RESEARCH ARTICLE Diversity of root-knot nematodes of the genus Meloidogyne Go¨eldi, 1892 (Nematoda: Meloidogynidae) associated with olive plants and environmental cues regarding their distribution in southern Spain Antonio Archidona-Yuste1, Carolina Cantalapiedra-Navarrete1, Gracia Lie´banas2, Hava a1111111111 F. Rapoport1, Pablo Castillo1, Juan E. Palomares-Rius1 a1111111111 a1111111111 1 Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Cientı´ficas (CSIC), Avenida Mene´ndez Pidal s/n, Co´rdoba, Spain, 2 Departmento de Biologı´a Animal, Biologı´a Vegetal y Ecologı´a, a1111111111 Universidad de Jae´n, Campus ‘Las Lagunillas’ s/n, Jae´n, Spain a1111111111 * [email protected] Abstract Citation: Archidona-Yuste A, Cantalapiedra- Root-knot nematodes of the genus Meloidogyne are recognised worldwide as a major pro- Navarrete C, Lie´banas G, Rapoport HF, Castillo P, duction constraint in crops of primary economic importance. Knowledge of their diversity Palomares-Rius JE (2018) Diversity of root-knot and prevalence, as well as the major environmental and agronomical cues for understand- nematodes of the genus Meloidogyne Go¨eldi, 1892 (Nematoda: Meloidogynidae) associated with olive ing their distribution in specific areas is of vital importance for designing control measures to plants and environmental cues regarding their reduce significant damage. We provide the first detailed information on the diversity, distri- distribution in southern Spain. PLoS ONE 13(6): bution and levels of Meloidogyne species infecting wild and cultivated olive soils in a wide- e0198236. https://doi.org/10.1371/journal. pone.0198236 region in southern Spain that included 499 sampling sites. Overall Meloidogyne spp. were found in 6.6% of sampled olive plants, with 6.6% and 6.5% for cultivated and wild olive, Editor: Raffaella Balestrini, Institute for Sustainable Plant Protection, C.N.R., ITALY respectively. We identified five previously described Meloidogyne spp. (Meloidogyne are- naria, M. baetica, M. hapla, M. incognita, M. javanica) and one new species (Meloidogyne Received: March 7, 2018 oleae sp. nov.) which, characterized using integrative taxonomy, increases the known biodi- Accepted: May 16, 2018 versity of Meloidogyne spp. affecting olive. Meloidogyne arenaria and M. incognita were Published: June 20, 2018 only found infecting cultivated olive varieties, while, M. baetica was only found infecting wild Copyright: ' 2018 Archidona-Yuste et al. This is an olive. Three major parameters drive the distribution of Meloidogyne spp. in cultivated olives open access article distributed under the terms of in southern Spain, cover vegetation on alley, irrigation and soil texture, but different species the Creative Commons Attribution License, which respond differently to them. In particular the presence of M. incognita is highly correlated permits unrestricted use, distribution, and reproduction in any medium, provided the original with sandy loamy soils, the presence of M. javanica with irrigated soils and cover vegetation, author and source are credited. while the presence of M. arenaria is correlated with the absence of cover vegetation on alley Data Availability Statement: The authors confirm and absence of irrigation. These parameters likely influence the selection of each particular that all data underlying the findings are fully Meloidogyne species from a major dispersal source, such as the rooted plantlets used to available without restriction. All genetic sequences establish the orchards. are available from GenBank (accession numbers MG996751-MG996760, MH011963-MH011983). All relevant data are within the paper. Funding: This work was supported by Project P12- AGR-1486 from the ‘Consejerı´a de Economı´a, PLOS ONE | https://doi.org/10.1371/journal.pone.0198236 June 20, 2018 1/40 Root-knot nematodes in olive in southern Spain Innovacio´n y Ciencia’ of Junta de Andalucı´a to PC, Introduction the grant 219262 ArimNET_ERANET FP7 2012- 2015 Project PESTOLIVE ‘Contribution of olive Root-knot nematodes (RKN) of the genus Meloidogyne Go¨eldi, 1892 [1] are recognised world- history for the management of soilborne parasites wide as one of the major production constraints of crops of primary economic importance, in the Mediterranean basin’ from the Instituto including vegetables, fruit-crops, ornamental and wild plants [2]. Meloidogyne species are Nacional de Investigacio´n y Tecnologı´a Agraria y among nature’s most successful plant parasites and have a significant economic impact on Alimentaria (INIA) to PC, Project AGL-2012-37521 host-plants due to their wide host range and distribution throughout temperate and tropical from the ‘Ministerio de Economı´a y Competitividad’ of Spain, FEDER financial support from the environments [2]. However species determination of Meloidogyne spp. is complex, difficult European Union, and grant 201740E042 “Ana´lisis and time-consuming even for experts. Identification of RKN species is essential for the design de diversidad molecular, barcoding, y relaciones of effective nematode management strategies such as crop rotation and plant resistance. filogene´ticas de nematodos fitopara´sitos en Recently 50 Meloidogyne species (about 50% of total species) have been characterized molecu- cultivos mediterra´neos” from the Spanish National larly by ribosomal (D2-D3 expansion segments of 28S rRNA and ITS1 rRNA and partial 18S) Research Council (CSIC) to PC. The funders had no role in study design, data collection and analysis, and mitochondrial genes (coxI, coxII-16S), constituting a useful tool for molecular-based spe- decision to publish, or preparation of the cies identification [3–6]. Additionally, the analysis of isozyme electrophoretic patterns, in par- manuscript. A. Archidona-Yuste is a recipient of ticular esterase (Est) and malate dehydrogenase (Mdh), have proven to be a valuable tool for research contract BES-2013063495 from the precise identification of Meloidogyne species, particularly the most important tropical species Ministerio de Economı´a y Competitividad, Spain. (M. incognita (Kofoid & White, 1919) Chitwood, 1949, M. javanica (Treub, 1885) Chitwood, Competing interests: The authors have declared 1949 and M. arenaria (Neal, 1889) Chitwood, 1949 among others) [7]. In fact the application that no competing interests exist. of molecular methods to studies of RKN and systematics has revealed that some long-assumed single species are cryptic species that are morphologically indistinguishable but may be phylo- genetically distant to one another [8]. For these reasons, the integration of molecular and iso- zyme electrophoretic pattern techniques with classical morphological approaches should help to provide tools for differentiating Meloidogyne species and significantly improve and facilitate the routine identification of these nematodes. Meloidogyne spp. and root-lesion nematodes (Pratylenchus spp.) are the most damaging plant-parasitic nematodes of cultivated olive (Olea europaea L. subsp. europaea var. europaea), especially in nurseries [9, 10]. Olive, in wild and cultivated forms, is widely distributed in the Mediterranean Basin, and particularly in southern Spain [11–14]. Wild (Olea europaea L. subsp. europaea var. sylvestris) and cultivated olives are hosts of and frequently suffer damage by RKN found in their rhizosphere, including M. arenaria, M. baetica Castillo, Vovlas, Subbo- tin, & Troccoli, 2003, M. javanica, M. incognita, M. hapla Chitwood, 1949, M. lusitanica Abrantes & Santos, 1991, M. spartelensis Ali et al. 2015 [15, 16]. Initially, with the aim of deci- phering the biodiversity of Meloidogyne spp. infecting wild and cultivated olives in southern Spain, we surveyed 499 sampling points in Andalusia covering the diversity of olive cropping systems from traditional groves to new intensive orchards, as well as agroforestry stands where both olive forms were present. Our survey found 33 infested sampling points containing 35 populations of Meloidogyne species, morphologically similar to known Meloidogyne spp. The definitive identification of those populations prompted us to carry out an integrative taxo- nomic study to identify the species within this complex and economically important genus. The suppression of the negative effects produced in crops by RKNs is considered as a diffi- cult task due to the biological traits of both crop and RKN species as well as the high complex- ity of the soil environment [2, 17]. Understanding the drivers of community structure, however, is an essential point for increasing our knowledge regarding ecological phenomena involved in RKN management. In this context, recent studies have been performed on culti- vated olives with the aim of finding the important factors influencing RKN population dynam- ics [18, 19]. Although both these studies suggested that the presence of RKN species could be determined by human activities (i.e. widespread introductions from nurseries), they also found habitat factors driving the distribution of RKNs among cultivated Moroccan olives [18, 19]. Nonetheless a general pattern for statistically significant environmental factors affecting PLOS ONE | https://doi.org/10.1371/journal.pone.0198236 June 20, 2018 2/40 Root-knot nematodes in olive in southern Spain RKN distribution in olive plants is lacking for Spain, which furthermore differs somewhat from African environmental conditions. The general objective of this research was to study the occurrence and abundance of Meloi- dogyne species in olive plants in