Cryptic diversity and species delimitation in theXiphinema americanum-group complex (Nematoda: Longidoridae) as inferred from morphometrics and molecular markers

Data on four species of Longidorus Micoletzky, 1922 (Nematoda: Longidoridae) from southern and southeastern Iran, including description of a new species

Four species of the genus Longidorus were recovered from southern (Bushehr province) and southeastern (Southern Khorasan province) Iran. The first species, L. paratabrizicus n. sp. represents a new member to the genus and is characterised by 4.8-5.6 mm long females with anteriorly flattened lip region separated from the rest of the body by depression, amphidial fovea pocket-shaped without lobes, tail conical, dorsally convex, ventrally almost straight with bluntly rounded tip and males in population. By having similar lip region and tail shape, the new species most closely resembles five species viz. L. artemisiae, L. globulicauda, L. patuxentensis, L. sturhani, and L. tabrizicus. It represents the cryptic form of the last species. The second species belongs to L. mirus, recovered in both southern and southeastern Iran, representing the first record of the species after its original description. As an update to the characteristics of this species, it's all juvenile developmental stages were recovered and described. The criteria to separate L. mirus from two closely related species, L. auratus and L. africanus, are discussed. The third species belongs to L. persicus, a new record in southern Iran. The fourth species, L. orientalis was recovered in high population density in association with date palm trees in Bushehr province. The phylogenetic relationships of the new species and recovered populations of L. mirus and L. persicus were reconstructed using two ribosomal markers and the resulted topologies were discussed.

A new species of the genus Hexamermis Steiner, 1924 (Nematoda: Mermithidae) from northern Iran: a nematode with an unusual uterine morphology

Hexamermis zirabi sp. n., recovered from a natural habitat of Mazandaran province, north of Iran, is described based on morphological and molecular data. The new species is characterized by its six cephalic papillae; cuticle with distinct cross fibers; conoid or sharply tapered head; mouth terminal; six hypodermal cords; J-shaped vagina oriented to the anterior end of body; uterus with Z-organs or sclerotized bodies; tail similar in both sexes and bluntly rounded; spicules paired, separate, slightly curved, shorter than body width at cloaca, with rounded tip; and male genital papillae arranged in five rows. In addition to the morphological study, molecular phylogenetic analyses using a partial large subunit (28S D2-D3) were also performed, and the new species formed a highly supported (1.00% Bayesian posterior probability (BPP)) clade with Hexamermis popilliae.

A new needle nematode, Longidorus zanjanensis sp. nov. (Nematoda: Longidoridae) from north-western Iran

During a survey of soil nematodes in 2022, a new species of the genus Longidorus, described here as Longidorus zanjanensis sp. nov., was discovered in the rhizosphere of Astragalus sp. in Zanjan Province, Iran. The new needle nematode is described and illustrated based on morphological, morphometric, and molecular traits. Further, its females are characterized by having a long body ranging 5.6-7.7 mm long, lip region anteriorly flattened and almost continuous or slightly offset by a depression with body contour, ca 16.5-18.5 μm wide, amphidial fovea pouch-like without basal lobes, guiding ring at 35-41 μm distance from the anterior end, and an odontostyle and odontophore ranging 102-115 and 47-75 μm long, respectively. The pharyngeal bulb is 123-153 μm long, female reproductive system didelphic-amphidelphic containing sperm, vulva almost equatorial, located at 46.7-51.4% of body length, tail short, rounded to bluntly conoid, bearing two pairs of caudal pores and terminus widely rounded with distinct radial lines in hyaline region (39-50 μm long, c = 122.4-189.4, c' = 0.6-0.8). Males are common, making up to 60% of the adults, and are functional, with spicules 68.0-80.0 μm long, as well as having 8-14 ventromedian copulatory supplements. All four juvenile life developmental stages were present, with the tail of first-stage juvenile conoid shape, dorso-ventrally curved with rounded terminus. The polytomous codes delimiting the new species are: A4-B3-C3-D3-E1-F34-G12-H1-I2-J1-K6. Morphologically, the new species comes close to eight known species of the genus, namely L. apulus, L. armeniacae, L. crassus, L. kheirii, L. soosanae, L. proximus, L. pauli, and L. ferrisi. The morphological differences between the new species and the aforementioned species are discussed. Molecular phylogenetic analyses based on D2-D3 of large subunit (LSU) and internal transcribed spacer 1 (ITS1) rRNA sequences indicate that Longidorus zanjanensis sp. nov. is closely related to L. hyrcanus, L. soosanae, and L. elongatus.

A Blind-Identification Test on Criconema annuliferum (de Man, 1921) Micoletzky, 1925 Species Complex Corroborate the Hyper-Cryptic Species Diversity Using Integrative Taxonomy

Ring nematodes are obligate ectoparasites on crops and natural herbaceous and woody plants, and some species are of economic importance and cause damage to roots of several crops. Recent integrative taxonomical analyses recognized the existence of two cryptic species within the Criconema annuliferum morphotype in Spain. In this study, we corroborated that morphometric, morphological and a multi-locus analysis (including the ribosomal markers D2-D3 expansion segments of 28S rRNA, ITS rRNA, 18S RNA, and the mitochondrial DNA cytochrome oxidase I gene) identified a new lineage clearly separated from C. annuliferum, C. paraannuliferum and C. plesioannuliferum. The new lineage was described herein as Criconema pseudoannuliferum sp. nov., confirming that C. annuliferum species complex species complex comprises a hyper-cryptic species complex. This research analysed soil samples from the rhizosphere of maritime pine (Pinus pinaster Ait.) forests in Bermeja-Crestellina Mountain, located at the western part of Málaga province, southern Spain. The integrative taxonomical analyses revealed the occurrence of a new cryptic species identified using females, males and juveniles with detailed morphology, morphometry and molecular markers, described herein as Criconema pseudoannuliferum sp. nov. All molecular markers (D2-D3, ITS, 18S and COI) were obtained from the same individual that was also used for morphological and morphometric analyses. This research demonstrated the hidden diversity within the C. annuliferum species complex species complex can reach to four lineages under ribosomal and mitochondrial gene markers for one morphospecies group, which includes four species, viz. C. annuliferum, C. paraannuliferum, C. plesioannuliferum, and C. pseudoannuliferum sp. nov. Criconema pseudoannuliferum sp. nov. was detected in moderate soil density in two maritime pine forests (5 and 25 nematodes/500 cm³ of soil) suggesting that does not cause damage to maritime pine.

Morphological and Molecular Characterization of Talanema eshtiaghii sp. n. (Dorylaimida, Qudsianematidae) from Iran

A new species of the genus Talanema, recovered from the northwest of Iran, was described based on morphological, morphometric, and molecular data. Talanema eshtiaghii sp. n. was characterized by its 1.45-1.68 mm long body, lip region offset by constriction and 13-15 μm wide, odontostyle 15-18 μm long, double guiding ring, neck 312-362 μm long, pharyngeal expansion occupying 41-43% of the total neck length, uterus tripartite, and 111-189 μm long or 2.1-3.2 body diameters, vulva transverse (V = 55-58), tail similar in both sexes, conical with a dorsal concavity (30-44 μm, c = 33-56, c' = 1.0-1.6), spicules 49-56 μm long, and 14-18 shortly spaced ventromedian supplements in front of the level of the anterior end of spicules, with distinct hiatus. It was compared to four closely similar species, with emphasis on the most relevant traits to distinguish them. Molecular phylogenetic studies using partial sequence of the 28S rDNA (D2-D3 segment) revealed that the new species forms a clade with other currently sequenced representatives of Talanema, tentatively supporting the monophyly of this genus.

Description of Xiphinema pupureum n. sp. (Nematoda: Longidoridae), a new Xiphinema americanum group species detected from the rhizosphere of Ilex purpurea from Japan

A new species of Xiphinema americanum group was recovered in the rhizosphere of holly (Ilex purpurea) imported from Japan. It is described and illustrated in the present study as X. purpureum n. sp. The new species is characterised by moderately long females 2267 (2115-2550) μm, round lip region slightly offset from the rest of the body, 103.5 (98.5-109.0) μm long odontostyle, genital branches without discernible endosymbiotic bacteria, vulva located at 54.1 (51.6-57.1)% of the body, tail 30 (24.3-33.4) μm long with a broadly rounded terminus, male absent and four juvenile developmental stages. The polytomous codes of the new species are as follows: A4/5, B2/3, C1/2, D2/3, E3, F1, G1, H2, I1/2/3. The new species was molecularly characterised using near full length 18S, ITS1, and 28S D2-D3 regions of rRNA, and mitochondrial cytochrome c oxidase subunit I gene sequences. The phylogenetic analyses placed X. purpureum n. sp. with X. americanum group species, particularly with X. brevicolle complex species. This is the third X. americanum group species described from Japan.

A Proposed New Species Complex within the Cosmopolitan Ring Nematode Criconema annuliferum (de Man, 1921) Micoletzky, 1925

Ring nematodes are obligate ectoparasites on cultivated and wild herbaceous and woody plants, inhabiting many types of soil, but particularly sandy soils. This study explored the morphometrical and molecular diversity of ring nematodes resembling Criconema annuliferum in 222 soil samples from fruit crops in Spain, including almond, apricot, peach and plum, as well as populations from cultivated and wild olives, and common yew. Ring nematodes of the genus Criconema were detected in 12 samples from under Prunus spp. (5.5%), showing a low to moderate nematode soil densities in several localities from southeastern and northeastern Spain. The soil population densities of Criconema associated with Prunus spp. ranged from 1 nematode/500 cm³ of soil in apricot at Sástago (Zaragoza province) to 7950 and 42,491 nematodes/500 cm³ of soil in peach at Ricla and Calasparra (Murcia province), respectively. The integrative taxonomical analyses reveal the presence of two cryptic species identified using females, males (when available), and juveniles with detailed morphology, morphometry, and molecular markers (D2-D3, ITS, 18S, and COI), described herein as Criconema paraannuliferum sp. nov. and Criconema plesioannuliferum sp. nov. All molecular markers from each species were obtained from the same individuals, and these individuals were also used for morphological and morphometric analyses. Criconema paraannuliferum sp. nov. was found in a high soil density in two peach fields (7950 and 42,491 nematodes/500 cm³ of soil) showing the possibility of being pathogenic in some circumstances.

First report of Xiphinema ifacolum Luc, 1961 (Dorylaimida: Longidoridae) from Nigeria

A population of a species of dagger nematode (Xiphinema) belonging to the non-americanum group was recovered from the fields of kola nut (Cola sp.) in southern Nigeria. The morphological and morphometric data obtained from this population were consistent with the characteristics of the species Xiphinema ifacolum. In addition, molecular identification based on D2-D3 expansion segments of 28S rRNA and partial mitochondrial COI gene regions confirmed its identity. According to our knowledge, this is the first report of the species from Nigeria, and the second report from Africa, after the original description from Foulaya, Guinea.

A new species of Xiphinema americanum group (Nematoda: Longidoridae) from Iran, with additional data on three known species

One new and three known species of the genus Xiphinema from the rhizosphere of fruit trees and rose shrubs in East Azarbaijan province, Iran, are presented based on the morphological, morphometric and molecular characters. The new species is distinguished by its 2.0-2.1 mm long body, relatively flattened lip region with 8.7-10.0 µm width, set off from body contour by a deep constriction, odontostyle 82.5-88.0 µm long, V = 52-54, reproductive system didelphic-amphidelphic with symbiotic bacteria in the reflexed ovaries, tail conoid, dorsally convex with rounded to slightly subdigitate tip (42.0-43.5 µm long, c = 61-65, c' = 1.6-1.8), and males unknown. The new species, X. babaii sp. n., looks very close to X. californicum, and is regarded as its cryptic species, being separated from it using some morphological differences. Their separation was further corroborated using molecular data. Three known species belonging to the Xiphinema americanum group namely X. primum, X. pachtaicum and X. simile were also collected during present study, and new data were provided for them. Xiphinema simile is a new record for the Iran's nematode fauna. Molecular phylogenetic studies using partial sequences of 28S rRNA gene D2-D3 fragments were performed, and the phylogenetic relationships of the new species were discussed.

New insights into the identity of Discolaimium dubium Das, Khan and Loof, 1969 (Dorylaimida) as derived from its morphological and molecular characterization, with the proposal of its transference to Aporcella Andrássy, 2002

Three Iranian populations of Discolaimium dubium are studied, including their morphological and morphometric characterization, molecular analysis (LSU-rDNA) and the description of the male for the first time. For comparative purposes, this species is distinguished by its 1.10 to 1.40 mm long body, lip region offset by constriction and 8 to 10 µm wide, odontostyle 7.5 to 10.5 µm long with aperture occupying 59 to 76% of total length, neck 300 to 362 µm, pharyngeal expansion 127 to 181 µm long or 44 to 46% of the total neck length, uterus simple and 38 to 53 µm or 1.2 to 1.5 times the body diameter long, V = 52 to 58, tail conical (32-38 µm, c = 32-43, c' = 1.6-2.0) with rounded tip and a hyaline portion occupying 14 to 15% of tail length, spicules 30 to 32 µm long, and two or three widely space ventromedian supplements with hiatus. Both morphological and molecular data support its belonging to the genus Aporcella, whose monophyly is confirmed and to which the species is formally transferred as A. dubia (Das et al., 1969) comb. n.

Essential Amino Acid Enrichment and Positive Selection Highlight Endosymbiont's Role in a Global Virus-Vectoring Pest

Host-associated microbes display remarkable convergence in genome repertoire resulting from selection to supplement missing host functions. Nutritional supplementation has been proposed in the verrucomicrobial endosymbiont Xiphinematobacter sp., which lives within a globally widespread group of plant-parasitic nematodes that vector damaging nepoviruses to plants. Only one genome sequence has been published from this symbiont, leaving unanswered questions about its diversity, host range, role, and selective pressures within its hosts. Because its hosts are exceptionally resistant to culturing, this symbiont is best studied through advanced genomic approaches. To analyze the role of Xiphinematobacter sp. in its host, sequencing was performed on nematode communities, and then genomes were extracted for comparative genomics, gene ontology enrichment tests, polymorphism analysis, de Bruijn-based genome-wide association studies, and tests of pathway- and site-specific selection on genes predicted play a role in the symbiosis. Results showed a closely clustered set of Xiphinematobacter isolates with reduced genomes of ∼917 kbp, for which a new species was proposed. Symbionts shared only 2.3% of genes with outgroup Verrucomicrobia, but comparative analyses showed high conservation of all 10 essential amino acid (EAA) biosynthesis pathways plus several vitamin pathways. These findings were supported by gene ontology enrichment tests and high polymorphisms in these pathways compared with background. Genome-wide association analysis confirmed high between-species fixation of alleles with significant functional enrichment for EAA and thiamine synthesis. Strong positive selection was detected on sites within these pathways, despite several being under increased purifying selection. Together, these results suggest that supplementation of EAAs missing in the host diet may drive this widespread symbiosis.IMPORTANCE Xiphinematobacter spp. are distinctly evolved intracellular symbionts in the phylum Verrucomicrobia, which includes the important human gut-associated microbe Akkermansia muciniphila and many highly abundant free-living soil microbes. Like Akkermansia sp., Xiphinematobacter sp. is obligately associated with the gut of its hosts, which in this case consists of a group of plant-parasitic nematodes that are among the top 10 most destructive species to global agriculture, by vectoring plant viruses. This study examined the hypothesis that the key to this symbiont's stable evolutionary association with its host is through provisioning nutrients that its host cannot make that may be lacking in the nematode's plant phloem diet, such as essential amino acids and several vitamins. The significance of our research is in demonstrating, using population genomics, the signatures of selective pressure on these hypothesized roles to ultimately learn how this independently evolved symbiont functionally mirrors symbionts of phloem-feeding insects.

Three Species of Xiphinema Americanum-group Complex (Nematoda: Longidoridae), from Lorestan Province, Iran

The dagger nematodes of the longidorids can cause diseases of various agronomic and horticultural crops, and are consisted of more than 260 valid species. In a forest survey of ecotypes of longidorid nematodes, from the root zone soil of Brant’s oak, (Quercus brantii Lindl.) and hawthorn (Crataegus aronia L.) trees, three species of Xiphinema americanum group namely Xiphinema pachtaicum, X. oxycaudatum and X. plesiopachtaicum were collected and studied based on their morphological and morphometric characters. X. pachtaicum is prevalent Xiphinema species in Iran. In this paper additional data for X. oxycaudatum and X. plesiopachtaicum species are presented. X. plesiopachtaicum is a new record for nematode fauna of Iran.

Morphostatic Speciation within the Dagger Nematode Xiphinema hispanum-Complex Species (Nematoda: Longidoridae)

Dagger nematodes of the genus Xiphinema include a remarkable group of invertebrates of the phylum Nematoda comprising ectoparasitic animals of many wild and cultivated plants. Damage is caused by direct feeding on root cells and by vectoring nepoviruses that cause diseases on several crops. Precise identification of Xiphinema species is critical for launching appropriate control measures. We deciphered the cryptic diversity of the Xiphinema hispanum-species complex applying integrative taxonomical approaches that allowed us to verify a paradigmatic example of the morphostatic speciation and the description of a new species, Xiphinema malaka sp. nov. Detailed morphological, morphometrical, multivariate and genetic studies were carried out, and mitochondrial and nuclear haploweb analyses were used for species delimitation of this group. The new species belongs to morphospecies Group 5 from the Xiphinema nonamericanum-group species. D2-D3, ITS1, partial 18S, and partial coxI regions were used for inferring the phylogenetic relationships of X. malaka sp. nov. with other species within the genus Xiphinema. Molecular analyses showed a clear species differentiation not paralleled in morphology and morphometry, reflecting a clear morphostatic speciation. These results support the hypothesis that the biodiversity of dagger nematodes in southern Europe is greater than previously assumed.

Study of two species, one new and one known, of the genus Aporcella Andrássy, 2002 (Dorylaimida, Aporcelaimidae) from Iran, with a note on its phylogeny

Two species of the genus Aporcella, one new and one previously known, collected from cultivated fields in Iran are studied. Description, morphometrics, illustrations (both line and microphotographs) and D2-D3 sequences are provided for Aporcella talebii sp. n., which is characterized by its 1.66-2.02-mm-long body, lip region offset by constriction and 15-17 μm broad, odontostyle 14-17.5 μm long, neck 412-484 μm long, pharyngeal expansion occupying 46-50% of total neck length, uterus simple and 1.6-2.0 times the corresponding body diameter long, V = 52-59, tail conical (40-50 μm, c = 37-47, c' = 1.1-1.4) with a weak but perceptible dorsal concavity at the end and male absent. Morphometrics, microphotographs and D2-D3 sequences of Aporcella simplex are also presented, this being its first Asian record. Molecular analyses confirm the monophyly of the genus, its close relationship with other taxa lacking pars refringens vaginae and the polyphyly of Aporcelaimidae.

Can bacterial indicators of a grassy woodland restoration inform ecosystem assessment and microbiota-mediated human health?

Understanding how microbial communities change with environmental degradation and restoration may offer new insights into the understudied ecology that connects humans, microbiota, and the natural world. Immunomodulatory microbial diversity and 'Old Friends' are thought to be supplemented from biodiverse natural environments, yet deficient in anthropogenically disturbed or degraded environments. However, few studies have compared the microbiomes of natural vs. human-altered environments and there is little knowledge of which microbial taxa are representative of ecological restoration-i.e. the assisted recovery of degraded ecosystems typically towards a more natural, biodiverse state. Here we use novel bootstrap-style resampling of site-level soil bacterial 16S rRNA gene environmental DNA data to identify genus-level indicators of restoration from a 10-year grassy eucalypt woodland restoration chronosequence at Mt Bold, South Australia. We found two key indicator groups emerged: 'opportunistic taxa' that decreased in relative abundance with restoration and more stable and specialist, 'niche-adapted taxa' that increased. We validated these results, finding seven of the top ten opportunists and eight of the top ten niche-adapted taxa displayed consistent differential abundance patterns between human-altered vs. natural samples elsewhere across Australia. Extending this, we propose a two-dimensional mapping for ecosystem condition based on the proportions of these divergent indicator groups. We also show that restoring a more biodiverse ecosystem at Mt Bold has increased the potentially immune-boosting environmental microbial diversity. Furthermore, environmental opportunists including the pathogen-containing genera Bacillus, Clostridium, Enterobacter, Legionella and Pseudomonas associated with disturbed ecosystems. Our approach is generalizable with potential to inform DNA-based methods for ecosystem assessment and help target environmental interventions that may promote microbiota-mediated human health gains.

Integrative taxonomy of Xiphinema histriae and Xiphinema lapidosum from Spain

Three populations of Xiphinema non-americanum group species were detected in agricultural and natural ecosystems, during routine surveys for plant-parasitic nematodes in Spain. Based on morphological and molecular analyses, the species were identified as Xiphinema histriae and Xiphinema lapidosum, being this the first record and molecular characterization of both species in Spain. The morphometrics and morphology of the Spanish populations agree with those of the original description and paratype specimens and the present study provided a first description of the second to fourth juvenile stages of both species. A detailed study on the morphology in the Spanish populations of X. histriae, as well as in paratypes, showed a pseudo-Z-organ with weakly muscularized wall and containing numerous small dense granular bodies, which was different to the original description by Lamberti et al. (1993). This new finding suggests that X. histriae must be considered a member of the morphospecies Group 5 of X. non-americanum. Phylogenetic analysis based on D2 to D3 expansion segments of 28S gene, ITS1 and partial CoxI gene indicated that X. histriae and X. lapidosum are phylogenetically related with other Xiphinema non-americanum group spp. reported from Spain. Considering the pathological and economic importance of this group of nematodes, the combination of morphological characters, measurements, and molecular analysis is crucial for accurate identification of these species.

New evidence of nematode-endosymbiont bacteria coevolution based on one new and one known dagger nematode species of Xiphinema americanum-group (Nematoda, Longidoridae)

Three populations of Xiphinema primum n. sp. and two populations of X. pachtaicum were recovered from natural forests and cultural regions of northern Iran. Both species belong to the X. americanum-group and were characterized by their morphological, morphometric and molecular data. The new species, which was recovered in three locations, belongs to the X. brevicolle-complex and is characterized by 2124–2981 μm long females with a widely rounded lip region separated from the rest of the body by a depression, 103–125 μm long odontostyle, two equally developed genital branches with endosymbiont bacteria inside the ovary, which are visible under light microscope (LM), vulva located at 51.8–58.0%, the tail is 26–37 μm long with a bluntly rounded end and four juvenile developmental stages. It was morphologically compared with nine similar species viz. X. brevicolle, X. diffusum, X. incognitum, X. himalayense, X. luci, X. parabrevicolle, X. paramonovi, X. parataylori and X. taylori. The second species, X. pachtaicum, was recovered in two geographically distant points close to city of Amol. Molecular phylogenetic studies of the new species were performed using partial sequences of the D2-D3 expansion segments of the large subunit ribosomal RNA gene (LSU rDNA D2-D3), the internal-transcribed spacer rDNA (ITS = ITS1+5.8S+ITS2), and the mitochondrial cytochrome c oxidase I gene (COI mtDNA) regions. The Iranian population of X. pachtaicum was also phylogenetically studied based upon its LSU rDNA D2-D3 sequences. Both species were also inspected for their putative endosymbiont bacteria. Candidatus Xiphinematobacter sp. was detected from two examined populations of the new species, whereas the second endosymbiont bacterium, detected from three examined isolates of X. pachtaicum, was related to the plant and fungal endosymbionts of the family Burkholderiaceae. The phylogenetic analyses of the two endosymbiont bacteria were performed using partial sequences of 16S rDNA. In cophylogenetic analyses, significant levels of cophylogenetic signal were observed using both LSU rDNA D2-D3 and COI mtDNA markers of the host nematodes and 16S rDNA marker of the endosymbiont bacteria.

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.

Endosymbionts of Plant-Parasitic Nematodes

Some of the most agriculturally important plant-parasitic nematodes (PPNs) harbor endosymbionts. Extensive work in other systems has shown that endosymbionts can have major effects on host virulence and biology. This review highlights the discovery, development, and diversity of PPN endosymbionts, incorporating inferences from genomic data. Cardinium, reported from five PPN hosts to date, is characterized by its presence in the esophageal glands and other tissues, with a discontinuous distribution across populations, and genomic data suggestive of horizontal gene exchange. Xiphinematobacter occurs in at least 27 species of dagger nematode in the ovaries and gut epithelial cells, where genomic data suggest it may serve in nutritional supplementation. Wolbachia, reported in just three PPNs, appears to have an ancient history in the Pratylenchidae and displays broad tissue distribution and genomic features intermediate between parasitic and reproductive groups. Finally, a model is described that integrates these insights to explain patterns of endosymbiont replacement.

Pest categorisation of Xiphinema americanum sensu lato

The Panel on Plant Health performed a pest categorisation of Xiphinema americanum sensu lato (Nematoda: Longidoridae) for the EU. Sixty‐one species in this group are recognised. They are polyphagous pests found in soil associated with a number of plant species. As a migratory ectoparasitic species, it punctures cells of plant roots. Nematodes were classified in four categories based on their distribution and ability to transmit viruses. Category I contains the seven virus vector species present outside the EU: X. americanum sensu stricto, X. bricolense, X. californicum, X. inaequale, X. intermedium, X. rivesi (non‐EU populations) and X. tarjanense. Category II contains the 28 species not present in the EU and not known to transmit any virus. Twenty‐six species are present in the EU and are not known to be virus vectors (category III). Category IV contains the species present in the EU, which is a virus vector (EU populations of X. rivesi). All nematodes known to be virus vectors occurring outside the EU (category I) satisfy all the criteria that are within the remit of EFSA to assess to be regarded as Union quarantine pests. This is mainly due to their association with non‐EU virus isolates. Categories II and III contain species that are not reported to transmit viruses or cause economic damage to crop plants. Although uncertainty concerning their ability to transmit viruses exists, those species do not satisfy all the criteria to be regarded as Union quarantine pests. Category IV contains the EU populations of X. rivesi. The species is a virus vector but current EU populations of X. rivesi have not been reported to be associated with any of the EU viruses or their non‐EU isolates under field conditions. Xiphinema rivesi (EU populations) is widespread in some Member States and does not satisfy all the criteria to be regarded as a Union quarantine. None of the species can be regarded as a regulated non‐quarantine pest.

A new dagger nematode, Xiphinema poasense n. sp. (Nematoda: Longidoridae), from Costa Rica

A new dagger nematode,Xiphinema poasensen. sp., is described and illustrated from three populations extracted from soil associated with a combined plantation ofEucalyptussp.,Cupressussp. andPennisetumsp. and wild plants from a tropical pre-montane forest in Costa Rica. The new dagger nematode is characterised by a moderate body size 2612 (2416-3042) μm long, a rounded lip region 15.0 (13.5-16.5) μm broad, separated from the body contour by a shallow depression, amphidial fovea large, stirrup-shaped, a very long odontostyle (175 (164-188) μm), stylet guiding ring located 167 (136-181) μm from anterior end, vulva situated anterior to mid-body (36-40%), anterior genital branch complete but strongly reduced, without uterine differentiation, female tail short, hemispherical to convex-conoid with a c′ ratio = 0.7 (0.6-0.8) and bearing two pairs of caudal pores, and male absent. Integrative diagnosis was completed with molecular data using D2-D3 expansion segments of 28S rRNA, ITS1 region, partial 18S-rRNA and the partial mitochondrial gene cytochrome c oxidase subunit 1 (coxI). The phylogenetic relationships based on D2-D3 segments of this species with otherXiphinemaspp. of theX.non-americanumgroup indicated thatX. poasensen. sp. clustered with other species with a reduced anterior genital branch from the morphospecies Group 2,viz.,X. costaricenseandX. krugi. However, the phylogeny ofcoxIand partial 18S rRNA gene revealed that the new species did not cluster withXiphinemaspecies having the anterior genital branch absent or reduced (i.e., morphospecies Groups 1 and 2, respectively).

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.

Mitochondrial genome diversity in dagger and needle nematodes (Nematoda: Longidoridae)

Dagger and needle nematodes included in the family Longidoridae (viz. Longidorus, Paralongidorus, and Xiphinema) are highly polyphagous plant-parasitic nematodes in wild and cultivated plants and some of them are plant-virus vectors (nepovirus). The mitochondrial (mt) genomes of the dagger and needle nematodes, Xiphinema rivesi, Xiphinema pachtaicum, Longidorus vineacola and Paralongidorus litoralis were sequenced in this study. The four circular mt genomes have an estimated size of 12.6, 12.5, 13.5 and 12.7 kb, respectively. Up to date, the mt genome of X. pachtaicum is the smallest genome found in Nematoda. The four mt genomes contain 12 protein-coding genes (viz. cox1-3, nad1-6, nad4L, atp6 and cob) and two ribosomal RNA genes (rrnL and rrnS), but the atp8 gene was not detected. These mt genomes showed a gene arrangement very different within the Longidoridae species sequenced, with the exception of very closely related species (X. americanum and X. rivesi). The sizes of non-coding regions in the Longidoridae nematodes were very small and were present in a few places in the mt genome. Phylogenetic analysis of all coding genes showed a closer relationship between Longidorus and Paralongidorus and different phylogenetic possibilities for the three Xiphinema species.

Remarkable Diversity and Prevalence of Dagger Nematodes of the Genus Xiphinema Cobb, 1913 (Nematoda: Longidoridae) in Olives Revealed by Integrative Approaches

The genus Xiphinema includes a remarkable group of invertebrates of the phylum Nematoda comprising ectoparasitic animals of many wild and cultivated plants. Damage is caused by direct feeding on root cells and by vectoring nepoviruses that cause diseases on several crops. Precise identification of Xiphinema species is critical for launching appropriate control measures. We make available the first detailed information on the diversity and distribution of Xiphinema species infesting wild and cultivated olive in a wide-region in southern Spain that included 211 locations from which 453 sampling sites were analyzed. The present study identified thirty-two Xiphinema spp. in the rhizosphere of olive trees, ten species belonging to Xiphinema americanum-group, whereas twenty-two were attributed to Xiphinema non-americanum-group. These results increase our current knowledge on the biodiversity of Xiphinema species identified in olives and include the description of four new species (Xiphinema andalusiense sp. nov., Xiphinema celtiense sp. nov., Xiphinema iznajarense sp. nov., and Xiphinema mengibarense sp. nov.), and two new records for cultivate olives (X. cadavalense and X. conurum). We also found evidence of remarkable prevalence of Xiphinema spp. in olive trees, viz. 85.0% (385 out of 453 sampling sites), and they were widely distributed in both wild and cultivated olives, with 26 and 17 Xiphinema spp., respectively. Diversity indexes (Richness, Hill´s diversity, Hill´s reciprocal of D and Hill´s evenness) were significantly affected by olive type. We also developed a comparative morphological and morphometrical study together with molecular data from three nuclear ribosomal RNA genes (D2-D3 expansion segments of 28S, ITS1, and partial 18S). Molecular characterization and phylogenetic analyses allowed the delimitation and discrimination of four new species of the genus described herein and three known species. Phylogenetic analyses of Xiphinema spp. resulted in a general consensus of these species groups. This study is the most complete phylogenetic analysis for Xiphinema non-americanum-group species to date.

Morphological and molecular characterisation, and phylogenetic position of X. browni sp. n., X. penevi sp. n. and two known species of Xiphinema americanum-group (Nematoda, Longidoridae)

Using ribosomal (18S, ITS1, ITS2, D2-D3 expansion segments of 28S rDNA) and mitochondrial (partial cox1 and nad4) DNA markers in a study of several populations of Xiphinemaamericanum-group from Europe and Morocco, two cryptic species Xiphinemabrownisp. n. (formerly reported as Xiphinemapachtaicum) and Xiphinemapenevisp. n. were revealed. The species are described, illustrated and their phylogenetic relationships discussed. The first species is most similar to Xiphinemaparasimile and is a member of Xiphinemasimile species complex. The phylogenetic reconstructions inferred from three molecular markers (18S, D2-D3 28S rDNA and cox1) showed that Xiphinemapenevisp. n. is part of Xiphinemapachtaicum-subgroup and is closely related to Xiphinemaincertum, Xiphinemapachtaicum, Xiphinemaparapachydermum, Xiphinemaplesiopachtaicum, Xiphinemaastaregiense and Xiphinemapachydermum. Also, a separate “Xiphinemasimile-subgroup”, outside the Xiphinemapachtaicum-subgroup and so far consisting only of the parthenogenetic species Xiphinemasimile, Xiphinemaparasimile, Xiphinemabrownisp. n. and probably Xiphinemavallense was formed. New primers for amplification and sequencing of part of the nad4 mitochondrial gene were designed and used.

Molecular and morphological characterisation of Xiphinema americanum-group species (Nematoda: Dorylaimida) from California, USA, and other regions, and co-evolution of bacteria from the genus Candidatus Xiphinematobacter with nematodes

The Xiphinema americanum-group is a large species complex containing more than 50 nematode species. They are economically important because they are vectors of nepoviruses. The species differentiation of X. americanum-group is problematic because the species share similar morphological characters. In the present study we collected nematode samples from different locations in the USA, Italy and Russia. Six valid species, X. americanum s. str., X. brevicolle, X. californicum, X. pachtaicum, X. rivesi and X. simile, and four unidentified putative Xiphinema species were characterised by morphology and sequencing of D2-D3 of 28S rRNA, ITS1 rRNA and mitochondrial COI genes. New nematode sequences generated totalled 147. Phylogenetic relationships of the X. americanum-group species reconstructed by Bayesian inference for D2-D3 of 28S rRNA gene sequences did not provide clear species delimitation of the samples studied, although the mtDNA presented interspecific variations useful for demarcation among species. Xiphinema americanum s. str., X. californicum, X. pachtaicum, X. rivesi, and two unidentified Xiphinema species were found in 72 soil samples from California. We also reconstructed the phylogenetic relationships using partial 16S rRNA gene sequences within endosymbiotic bacteria of the genus Candidatus Xiphinematobacter and provided solid evidence for distinguishing 17 species of this genus based on the analysis of new and previously published sequences. Fifty-five new bacterial sequences were obtained in the present study and comparison of the bacterial 16S rRNA and nematode COI phylogenies revealed a high level of co-speciation events between host and symbiont.

Molecular phylogenetic analysis and comparative morphology resolve two new species of olive-tree soil related dagger nematodes of the genus Xiphinema (Dorylaimida : Longidoridae) from Spain

The genus Xiphinema constitutes a large group of ~275 species of polyphagous, plant-ectoparasitic nematodes that are distributed almost worldwide. Some species affect agricultural crops by feeding directly on root cells as well as by transmitting nepoviruses. Despite their agricultural importance, species discrimination in Xiphinema is difficult, leading to potential misidentification. Integrative taxonomy, based on the combination of molecular analyses and morphology, constitutes a new insight into Xiphinema species identification. In this study we describe two new species of Xiphinema from the Iberian Peninsula (X. macrodora, sp. nov. and X. oleae, sp. nov.) associated with cultivated and wild olive trees. Both species have specific rRNA sequences. Morphologically, Xiphinema macrodora, sp. nov. is characterised by a very long body (7.2–8.7 mm), a very long odontostyle and odontophore (190–206 and 105–120 µm, respectively), and a well developed pseudo-Z-organ, comprising 8 to 12 sclerotised bodies. Xiphinema oleae, sp. nov. is characterised by an odontostyle and an odontophore 136–149 and 65–80 µm long, respectively, and a well developed Z-organ with refractive inclusions (3–5), variable in shape. Additionally, X. macrodora, sp. nov. has the longest body size, and the longest odontostyle and odontophore of any Xiphinema, whereas X. oleae, sp. nov. is the first species with a well developed Z-organ from the Iberian Peninsula. http://zoobank.org/urn:lsid:zoobank.org:pub:E4CE8711-22EF-40E4-9D39-6FE962F25225