DOCSLIB.ORG

A Case Study Within the Genus Pratylenchus (Nematoda

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Case Study Within the Genus Pratylenchus (Nematoda Nematology 19 (2017) 1179-1199 brill.com/nemy The pitfalls of molecular species identification: a case study within the genus Pratylenchus (Nematoda: Pratylenchidae) ∗ Toon JANSSEN 1,2, , Gerrit KARSSEN 3, Marjolein COUVREUR 1, ∗ Lieven WAEYENBERGE 4 and Wim BERT 1, 1 Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium 2 Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium 3 National Plant Protection Organization, Wageningen Nematode Collection, P.O. Box 9102, 6700 HC Wageningen, The Netherlands 4 ILVO, Crop Protection, Burg. Van Gansberghelaan 96 bus 2, 9820 Merelbeke, Belgium Received: 27 February 2017; revised: 13 September 2017 Accepted for publication: 13 September 2017; available online: 20 October 2017 Summary – Comprehensive morphological and molecular analyses revealed that published ITS sequences of the economically important plant-parasitic nematode Pratylenchus goodeyi are actually sequences from distantly free-living bacterivorous ‘cephalobids’. We demonstrated that this incorrect labelling resulted in a cascade of erroneous interpretations, as shown by the reports of ‘P. goodeyi’ on banana in China and on cotton in India. This clearly illustrates the risk of mislabelled sequences in public databases. Other mislabelled Pratylenchus cases are discussed to illustrate that this is not an isolated case. Herein, P. lentis n. syn. is considered a junior synonym of P. pratensis while P. flakkensis was for the first time linked to DNA sequences using topotype material. As taxonomic expertise is decreasing and sequence-based identification is growing rapidly, the highlighted problem may yet increase and a strong link between morphology and DNA sequences will be of crucial importance in order to prevent, or at least minimise, sequence-based misidentifications. Keywords – Acrobeloides cf. nanus, diagnostics, mislabelled sequences, molecular phylogeny, new synonym, Pratylenchus flakkensis, Pratylenchus goodeyi, Pratylenchus lentis n. syn., Pratylenchus pratensis, topotypes. Molecular taxonomy and DNA barcoding provide a Nilsson et al. (2006) estimate that up to 20% of fungal powerful tool for the identification of organisms and for sequences are actually misidentified. For eukaryotes, er- studying biodiversity (Hebert et al., 2003; Savolainen et roneous linking of sequence and organism was thought al., 2005; Kress & Erickson, 2008). Molecular identifi- to be relatively uncommon due to the availability of mor- cation is especially important for organisms for which phological characters for their identification (Nilsson et morphological diagnostic characteristics are scarce. Due al., 2006). However, this problem appears not to be re- to the decreasing price and increased availability of se- stricted to microbiology, as demonstrated here for Ne- quence instruments, the amount of sequence data avail- matoda, using three case studies within the genus Praty- able on public DNA databases has grown exponentially lenchus (Pratylenchidae). Many species of Pratylenchus over the last 10 years (Muir et al., 2016). However, a sub- are very difficult to identify morphologically, due to a stantial part of this sequence data appears to be incor- lack of robust diagnostic characters, morphological inter- rect, with faults ranging from sequence errors over mis- specific plasticity, and incomplete taxonomic descriptions assemblies to mislabelled, unlabelled, and misidentified (Castillo & Vovlas, 2007; Subbotin et al., 2008; Troccoli sequences. In microbiology where morphological infor- et al., 2016). As a result, DNA-based identification strate- mation is almost absent and identification is often purely gies are becoming more important (Waeyenberge et al., based on 16S rDNA sequences the problem is well known 2000, 2009; Al-Banna et al., 2004; Powers, 2004; Mokrini (Vilgalys, 2003; Nilsson et al., 2006; Lal & Lal, 2011). et al., 2013). * Corresponding authors, e-mail: [email protected]; [email protected] © Koninklijke Brill NV, Leiden, 2017 DOI 10.1163/15685411-00003117 Downloaded from Brill.com10/06/2021 03:12:39AM via free access T. Janssen et al. CASE STUDY 1: Pratylenchus goodeyi SHER & Castillo & Vovlas, 2007). Pratylenchus pratensis has ALLEN, 1953 been recorded in Africa (Algeria, Libya, South Africa), Asia (Azerbaijan, China, India, Pakistan, Uzbekistan) and Pratylenchus goodeyi is considered a major pest of North America (Canada, Mexico, USA) but has mainly banana and plantain (Castillo & Vovlas, 2007). It was been reported from Europe, occurring in Belgium, Bul- originally described by Sher & Allen (1953) from Kew garia, Finland, Germany, Italy, Moldavia, Poland, Rus- Gardens in London from the roots of banana trees. Since sia, Slovakia, Slovenia, Spain and The Netherlands on a then it has been reported from many banana-producing wide variety of crops (Castillo & Vovlas, 2007). Despite regions, especially from Africa and southern European the numerous morphological reports of P. pratensis, there countries: the Canary Islands (Spain), Crete (Greece) and is relatively little sequence information available for this Madeira (Portugal) (Castillo & Vovlas, 2007). In Africa, species. Nevertheless, seven 28S rDNA sequences were the parasite is often associated with higher altitudes and generated from five coastal areas in Belgium, Portugal, cooler temperatures (Price & Bridge, 1995). Surprisingly, Spain and the UK, by de la Peña et al. (2007). In addi- it has not been recorded in North or South America. tion five β-1,4-endoglucanase gene sequences, five 18S Pratylenchus goodeyi is differentiated from other root- rDNA sequences and two RNA polymerase II gene se- lesion nematodes by the presence of four lip annuli, quences were generated (Rybarczyk-Mydlowska et al., a large oblong spermathecal, and tail conoid, ventrally 2012, 2014) although morphological vouchers of these concave with a smooth tail tip (Sher & Allen, 1953; Loof, populations were not provided. In 2008, P. lentis Troccoli, 1991; Castillo & Vovlas, 2007). De Luca, Handoo & Di Vito, 2008, a taxon morphologi- In 2007, P. goodeyi was labelled as a cryptic species cally very similar to P. pratensis, was described parasitis- complex using sequence-based taxonomy (Waeyenberge, ing roots of lentil (Lens culinaris Medik.) in Sicily (Italy) 2007) and, in this study, five ITS sequences originating (Troccoli et al., 2008), the description being associated from Tenerife (Canary Islands, Spain) were made pub- with 12 ITS sequences. In later studies, P. lentis appeared licly available (FJ712922-FJ712926). In 2011, another to be embedded within the P. fallax clade (Palomares- P. goodeyi population (FR692324) was reported from Rius et al., 2010), although this relationship has recently the Canary Islands by De Luca et al. (2011). Praty- been shown to be the result of a P. fallax misidentification lenchus goodeyi was also reported by Gokte-Narkhedkar (Janssen et al., 2017). et al. (2013) from cotton in India at three different lo- cations and six P. goodeyi sequences were deposited in GenBank (KF275665, KF700243, KF840454, KF840455, CASE STUDY 3: Pratylenchus flakkensis KF840456, KF856291). In 2015, P. goodeyi was reported SEINHORST, 1968 for the first time on banana in China (Zhang et al., 2015). Both Waeyenberge (2007) and De Luca et al. (2011) re- Pratylenchus flakkensis was originally described by ported a large discrepancy between P. goodeyi sequences Seinhorst (1968) from Middelharnis (The Netherlands) from different geographical locations. This could indicate from a heavy loam soil under grass. Seinhorst (1968) either the presence of a species complex, as suggested by also reported it from Ouddorp (The Netherlands) and Waeyenberge (2007), or alternatively it could point to in- from Beckenham (UK). Later, P. flakkensis was reported correctly labelled sequences as suggested by De Luca et by Ryss from Estonia and Russia (Ryss, 1986, 1988, al. (2011). 1992). Pratylenchus flakkensis appears to be geograph- ically widespread as it has also been recorded from CASE STUDY 2: Pratylenchus pratensis (DE MAN, Guadeloupe, Pakistan, Peru, and South Africa (Castillo 1880) FILIPJEV, 1936 & Vovlas, 2007). Despite the numerous morphological records of this species, no molecular data are currently Pratylenchus pratensis was originally described as Ty- available for the taxon. lenchus pratensis by de Man (1880). The species was In order unequivocally to link DNA sequences with the subsequently transferred to Anguillulina (Goffart, 1929) above mentioned species of Pratylenchus, and to clarify and then appointed as the type species of the newly their taxonomic status, the goals of these case studies erected genus Pratylenchus by Filipjev (1936). Later, were: i) to characterise these species using a combination P. helophilus Seinhorst, 1959 and P. irregularis Loof, of morphological characteristics and molecular sequences 1960 were synonymised with P. pratensis (Loof, 1974; from geographically different locations; ii) to determine 1180 Nematology Downloaded from Brill.com10/06/2021 03:12:39AM via free access Pitfalls of molecular species identification their phylogenetic position within the genus; and iii)to of 4.5% Tween-20. The mixture was heated to 95°C for enable reliable molecular diagnostics. 15 min and, after cooling to room temperature, 40 μlof double-distilled water was added. PCR amplification was performed using Toptaq DNA
Load more

Recommended publications
  • Reproduction of the Banana Root-Lesion Nematode, Pratylenchus Goodeyi, in Monoxenic Cultures
    Nematol. medit. (1999), 27: 187-192 1 Instituto de Agricultura Sostenible CS.I.C, Apdo. 4084) 14080 Cordoba, Spain 2 Istituto di Nematologia Agraria) CN.R.) 70126Bari, Italy REPRODUCTION OF THE BANANA ROOT-LESION NEMATODE, PRATYLENCHUS GOODEYI, IN MONOXENIC CULTURES by A. 1. NICO 1, N. VOVLAS 2, A. TRoccoLI 2 and P. CASTILLO 1 Summary. Pratylenchus goodeyi obtained from a field population, infecting banana roots at Madeira island, Portugal, was cultured on carrot discs at 25 QC in a growth chamber to determine its rate of reproduction and to compare the morphometry of the axenically produced population with that of specimens from a field popula­ tion and from previous published descriptions. An initial inoculum level of 12 specimens (ten females and two males) produced, after four months, up to 39,000 specimens/single disc, in all stages of development (eggs, juveniles and adults with a sex ratio between females and males of 12:1). The main morphometric features with stable value (such as stylet length, V%, spicules and gubernaculum length, etc.) of specimens from the carrot disc culture closely agreed with the original description, and the banana populations from Cameroon and Ma­ deira. The root-lesion nematode, Pratylenchus goo­ with data of previous descriptions. These obser­ deyi, was first isolated from banana roots in Gre­ vations may be useful to others for additional nada (Cobb, 1919) and later was found in bana­ studies on such migratory species. na plantations in the Canary Islands (Spain) (de Guiran and Vilardebo, 1982), Kenya (Gichure and Ondieki, 1977; Waudo et al., 1990; Prasad et Materials and methods al., 1995), Tanzania (Walker et al., 1984), Came­ roon (Sakwe and Geraert, 1994), Greece (Vovlas A population of P.
    [Show full text]
  • Description of Pratylenchus Dunensis Sp. N. (Nematoda: Pratylenchidae
    Nematology, 2006, Vol. 8(1), 79-88 Description of Pratylenchus dunensis sp.n.(Nematoda: Pratylenchidae), a root-lesion nematode associated with the dune grass Ammophila arenaria (L.) Link ∗ Eduardo DE LA PEÑA 1, , Maurice MOENS 1,2, Adriaan VA N AELST 3 and Gerrit KARSSEN 4,5 1 Agricultural Research Centre, Crop Protection Department, Burg. van Gansberghelaan 96, 9820, Merelbeke, Belgium 2 Gent University, Laboratory for Agrozoology, Coupure 653, 9000 Gent, Belgium 3 Wageningen University & Research Centre, Laboratory of Plant Cell Biology, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands 4 Plant Protection Service, Nematology Section, P.O. Box 9102, 6700 HC Wageningen, The Netherlands 5 Wageningen University & Research Centre, Laboratory of Nematology, Binnenhaven 5, 6709 PD Wageningen, The Netherlands Received: 4 April 2005; revised: 7 November 2005 Accepted for publication: 7 November 2005 Summary – A root-lesion nematode, Pratylenchus dunensis sp. n., is described and illustrated from Ammophila arenaria (L.) Link, a grass occurring abundantly in coastal dunes of Atlantic Europe. The new species is characterised by medium sized (454-579 µm) slender, vermiform, females and males having two lip annuli (sometimes three to four; incomplete incisures only visible with scanning electron microscopy), medium to robust stylet (ca 16 µm) with robust stylet knobs slightly set off, long pharyngeal glands (ca 42 µm), lateral field with four parallel, non-equidistant, lines, the middle ridge being narrower than the outer ones, lateral field with partial areolation and lines converging posterior to the phasmid which is located between the two inner lines of the lateral field in the posterior half of the tail, round spermatheca filled with round sperm, vulva at 78% of total body length and with protruding vulval lips, posterior uterine sac relatively short (ca 19 µm), cylindrical tail (ca 33 µm) narrowing in the posterior third with smooth tail tip and with conspicuous hyaline part (ca 2 µm).
    [Show full text]
  • Nematodes and Agriculture in Continental Argentina
    Fundam. appl. NemalOl., 1997.20 (6), 521-539 Forum article NEMATODES AND AGRICULTURE IN CONTINENTAL ARGENTINA. AN OVERVIEW Marcelo E. DOUCET and Marîa M.A. DE DOUCET Laboratorio de Nematologia, Centra de Zoologia Aplicada, Fant/tad de Cien.cias Exactas, Fisicas y Naturales, Universidad Nacional de Cordoba, Casilla df Correo 122, 5000 C6rdoba, Argentina. Acceplecl for publication 5 November 1996. Summary - In Argentina, soil nematodes constitute a diverse group of invertebrates. This widely distributed group incJudes more than twO hundred currently valid species, among which the plant-parasitic and entomopathogenic nematodes are the most remarkable. The former includes species that cause damages to certain crops (mainly MeloicU:igyne spp, Nacobbus aberrans, Ditylenchus dipsaci, Tylenchulus semipenetrans, and Xiphinema index), the latter inc1udes various species of the Mermithidae family, and also the genera Steinernema and Helerorhabditis. There are few full-time nematologists in the country, and they work on taxonomy, distribution, host-parasite relationships, control, and different aspects of the biology of the major species. Due tO the importance of these organisms and the scarcity of information existing in Argentina about them, nematology can be considered a promising field for basic and applied research. Résumé - Les nématodes et l'agriculture en Argentine. Un aperçu général - Les nématodes du sol représentent en Argentine un groupe très diversifiè. Ayant une vaste répartition géographique, il comprend actuellement plus de deux cents espèces, celles parasitant les plantes et les insectes étant considèrées comme les plus importantes. Les espèces du genre Me/oi­ dogyne, ainsi que Nacobbus aberrans, Dùylenchus dipsaci, Tylenchulus semipenetrans et Xiphinema index représentent un réel danger pour certaines cultures.
    [Show full text]
  • Burrowing Nematode Radopholus Similis (Cobb, 1893) Thorne, 1949 (Nematoda: Secernentea: Tylenchida: Pratylenchidae: Pratylenchinae)1 Nicholas Sekora and William T
    EENY-542 Burrowing Nematode Radopholus similis (Cobb, 1893) Thorne, 1949 (Nematoda: Secernentea: Tylenchida: Pratylenchidae: Pratylenchinae)1 Nicholas Sekora and William T. Crow2 Introduction by fine textured soils rich in organic matter. However, soil texture plays a less important role on nematode population Radopholus similis, the burrowing nematode, is the most levels on banana (O’Bannon 1977). economically important nematode parasite of banana in the world. Infection by burrowing nematode causes toppling disease of banana, yellows disease of pepper and spreading Life Cycle and Biology decline of citrus. These diseases are the result of burrowing Burrowing nematode is an endoparasitic migratory nema- nematode infection destroying root tissue, leaving plants tode, meaning it completes its life cycle within root tissue. with little to no support or ability to take up water and All motile juvenile stages and females can infect root tissue translocate nutrients. Because of the damage that it causes at any point along the length of a root. After root penetra- to citrus, ornamentals and other agricultural industries, tion, these life stages mainly feed and migrate into the worldwide, burrowing nematode is one of the most regu- cortical parenchyma and also into the stele. Mature males lated nematode plant pests (Hockland et al. 2006). of burrowing nematode are not infective. As the mature females migrate through root tissue, they lay eggs that are Distribution produced through either sexual reproduction with males or by hermaphroditistim (Thorne 1961, Kaplan and Burrowing nematode is native to Australasia, but is found worldwide in tropical and subtropical regions of Africa, Opperman 2000). Once an egg hatches, the emergent Asia, Australia, North and South America, and many second-stage juvenile can migrate within the root and island regions.
    [Show full text]
  • Introduction 1.1. Banana Bananas
    Chapter 1: Introduction 1.1. Banana Bananas (Musa spp.) are an important fruit in agriculture and to the world economy. This fruit provides carbohydrates, proteins, vitamin and minerals to more than 400 million people worldwide (Musabyimana et al., 1999). A banana plant is considered as a herbaceous perennial plant; herbaceous because this plant do not have any woody parts and after the ripening of the fruits, the aerial parts would wither and die while at the same time being perennial due to the fact that new shoots would sprout from the base mature banana and forming a new tree. A mature banana plant can be divided into three integral parts, namely a corm, pseudostems with leaves and a bunch with fruits (Speiger et al., 1997). A corm is the underground part of a banana plant that consists of the roots and suckers. The corm is actually the true stem of the plant because it is the apical meristem or the growing point of the leaves which are developed from the tip of the corm. The corm is composed of a middle cylinder bounded by a cortex. Primary roots separate from the central cylinder and the cortex. Primary roots are formed in three to four waves and the majority of them are created within four months after planting. Primer roots grow horizontally all over the cortex and stay above 50 cm of soil. They are one centimeter thick and are three to four meters in length. A subsequent system of secondary and tertiary roots and root hairs would emerge from the primary roots.
    [Show full text]
  • Phylogenetic Analysis of Nematodes of the Genus Pratylenchus Using Nuclear 26S Rdna
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications from the Harold W. Manter Laboratory of Parasitology Parasitology, Harold W. Manter Laboratory of February 1997 Phylogenetic Analysis of Nematodes of the Genus Pratylenchus Using Nuclear 26S rDNA Luma Al-Banna University of Jordan, [email protected] Valerie M. Williamson University of California, Davis, [email protected] Scott Lyell Gardner University of Nebraska - Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/parasitologyfacpubs Part of the Parasitology Commons Al-Banna, Luma; Williamson, Valerie M.; and Gardner, Scott Lyell, "Phylogenetic Analysis of Nematodes of the Genus Pratylenchus Using Nuclear 26S rDNA" (1997). Faculty Publications from the Harold W. Manter Laboratory of Parasitology. 52. https://digitalcommons.unl.edu/parasitologyfacpubs/52 This Article is brought to you for free and open access by the Parasitology, Harold W. Manter Laboratory of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications from the Harold W. Manter Laboratory of Parasitology by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published in Molecular Phylogenetics and Evolution (ISSN: 1055-7903), vol. 7, no. 1 (February 1997): 94-102. Article no. FY960381. Copyright 1997, Academic Press. Used by permission. Phylogenetic Analysis of Nematodes of the Genus Pratylenchus Using Nuclear 26S rDNA Luma Al-Banna*, Valerie Williamson*, and Scott Lyell Gardner1 *Department of Nematology, University of California at Davis, Davis, California 95676-8668 1H. W. Manter Laboratory, Division of Parasitology, University of Nebraska State Museum, W-529 Nebraska Hall, University of Nebraska-Lincoln, Lincoln, NE 68588-0514; [email protected] Fax: (402) 472-8949.
    [Show full text]
  • Diversity, Phylogeny, Characterization and Diagnostics of Root-Knot and Lesion Nematodes
    Diversity, phylogeny, characterization and diagnostics of root-knot and lesion nematodes Toon Janssen Promotors: Prof. Dr. Wim Bert Prof. Dr. Gerrit Karssen Thesis submitted to obtain the degree of doctor in Sciences, Biology Proefschrift voorgelegd tot het bekomen van de graad van doctor in de Wetenschappen, Biologie 1 Table of contents Acknowledgements Chapter 1: general introduction 1 Organisms under study: plant-parasitic nematodes .................................................... 11 1.1 Pratylenchus: root-lesion nematodes ..................................................................................... 13 1.2 Meloidogyne: root-knot nematodes ....................................................................................... 15 2 Economic importance ..................................................................................................... 17 3 Identification of plant-parasitic nematodes .................................................................. 19 4 Variability in reproduction strategies and genome evolution ..................................... 22 5 Aims .................................................................................................................................. 24 6 Outline of this study ........................................................................................................ 25 Chapter 2: Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution. 1 Abstract
    [Show full text]
  • Description of Pratylenchus Gutierrezi N. Sp. (Nematoda: Pratylenchidae
    Journal of Nematology 24(2):298-304. 1992. © The Society of Nematologists 1992. Description of Pratylenchus 9utierrezi n. sp. (Nematoda: Pratylenchidae) from Coffee in Costa Rica A. MORGAN GOLDEN, 1 ROGER L6PEZ CH., 2 AND HERNAN VILCHEZ R. 2 Abstract: A lesion nematode, Pratylenchu6 gutierrezi n. sp., collected from the roots of coffee in the Central Plateau of Costa Rica, is described and illustrated. Its relationships to Pratylenchusflakkensis, P. similis, and P. gibbicaudatus, the only other species of the genus having two head annules, males, or spermatheca with sperm, and an annulated tail terminus, is discussed. Other distinctive characters are its posterior vulva (mean of 80%); its prominently rounded stylet knobs, low head, and subcy- lindrical tail. SEM observations provide additional details of females and males, especially face views, which show for the first time sexual dimorphism. Key words: Coffea arabica, Costa Rica, lesion nematode, morphology, nematode, new species, Pra- tylenchus flakkensis, P. gibbicaudatus, P. gutierrezi n. sp., P. similis, scanning electron microscopy, SEM, taxonomy. Certain species of lesion nematodes to be a new Pratylenchus species, which is (Pratylenchus spp.) are important parasites described and illustrated herein. of coffee (Coffea spp.). In a recent excellent review of nematodes reported to occur on MATERIALS AND METHODS coffee (1), the following five Pratylenchus species were listed: P. brachyurus (Godfrey, Nematodes were extracted from in- 1929) Filipjev & Schuurmans Stekhoven, fected coffee roots by placing chopped or 1941; P. coffeae (Zimmermann, 1889) Fil- blenderized roots on filter paper over wa- ipjev & Schuurmans Stekhoven, 1941; P. ter in a Baermann funnel. Specimens were goodeyi Sher & Alien, 1953; P.
    [Show full text]
  • Evaluation of Metabarcoding Primers for Analysis of Soil Nematode Communities
    diversity Article Evaluation of Metabarcoding Primers for Analysis of Soil Nematode Communities Md. Maniruzzaman Sikder 1,2 , Mette Vestergård 1 , Rumakanta Sapkota 3 , Tina Kyndt 4 and Mogens Nicolaisen 1,* 1 Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200 Slagelse, Denmark; [email protected] (M.M.S.); [email protected] (M.V.) 2 Department of Botany, Faculty of Biological Sciences, Jahangirnagar University, 1342 Savar, Dhaka, Bangladesh 3 Department of Environmental Science, Faculty of Technical Sciences, Aarhus University, 4000 Roskilde, Denmark; [email protected] 4 Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Gent, Belgium; [email protected] * Correspondence: [email protected]; Tel.: +45-24757668 Received: 5 August 2020; Accepted: 7 October 2020; Published: 9 October 2020 Abstract: While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the application of high throughput approaches to study the ecology of nematodes remains unresolved due to several issues, e.g., whether to include an initial nematode extraction step or not, the lack of consensus on the best performing primer combination, and the absence of a curated nematode reference database. The objective of this method development study was to compare different primer sets to identify the most suitable primer set for the metabarcoding of nematodes without initial nematode extraction. We tested four primer sets for amplicon sequencing: JB3/JB5 (mitochondrial, I3-M11 partition of COI gene), SSU_04F/SSU_22R (18S rRNA, V1-V2 regions), and Nemf/18Sr2b (18S rRNA, V6-V8 regions) from earlier studies, as well as MMSF/MMSR (18S rRNA, V4-V5 regions), a newly developed primer set.
    [Show full text]
  • Research/Investigación Plant Parasitic Nematodes
    RESEARCH/INVESTIGACIÓN PLANT PARASITIC NEMATODES ASSOCIATED WITH BANANA AND PLANTAIN IN EASTERN AND WESTERN DEMOCRATIC REPUBLIC OF CONGO M. Kamira1, 3, S. Hauser2, P. van Asten1,2, D. Coyne2, and H. L. Talwana3 1Consortium for Improving Agricultural-based Livelihoods in Central Africa (CIALCA) Project, Bukavu, Democratic Republic of Congo; 2International Institute of Tropical Agriculture (IITA); 3School of Agricultural Sciences Makerere University, Kampala, Uganda; Corresponding author [email protected] ABSTRACT Kamira M., S. Hauser, P. Van Asten, D. Coyne, and H. L. Talwana. 2013. Plant parasitic nematodes associated with banana and plantain in eastern and western Democratic Republic of Congo. Nematropica 43:216-225. Plant-parasitic nematode incidence, population densities and associated damage were determined from 153 smallholder banana and plantain gardens in Bas Congo (9 – 646 meters above sea level, m.a.s.l) and South Kivu (1043 – 2005 m.a.s.l), Democratic Republic of Congo, during 2010. Based on the frequency of total nematode soil and root extraction, Helicotylenchus multicinctus (89%), Meloidogyne spp. (54%) and Radopholus similis (30%) were the most widespread, while Pratylenchus goodeyi (18%) Helicotylenchus dihystera (18%), Rotylenchulus reniformis (14%), and Pratylenchus spp. (6%) were localized in occurrence. The occurrence and abundance of the nematode species was influenced by altitude:R. similis declined at elevations above 1300 m; P. goodeyi declined at elevations below 1200 m; H. multicinctus and Meloidogyne spp. were found everywhere with higher but non-dominant densities at lower altitudes; Pratylenchus spp. was restricted to lower altitudes; while H. dihystera and R. reniformis were scattered at both low and high altitudes.
    [Show full text]
  • Root-Lesion Nematodes: Biology and Management in Pacific Northwest Wheat Cropping Systems Richard W
    A Pacific Northwest Extension Publication Oregon State University • University of Idaho • Washington State University PNW 617 • October 2015 Root-lesion nematodes: Biology and management in Pacific Northwest wheat cropping systems Richard W. Smiley ematodes are microscopic but complex symptoms on small grain cereals are nonspecific unsegmented roundworms that are anatomi- and easily confused with other ailments such as Ncally differentiated for feeding, digestion, nitrogen deficiency, low water availability, and root locomotion, and reproduction. These small animals rots caused by fungi such as Pythium, Rhizoctonia, occur worldwide in all environments. Most species and Fusarium. Farmers, pest management advi- are beneficial to agriculture; they make important sors, and scientists routinely underestimate or fail to contributions to organic matter decomposition recognize the impact of root-lesion nematodes on and are important members of the soil food chain. wheat. It is now estimated that these root parasites However, some species are parasitic to plants or reduce wheat yields by about 5 percent annually in animals. each of the Pacific Northwest (PNW) states of Idaho, Plant-parasitic nematodes in the genus Oregon, and Washington. This generally unrecog- Pratylenchus are commonly called either root-lesion nized pest annually reduces wheat profitability by as nematodes or lesion nematodes. These parasites much as $51 million in the PNW. can be seen only with the aid of a microscope. They Description are transparent, eel-shaped, and about 1/64 inch (0.5 mm) long. They puncture root cells and There are nearly 70 species in the genus damage underground plant tissues. Feeding by these Pratylenchus, at least eight of which are parasitic to nematodes reduces plant vigor, causes lesions, and wheat.
    [Show full text]
  • Functional Diversity of Soil Nematodes in Relation to the Impact of Agriculture—A Review
    diversity Review Functional Diversity of Soil Nematodes in Relation to the Impact of Agriculture—A Review Stela Lazarova 1,* , Danny Coyne 2 , Mayra G. Rodríguez 3 , Belkis Peteira 3 and Aurelio Ciancio 4,* 1 Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Y. Gagarin Str., 1113 Sofia, Bulgaria 2 International Institute of Tropical Agriculture (IITA), Kasarani, Nairobi 30772-00100, Kenya; [email protected] 3 National Center for Plant and Animal Health (CENSA), P.O. Box 10, Mayabeque Province, San José de las Lajas 32700, Cuba; [email protected] (M.G.R.); [email protected] (B.P.) 4 Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, 70126 Bari, Italy * Correspondence: [email protected] (S.L.); [email protected] (A.C.); Tel.: +359-8865-32-609 (S.L.); +39-080-5929-221 (A.C.) Abstract: The analysis of the functional diversity of soil nematodes requires detailed knowledge on theoretical aspects of the biodiversity–ecosystem functioning relationship in natural and managed terrestrial ecosystems. Basic approaches applied are reviewed, focusing on the impact and value of soil nematode diversity in crop production and on the most consistent external drivers affecting their stability. The role of nematode trophic guilds in two intensively cultivated crops are examined in more detail, as representative of agriculture from tropical/subtropical (banana) and temperate (apple) climates. The multiple facets of nematode network analysis, for management of multitrophic interactions and restoration purposes, represent complex tasks that require the integration of different interdisciplinary expertise. Understanding the evolutionary basis of nematode diversity at the field Citation: Lazarova, S.; Coyne, D.; level, and its response to current changes, will help to explain the observed community shifts.
    [Show full text]