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Integrative Taxonomy, Molecular Diagnosis and Phylogenetic Relationships of Plant-Parasitic Nematodes
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Integrative Taxonomy, Molecular Diagnosis and Phylogenetic Relationships of Plant-Parasitic Nematodes

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: closed (20 June 2023) | Viewed by 12081

Special Issue Editors

Dr. Antonio Archidona-Yuste

E-Mail Website
Guest Editor
Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Córdoba, Spain
Interests: nematology; integrated pest management; plant protection; phylogenetics
Dr. Francesca De Luca

E-Mail Website
Guest Editor
Institute for Sustainability Plant Protection- National Research Council of Italy, Rome, Italy
Interests: plant parasitic and entomopathogenic nematodes; parasitism genes; soil nematofauna biodiversity; nematodes associated to insects
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Unravelling the diversity of PPNs infesting soils from an agricultural ecosystem is an essential task in order to design useful management practices for controlling potential nematode diseases. Species discrimination in nematodes has classically been based mainly on morphology and morphometrics of diagnostic features. However, morphologically based species characterization is complicated by a high degree of intraspecific variability within morphometrics, as well as small interspecific differences that lead to substantial overlapping among species and increase the risk of species misidentification. In addition, the identification of nematode species based solely on morphological diagnostics is also quite complex due to the occurrence of complexes of cryptic species. For this reason, it is essential to implement approaches to ensure accurate species identification. Sequences of nuclear rDNA and mtDNA genes, particularly D2-D3, ITS1, and partial coxI, have proven to be a powerful tool for providing accurate and molecular species identification. Their close morphological similarities are usually not associated with their ecological traits or association with plant resistance or vectoring of plant viruses. In this regard, only an accurate description is the way forward for improving their integrated management as well as for quarantine purposes. This demonstrates the importance of using integrative taxonomic identification, highlighting the time-consuming aspect and difficulty of correct identification at the species level. Although this approach is more complex and has a higher cost than traditional taxonomy, its application reduces the degree of subjectivity that is common in traditional taxonomic practices.

Dr. Antonio Archidona-Yuste
Dr. Francesca De Luca
Guest Editors

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Keywords

  • diversity
  • nematodes
  • plant-parasitic nematodes
  • integrative taxonomy
  • new species
  • description
  • morphology
  • agricultural and natural ecosystems
  • phylogeny
  • molecular markers
  • cytochrome oxidase c subunit 1
  • D2-D3 of 28S rDNA
  • ITS rDNA

Published Papers (7 papers)

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63 pages, 32055 KiB  
Article
Morphological and Molecular Diversity among Pin Nematodes of the Genus Paratylenchus (Nematoda: Paratylenchidae) from Florida and Other Localities and Molecular Phylogeny of the Genus
by Sergio Álvarez-Ortega, Sergei A. Subbotin, Koon-Hui Wang, Jason D. Stanley, Silvia Vau, William Crow and Renato N. Inserra
Plants 2023, 12(15), 2770; https://doi.org/10.3390/plants12152770 - 26 Jul 2023
Cited by 3 | Viewed by 1430
Abstract
Pin nematodes (Paratylenchus spp.) are root parasites found worldwide. They have different life cycles and feeding habits and can damage a wide range of plants. A remarkable diversity of pin nematode species was found in soil samples from Florida and other states [...] Read more.
Pin nematodes (Paratylenchus spp.) are root parasites found worldwide. They have different life cycles and feeding habits and can damage a wide range of plants. A remarkable diversity of pin nematode species was found in soil samples from Florida and other states of the USA, Canada, and Spain. Using integrative taxonomy, two new species (Paratylenchus hawaiiensis sp. n. and P. roboris sp. n.), six valid species (Paratylenchulus acti, P. aquaticus, P. goldeni, P. paralatescens, P. minutus (=P. shenzhenensis syn. n.), and P. straeleni), and two undescribed species were identified from Florida; P. goldeni, P. hamatus, P. hamicaudatus, P. holdemani, and P. pedrami were found in California, P. minutus in Hawaii, P. goldeni in Oregon and Washington, and one new species, Paratylenchus borealis sp. n., in Alaska. Outside the USA, Paratylenchus projectus was detected in samples from Canada and Spain as well as P. holdemani and Paratylenchus sp. from Spain. The pin nematode species from Belgium and Russia identified in former studies as Paratylenchus sp. F was herein described as a new species with the name of P. borealis sp. n., using a population from Alaska. Previously reported molecular type A of P. aquaticus from Hawaii was reclassified as P. hawaiiensis sp. n., using a population from Florida. Paratylenchus roboris sp. n. from Florida has obese sedentary females with a stylet 63–71 µm long. The results of the molecular analysis of P. shenzhenensis from Florida and China indicated that it was conspecific with P. minutus from Hawaii and considered here as its junior synonym. New 26 D2–D3 expansion segments of 28S rRNA, 17 ITS rRNA, and 20 COI gene sequences were obtained in this study. Phylogenetic relationships of Paratylenchus are reconstructed using the D2–D3 of 28S rRNA, ITS rRNA, and COI gene sequences. Congruence of molecular and morphological evolution and species identification problems are discussed. Obese females were found in two major clades of Paratylenchus. The problem of reference materials is discussed, and it is proposed to make more efforts to collect topotype materials of known Paratylenchus species for molecular study. Full article
(This article belongs to the Special Issue Integrative Taxonomy, Molecular Diagnosis and Phylogenetic Relationships of Plant-Parasitic Nematodes)
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27 pages, 6175 KiB  
Article
A Blind-Identification Test on Criconema annuliferum (de Man, 1921) Micoletzky, 1925 Species Complex Corroborate the Hyper-Cryptic Species Diversity Using Integrative Taxonomy
by Antonio Archidona-Yuste, Juan Emilio Palomares-Rius, Ilenia Clavero-Camacho, Carolina Cantalapiedra-Navarrete, Gracia Liébanas and Pablo Castillo
Plants 2023, 12(5), 1044; https://doi.org/10.3390/plants12051044 - 24 Feb 2023
Cited by 3 | Viewed by 1577
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Integrative Taxonomy, Molecular Diagnosis and Phylogenetic Relationships of Plant-Parasitic Nematodes)
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26 pages, 10157 KiB  
Article
New Records of Ditylenchus Species from Southern Alberta, Canada
by Maria Munawar, Atta Ur Rahman, Pablo Castillo and Dmytro P. Yevtushenko
Plants 2023, 12(5), 998; https://doi.org/10.3390/plants12050998 - 22 Feb 2023
Cited by 3 | Viewed by 1761
Abstract
The presence of plant-parasitic nematodes (PPNs) in cultivated areas is a limiting factor in achieving marketable crop yield. To control and alleviate the effects of these nematodes and determine appropriate management strategies, species-level identification is crucial. Therefore, we conducted a nematode diversity survey, [...] Read more.
The presence of plant-parasitic nematodes (PPNs) in cultivated areas is a limiting factor in achieving marketable crop yield. To control and alleviate the effects of these nematodes and determine appropriate management strategies, species-level identification is crucial. Therefore, we conducted a nematode diversity survey, which resulted in the detection of four Ditylenchus species in cultivated areas of southern Alberta, Canada. The recovered species had six lines in the lateral field, delicate stylets (>10 µm long), distinct postvulval uterine sacs, and pointed to rounded tail tips. The morphological and molecular characterization of these nematodes revealed their identity as D. anchilisposomus, D. clarus, D. tenuidens and D. valveus, all of which are members of the D. triformis group. All of the identified species were found to be new records in Canada except for D. valveus. Accurate Ditylenchus species identification is crucial because false-positive identification can result in the implementation of quarantine measures over the detected area. Our current study not only documented the presence of Ditylenchus species from southern Alberta, but also described their morpho-molecular characteristics and subsequent phylogenetic relationships with related species. The results of our study will aid in the decision on whether these species should become a part of nematode management programs since nontarget species can become pests due to changes in cropping patterns or climate. Full article
(This article belongs to the Special Issue Integrative Taxonomy, Molecular Diagnosis and Phylogenetic Relationships of Plant-Parasitic Nematodes)
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25 pages, 4709 KiB  
Article
New Records of Wood- and Bark-Inhabiting Nematodes from Woody Plants with a Description of Bursaphelenchus zvyagintsevi sp. n. (Aphelenchoididae: Parasitaphelenchinae) from Russia
by Alexander Y. Ryss and Sergei A. Subbotin
Plants 2023, 12(2), 382; https://doi.org/10.3390/plants12020382 - 13 Jan 2023
Cited by 3 | Viewed by 2556 | Correction
Abstract
Wood- and bark-inhabiting parasitic nematodes are of great economic importance. Nematodes can cause wilt diseases in conifers and deciduous trees. In 2014–2022, during nematology surveys conducted in different regions of Russia and Belarus, adults and dauer juveniles of nematodes were collected from wood, [...] Read more.
Wood- and bark-inhabiting parasitic nematodes are of great economic importance. Nematodes can cause wilt diseases in conifers and deciduous trees. In 2014–2022, during nematology surveys conducted in different regions of Russia and Belarus, adults and dauer juveniles of nematodes were collected from wood, bark and beetle vectors. Using traditional morphological taxonomic characters integrated with molecular criteria, we identified in the studied samples the following nematode species: Aphelenchoides heidelbergi, Bursaphelenchus eremus, B. fraudulentus, B. michalskii, B. mucronatus, B. willibaldi, Deladenus posteroporus, Diplogasteroides nix and Laimaphelenchus hyrcanus, several unidentified species: Aphelenchoides sp.1 and sp.2, Cryptaphelenchus sp.1, sp.2 and sp.3, Laimaphelenchus sp.1, Micoletzkya sp.1, Parasitaphelenchus sp.1, Parasitorhabditis sp.1, three unidentified tylenchid nematodes and a new species, Bursaphelenchus zvyagintsevi sp.n. Morphological descriptions and molecular characterization are provided for B. zvyagintsevi sp. n. belonging to the Abietinus group and B. michalskii belonging to the Eggersi group. Findings of Aphelenchoides heidelbergi, Bursaphelenchus eremus, B. michalskii, Deladenus posteroporus, Diplogasteroides nix and Laimaphelenchus hyrcanus are new records for Russia. Phylogenetic positions of studied species were reconstructed using D2–D3 expansion segments of 28S rRNA gene sequence analysis. The data obtained in this study may help to detect the refugia of opportunistic plant pests and find possible native biocontrol nematode agents of insect vectors causing diseases. Full article
(This article belongs to the Special Issue Integrative Taxonomy, Molecular Diagnosis and Phylogenetic Relationships of Plant-Parasitic Nematodes)
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37 pages, 8781 KiB  
Article
DNA Barcoding and Morphometry Reveal Further Cryptic Bio-Diversity within the Pin Nematode Genus Paratylenchus (Nematoda: Tylenchulidae)
by Juan Emilio Palomares-Rius, Antonio Archidona-Yuste, Ilenia Clavero-Camacho, José A. Carreira de la Fuente, Ana Rey, Benjamín Viñegla, Gracia Liébanas, Carolina Cantalapiedra-Navarrete and Pablo Castillo
Plants 2022, 11(23), 3385; https://doi.org/10.3390/plants11233385 - 5 Dec 2022
Cited by 4 | Viewed by 1546
Abstract
Paratylenchus species are obligate ectoparasitic nematodes on cultivated and wild herbaceous and woody plants occupying numerous soil categories. Several species may cause damage to several crops (viz. P. dianthus, P. enigmaticus, P. microdorus, P. hamatus and P. epacris [...] Read more.
Paratylenchus species are obligate ectoparasitic nematodes on cultivated and wild herbaceous and woody plants occupying numerous soil categories. Several species may cause damage to several crops (viz. P. dianthus, P. enigmaticus, P. microdorus, P. hamatus and P. epacris on carnation, lettuce, rose and walnut, respectively). This investigation proves and emphasizes the relevance of applying integrative taxonomy for the accurate detection of Paratylenchus species in mountainous wild environments in the Malaga province, Southern Spain. This research analyzed 45 soil samples of maritimus pine and one of green heather in southern Spain and identified fourteen Paratylenchus species, two of them are described herein as new species (P. paraaonli sp. nov., P. plesiostraeleni sp. nov.), six of them were first reports for Spain (P. canchicus, P. nainianus, P. neonanus, P. salubris, Paratylenchus sp. 2 SAS, and P. wuae), and six species (P. caravaquenus, P. microdorus, P. nanus, P. neoamblycephalus, P. sheri, and P. variabilis) have been already reported in Spain. Accordingly, these data increase the biodiversity of pin nematodes in Spain comprising a total of 47 species (33.1% out of 142 total species of this genus). Phylogenetic analyses based on ribosomal and mitochondrial markers (D2-D3, ITS, and partial COI) resulted in a consistent position for the newly described Paratylenchus species in this study (P. plesiostraeleni sp. nov., P. paraaonli sp. nov.). Paratylenchus plesiostraeleni sp. nov. grouped in a separated subclade as unequivocal species from the P. straeleni-complex species (including P. straeleni and P. parastraeleni), and P. paraaonli sp. nov. clustered with P. vitecus, but clearly separate from this species. This study indicates that Paratylenchus species diversity in natural environments may be higher than expected, and this study may help in accurate identifications. Full article
(This article belongs to the Special Issue Integrative Taxonomy, Molecular Diagnosis and Phylogenetic Relationships of Plant-Parasitic Nematodes)
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36 pages, 8247 KiB  
Article
A Proposed New Species Complex within the Cosmopolitan Ring Nematode Criconema annuliferum (de Man, 1921) Micoletzky, 1925
by Ilenia Clavero-Camacho, Juan Emilio Palomares-Rius, Carolina Cantalapiedra-Navarrete, Pablo Castillo, Gracia Liébanas and Antonio Archidona-Yuste
Plants 2022, 11(15), 1977; https://doi.org/10.3390/plants11151977 - 29 Jul 2022
Cited by 5 | Viewed by 1813
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Integrative Taxonomy, Molecular Diagnosis and Phylogenetic Relationships of Plant-Parasitic Nematodes)
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1 pages, 173 KiB  
Correction
Correction: Ryss, A.Y.; Subbotin, S.A. New Records of Wood- and Bark-Inhabiting Nematodes from Woody Plants with a Description of Bursaphelenchus zvyagintsevi sp. n. (Aphelenchoididae: Parasitaphelenchinae) from Russia. Plants 2023, 12, 382
by Alexander Y. Ryss and Sergei A. Subbotin
Plants 2023, 12(16), 2949; https://doi.org/10.3390/plants12162949 - 15 Aug 2023
Viewed by 468
Abstract
In the original publication [...] Full article
(This article belongs to the Special Issue Integrative Taxonomy, Molecular Diagnosis and Phylogenetic Relationships of Plant-Parasitic Nematodes)
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