Dataset on the diversity of plant-parasitic nematodes in cultivated olive trees in southern Spain

Datasets presented here were employed in the main work “Spatial structure and soil properties shape local community structure of plant-parasitic nematodes in cultivated olive trees in southern Spain” Archidona-Yuste et al., 2020. In this research, we aimed to unravel the diversity of plant-parasitic nematodes (PPN) associated with cultivated olive (Olea europaea subsp. europaea var. europaea) in southern Spain, Andalusia. The olive growing area of Andalusia is of high agriculture and socio-economic importance with an extensive distribution of this crop. To this end, we conducted a systematic survey comprising 376 commercial olive orchards covering the diversity of cropping systems applied. Data showed 128 species of PPN belonging to 38 genera and to 13 families. In addition, an extensive data set regarding to potential factors in structuring the community patterns of PPN found in the 376 commercial olive orchards sampled is provided. Three variables data set were compiled including above-ground environment, soil and agronomic management. Overall, 48 explanatory variables were selected as determinist processes on shaping the diversity of PPN. Finally, data also showed the values regarding to the partition of beta diversity into contributions of single sites to overall beta diversity (LCBD) and intro contributions of individual species to overall beta diversity (SCBD). Data may serve as benchmarks for other groups working in the field of PPN diversity associated with crops and of belowground communities and ecosystems.

overall beta diversity (LCBD) and intro contributions of individual species to overall beta diversity (SCBD). Data may serve as benchmarks for other groups working in the field of PPN diversity associated with crops and of belowground communities and ecosystems. © 2019 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).

Data
The data presented in this article include the information of the 376 commercial olive orchards sampled, as well as the total abundance of nematodes and species richness for each commercial orchard in Table 1, information about the diversity of PPN found from the systematic survey performed in Table 2, Figs. 1 and 2 In addition, Fig. 1 showed the distribution of species diversity of PPN detected by classes including feeding habit and family. Finally, values of Local Contributions to Beta diversity (LCBD) and Species Contributions to Beta Diversity (SCBD) indexes are provided in Tables 1 and 2, respectively. Table 2 showed the 27 commercial olive orchards with significant values as described by Archidona-Yuste et al. [1].
The diversity, prevalence and abundance of PPN associated with cultivated olive are presented in Table 2, Figs. 1 and 2. Data were characterized by performing species diversity under integrative taxonomy identification at species level of PPN infesting soils from 376 sampled commercial olive Specifications Table   Subject area Ecology More specific subject area Plant-parasitic nematode ecology. A case of study: cultivated olive trees in southern Spain Type of data Tables and figures How data was acquired Nematode identification was acquired by using integrative taxonomy (using a Zeiss III compound microscope with Nomarski differential interference contrast at up to Â 1000 magnification and molecular methods standardized). Variable data sets were compiled from GIS, directly provided by landowner and/or data collection Data format Raw and analyzed Experimental factors Soil samples were collected with a hoe from four to five trees randomly selected in each commercial olive orchard for both taxa identification and explanatory variables data collection. Experimental features Evaluate diversity, prevalence and abundance of plant-parasitic nematodes infesting soils from cultivated olive trees in southern Spain. Data source location Andalusia, southern Spain. Coordinates of sampling points are provided. Data accessibility Data is provided in this article, and raw data as supplementary material.

Related research article
Archidona-Yuste A., Wiegand T., Castillo P., and Navas-Cort es J. A. 2020. Spatial structure and soil properties shape local community structure of plant-parasitic nematodes in cultivated olive trees in southern Spain. Submitted to: Agriculture, Ecosystems and Environment, 287 (1), https://doi.org/10.1016/j.agee.2019.106688 Value of the Data Data may serve as benchmarks for other groups working in the field of PPN diversity infesting soils from agricultural ecosystems, and for belowground communities and ecosystems. Data are based on the systematic survey with the largest sampling effort done on cultivated olive to date. Data show a species list of PPN attacking to cultivated olive. Data increase the number of PPN associated with olive trees, being estimated in about 250 species documented worldwide Table 1 Olive orchards from cultivated olive in Andalusia (southern Spain) for detecting plant-parasitic nematodes. Olive growing areas in Andalusia have been classified into 70 biologically homogeneous zones based on environmental similarities [11]. Based on these zones, 376 commercial olive orchards were selected for this study. This was done in a way that the number of sampled olive orchards per biological zone was proportional to the total olive area in each zone.    (Table 1). Thus, 128 PPN species belonging to 38 genera and to 13 families were recorded, which highlights a high taxonomical diversity of PPN communities. However, it should be pointed out that species belonging to genus Filenchus were not included because of its feeding habits as plant feeding are not fully clarified [2]. Other PPN species such as Heterodera avenae, Pratylenchus neglectus, Pratylenchus thornei, Zygotylenchus guevarai or other species from the genera Ditylenchus, Heterodera and Globodera were included in the analysis although olive is not a suitable host for them but they were detected from the rhizosphere of olive tree and could be associated with host plants growing as cover crops in the orchards. The nematode abundance in each commercial olive orchard ranged from 7 to (O31) to 19,796 (O333) nematode specimens per 500 cm 3 of soil [1] ( Table 1). The number of PPN species per nematode family ranged from one in the case of the family Rotylenchulidae to 28 species for the family Longidoridae. Other families comprising species among the most damaging plant pathogens worldwide such as Meloidogynidae encompassed six sedentary endoparasite nematodes species (Meloidogyne spp.). The three most prevalent families were Tylenchidae, Paratylenchidae and Criconematidae, and the nematodes families with the highest average nematode densities were Meloidogynidae, Hoplolaimidae and Paratylenchidae. In fact, migratory ectoparasite PPN such as Helicotylenchus oleae and Ogma rhombosquamatum showed the highest nematode abundance (19,720 and 9800 nematodes per 500 cm 3 of soil, respectively); however, a rare (low prevalence) of sedentary endoparasitic PPN species such as Meloidogyne javanica was also detected at a high nematode abundance, i.e. 10,000 nematodes per 500 cm 3 of soil. The species

Sampling design
Data was obtained by systematic survey based on sampling design described by Archidona-Yuste et al. [1]. A total of 376 commercial olive orchards were selected across the entire olive area of Andalusia (Table 1). In brief, soil samples were collected from 2011 to 2016 during the spring season. In each commercial olive orchard, soil samples were taken from four to five healthy-looking trees that were georeferenced. Soil samples were collected with a hoe discarding the upper 5-cm top soil profile, from a 5-to 50-cm depth, in the close vicinity of active olive roots. In fact, we ensured that roots from other plants including weeds or other herbaceous plants were not included. Finally, all individual samples were thoroughly mixed to obtain a single representative sample per each commercial olive orchard before nematode extraction and physicochemical parameters determination [1].

Nematode extraction
From each soil sample, nematodes were extracted separately from two 250-cm 3 subsamples using magnesium sulfate centrifugal-flotation method [6,8]. Soil was washed thoroughly with tap water  [17]. c Prevalence was calculated as the percentage of samples in which a nematode species was diagnosed with respect to total number of samples. d Relative nematode wet biomass according to an adjusted Andrassy's formula [10]; relative biomass (mg) ¼ L x D2/1.600.000; where L is nematode body length (in mm). and D is nematode maximum body width (in mm). (*) Biomass based on second-stage juveniles. e SCBD: species contribution to beta diversity [12]. f Plant-parasitic nematodes species could be associated with cultivated and wild legumes growing as cover crops rather than with cultivated olives; as olive is not a suitable host for this PPN species [4].
through a 710-mm mesh sieve, and the filtered water was collected in a beaker and extensively mixed with 4% kaolin (v/v). This mixture was centrifuged at 1100Âg for 4 min, and the supernatants discarded.
Pellets were re-suspended in 250 ml MgSO4 (d ¼ 1.16) and the new suspensions were centrifuged at 1100Âg for 3 min. The supernatants were sieved through a 5 mm mesh, and nematodes collected on the sieve were washed with tap water [4]. Water solution containing nematodes collected from each of the two 250 cm 3 were mixed in a single one in order to carry out the diagnostic and identification of nematodes from a 500 cm 3 soil subsample.

Nematode identification
In order to select the PPN from the global nematode community in the soil, the nematode sample was poured into a counting dish (8 cm L x 8 cm W x 1.5 cm H), where they were identified and then, counted under a stereo-microscope (Leica MZ12; Leica Microsystems, Wetzler, Germany). PPN were identified to genus, and then we focused on the species delineation selecting adult nematode specimens which were fixed in a solution of 4% formaldehyde þ1% propionic acid and processed to pure glycerine using Seinhorst's method [9], and identified by morphological traits and molecular markers to species level. The morphological study at nematode species level was performed by classical diagnostic features using general and specific taxonomic keys from each nematode family and genus. However, the identification of nematode species based solely on morphological diagnostic is quite complex due to the occurrence of cryptic species and/or overlapping of morphological diagnostic characters among PPN species [5e7]. Therefore, polyphasic identification, based on an integrative taxonomy of combining both molecular and morphological techniques, was performed to get an efficient and reliable identification of PPN species (see Notes in Table 2).

Prevalence, abundance, biomass and species richness calculation
Prevalence was calculated by dividing the number of samples in which PPN species was detected by the total number of samples and expressed as a percentage. Total nematode abundance in each commercial orchard was calculated as the total number of specimens from all species identified per 500 cm 3 of soil for each commercial olive orchard. For each species identified, the abundance was calculated as the total number of specimens per 500 cm 3 of soil. Relative nematode individual fresh biomass was calculated according to an adjusted Andrassy's formula [10], wherein relative biomass (mg) ¼ L x D 2 * 1,600,000 À1 ; where L is nematode body length (in mm), and D is nematode maximum body width (in mm). Nematode size was determined with indications described by Archidona-Yuste et al., [1]. In addition, nematode species richness was determined for each olive orchard.