei was found associated with P. archon, and this recurrent association was discussed.

Oswaldocruzia franciscoensis n. sp. (Nematoda: Molineidae) in Leptodactylus macrosternum Miranda-Ribeiro, 1926 (Anura: Leptodactylidae) from Caatinga morphoclimatic domain, Brazil: morphological and molecular characterisation

A new species of Oswaldocruzia Travassos, 1917 (Nematoda, Molineidae), parasite of Leptodactylus macrosternum Miranda-Ribeiro, 1926 (Anura: Leptodactylidae), from Caatinga morphoclimatic domain, Brazil, is described based on morphological and molecular data. Oswaldocruzia franciscoensis n. sp. is characterised by an anterior extremity with a cephalic vesicle divided into two portions, a body covered by cuticular longitudinal ridges, and cervical alae. Males of the new species have caudal bursa of type I with a 2-1-2 pattern, spicules divided into a shoe, bifurcated fork, and blade with two unequal branches, in which the longer branch bifurcates at its distal portion end and the smaller branch with three distal processes, each with distal bifurcations. Females have didelphic and amphidelphic uteri, an ovijector divided into vestibule, anterior and posterior sphincters, and anterior and posterior infundibula. The new species differs from its Neotropical congeners that have caudal bursa of type I, based on the presence of cervical alae and by having a spicular blade distally divided into two unequal branches, with the longer branch bifurcating at its distal portion and smaller branch with three distal processes, each distally bifurcated. The partial 18S rDNA sequence generated for Oswaldocruzia franciscoensis n. sp. is the first of a representative belonging to this genus in the Neotropical region.

Redescription and molecular characterization of Panagrellus ceylonensis (Nematoda, Rhabditida, Panagrolaimidae) from India

A species of genus Panagrellus was discovered from a wet season form of an oriental common evening brown butterfly Melanitis leda. In this study, a detailed description of Panagrellus ceylonensis is provided including the morphometry, light microscopy and molecular (18S and 28S rDNA genes) studies. Morphological studies on the species agree with original description and characterized by having 12501481m long body in females and 9491305m in males, lateral fields with four longitudinal incisures, lip region continuous and 811 m wide, six offset lips with protruding labial sensilla, neck 124173 m long, excretory pore at the level of basal bulb, vulva post-equatorial (V = 6871), vagina anteriorly orientated with heavily muscled vaginal walls, post-vulval uterine sac 111135 m long or 1.72.6 times as long as the corresponding body diameter, tail conical elongate with an acute terminus in both sexes, spicule 7191 m long, ventrally curved having hooked manubrium and bifurcated lamina tip, lamina ventrally curved with dorsal deflexion at about 60% of spicule length, gubernaculum 2631 m long and well developed. Morphologically, the Indian population of P. ceylonensis does not show a significant difference from the type material of P. ceylonensis in the original description. For molecular studies of this species, the sequence of 18S rDNA is obtained for the first time. Phylogenetic trees based on 18S and 28S rDNA sequences are provided in this study. Additionally, bionomics and global distribution of the species of Panagrellus genus are also discussed. In conclusion, our study provides a comprehensive morphological characterisation and molecular marker sequences of 18S, and 28S genes that can be used to support future taxonomical research on this species and emphasizes the importance of combining molecular data with morphological data to describe the species accurately.

Transcriptomics of Cruznema velatum (Nematoda: Rhabditidae) with a redescription of the species

Cruznema velatum isolated from soil in a chestnut orchard located at Guangdong province, China, is redescribed with morphology, molecular barcoding sequences, and transcriptome data. The morphological comparison for C. velatum and six other valid species is provided. Phylogeny analysis suggests genus Cruznema is monophyletic. The species is amphimix, can be cultured with Escherichia coli in 7-9 days from egg to egg-laying adult, and has a lifespan of 11 to 14 days at 20°C. The transcription data generated 45,366 unigenes; 29.9%, 31.3%, 24.8%, and 18.6% of unigenes were annotated in KOG, SwissProt, GO, and KEGG, respectively. Further gene function analysis demonstrated that C. velatum share the same riboflavin, lipoic acid, and vitamin B6 metabolic pathways with Caenorhabditis elegans and Pristionchus pacificus.

Advancing the knowledge of the nematode Echinocephalus pseudouncinatus (Gnathostomatidae, Spirurida): morphological and molecular identification, new host, and host specificity in two coexisting pen shells (Bivalvia: Pinnidae)

The life cycle of Echinocephalus pseudouncinatus has not been described in detail to date, as is also the case of other species in the genus. This study contributes to the information available about the life history of the genus, particularly E. pseudouncinatus, by (1) using molecular techniques (small subunit rRNA gene [SSU rRNA] sequences) to identify larvae of this species; (2) describing the most conspicuous morphological characteristics that distinguish the species by scanning electron microscopy; (3) describing histological characteristics of the internal anatomy of larvae and the lesions caused by them in the gonads of hosts; (4) reporting new host and reporting evidence of host specificity of E. pseudouncinatus between two species of edible pen shells coexisting in the northern Pacific of Mexico; and (5) analyzing the frequency of infested gonads by host sex, size, and gonadal development stage. The molecular analysis confirmed the morphological and histological diagnosis of E. pseudouncinatus larvae infesting gonads of Atrina maura and Pinna rugosa in Ojo de Liebre and San Ignacio lagoons. The morphological characterization of larvae provides internal details of the cephalic bulb (including rows of hooks and ballonets), neural chord, and cell types of the body wall. Histopathological findings such as degenerated and atretic gametes and the displacement of gonadal tissue in hosts infested with E. pseudouncinatus larvae are discussed in terms of temperature anomalies caused by the "Godzilla El Niño." The frequency of infestation increased with shell length and gonadal development in A. maura, with a higher infestation frequency in females versus males observed at both study sites. Our findings expand the list of hosts of E. pseudouncinatus, which was previously unknown as a parasite of P. rugosa. In P. rugosa, infestation frequencies are noticeably lower (<1%) compared with those observed in A. maura (>30%) at both study sites, suggesting host-specific requirements or preferences in E. pseudouncinatus larvae.

Aphelenchoides varicaudatus (Nematoda: Aphelenchoididae) and Helicotylenchus erythrinae (Nematoda: Hoplolaimidae) from Garlic Plantation in Magelang, Central Java, Indonesia

There were two most found genera of plant parasitic nematodes from garlic plantation in Magelang, Central Java, Indonesia which suffered losses due to bulb rot, Aphelenchoides and Helicotylenchus. Polymerase Chain Reaction (PCR) was conducted using a pair of universal nematode primer (D2A/D3B) to determine the Aphelenchoides and Helicotylenchus species from those host. Both genera were amplified at ~780 bp. The Blast-N results for the Aphelenchoides showed high identity to Aphelenchoides varicaudatus from Yunnan China (HQ283353) with 99.47 % identity, while the Helicotylenchus showed 95.22 % identity to Helicotylenchus erythrinae from Colombia (MT321739). From morphological and molecular data, we confirm that the Aphelenchoides species is A. varicaudatus. Based on female morphological character, Helicotylenchus species refers to H. erythrinae. Which is also supported by its nucleotide alignment which has same region character as H. erythrinae (MT321739). This is the first report of molecular characterization of H. erythrinae in Indonesia.

Molecular and Morphological Characterization of Tylenchus Zeae n. Sp. (Nematoda: Tylenchida) from Corn (Zea Mays) in South Carolina

Specimens of a tylenchid nematode were recovered in 2019 from soil samples collected from a corn field, located in Pickens County, South Carolina, USA. A moderate number of Tylenchus sp. adults (females and males) were recovered. Extracted nematodes were examined morphologically and molecularly for species identification, which indicated that the specimens of the tylenchid adults were a new species, described herein as Tylenchus zeae n. sp. Morphological examination and the morphometric details of the specimens were very close to the original descriptions of Tylenchus sherianus and T. rex. However, females of the new species can be differentiated from these species by body shape and length, shape of excretory duct, distance between anterior end and esophageal intestinal valve, and a few other characteristics given in the diagnosis. Males of the new species can be differentiated from the two closely related species by tail, spicules, and gubernaculum length. Cryo-scanning electron microscopy confirmed head bearing five or six annules; four to six cephalic sensilla represented by small pits at the rounded corners of the labial plate; a small, round oral plate; and a large, pit-like amphidial opening confined to the labial plate and extending three to four annules beyond it. Phylogenetic analysis of 18S rRNA gene sequences placed Tylenchus zeae n. sp. in a clade with Tylenchus arcuatus and several Filenchus spp., and the mitochondrial cytochrome oxidase c subunit 1 (COI) gene region separated the new species from T. arcuatus and other tylenchid species. In the 28S tree, T. zeae n. sp. showed a high level of sequence divergence and was positioned outside of the main Tylenchus-Filenchus clade.

First report of barley root-knot nematode, Meloidogyne naasi from turfgrass in Idaho, with multigene molecular characterization

Barley root-knot nematode, Meloidogyne naasi Franklin, 1965, is one of the most important pest nematodes infecting monocots (Franklin, 1965). Two-inch core soil samples collected from a golf course in Ada County, Idaho were submitted for identification in November of 2019. A high number of Meloidogyne sp. juveniles were recovered from both soil samples using sieving and decantation followed by the sugar centrifugal flotation method. They were examined by light microscopy, morphometric measurements, and multiple molecular markers, including the ribosomal 28S D2-D3 and intergenic spacer 2 (IGS-2) regions, mitochondrial markers cytochrome oxidase I (COI) and the interval from COII to 16S, and the protein-coding gene Hsp90. Morphometrics as well as BlastN comparisons with other root-knot nematode sequences from GenBank were consistent with identification as M. naasi. Phylogenetic trees inferred from 28S, IGS-2, COI, or Hsp90 alignments each separated the Idaho population into a strongly supported clade with other populations of M. naasi, while the COII-16S interval could not resolve M. naasi from M. minor. This report represents the first morphological and molecular characterization of Meloidogyne naasi from turfgrass in Idaho.

Morphological description and molecular characterization of Ancyracanthus electrophori n. sp. (Gnathostomatoidea: Gnathostomatidae): a new nematode parasitic in the electric eel Electrophorus varii (Gymnotiformes: Gymnotidae), from the Brazilian Amazon

A new species of Ancyracanthus, parasite of the electric eel Electrophorus varii, in the Brazilian Amazon, is described based on morphological and molecular characterization. Ancyracanthus electrophori n. sp. differs from the two congeners namely, Ancyracanthus pinnatifidus and Ancyracanthus schubarti, based on the structure of cephalic appendages, number and arrangement of caudal papillae in males, vulva very close to anus in females, eggs with smoothly mamillated shell, host taxon and geographical origin. Moreover, the new species is the first in the genus to be described with thorny cuticular rings and to be observed with the use of scanning electron microscopy (SEM). The morphology of A. pinnatifidus and A. schubarti is still poorly-known and should be revised in details; however, the separation between them and the new species was clear. Genetic characterization based on 28S rDNA and cytochrome c oxidase subunit I (cox1) mtDNA partial sequences, performed for the first time in Acyracanthus, along with phylogenetic reconstructions using both genetic markers, placed Ancyracanthus electrophori n. sp. in a suggestive basal position within Gnathostomatidae. Phylogenetic reconstructions using cox1 sequences also suggested lack of monophyly in the genera Gnathostoma and Spiroxys and, consequently, in the subfamilies Gnathostominae and Spiroxyinae. However, such results are preliminary. With the first genetic characterization and observations using SEM in Ancyracanthus, resulting in the discovery of a new species and in the expansion of the geographical occurrence of the genus to Amazonian fish, an important step towards a better understanding of these nematodes has been taken.

Geographical distribution and phylogenic relationships of Hirschmanniella diversa Sher (Nematoda: Pratylenchidae) in Japan

Hirschmanniella diversa and H. imamuri parasitise the lotus, Nelumbo nucifera. Hirschmanniella spp. are the most important pests of lotus cultivation in Japan, but the distribution and species dominancy are not fully understood. In this study, we aimed to collect Hirschmanniella spp. individuals from lotus roots in the major lotus cultivation areas in Japan and identify them morphologically and molecularly using the 18S, D2-D3 regions of rRNA and mitochondrial cytochrome c oxidase subunit I (mtCOI). Hirschmanniella oryzae, commonly known to cause damage on rice in Japan, was also obtained and analysed for inter- and intraspecies sequence variations. All individuals of the genus Hirschmanniella extracted from lotus roots in 16 fields in ten prefectures were identified as H. diversa morphologically and molecularly. This result revealed that H. diversa is a dominant Hirschmanniella species parasitising lotus in Japan. Meanwhile, intraspecific sequence variations in H. diversa were relatively higher in the mtCOI (1-21 bases, ≦5.3%) than in the 18S rRNA and D2-D3 of 28S rRNA (0.0-0.3% and 0.0-0.4%, respectively) and in those of H. oryzae. Based on the mtCOI sequences, five haplotypes were identified and each haplotype was distributed in relatively close regions or regions in which the same lotus cultivars were grown, although further studies are required to verify this assertion. The morphological and genetic variations were higher in H. diversa than in H. oryzae (no intraspecific sequence variation in mtCOI), suggesting that H. diversa was not a recent invasive species.

Morphological Characterization of Fresh and 20-Yr-Old Fixed Nematode Specimens of Sauertylenchus maximus (Allen, 1955) Siddiqi, 2000 Deposited in the USDA Nematode Collection from Arlington National Cemetery, VA, USA

Sauertylenchus maximus was discovered during a survey conducted at the Arlington National Cemetery, Virginia, for the type specimens of Hoplolaimus galeatus. Besides the fresh material, the fixed specimens of S. maximus were also studied by molecular and morphological means. The morphological and morphometric characteristics of the recovered fresh material were consistent with the original and other description(s) of this species. The fixed specimens used in this study were preserved in a 3% formaldehyde and 2% glycerin solution for over 20 yr. Molecular analyses of the fresh and fixed specimens were performed using internal transcribed spacer, D2–D2 expansion segments of 28S large subunits, and 18S small subunit ribosomal DNA sequences. To our knowledge, this represents the first report of S. maximus from Virginia and the first report of a successful DNA extraction from fixed nematode specimens.

Virulence and Reproductive Fitness of Meloidogyne paranaensis Field Populations in Coffee Genotypes

The aim of this study was to characterize Meloidogyne paranaensis populations collected from infested coffee crops. Methodologies used to characterize the 11 studied populations from municipalities in Paraná and Minas Gerais States involved the morphological analysis of perineal patterns, biochemical analysis by isozyme electrophoresis, sequencing of internal transcribes spacer 1 (ITS-1) and D2/D3 ribosomal DNA (rDNA) regions, reproductive fitness, and virulence characterization in coffee genotypes. Morphological evaluations showed the existence of variation between populations, although the majority of them showed typical perineal patterns. The biochemical identification was based on α-esterase isozyme analyses and resulted in the appearance of three distinct profiles: P1 (typical), P2 (atypical), and a nondescribed profile, P2b. BLAST of the ITS-1 and D2/D3 rDNA regions indicated homology (>95%) with other sequences deposited in GenBank. For reproductive fitness and virulence characterization, 13 coffee genotypes (5 Coffea arabica and 8 C. canephora) were inoculated with 11 M. paranaensis populations. Variation in the reproductive fitness of populations was observed for cultivar Mundo Novo, a genotype without resistance genes, and variation in the virulence of populations was observed in genotypes carrying resistance genes. Three populations exhibited virulence combined with high reproductive fitness, while one showed virulence with low reproductive fitness. Some hosts were resistant to 11 populations, while one of the hosts was resistant to only one population, indicating the presence of different resistance genes. Nevertheless, no relationship was observed between the origin of population and their variations in perineal patterns, esterase profiles, phylogeny, or reproductive fitness in coffee genotypes, or between the different characterizations, although differences were observed within each characteristic.

Occurrence of Hookworm and the First Molecular and Morphometric Identification of Uncinaria stenocephala in Dogs in Central Europe

PURPOSE

Hookworms are hematophagous parasitic nematodes that occur in the intestinal tract of various mammals, including humans. The objective of this work was to develop a two-step morphology-molecular analysis-based strategy to identify the genus and the species of eggs and larvae of the Ancylostomatidae family in dogs, which were kept in various living conditions in Slovakia.

METHODS

Faecal samples were collected from 270 dogs kept in two different shelters (160 samples) and in a marginalised Roma community (110 samples). Faecal samples were processed using the flotation method. Microscopically positive faecal samples with hookworm eggs were subjected to a coproculture and the hatched larvae were identified morphometrically, prior to molecular testing. The faecal samples with hookworm´s eggs and individual larvae were identified by a molecular assay based on the amplification of the 18S ribosomal RNA gene fragment. Further, species-specific primer sets were designed for the internal transcribed spacer (ITS 1 region) and the mitochondrial cytochrome c oxidase subunit I (COX1) gene section.

RESULTS

Hookworm eggs were microscopically detected in 9.6% (26/270) of the total number of faecal samples. The prevalence in the Roma settlement was higher, 14.5% (16/110), than in shelters, 6.3% (10/160). Using PCR and subsequent Sanger sequencing, we identified the canine hookworm species Uncinaria stenocephala in all positive samples.

CONCLUSION

Our results have provided new data on the molecular identification of the neglected species U. stenocephala affecting dogs in Slovakia and supplemented the missing information on the prevalence and incidence of hookworms in dogs in Europe.

A New Species of Free-living Marine Nematode (Ptycholaimellus: Chromadoridae: Chromadorida: Nematoda) from Mangrove Wetlands in China

This study presents a new species of free-living marine nematode, Ptycholaimellus luoyang sp. nov., from mangrove wetlands in China. The identification was confirmed by analyzing morphological characteristics and three genes: COI, 18S rDNA, and 28S rDNA. This species is distinguished from allied species by its short cephalic setae, cylindrical pharynx with anterior swelling, sclerotized transverse ridges occurring near the dorsal tooth, rod-like gubernaculum and proximal, arch-like, slightly waved, middle curved, and distally pointed spicules. The Bayesian topology was regarded as morphological evidence of P. luoyang sp. nov. being a distinct species. Interspecific and intrageneric thresholds of the K2P distance divergence have been presented here for the first time.

Report of the Parana coffee root-knot nematode, Meloidogyne paranaensis (Tylenchida: Meloidogynidae) from Caladium sp. in the continental United States

In May 2021, the Parana coffee root-knot nematode, Meloidogyne paranaensis was identified using molecular markers from a potted elephant ear plant (Caladium sp.) originated from San Antonio, Texas, USA. This nematode was found in a mixture with the peanut root-knot nematode, Meloidogyne arenaria. The molecular analysis showed that the intergenic COII-16S gene region and the D2–D3 of 28S rRNA gene sequences allowed differentiating M. paranaensis from the related root-knot nematode species of the tropical group. To the best of our knowledge, it is the first report of M. paranaensis in the continental United States.

First report of Seville root-knot nematode, Meloidogyne hispanica (Nematoda: Meloidogynidae) in the USA and North America

A high number of second stage juveniles of the root-knot nematode were recovered from soil samples collected from a corn field, located in Pickens County, South Carolina, USA in 2019. Extracted nematodes were examined morphologically and molecularly for species identification which indicated that the specimens of root knot juveniles were Meloidogyne hispanica. The morphological examination and morphometric details from second-stage juveniles were consistent with the original description and redescriptions of this species. The ITS rRNA, D2-D3 expansion segments of 28S rRNA, intergenic COII-16S region, nad5 and COI gene sequences were obtained from the South Carolina population of M. hispanica. Phylogenetic analysis of the intergenic COII-16S region of mtDNA gene sequence alignment using statistical parsimony showed that the South Carolina population clustered with Meloidogyne hispanica from Portugal and Australia. To our best knowledge, this finding represents the first report of Meloidogyne hispanica in the USA and North America.

Genetic variability, cryptic species and phylogenetic relationship of six cyathostomin species based on mitochondrial and nuclear sequences

Cyathostomins are important intestinal nematode parasites of equines and include 50 accepted species. Their taxonomy has been frequently revised and the presence of cryptic species suggested. Furthermore, usually molecular- and morphology-based phylogenetic analyses give divergent results. In this study, the nucleotide sequences of the nuclear second internal transcribed spacer (ITS-2) and the mitochondrial partial cytochrome c oxidase subunit I (COI) were determined for adults of six cyathostomin species (Coronocyclus coronatus, Coronocyclus labiatus, Cylicocyclus nassatus, Cylicostephanus calicatus, Cylicostephanus longibursatus, Cylicostephanus minutus) collected from different equine species within two geographic regions. Maximum likelihood trees were calculated for ITS-2, COI, and concatenated data. No obvious differentiation was observed between geographic regions or equine host species. As previously reported, Coronocyclus coronatus and Cylicostephanus calicatus revealed a close relationship. Cryptic species were detected in Cylicostephanus minutus and Cylicostephanus calicatus. Cylicocyclus nassatus and Coronocyclus labiatus showed diverse mitochondrial and nuclear haplotypes occurring in different combinations, while Cylicostephanus longibursatus was comparatively homogenous. In conclusion, a combined analysis of nuclear and mitochondrial haplotypes improved resolution of the phylogeny and should be applied to the remaining cyathostomin species and across additional equine host species and geographic regions.

A new cyst-forming nematode, Cactodera tianzhuensis n. sp. (Nematoda:Heteroderinae) from Polygonum viviparum in China with a key to the Genus Cactodera

A new cyst-forming nematode, Cactodera tianzhuensis n. sp. was isolated from the rhizosphere soil of Polygonum viviparum L. in Tianzhu county, China. Morphologically, the new species is characterized by lemon-shaped or rounded cysts that have protruding necks and vulval cones. The vulval cone of the new species appeared to be circumfenestrate without bullae and underbridge, vulval denticle present and anus distinct. Second-stage juveniles are vermiform, stylet well-developed with the rounded stylet knobs to slightly concave anteriorly. Lateral field with four incisures. Tail gradually tapering to a finely rounded terminus with a length of ca 54 (47–59) µm, outline of hyaline portion is V-shaped or U-shaped. Egg shells without visible markings or punctations. The phylogenetic analyses based on ITS-rDNA, D2-D3 of 28S-rDNA clearly revealed that the new species formed a separate clade from other Cactodera species, which further support the unique status of C. tianzhuensis n. sp. Therefore, it is described herein as a new species of the genus Cactodera.

First report of Cactodera milleri Graney and Bird, 1990 from Colorado and Minnesota

In 2019, Cactodera milleri cysts were discovered from soil samples collected from a Chenopodium quinoa field, located in Mosca, Alamosa county, Colorado, USA. Approximately 200 lemon shaped cysts and several hundred juveniles were recovered from the affected quinoa plants. The same species was also identified from several counties in Minnesota from samples submitted over the years by the Minnesota Department of Agriculture as part of the Animal and Plant Health Inspection Service (APHIS) efforts to survey states for the presence of Pale Potato Cyst Nematode. The cysts and juveniles (J2) were recovered from soil samples through sieving and Baermann funnel extraction. The nematode species was identified by both morphological and molecular means as Cactodera milleri (Graney and Bird, 1990). To our knowledge this represents the first report of Cactodera milleri from Colorado and Minnesota.

Xenobiotic metabolism and transport in Caenorhabditis elegans

Caenorhabditis elegans has emerged as a major model in biomedical and environmental toxicology. Numerous papers on toxicology and pharmacology in C. elegans have been published, and this species has now been adopted by investigators in academic toxicology, pharmacology, and drug discovery labs. C. elegans has also attracted the interest of governmental regulatory agencies charged with evaluating the safety of chemicals. However, a major, fundamental aspect of toxicological science remains underdeveloped in C. elegans: xenobiotic metabolism and transport processes that are critical to understanding toxicokinetics and toxicodynamics, and extrapolation to other species. The aim of this review was to initially briefly describe the history and trajectory of the use of C. elegans in toxicological and pharmacological studies. Subsequently, physical barriers to chemical uptake and the role of the worm microbiome in xenobiotic transformation were described. Then a review of what is and is not known regarding the classic Phase I, Phase II, and Phase III processes was performed. In addition, the following were discussed (1) regulation of xenobiotic metabolism; (2) review of published toxicokinetics for specific chemicals; and (3) genetic diversity of these processes in C. elegans. Finally, worm xenobiotic transport and metabolism was placed in an evolutionary context; key areas for future research highlighted; and implications for extrapolating C. elegans toxicity results to other species discussed.

Description of Heterodera microulae sp. n. (Nematoda: Heteroderinae) from China - a new cyst nematode in the Goettingiana group

A new cyst-forming nematode, Heterodera microulae sp. n., was isolated from the roots and rhizosphere soil of Microula sikkimensis in China. Morphologically, the new species is characterized by lemon-shaped body with an extruded neck and obtuse vulval cone. The vulval cone of the new species appeared to be ambifenestrate without bullae and a weak underbridge. The second-stage juveniles have a longer body length with four lateral lines, strong stylets with rounded and flat stylet knobs, tail with a comparatively longer hyaline area, and a sharp terminus. The phylogenetic analyses based on ITS-rDNA, D2-D3 of 28S rDNA, and COI sequences revealed that the new species formed a separate clade from other Heterodera species in Goettingiana group, which further support the unique status of H. microulae sp. n. Therefore, it is described herein as a new species of genus Heterodera; additionally, the present study provided the first record of Goettingiana group in Gansu Province, China.

Evaluation of Metabarcoding Primers for Analysis of Soil Nematode Communities

While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the application of high throughput approaches to study the ecology of nematodes remains unresolved due to several issues, e.g., whether to include an initial nematode extraction step or not, the lack of consensus on the best performing primer combination, and the absence of a curated nematode reference database. The objective of this method development study was to compare different primer sets to identify the most suitable primer set for the metabarcoding of nematodes without initial nematode extraction. We tested four primer sets for amplicon sequencing: JB3/JB5 (mitochondrial, I3-M11 partition of COI gene), SSU_04F/SSU_22R (18S rRNA, V1-V2 regions), and Nemf/18Sr2b (18S rRNA, V6-V8 regions) from earlier studies, as well as MMSF/MMSR (18S rRNA, V4-V5 regions), a newly developed primer set. We used DNA from 22 nematode taxa, 10 mock communities, 20 soil samples, 4 root samples, and one bulk soil. We amplified the target regions from the DNA samples with the four different primer combinations and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the Nemf/18Sr2b primer set was superior for detecting soil nematodes compared to the other primer sets based on our sequencing results and on the annotation of our sequence reads at the genus and species ranks. This primer set generated 74% reads of Nematoda origin in the soil samples. Additionally, this primer set did well with the mock communities, detecting all the included specimens. It also worked better in the root samples than the other primer set that was tested. Therefore, we suggest that the Nemf/18Sr2b primer set could be used to study rhizosphere soil and root associated nematodes, and this can be done without an initial nematode extraction step.

New records of plant-parasitic nematodes from Iceland

The plant-parasitic nematodes of Iceland are poorly understood. To address this, a study of the nematodes of the families Criconematidae and Hemicycliophoridae was performed in 2015. Soil samples were taken from underneath various host plants in different locations in Iceland. The identification was performed on the basis of the general morphology and subsequently confirmed by molecular markers (D2-D3 28S rDNA). The study revealed the presence of nematode specimens belonging to four species of the family Criconematidae: Criconemoides amorphus, Criconema demani, Mesocriconema xenoplax and Mesocriconema curvatum, as well as one species Hemicycliophora conida of the family Hemicycliophoridae. To our knowledge, this is the first record of the occurrence of these nematode species in Iceland. The species identified are economically important plant-parasitic nematodes of likely interest to—among others—Icelandic plant protection professionals. This report broadens our knowledge of Iceland’s nematode biodiversity; moreover, morphological analyses and molecular data may contribute to better understanding the origin of nematode species on the island of Iceland.

New Molecular Data on Filaria and its Wolbachia from Red Howler Monkeys (Alouatta macconnelli) in French Guiana-A Preliminary Study

Previous studies have reported filarial parasites of the genus Dipetalonema and Mansonella from French Guiana monkeys, based on morphological taxonomy. In this study, we screened blood samples from nine howler monkeys (Alouatta macconnelli) for the presence of filaria and Wolbachia DNA. The infection rates were 88.9% for filaria and 55.6% for wolbachiae. The molecular characterization, based on the 18S gene of filariids, revealed that A. macconnelli are infected with at least three species (Mansonella sp., Brugia sp. and an unidentified Onchocercidae species.). Since the 18S and cox1 generic primers are not very effective at resolving co-infections, we developed ITS genus-specific PCRs for Mansonella and Brugia genus. The results revealed coinfections in 75% of positives. The presence of Mansonella sp. and Brugia sp. was also confirmed by the 16S phylogenetic analysis of their associated Wolbachia. Mansonella sp., which close to the species from the subgenus Tetrapetalonema encountered in New World Monkeys, while Brugia sp. was identical to the strain circulating in French Guiana dogs. We propose a novel ITS1Brugia genus-specific qPCR. We applied it to screen for Brugia infection in howler monkeys and 66.7% were found to be positive. Our finding highlights the need for further studies to clarify the species diversity of neotropics monkeys by combining molecular and morphological features. The novel Brugia genus-specific qPCR assays could be an effective tool for the surveillance and characterization of this potential zoonosis.

DNA Barcoding for Delimitation of Putative Mexican Marine Nematodes Species

Nematode biodiversity is mostly unknown; while about 20,000 nematode species have been described, estimates for species diversity range from 0.1 to 100 million. The study of nematode diversity, like that of meiofaunal organisms in general, has been mostly based on morphology-based taxonomy, a time-consuming and costly task that requires well-trained specialists. This work represents the first study on the taxonomy of Mexican nematodes that integrates morphological and molecular data. We added eleven new records to the Mexican Caribbean nematode species list: Anticomidae sp.1, Catanema sp.1, Enoploides gryphus, Eurystomina sp.1, Haliplectus bickneri, Metachromadora sp.1, Odontophora bermudensis, Oncholaimus sp.1, Onyx litorale, Proplatycoma fleurdelis, and Pontonema cf. simile. We improved the COI database with 57 new sequences from 20 morphotypes. All COI sequences obtained in this work are new entries for the international genetic databases GenBank and BOLD. Among the studied sites, we report the most extensive species record (12 species) at Cozumel. DNA barcoding and species delineation methods supported the occurrence of 20 evolutionary independent entities and confirmed the high taxonomic resolution of the COI gene. Different approaches provided consistent results: ABGD and mPTP methods disentangled 20 entities, whereas Barcode Index Numbers (BINs) recovered 22 genetic species. Results support DNA barcoding being an efficient, fast, and low-cost method to integrate into morphological observations in order to address taxonomical shortfalls in meiofaunal organisms.

Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities

Biomonitoring approaches and investigations of many ecological questions require assessments of the biodiversity of a given habitat. Small organisms, ranging from protozoans to metazoans, are of great ecological importance and comprise a major share of the planet's biodiversity but they are extremely difficult to identify, due to their minute body sizes and indistinct structures. Thus, most biodiversity studies that include small organisms draw on several methods for species delimitation, ranging from traditional microscopy to molecular techniques. In this study, we compared the efficiency of these methods by analyzing a community of nematodes. Specifically, we evaluated the performances of traditional morphological identification, single-specimen barcoding (Sanger sequencing), and metabarcoding in the identification of 1500 nematodes from sediment samples. The molecular approaches were based on the analysis of the 28S ribosomal large and 18S small subunits (LSU and SSU). The morphological analysis resulted in the determination of 22 nematode species. Barcoding identified a comparable number of operational taxonomic units (OTUs) based on 28S rDNA (n = 20) and fewer OTUs based on 18S rDNA (n = 12). Metabarcoding identified a higher OTU number but fewer amplicon sequence variants (AVSs) (n = 48 OTUs, n = 17 ASVs for 28S rDNA, and n = 31 OTUs, n = 6 ASVs for 18S rDNA). Between the three approaches (morphology, barcoding, and metabarcoding), only three species (13.6%) were shared. This lack of taxonomic resolution hinders reliable community identifications to the species level. Further database curation will ensure the effective use of molecular species identification.

Characterization of Vittatidera zeaphila (Nematoda: Heteroderidae) from Indiana with molecular phylogenetic analysis of the genus

In the summer of 2016, a field of corn (Zea mays) in Spencer County, Indiana was observed with heavily stunted plants, and from the affected roots a large number of cysts were recovered. Soil samples were submitted to one of us (JF), who extracted the nematode cysts and sent them to the USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory (MNGDBL), Beltsville, MD for morphological and molecular identification. Cysts and the recovered second-stage juveniles (J2) that were examined morphologically conformed to the measurements of Vittatidera zeaphila, the goose cyst nematode originally described from Tennessee, USA in 2010. The molecular analysis of J2 showed the sample from Spencer County matched exactly with V. zeaphila according to ribosomal DNA markers ITS, 28S, and 18S, and with mitochondrial cytochrome oxidase I (COI). The nuclear marker heat shock protein 90 (Hsp90) was also analyzed for the first time from the Indiana population of V. zeaphila. Similarities to existing cyst nematode sequences are reported herein. Geographically, although the county is across the Ohio River from Kentucky, the previously reported Hickman County, Kentucky location and Indiana detection are approximately 200 miles apart. To the best of our knowledge, this is the first report of V. zeaphila in Indiana.

In the summer of 2016, a field of corn (Zea mays) in Spencer County, Indiana was observed with heavily stunted plants, and from the affected roots a large number of cysts were recovered. Soil samples were submitted to one of us (JF), who extracted the nematode cysts and sent them to the USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory (MNGDBL), Beltsville, MD for morphological and molecular identification. Cysts and the recovered second-stage juveniles (J2) that were examined morphologically conformed to the measurements of Vittatidera zeaphila, the goose cyst nematode originally described from Tennessee, USA in 2010. The molecular analysis of J2 showed the sample from Spencer County matched exactly with V. zeaphila according to ribosomal DNA markers ITS, 28S, and 18S, and with mitochondrial cytochrome oxidase I (COI). The nuclear marker heat shock protein 90 (Hsp90) was also analyzed for the first time from the Indiana population of V. zeaphila. Similarities to existing cyst nematode sequences are reported herein. Geographically, although the county is across the Ohio River from Kentucky, the previously reported Hickman County, Kentucky location and Indiana detection are approximately 200 miles apart. To the best of our knowledge, this is the first report of V. zeaphila in Indiana.

Molecular and morphological characterization of the amaryllis lesion nematode, Pratylenchus hippeastri (Inserra et al., 2007), from California

Root-lesion nematodes (Pratylenchus spp.) are among the most important nematode pests on grapevine along with root-knot, dagger, and ring nematodes. In 2019, two samples of both soil and roots were collected from a vineyard in Delano, Kern County, California and submitted to the United States Department of Agriculture, ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD, for identification purposes. Females and juveniles of Pratylenchus sp. were recovered from the root and soil samples using the sugar centrifugal flotation and Baermann funnel extraction methods. Both morphological observations and molecular analysis of internal transcribed spacer (ITS), 28S large subunit ribosomal DNA, and mitochondrial cytochrome oxidase (COI) sequences indicated that the specimens recovered from the soil and roots were Pratylenchus hippeastri. To the best of the authors' knowledge, this is the first report of P. hippeastri from California including the first record of this species on grapevine and the second state record in North America. Damages caused by nematodes cannot be over-emphasized, although economic importance of P. hippeastri has never been established. Hence, there is an urgent need to investigate the economic impact of this nematode in vineyards in California State in order to develop sustainable management strategies.

Root-lesion nematodes (Pratylenchus spp.) are among the most important nematode pests on grapevine along with root-knot, dagger, and ring nematodes. In 2019, two samples of both soil and roots were collected from a vineyard in Delano, Kern County, California and submitted to the United States Department of Agriculture, ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD, for identification purposes. Females and juveniles of Pratylenchus sp. were recovered from the root and soil samples using the sugar centrifugal flotation and Baermann funnel extraction methods. Both morphological observations and molecular analysis of internal transcribed spacer (ITS), 28S large subunit ribosomal DNA, and mitochondrial cytochrome oxidase (COI) sequences indicated that the specimens recovered from the soil and roots were Pratylenchus hippeastri. To the best of the authors’ knowledge, this is the first report of P. hippeastri from California including the first record of this species on grapevine and the second state record in North America. Damages caused by nematodes cannot be over-emphasized, although economic importance of P. hippeastri has never been established. Hence, there is an urgent need to investigate the economic impact of this nematode in vineyards in California State in order to develop sustainable management strategies.

PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes

Motivation

The phylum Nematoda comprises the most cosmopolitan and abundant metazoans on Earth and plant-parasitic nematodes represent one of the most significant nematode groups, causing severe losses in agriculture. Practically, the demands for accurate nematode identification are high for ecological, agricultural, taxonomic and phylogenetic researches. Despite their importance, the morphological diagnosis is often a difficult task due to phenotypic plasticity and the absence of clear diagnostic characters while molecular identification is very difficult due to the problematic database and complex genetic background.

Results

The present study attempts to make up for currently available databases by creating a manually-curated database including all up-to-date authentic barcoding sequences. To facilitate the laborious process associated with the interpretation and identification of a given query sequence, we developed an automatic software pipeline for rapid species identification. The incorporated alignment function facilitates the examination of mutation distribution and therefore also reveals nucleotide autapomorphies, which are important in species delimitation. The implementation of genetic distance, plot and maximum likelihood phylogeny analysis provides more powerful optimality criteria than similarity searching and facilitates species delimitation using evolutionary or phylogeny species concepts. The pipeline streamlines several functions to facilitate more precise data analyses, and the subsequent interpretation is easy and straightforward.

Availability and implementation

The pipeline was written in vb.net, developed on Microsoft Visual Studio 2017 and designed to work in any Windows environment. The PPNID is distributed under the GNU General Public License (GPL). The executable file along with tutorials is available at https://github.com/xueqing4083/PPNID.

Supplementary information

Supplementary data are available at Bioinformatics online.

First report with morphometrics and molecular characterization of phtyonematodes associating mango trees in the tropics of Saudi Arabia

A sum of 218 composite rhizosphere soil samples were collected from around the feeder roots of mango, Mangifera indica growing in Jazan region, the tropical south west corner of Saudi Arabia. Samples were rendered for nematodes extraction using the centrifugal floatation method, and the stylet-bearing nematodes were morphologically identified according to the standardized taxonomical keys. A list of 14 stylet-bearing nematode genera and/or species were found to be associating the roots of mango in this study. Species identification of the most important parasitic nematodes, in this list, was carried-out, based on morphometrics and morphological features. Identification of these species was then molecularly confirmed using the D3 expansion region of 28S ribosomal RNA (rRNA) gene. These nematodes included; Tylenchorhynchus mediterraneus, Hoplolaimus seinhorsti, Hemicriconemoides strictathecatus, Longidorus latocephalus and Xiphinema elongatum. Some new local nematode-host records in Saudi Arabia were recorded including; Aphelenchus sp., H. strictathecatus, L. latocephalus, and T. mediterraneus. Some new world nematode-host records were also reported including; L. latocephalus and T. mediterraneus.

Metabarcoding free-living marine nematodes using curated 18S and CO1 reference sequence databases for species-level taxonomic assignments

High-throughput sequencing has the potential to describe biological communities with high efficiency yet comprehensive assessment of diversity with species-level resolution remains one of the most challenging aspects of metabarcoding studies. We investigated the utility of curated ribosomal and mitochondrial nematode reference sequence databases for determining phylum-specific species-level clustering thresholds. We compiled 438 ribosomal and 290 mitochondrial sequences which identified 99% and 94% as the species delineation clustering threshold, respectively. These thresholds were evaluated in HTS data from mock communities containing 39 nematode species as well as environmental samples from Vietnam. We compared the taxonomic description of the mocks generated by two read-merging and two clustering algorithms and the cluster-free Dada2 pipeline. Taxonomic assignment with the RDP classifier was assessed under different training sets. Our results showed that 36/39 mock nematode species were identified across the molecular markers (18S: 32, JB2: 19, JB3: 21) in UClust_ref OTUs at their respective clustering thresholds, outperforming UParse_denovo and the commonly used 97% similarity. Dada2 generated the most realistic number of ASVs (18S: 83, JB2: 75, JB3: 82), collectively identifying 30/39 mock species. The ribosomal marker outperformed the mitochondrial markers in terms of species and genus-level detections for both OTUs and ASVs. The number of taxonomic assignments of OTUs/ASVs was highest when the smallest reference database containing only nematode sequences was used and when sequences were truncated to the respective amplicon length. Overall, OTUs generated more species-level detections, which were, however, associated with higher error rates compared to ASVs. Genus-level assignments using ASVs exhibited higher accuracy and lower error rates compared to species-level assignments, suggesting that this is the most reliable pipeline for rapid assessment of alpha diversity from environmental samples.

Taxonomic status of Rhabdochona ictaluri (Nematoda: Rhabdochonidae) based on molecular and morphological evidence

The genus Rhabdochona includes more than 100 species infecting freshwater fishes in all zoogeographical regions of the world. In Mexico, 12 nominal species of Rhabdochona have been recorded. Of these, Rhabdochona ictaluri was originally described as a parasite of endemic catfishes of the family Ictaluridae; however, the species was later considered on morphological grounds as a junior synonym of Rhabdochona kidderi. In this study, newly sampled specimens of R. ictaluri were obtained from the type host and type locality and were used to perform a detailed morphological analysis and molecular phylogenetic inferences through one mitochondrial and two nuclear genes; data were used in an integrative taxonomy context to test the taxonomic status of R. ictaluri. This approach proved to be very useful to confirm the validity of this species, and robust species limits were established between these two putative species considering morphology, molecular data, host association, and biogeography.

Unexpected rDNA divergence between two morphologically minimalistic nematodes with description of a new species (Tylenchomorpha: Tylenchidae)

Species of the family Tylenchidae are encountered in large numbers in soils. The genus Labrys was recently described characterised by a remarkable lip pattern that differs from all other known Tylenchidae genera. Here we describe a curious new species, Labrys fujianensis sp. n., that morphologically fits the genus Labrys but which is genetically divergent. The phylogeny was inferred based on 18S and 28S rDNA and light and scanning electron microscopy were used to extract detailed morphologies. The phylogenetic position of this species and its phenotypic convergence are discussed. The possibility of a long-branch attraction artefact was inspected both by removal of variable nucleotide sites and monophyletic testing of topologies. The results confirmed the divergent positioning of the presented species and it is demonstrated that the genetic diversity in Tylenchidae may be much higher than expected due to morphological homoplasy.

Morphological and molecular characterisation of Spirinia antipodea Leduc n. sp. (Nematoda: Desmodoridae), a cryptic species related to S. parasitifera, from the coast of New Zealand

Spirinia parasitifera is a common nematode species recorded from coastal habitats of the White, North and Barents Seas, the Northwest Atlantic, the Maldives and Australia, and exhibits a high degree of variability in some morphological characters. For these reasons it has been suggested that S. parasitifera is a species complex comprised of several distinct but potentially cryptic species. However, no study has yet combined molecular and morphological approaches to verify this assertion. Here, we describe S. antipodea n. sp., a species morphologically very similar to S. parasitifera, from the coast of New Zealand. Spirinia antipodea n. sp. differs from the original description of S. parasitifera as well as subsequent descriptions by other authors in at least one body dimension, but no single trait differs consistently between the New Zealand specimens and all descriptions of S. parasitifera. Phylogenetic analyses showed that the new species is distinct from other species of the genus, including S. parasitifera specimens sampled near the type locality. The S. antipodea n. sp. SSU sequence differed from other Spirinia sequence by 2.1-5.3%, whilst D2-D3 of LSU sequences differed by 12.5-18.9%. The consensus SSU tree also recovered three distinct S. parasitifera clades, which provides support for the existence of a species complex. Because it is not possible to determine whether the variability in morphological characters observed among descriptions of S. parasitifera is intra- or interspecific, and therefore to determine which trait can reliably be used to differentiate between S. antipodea n. sp. and S. parasitifera, the new species is best differentiated from S. parasitifera and other closely related species based on SSU sequences rather than morphological characters.

Phylogenetic position of the parasitic nematode Trophomera (Nematoda, Benthimermithidae): A molecular analysis

Benthimermithid nematodes are parasites of invertebrates currently classified within their own order. Relationships between the Benthimermithida and other nematode orders, however, remain unclear due to their relatively simple morphology, their rarity, and paucity of molecular sequence data. Here, we combine molecular sequences obtained from Trophomera cf. marionensis in the Kermadec Trench with existing Trophomera sequences to determine the phylogenetic position of benthimermithids. Our SSU analyses showed Trophomera to be most closely-related to the order Plectida, subclass Chromadorea. Trophomera sequences formed a well-supported monophyletic clade placed within the Plectida, however relationships with other taxa within the order could not be resolved. Based on the result of these analyses, we propose that the family Benthimermithidae be moved to the order Plectida, however, future research on the classification of the family should focus on the benthimermithid genera Bathynema and Adenodelphis, for which no molecular sequences are yet available. We could not confirm a relationship between Trophomera and the family Camacolaimidae, which are both characterised by the presence of a stylet or stylet-like structure in the buccal cavity. Stylets are a common feature of parasitic nematodes, and its presence in a free-living benthimermithid ancestor perhaps similar to present-day camacolaimids could have facilitated a transition to a parasitic lifestyle. Our SSU phylogenetic analyses show that some features of benthimermithids, including the trophosome and a parasitic life cycle where the adults mate outside the host, have evolved independently in different groups of parasitic nematodes.

Phylogenetic position of the enigmatic deep-sea nematode order Rhaptothyreida: A molecular analysis

The placement of the rare deep-sea nematode order Rhaptothyreida remains unclear due to the unique morphology of this group, an unknown life cycle with morphologically distinct juvenile stages which may or may not be parasitic, and lack of molecular sequences. Here, we investigate the phylogenetic placement and status of the Rhaptothyreida based on SSU and D2-D3 of LSU rDNA sequences of Rhaptothyerus typicus specimens obtained from the continental slope of New Zealand. Molecular sequences of three adults and a late stage juvenile were identical, confirming that they belong to the same species despite pronounced morphological differences. We observed the presence of the rare nucleotide transition A → G and transversion G → Y in the loops of Hairpin 35 and 48 regions, which is consistent with the placement of R. typicus within the order Enoplida. Rhaptothyreus typicus was consistently recovered as a long branch clade in SSU and D2-D3 of LSU analyses, which can have a destabilising effect on tree topology. After Gblocks were used to remove sites of questionable alignment, R. typicus was placed in a clade comprising Trissonchulus, Dolicholaimus and Ironus sequences (family Ironidae, order Enoplida) in both Bayesian and Maximum Likelihood SSU topologies. Depending on which alignment algorithm was used, analyses of LSU sequences focusing on enoplid taxa either suggested a relationship between R. typicus and Halalaimus (family Oxystominidae) or did not identify any clear relationships. Overall, our results provide strong evidence for placing R. typicus and the family Rhaptothyreidae within the order Enoplida, although further work is required to clarify relationships between rhaptothyreids and other enoplid taxa. A parasitic lifestyle could explain the unique morphology of this group, their highly divergent SSU and LSU rDNA molecular sequences, and the marked morphological differences between late juveniles and adults. Further molecular investigations targeting both free-living and parasitic early juvenile life stages in potential deep-sea hosts are needed to better understand the evolution of this unusual nematode taxon.

Soil nematode abundance and diversity from four vegetation types in Central Mexico

Soil nematode abundance and MOTU diversity were estimated from a geographically broad area of Mexico that included four out of seven recognised vegetation types. Vegetation types were assessed for abundance and diversity of nematode communities and inferred ecological relationships between them. Soils were sampled from tropical rainforest, tropical dry deciduous forest, temperate coniferous forest and xerophytic shrub during 2013, 2014 and 2015. Fourteen sampling sites withca10-20 samples per site from 11 localities spread across Central Mexico were assessed. Altitudes sampled ranged from 113 m a.s.l. (tropical coastal plain) to 2400 m a.s.l. (Trans-Mexican Volcanic Belt). Samples were drawn from conserved and cultivated plots from each sampling site covering an area of ⩾100 m2. A total of 13 263 individuals from 25 identified families of nematodes were collected. Family abundance and complementarity indices between sites revealed to some extent the affinities between vegetation types. Nevertheless, statistical analyses revealed no differences between nematode family abundances between sites, only between families across all sites. Molecular operational taxonomic units (MOTU) methods were employed as a framework to assess biodiversity. From these, 77 high-quality sequences for taxonomic barcoding were recovered and later identified with morphological traits. Only six sequences matched at a 98-99% level with those reported in GenBank. Sequences amounted to a total of 41 MOTU, where 100% of the MOTU from both conserved and disturbed tropical rainforest, tropical dry deciduous forest and xerophytic shrub exhibited a ⩾3% cut-off genetic identity, whilst temperate coniferous forest and disturbed temperate coniferous forest showed 73% and 70% respectively. In addition, 12.2% MOTU were shared among localities and 87.8% exhibited an apparently locality-limited distribution. The potential for a considerable diversity of nematodes, as revealed from a small sample of MOTU diversity, is discussed.

A new species of Malenchus (Nematoda: Tylenchomorpha) with an updated phylogeny of the Tylenchidae

The family Tylenchidae is one of most abundant and diverse nematode groups found in soil habitats. In this study, a new species named Malenchus cylindricus sp. n. is described based on light and scanning electron microscopy and molecular data. The new species is characterised by elongate-cylindrical vulva-anus body shape and a narrow annulation. We updated the phylogeny of Tylenchidae by including molecular data for the rare genera Miculenchus and Tenunemellus and by improving the morphological characterisation of the genus Lelenchus. Additionally, we compared the effect of alignment methods on the tree topologies and branch support values. The results suggest that the position of subfamily Ecphyadophorinae within Tylenchidae needs to be further revised. Phylogenies inferred from different sequence-based alignments were relatively more similar (i.e., tree topology and branch support) to one another than to secondary structure-aided methods. Finally, conflicting branch support values can be reconciled by properly selecting the alignment method.

A molecular phylogeny of the Rhigonematomorpha De Ley & Blaxter, 2002 as inferred from SSU and LSU rDNA sequences

A molecular hypothesis of the Infraorder Rhigonematomorpha is presented. The phylogeny recovered using combined SSU and LSU markers suggests that the Rhigonematomorpha is nested within a larger clade that includes Ascaridomorpha, Spiruromorpha and Oxyuridomorpha and is strongly supported by maximum likelihood (ML) bootstrap support values (BS) and Bayesian posterior probabilities (BPP). SSU and LSU ML and Bayesian analyses recovered Rhigonematomorpha as a paraphyletic clade. In the ML and Bayesian analyses of a combined matrix of complete to partial sequences of SSU and LSU, respectively, Rhigonematomorpha is recovered as a monophyletic clade with moderate BPP but low BS. Highly supported BS and BPP of a combined SSU and LSU matrix support a hypothesis of a monophyletic Superfamily Ransomnematoidea that includes the families Carnoyidae, Hethidae, Ransomnematidae plus a Brumptaemilius, Cattiena, Insulanema clade, and a monophyletic Superfamily Rhigonematoidea that probably includes the paraphyletic families Rhigonematidae and Ichthyocephalidae. It is suggested that the future inclusion of more families and genera might help resolve the monophyly of the Infraorder Rhigonematomorpha as advanced here.

The utility of mtDNA and rDNA for barcoding and phylogeny of plant-parasitic nematodes from Longidoridae (Nematoda, Enoplea)

The traditional identification of plant-parasitic nematode species by morphology and morphometric studies is very difficult because of high morphological variability that can lead to considerable overlap of many characteristics and their ambiguous interpretation. For this reason, it is essential to implement approaches to ensure accurate species identification. DNA barcoding aids in identification and advances species discovery. This study sought to unravel the use of the mitochondrial marker cytochrome c oxidase subunit 1 (coxI) as barcode for Longidoridae species identification, and as a phylogenetic marker. The results showed that mitochondrial and ribosomal markers could be used as barcoding markers, except for some species from the Xiphinema americanum group. The ITS1 region showed a promising role in barcoding for species identification because of the clear molecular variability among species. Some species presented important molecular variability in coxI. The analysis of the newly provided sequences and the sequences deposited in GenBank showed plausible misidentifications, and the use of voucher species and topotype specimens is a priority for this group of nematodes. The use of coxI and D2 and D3 expansion segments of the 28S rRNA gene did not clarify the phylogeny at the genus level.

Taxonomy assignment approach determines the efficiency of identification of OTUs in marine nematodes

Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of data. Identification of operational taxonomic units (OTUs) is one of the crucial steps in the process and can be accomplished using several different approaches, namely, alignment-based, probabilistic, tree-based and phylogeny-based. The number of identified sequences in the reference databases affects the precision of identification. This paper compares the identification of marine nematode OTUs using alignment-based, tree-based and phylogeny-based approaches. Because the nematode reference dataset is limited in its taxonomic scope, OTUs can only be assigned to higher taxonomic categories, families. The phylogeny-based approach using the evolutionary placement algorithm provided the largest number of positively assigned OTUs and was least affected by erroneous sequences and limitations of reference data, compared to alignment-based and tree-based approaches.