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)

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.

Boolean implication analysis unveils candidate universal relationships in microbiome data

BACKGROUND

Microbiomes consist of bacteria, viruses, and other microorganisms, and are responsible for many different functions in both organisms and the environment. Past analyses of microbiomes focused on using correlation to determine linear relationships between microbes and diseases. Weak correlations due to nonlinearity between microbe pairs may cause researchers to overlook critical components of the data. With the abundance of available microbiome, we need a method that comprehensively studies microbiomes and how they are related to each other.

RESULTS

We collected publicly available datasets from human, environment, and animal samples to determine both symmetric and asymmetric Boolean implication relationships between a pair of microbes. We then found relationships that are potentially invariants, meaning they will hold in any microbe community. In other words, if we determine there is a relationship between two microbes, we expect the relationship to hold in almost all contexts. We discovered that around 330,000 pairs of microbes universally exhibit the same relationship in almost all the datasets we studied, thus making them good candidates for invariants. Our results also confirm known biological properties and seem promising in terms of disease diagnosis.

CONCLUSIONS

Since the relationships are likely universal, we expect them to hold in clinical settings, as well as general populations. If these strong invariants are present in disease settings, it may provide insight into prognostic, predictive, or therapeutic properties of clinically relevant diseases. For example, our results indicate that there is a difference in the microbe distributions between patients who have or do not have IBD, eczema and psoriasis. These new analyses may improve disease diagnosis and drug development in terms of accuracy and efficiency.

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.

First report and molecular characterization of the dagger nematode, Xiphinema oxycaudatum (Nematoda, Dorylaimidae) from South Africa

Plant-parasitic nematodes of the genus Xiphinema Cobb, 1913 comprise a complex group of nematode species, some of which are important vectors of plant viruses. During a field survey to determine the soil health of an abandoned honeybush (Cyclopiagenistoides) monoculture, a high density of the dagger nematode, Xiphinemaoxycaudatum Lamberti & Bleve-Zacheo, 1979 (Nematoda, Dorylaimidae), was observed in soil around the roots of honeybush plants in an abandoned farmland at Bereaville, an old mission station in the Western Cape province of South Africa. Soil samples were taken from the rhizosphere of plants and nematodes were extracted from the soil using a modified extraction tray method. Specimen of the dagger nematodes were processed for scanning electron microscopy, morphological and molecular analysis. Molecular profiling of the nematode species was done in order to give an accurate diagnosis and to effectively discriminate the nematode from other species within the Xiphinemaamericanum group. Phylogenetic analysis based on the D2D3 expansion segment of the 28S gene supported a close relationship of species within the americanum group, however, the protein-coding cytochrome oxidase (coxI) of the mitochondrial gene provided a useful tool for distinguishing the nematode from other species within the group. This study represents the first report of X.oxycaudatum from South Africa.

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.

Molecular and morphological characterisation of Longidoruspolyae sp. n. and L.pisi Edward, Misra & Singh, 1964 (Dorylaimida, Longidoridae) from Bulgaria

Longidoruspolyaesp. n., a bisexual nematode species found in the rhizosphere of pear tree (Pyruscommunis L.), is described and characterised using an integrative approach. The new species has a female body length of 6.8–9.1 mm; a comparatively long odontostyle (114.0–127.5 μm); a narrow lip region (14.0–15.5 μm), anteriorly flattened and almost continuous with the body profile; pocket-like amphidial pouches long, deeply bilobed, and slightly asymmetrical, a guide ring at 37–42 μm from the anterior end; normal arrangement of pharyngeal glands; and a short bluntly rounded to hemispherical tail. Four juvenile stages identified: the first stage with a digitate tail, and the second and subsequent stages with a bluntly rounded tail. Males have one adcloacal pair and a row of 10 or 11 single ventromedian supplements; spicules 71.0–74.5 μm long. Based on morphometric data, the new species belongs to a group of species spread over Europe (L.arthensis, L.silvae, L.uroshis,), Iran (L.kheirii), and Syria (L.pauli), which share common characters such as amphidial fovea, lip region and tail shapes, similar odontostyle and body length, and similar first-stage juvenile tail shape. Codes for identifying the new species are A5, B2, C34, D3, E3, F45, G12, H1, I2, J1, K7. The phylogenetic analysis based on D2-D3 expansion domains of the rRNA gene revealed that the new species has the closest relationships with L.athesinus from Italy and three unidentified Longidorus spp. from USA (Longidorus sp. 1, Longidorus sp. 2, and Longidorus sp. 6). New morphometric and molecular data (18S rRNA gene, ITS1-5.8S-ITS2 regions and D2-D3 28S rRNA gene sequences) for three populations of L.pisi from Bulgaria were obtained and variations between populations are discussed.

Description of a new dagger nematode, Xiphinema barooghii n. sp. (Nematoda: Longidoridae) and additional data on the three known species of the genus from northwest of Iran

Xiphinema barooghii n. sp. collected from the rhizosphere of common wheat (Triticum aestivum L.) in Roodghat area, Sufiyan, East-Azarbaijan province, northwest of Iran, is described on the basis of the morphological, morphometric and molecular data. The new species belongs to morphospecies group 6 of the polytomous key prepared by Loof and Luc, 1990. Xiphinema barooghii n. sp. is characterized by having two almost equally developed female reproductive branches with spines in the tubular portion of the uterus, a body length of 3.67-4.25 mm, a flat lip region, rounded cephalic region, separated from body contour by a shallow depression, a spear 215-225 μm long, mid-body diameter of 60-79 μm, vulva (46-48%), a short tail (30-38 µm, c = 103-133, c' = 0.7-0.9), conoid, dorsally convex, ventrally directed with a small terminal peg and a distinct terminal blind canal, the presence of four juvenile stages and the absence of males. The polytomous identification codes of the new species are: A4, B3, C5a, D6, E5, F4, G3, H2, I3, J4, K2, L1. In addition to morphological and morphometric data, molecular analyses of the D2-D3 expansion regions of the 28S rDNA gene placed the new species as a sister species of X. herakliense (Group 5) with 65% Bayesian posterior probability and further separated this species from the other members in group 6. In this study, X. index, X. pachtaicum and X. vuittenezi were also collected and additional data for the species were provided.

Xiphinema barooghii n. sp. collected from the rhizosphere of common wheat (Triticum aestivum L.) in Roodghat area, Sufiyan, East-Azarbaijan province, northwest of Iran, is described on the basis of the morphological, morphometric and molecular data. The new species belongs to morphospecies group 6 of the polytomous key prepared by Loof and Luc, 1990. Xiphinema barooghii n. sp. is characterized by having two almost equally developed female reproductive branches with spines in the tubular portion of the uterus, a body length of 3.67–4.25 mm, a flat lip region, rounded cephalic region, separated from body contour by a shallow depression, a spear 215–225 μm long, mid-body diameter of 60–79 μm, vulva (46–48%), a short tail (30–38 µm, c = 103–133, c′ = 0.7–0.9), conoid, dorsally convex, ventrally directed with a small terminal peg and a distinct terminal blind canal, the presence of four juvenile stages and the absence of males. The polytomous identification codes of the new species are: A4, B3, C5a, D6, E5, F4, G3, H2, I3, J4, K2, L1. In addition to morphological and morphometric data, molecular analyses of the D2–D3 expansion regions of the 28S rDNA gene placed the new species as a sister species of X. herakliense (Group 5) with 65% Bayesian posterior probability and further separated this species from the other members in group 6. In this study, X. index, X. pachtaicum and X. vuittenezi were also collected and additional data for the species were provided.

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.

Description of Longidorus cheni sp. n. (Nematoda, Longidoridae) from China

Longidoruschenisp. n., an amphimictic species recovered from the rhizosphere of Larixprincipis-rupprechtii and Pyracanthafortuneana in Shanxi and Beijing, China, is described and illustrated. The taxonomic position of L.chenisp. n. among other species within the genus was elucidated using morphometric and molecular data, and phylogenetic relationships were inferred using D2–D3 expansion domains of 28S and 18S rRNA genes by Bayesian Inference (BI) method. The new species is characterised by females with a medium body size (L = 4.9–6.6 mm), a lip region slightly expanded, broadly rounded frontally and laterally, the amphidial fovea broad and symmetrically bilobed at base, odontostyle long and slender (143–168 μm), odonthophore slightly swollen at the base, tail short bluntly conoid to rounded. Guide ring located far posterior from the oral aperture (70–93 μm). Males with two ad-cloacal pairs of supplements preceded by a row of 10–14 ventromedian supplements, with robust spicules measuring 111–126 μm along the median line. Three juvenile stages were present, tail shape of J1 elongate conoid while in J2 and J3 the tail gradually becomes bluntly rounded. Codes for identifying the new species are: A6-B3-C5-D2-E2-F3-G1-H1-I2-J2-K2. Longidoruschenisp. n. belongs to a group of species with a guide ring at the mid-odontostyle position that have a predominantly Asiatic origin. It differs from all of them by a combination of morphological characters and unique sequences of partial 18S and D2–D3 region of 28S rRNA genes. The percentage dissimilarities in partial 18S and D2–D3 28S rRNA genes of L.cheni to the closest species (L.litchii, L.fangi, L.jonesi and L.juglans) were 1.5 %–1.8 % and 16.8–18.3 %, respectively.

Biogeography and phylogenetic position of Enchodeloides signyensis (Loof, 1975), gen. n., comb. n. from Maritime Antarctic (Nematoda, Nordiidae)

The taxonomic position of the endemic Antarctic species Enchodeloidessignyensis (Loof, 1975), gen. n., comb. n. (= Enchodelussignyensis Loof, 1975) is discussed on the basis of morphological study, including SEM, morphometric data, postembryonic observations, and sequence data of 18S rDNA and the D2-D3 expansion fragments of the large subunit rDNA. A number of characters such as the cuticle and stoma structures, including the presence of moderately developed cuticularised ring around the oral aperture, peculiarities of pharynx expansion, size and position of the posterior pair of pharyngeal nuclei, a less complex uterus, and the position of a posterior ventromedian supplement show that this species differs substantially from the other members of the genus Enchodelus. Furthermore, both the 18S and 28S rDNA-based phylogenetic trees of the Enchodelus sequences available in the GenBank formed two distinct clusters with E.signyensis being a part of a well-supported group with species of the genus Pungentus; therefore, it is proposed that its taxonomic position should be reconsidered.

The morphological and molecular identity of Longidorus piceicola Lišková, Robbins & Brown, 1997 from Romania (Nematoda, Dorylaimida)

Longidoruspiceicola, a new geographical and host record from Romania, was described and illustrated on the basis of two populations originating from a coniferous and a deciduous forest. The main morphological characters of specimens from Romania correspond very well with the type material collected from the soil around Piceaabies L. (Slovakia) except for the shorter body and tail. The D2-D3 fragment of 28S rDNA from both populations was amplified and sequenced, and the sequences were identical to L.piceicola sequence from Slovakia. The partial 18S-ITS1-5.8S-ITS2 rDNA regions from one of the populations were sequenced for the first time. The evolutionary relationships between L.piceicola and the closest species L.intermedius based on D2-D3 sequence divergence and single-nucleotide polymorphisms are discussed. Although having very low sequence dissimilarity (0.3–0.9 %) both species have distinct morphology and biology. Longidoruspiceicola differs from L.intermedius in having a much longer odontostyle, body, distance anterior end - guide ring, a wider lip region, more ventromedian supplements (11 vs 5–7) in the male, and develops through four rather than three juvenile stages. Furthermore, L.piceicola occurs more frequently in association with conifers, while L.intermedius is found mainly in oak forests.

A new record of Xiphinema dentatum Sturhan, 1978 and description of X. paradentatum sp. n. (Nematoda: Dorylaimida) from Serbia

A population of Xiphinema dentatum, found in a new locality in Serbia, is briefly described and illustrated. Xiphinema paradentatum sp. n. is described and illustrated. It is a parthenogenetic species characterised by its medium to moderately long body (3.71-5.02 mm), open C-shaped when heat-relaxed, lip region frontally almost flattened, laterally rounded and separated from the rest of the body by a weak depression; a moderately long odontostyle (147-166 μm), guide ring located at 137-153 μm from anterior end; two equally developed genital tracts having a pseudo-Z-organ in uterus in the form of several irregular angular sclerotised bodies – apophyses located in the vicinity of the pars dilatata uteri and devoid of spines; tail broadly and symmetrically rounded, and four juvenile developmental stages. Molecular characterisation using the ribosomal ITS and the D2-D3 expansion domains of the 28S rRNA gene was done and maximum likelihood analysis was used to reconstruct the phylogenetic relationships of X. dentatum and X. paradentatum sp. n. from Serbia with other longidorids.