Russian Journal of Nematology, 2012, 20 (1), 37-44
Molecular and morphological characterization of Ektaphelenchoides hunti sp. n. (Nematoda: Ektaphelenchinae) from northern Iran
12 2 2 3
Mohammad Reza Atighi ' , Ebrahim Pourjam , Majid Pedram , Weimin Ye
and Robert T. Robbins4
department of Plant Protection, Faculty of Agricultural Sciences and Engineering, University College of Agriculture and
Natural Resources, University of Tehran, Karaj, Iran 2Department of Plant Pathology, College of Agriculture, Tarbiat Modares University, Tehran, Iran;
e-mail: [email protected] 3Nematode Assay Section, North Carolina Department of Agriculture, Raleigh, NC 27607, USA ^Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USA
Accepted for publication 19 December 2011
Summary. Ektaphelenchoides hunti sp. n is described and illustrated based on morphological and molecular characters. The new species is characterized by its body length of 711-929 ^m in the female, offset head region, three incisures in lateral field, total stylet length of 16-23 ^m, excretory pore in middle of the metacorpus to slightly posterior to metacorpus base, hemizonid at 95-116 ^m distance from the anterior end and males with a body length of 572-809 ^m, 12.5-17.5 ^m long spicules with rounded condylus, moderately developed short rostrum with blunt end and without a cucullus. The new species most closely resembles E. compsi but differs by having three incisures in lateral field vs obscure, excretory pore in middle of the metacorpus to slightly posterior to metacorpus base, 75-93 ^m from anterior end vs posterior to the median bulb 91-113 ^m from the anterior end, shorter spicules (12.5-17.5 vs 19-24 ^m) and basic differences in shape of the posterior body (tail). The comparisons with other species of Ektaphelenchoides are also discussed. Molecular analyses were performed based on 793 bp partial ribosomal DNA large subunit D2D3 and showed E. hunti sp. n to be different but closest to E. compsi and E. spondylis.
Key words: Ektaphelenchoides compsi, E. pini, E. spondylis, Kelardasht, new species, taxonomy.
The genus Ektaphlenchoides Baujard, 1984 currently contains 6 valid species (Kanzaki et al., 2009) namely E. pini (Massey, 1966) Baujard, 1984, E. attenuata (Massey, 1974) Baujard, 1984, E. musae Baujard, 1984, E. compsi Baujard, 1984, E. winteri Hooper, 1995 and E. spondylis Kanzaki, Giblin-Davis & Center 2009. The species E. pini was described as Seinura pini by Massey (1966) in association with Dendroctonus adjunctus in ponderosa pine. In 1974, Massey added another species to Ektaphelenchoides as S. attenuatus associated with D. terebrans in loblolly pine.
Baujard (1984) erected the genus Ektaphelenchoides and described two species: E. compsi isolated from xylem of Pinus laricio Poir and E. musae isolated from banana corn tissue from the Ivory Coast. Baujard (1984) also recovered E. pini from the xylem of Pinus laricio in France. Hooper (1995) described E. winteri that was found attaching to larvae of Xylodiplosis sp. (Diptera: Cecidomyidae) emerging from logs of oak, Quercus robur L., cut from trees at Crickley Hill, Gloucestershire, England. Kanzaki et al. (2009)
described E. spondylus, which was recovered from the body cavity of Spondylis buprestoides in Tsukuba, Japan. The last species, E. sylvestris Pedram, Pourjam, Atighi, Ye and Houshmand, 2012 was recovered from bark of dead Pinus sylvestris L. in Tehran, Iran.
During nematode surveys in the north of Iran, a new species of Ektaphelenchoides was recovered from bark samples of a beech tree (Fagus orientalis Lispky) and described in present paper as E. hunti sp. n. This is the third report of Ektaphelenchoides from Iran. Ektaphelenchoides compsi, was first reported by Rafiee et al. (2011) from the rhizosphere of cucumber in a green house in the city of Jiroft.
MATERIALS AND METHODS
Several bark samples were collected from northern cities of Iran during September 2010. The nematodes were recovered from the wood samples by soaking in small amount of water for 48 hours, then handpicked under stereomicroscope. The
nematodeds were heat killed by adding boiling 4% formalin solution and then transferred to anhydrous glycerin and mounted in permanent slides according to De Grisse (1969). Permanent slides were made and examined using a Nikon Eclipse E600 light microscopy. Photographs were taken using an Olympus DP72 digital camera attached to an Olympus BX51 microscope powered with differential interference contrast (DIC). Drawings were made using a drawing tube attached to the microscope and were redrawn using CorelDRAW® software version 12.
For molecular study, a single nematode specimen was picked out and transferred to 10^l distilled water on a glass microscope slide, macerated with a pipette tip and collected in 50^l AE buffer (10 mM Tris-Cl, 0.5 mM EDTA; pH 9.0, QIAGEN Inc., Valencia CA, USA). DNA samples were stored at -20°C until used as a PCR template. Primers for 28S D2/D3 amplification were forward primer D2a (5' ACA AGT ACC GTG AGG GAA AGT 3') and reverse primer D3b (5'TGC GAA GGA ACC AGC TAC TA3') (Nunn, 1992). The 25-^l PCR contained 12.5-^l 2X GoTaq DNA polymerase mix (Promega Corporation, Madison, Wl, USA), 1 ^l each of a 0.4-^M forward and reverse primers solution, and 1 ^l of DNA template. The thermal cycling program was as follows: denaturation at 95°C for 6 min, followed by 35 cycles of denaturation at 94°C for 30 s, annealing at 55°C for 30 s, and extension at 72°C for 1 min. A final extension was performed at 72°C for 10 min. DNA sequencing was performed using PCR primers for direct sequencing by dideoxynucleotide chain termination using an ABI PRISM BigDye terminator cycle sequencing ready reaction kit (Applied Biosystems, Foster City, CA, USA) in an Applied Biosystems 377 automated sequencer (Applied Biosystems, Foster City, CA, USA) by the Genomic Sciences Laboratory in North Carolina State University (Raleigh, NC 27695, USA). The sequences were deposited into the GenBank database. DNA sequences were aligned by Clustal W (http:// workbench. sdsc.edu, Bioinformatics and Computational Biology group, Dept. Bioengineering, UC San Diego, CA). The molecular sequences of E. hunti sp. n. were compared with those of the other nematode species available in GenBank using the BLAST homology search program. The model of base substitution was evaluated using MODELTEST (Posada & Crandall, 1998; Huelsenbeck & Ronquist, 2001). The Akaike-supported model, the base frequencies, the
proportion of invariable sites and the gamma distribution shape parameters and substitution rates were used in phylogenetic analyses. Bayesian analysis was performed to confirm the tree topology for each gene separately using MrBayes 3.1.0 (Huelsenbeck & Ronquist, 2001) running the chain for one million generations and setting the "burnin" at 1,000. We used the Markov Chain Monte Carlo (MCMC) method within a Bayesian framework to estimate the posterior probabilities of the phylogenetic trees (Larget & Simon, 1999) using 50% majority rule. The 10001st tree was selected to represent the phylogenetic relationships with branch length and support level.
DESCRIPTION
Ektaphelenchoides hunti sp. n. (Figs 1, 2)
Measurements: See Table 1.
Male. Body slender, J-shaped, ventrally arcuate with the posterior end more ventrally bent after fixation. Cuticle finely annulated. Lateral field with three incisures (not clearly visible in some individuals). Head set off from body contour by a definite constriction, 3.0-4.5 high and 6.0-8.5 ^m wide. Stylet 14.5-22.0 ^m long without basal knobs, conus ca 44.5% of total stylet length. Procorpus cylindrical, connected to a muscular, rectangular metacorpus 9.0-11.5x14-22 ^m with the granular part ca 30% of its length. Oesophageal glands well-developed, overlapping intestine dorsally ca 1.82.1 times the distance from anterior end to the base of median bulb and ca 8.5-12.5 times body width at median bulb level. Excretory pore with slight variation in position, i.e. at the middle of metacorpus to slightly posterior and at 2-8 ^m distances from the base of metacorpus. Hemizonid 1.0-1.5 times stylet length posterior to excretory pore and 85-112 ^m from anterior body end. Gonad single, outstretched and in some individuals reflexed. Spicules ca 2.4 times longer than capitulum width, separate, lamina/calomus smoothly and symmetrically curved, rostrum short, moderately developed with blunt tip. Condylus rounded with round tip and more developed than rostrum. Seven precloacal and postcloacal papillae present with their arrangement as follows: A single midventral precloacal papilla (P1) ca 1.2 times cloacal body diameter anterior to cloacal aperture,
Table 1. Morphometrics of Ektaphelenchoides hunti sp. n. All measurements are in ^m and in the form: mean ± s.d.
(range).
Holotype male Paratype males Paratype females
n 1 15 20
L 795 702.5 ± 68.7 (572-809) 824 ± 70 (711-929)
a 39.8 46.2 ± 2.3 (39.9-47.2) 40.7 ± 2.3 (35.9-44.5)
b 8.5 8.2 ± 0.4 (7.6-9.2) 8.9 ± 0.7 (7.7-10.0)
b' 3.4 3.1 ± 0.2 (2.9-3.5) 3.3 ± 0.3 (2.9-3.8)
c 16.2 15.5 ± 0.8 (14.0-16.7) -
c' 4.1 3.8 ± 0.3 (3.3-4.3) -
V or T 63.8 53.4 ± 8.1 (40.8-66.1) 71.6 ± 0.6 (70.4-72.6)
Head height 3.5 3.7 ± 0.3 (3.0-4.0) 4.1 ± 0.3 (3.5-4.5)
Head width 7.5 6.9 ± 0.4 (6.0-7.5) 7.5 ± 0.5 (6.5-8.5)
Stylet 21 17 ± 2.3 (14.5-22) 19.5 ± 1.6 (16-23)
Stylet shaft 12 9.5 ± 1.5 (7.5-12) 10.8 ± 0.8 (9.0-12)
Conus 9 7.6 ± 1.1 (6.0-10) 8.7 ± 1.0 (7.0-11)
m 1 43 44.5 ± 3.7 (38.7-51.6) 44.5 ± 2.4 (39-47.8)
MB2 87 87.4 ± 2.6 (83.5-95.5) 86 ± 2.0 (81.4-88.5)
Body width of MB 14 14.0 ± 1.6 (11-17) 16.4 ±1.7 (13.0-18.5)
Nerve ring from anterior body 97 88.6 ± 7.0 (75-97) 95.0 ± 5.5 (85-103)
Median bulb width 11 10.1 ± 0.8 (9.0-11.5) 12 ± 1.2 (9.5-14)
Median bulb length 20 19.9 ± 2.0 (14-22) 22.0 ± 1.4 (20-25)
Median bulb length/diam. ratio 1.8 2.0 ± 0.2 (1.6-2.2) 1.9 ± 0.2 (1.6-2.2)
Excretory pore 84 80.1 ± 6.5 (67-91) 84 ± 5 (75-93)
Hemizonid 107 100.3 ± 8.4 (85-112) 107.0 ± 6.2 (95-116)
Oesophagus 93 85.7 ± 6.4 (71-93) 92.0 ± 4.2 (82-99)
Overlapping3 138 139.5 ± 16.6 (92-160) 159.5 ± 12 (139-181)
Testis or ovary length 507 376.3 ± 77 (262-535) 341 ± 79.2 (210-453)
Anal (cloacal) body width 12 12 ± 0.9 (10.5-14) -
Tail 49 45.3 ± 4.6 (35-53) -
Spicule length (arc line) 15 15.8 ± 1.3 (12.5-17.5) -
Capitulum 6.5 6.5 ± 0.7 (5.5-7.5) -
1 Length of conus as percentage of total stylet length
2 Distance between anterior end of body and centre of median oesophageal bulb as percentage of oesophageal length
3 Distance from oesophagus-intestine junction to end of dorsal gland tip
one pair subventral papillae (P2) at level of or just posterior to cloacal aperture, one subventral pair of postcloacal papillae (P3) at ca 47% of tail length posterior to cloacal aperture and one small subventral pair of papillae (P4) at ca 54% of tail length posterior to cloacal aperture. Tail dorsally
convex, ventrally concave, about 2.5 times cloacal body width long with pointed tip.
Female. Body slightly curved ventrally when heat-killed. Anterior region similar to that in male. Ovary single and outstretched. Oocytes mostly in single file. Spermathecae oval to irregular in shape
and most filled with sperm. Uterus thick-walled, usually containing an egg. Crustaformeria visible in some individuals. Vagina not sclerotised, straight and directed somewhat anteriorly. Post-uterine sac ca 2.8 times vulva body diameter long and sometimes filled with large sperm. Intestine appears to end in a blind sac at about two thirds the distance from the vulva to posterior end; no rectum or anus seen. Distance of vulva to posterior end ca 12.5 times vulval-body width, posterior end (tail) dorsally convex, with a conical posteriorly bent pointed tip.
Molecular characterization and phylogeny of
Ektaphelenchoides hunti sp. n. For molecular analysis, the 793-bp ribosomal DNA large subunit (LSU) D2D3 (JN714466) was sequenced. A Blastn search of LSU sequence revealed the highest match as to E. compsi and E. spondylis. Sequence alignment of E. hunti sp. n. and E. compsi yielded 817 total characters with 613 constant nucleotides (75.0% identity) and 27 insertions/deletions. Sequence alignment of E. hunti sp. n. and E. spondylis yielded 768 total characters with 569 constant nucleotides (74.1% identity) and 23 insertions/deletions. Sequence alignment of E. hunti sp. n. and E. pini yielded 802 total characters with 576 constant nucleotides (71.8% identity) and 77 insertions/deletions. The large sequence disparity in LSU supported E. hunti sp. n. as a distinct unique species when compared with all available nematode species in GenBank.
Fig. 3 presents a phylogenetic tree based on the LSU of many representative Aphelenchids from a multiple alignment of 817 total characters, in which, 186 characters (22.8%) were constant. The average nucleotide composition was as follows: 18.71% A, 17.59% C, 31.91% G and 31.79% T. Using Aphelenchus avenae Bastian, 1865 as the outgroup, this tree inferred many highly supported monophyletic groups. Ektaphelenchoides hunti sp. n. is in a 100%-supported monophyletic clade which also includes E. compsi, E. spondylis, Aphelenchoides stammeri Körner, 1954, Devibursaphelenchus sp., Devibursaphelenchus hunanensis Yin, Fang & Tarjan, 1988, D. lini Braasch, 2004, Ektaphelenchoides pini, Ektaphelenchus obtusus Thorne & Malek, 1968 and Cryptaphelenchus sp. The four species of sequenced Ektaphelenchoides were not monophyletic and E. hunti sp. n. was basal to E. compsi and E. spondylis. The LSU data set in this study was very variable with a low number of constant characters. The identity between E. hunti sp. n. and the closest putative relatives of E. compsi
and E. spondylis had only about 75% identity. The large sequence divergence results in many ambiguous sites in multiple alignments making phylogenetic analysis challenging with the current available sequences of aphelenchids from GenBank.
Differential diagnosis and relationships.
Ektaphelenchoides hunti sp. n. is characterized by its distinctly offset head, three incisures in lateral field, a total stylet length of 16-23 ^m, position of excretory pore at the level of the middle of the metacorpus to slightly posterior to the metacorpus base and at 2-6 ^m distance from base of metacorpus. Position of hemizonid 95-116 ^m from anterior end. The new species is typologically closest to E. compsi, E. pini and E. spondylis.
The new species differs from E. compsi by having three incisures in lateral field vs lateral field obscure, position of excretory pore at level of the middle of the metacorpus to slightly posterior to metacorpus base 75-93 ^m from anterior end vs posterior to median bulb and at 91-113 ^m, shorter spicules (12.5-17.5 vs 19-24 ^m), different shape of posterior body (tail) in females and males (dorsally convex, with a conical slightly posteriorly bent pointed tip vs ventrally bent, regularly conical and dorsally convex, ventrally concave with pointed tip vs regularly conical with strongly ventrally bent end, respectively).
Compared to E. pini, the new species has a shorter stylet (16-23 vs 26 ^m), position of excretory pore is at the level of the middle of the metacorpus to slightly posterior to metacorpus base, 75-93 ^m from anterior end vs 1/3 body width posterior to median bulb, hemizonid 23 ^m from excretory pore vs immediately posterior to excretory pore, longer post-uterine sac (1.4-4.0 times body width vs 1.0), shorter spicules (12.5-17.5 vs 24 ^m) and different shape of tail in females.
Compared with E. spondylis, E. hunti sp. n. has a distinctly offset head vs without a sharp constriction, three incisures in lateral field vs obscure, position of excretory pore at level of the middle of the metacorpus to slightly posterior to metacorpus base 75-93 ^m from anterior end vs one metacorpal length posterior to metacorpus and 85-99 ^m from the anterior end and shorter spicules (12.5-17.5 vs 23-26) without cucullus vs having plate-like cucullus.
Taxonomic remark. Even though this species may fit typologically into Ektaphelenchoides, the molecular distances suggest that this is a tentative assignment requiring further comparisons with other more closely related nematodes.
Fig. 1. Ektaphelenchoides hunti sp. n. A & B: Entire body of male and female; C-E: Variation in excretory pore position; F: Pharyngeal region; G: Male caudal region; H: Female posterior end; I: Anterior end in detail; J & k: Spicules.
Fig. 2. A-C: Ektaphelenchoides hunti sp. n. Anterior end, A: Offset head, B: Lip morphology, C: Stylet; D: Part of female genital tract; E & F: Variation in excretory pore position (arrows); G: Three lateral lines; H: Blind end of the intestine; I & J: Male papillae (arrows), I: P1 and P2, J: P3 and P4; K: Female posterior end; L: Male posterior end, M: Spicule in detail. (All scale bars = 10 ^m).
Type habitat and locality. Recovered from bark samples of a beech tree (Fagus orientalis Lipsky) with bark beetle galleries in Kelardasht, Mazandaran Province, northern Iran.
Type material. Holotype male, 5 paratype males and females deposited at Nematode Collection of the Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran. Three female and three
male paratypes deposited at each of the following collections: CABI Europe-UK, Egham, Surrey, UK; USDA Nematode Collection, Beltsville, MD, USA and Department of Nematology, Agricultural
University, Wageningen, the Netherlands.
Etymology. The new species is named in honor of Prof. David J. Hunt, a pioneering scientist in the systematics of aphelenchids.
77
100
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-DQ912928 Schistonchus centerae
DQ912925 Schistonchus aureus
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-AB535566 Schistonchus aculeata
■ EU287595 Laimaphelenchusheidebergi - DQ328683 Aphelenchoides fragariae
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-AB368539 Laimaphelenchus sp.
- AB434933 Aphelenchoides xylocopae
- FJ643488 Aphelenchoides sp.
- HQ283353 Aphelenchoides varicaudatus
EU287597 Aphelenchoides sp. DQ328682 Aphelenchoides sp. — DQ912927 Schistonchus guangzhouensis - AB368540 Aphelenchoides fragariae
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100
- EU287598 Laimaphelenchuspreissii
EU287599 Aphelenchoides sp. -AY508035 Aphelenchoides besseyi
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100
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- DQ328684 Aphelenchoides besseyi
EU287600 Laimaphelenchus australis
- EU287654 Schistonchuscaprifici
AM269475 Ruehmaphelenchus asiaticus
- HQ283352 Tylaphelenchusjiaae
AB537560 Pseudaphelenchus vindai AB470972 Pseudaphelenchus yukiae -EU287596 Cryptaphelenchussp.
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98
100
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AB368533 Ektaphelenchus obtusus
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100
С
-DQ257623 Ektaphelenchoides pini
- FJ768944 Devibursaphelenchuslini
FJ768945 Devibursaphelenchushunanensis
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GQ903770 Devibursaphelenchus sp. - AB434934 Ektaphelenchoides spondylis DQ257625 Ektaphelenchoides compasi JN714488 Ektaphelenchoides hunti sp. n.
■ AM396582 Aphelenchoides stammeri 1EU295493 Bursaphelenchus mucronatus 100
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L GQ870257 Bursaphelenchus mucronatus I EU295504 Bursaphelenchus xylophilus 00 L FJ768948 Bursaphelenchus xylophilus
— FJ520229 Bursaphelenchus doui AM396569 Bursaphelenchus hildegardae
— AM396578 Bursaphelenchus vallesianus -EU295497 Bursaphelenchus thailandae
- AM396574 Bursaphelenchuspinasteri
AB368536 Aphelenchusavenae
50 changes
Fig. 3. Ektaphelenchoides hunti sp. n. The 10001st Bayesian tree inferred from LSU D2/D3 under GTR+I+G model (lnL= 16806.2656; freqA=0.1871; freqC=0.1759; freqG=0.3191; freqT=0.3179; R(a)=1.287; R(b)=3.2662; R(c)=1.4121; R(d)=0.8576; R(e)=4.1178; R(f)=1; Pinvar=0.1661; Shape=0.9103). Posterior probability values exceeding 50% are given on appropriate clades.
ACKNOWLEDGEMENT
The authors thank Azam Houshmand for her helps and Iranian National Science Foundation (ISNF) and Trabiat Modares University (Iran) for finnacial support.
REFERENCES
Baujard, P. 1984. Remarques sur la sous-famille des Ektaphelenchinae Paramonov, 1964 et proposition d''Ektaphelenchoides n. gen (Nematoda: Aphelencho-ididae). Revue de Nématologie 7: 147-171. De Grisse, A.T. 1969. Redescription ou modifications de quelques techniques utilisées dans l'étude des nematodes phytoparasitaires. Mededelingen Faculteit Landbouwwetenschappen Rijksuniversiteit Gent 34: 351-369.
Hooper, D.J. 1995. Ektaphelenchoides winteri sp. n. (Nematoda: Ektaphelenchidae) from wood fly larvae Xylodiplosis sp. (Diptera: Cecidomyidae). Fundamental and Applied Nematology 18: 465-470. Huelsenbeck, J.P. & Ronquist, F. 2001. MR BAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 1754-1755. Kanzaki, N., Giblin-Davis, R. M. & Center, B. J. 2009. Description of Ektaphelenchoides spondylis sp. n. (Nematoda: Ektaphelenchinae) isolated from Spondylis buprestoides (Coleoptera: Cerambycidae) in Japan. Nematology 11: 181-188.
Larget, B. & Simon, D.L. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology and Evolution 16: 750-759.
Massey, C.L. 1966. The nematode parasites and associates of Dendroctonus adjunctus (Coleoptera: Scolytidae) in New Mexico. Annals of the Entomological Society of America 59: 424-440.
MASSEY, C.L. 1974. Biology and taxonomy of nematode parasites and associates of bark beetles in the United States. Washington DC, USA, US Government Printing Office, USDA Agriculture Handbook No. 446, 233 pp.
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М. Я. Atighi, Е. Роиг|ат, М. Pedram, Weimin Ye, Я. Т. ЯоЬЫш. Молекулярная и морфологическая характеристика Ektaphelenchoides ЫпЫ sp. п. (Nematoda: Ektaphelenchinae) из северного Ирана.
Резюме. Дано молекулярное и морфологическое описание Ektaphelenchoides ЫпЫ sp. п. Новый вид характеризуется длиной тела 711-929 мкм у самок, обособленным головным концом, тремя инцизурами латерального поля, общей длиной стилета 16-23 мкм, экскреторной порой на уровне середины метакорпуса, гемизонидом на расстоянии 95-116 мкм от головного конца, длиной тела самцов 572-809 мкм и спикулами длиной 12,5-17,5 мкм с округленным кондилюсом, умеренно развитым коротким рострумом с притупленым концом и без кукулюса. Новый вид близок к E. compsi, но отличается наличием трех четких инцизур латерального поля (в отличие от плохо различимых), экскреторной порой на уровне середины метакорпуса (в отличие от ее положения сзади от основания метакорпуса у E. compsi) - т.е. в 75-93 мкм от головного конца, а не сзади от медианного бульбуса в 91-113 мкм от головного конца, более короткими спикулами (12,5-17,5 vs 19-24 мкм) и явными отличиями в форме задней части тела (хвостового конца). Обсуждаются отличия от других видов рода Ektaphelenchoides. Основанный на частичной последовательности Б2Б3-участка рибосомальной ДНК анализ показал, что E. ЫпЫ sp. п. отличается от ближайших видов E. compsi и E. spondylis.