Introduction

Entomopathogenic nematodes (EPNs) Steinernematidae and Heterorhabditidae can control pests due to mutualistic association with bacteria of the genus Xenorhabdus (Thomas & Poinar) and Photorhabdus (Boemare, Louis & Kuhl), respectively1,2. These nematodes penetrate the host through natural openings or through the cuticle transporting bacteria into the hemocele3,4 where they reproduce and kill the host from septicemia within 24 to 48 hours5,6, making the environment favorable for nematode development and reproduction7. Infective juveniles seek another host in the soil when the insect host resources run out8. Interest in these biological control agents is increasing9 due to the reduced efficiency of conventional chemical and cultural methods for insect soil management and the broad spectrum of EPN hosts10.

EPNs are globally distributed, with different species and groups according to geographic regions11,12. Information on EPNs and their symbiotic bacteria is scarce in many countries, including in Brazil. Heterorhabditis amazonensis Andaló and Steinernema brasiliensis Nguyen were reported as native species in Brazil13,14 and Heterorhabditids indica and H. baujardi were reported in Rondônia state, Brazil15. Isolates of H. amazonensis, H. baujardi, H. indica and H. mexicana were found in Minas Gerais state, Brazil16,17.

Nematode species can be identified by molecular characterization based on sequencing of rDNA subunit (28S)18,19,20, because low morphological variation and similar characteristics within this group hamper identification15. Infectivity, environmental tolerance and suitability for commercial formulations vary between EPN isolates and species21,22 which can be used to control pests of various orders, such as Coleoptera23,24,25, Hemiptera26,27,28,29,30 and Lepidoptera31,32,33.

EPN identification, adapted to environmental and climatic conditions of cultivated areas is important for sustainable pest suppression in integrated management programs in agricultural areas of Brazil. The objective was to identify EPNs from agricultural soils with annual, fruit and perennial crops in Brazil.

Methods

Nematode collection

Soil samples were collected in agricultural areas in Barretos, Botucatu, Garça, São Manuel (São Paulo State), and Palotina (Paraná State), Brazil from 2010 to 2013. Thirty-seven samples were collected in areas with annual crops, [Glycine max (L.) Merrill, Zea mays (L.), Avena sativa (L.), Saccharum officinarum (L.) and irrigated Oryza sativa (L.)], 20 in areas with forest plantations [Anadenanthera falcata (Benth.) Speg.), Peltophorum dubium (Spreng.) Taub., Khaya ivorensis, Swietenia macrophylla, Hevea brasiliensis (L.), Eucalyptus spp., Cedrela odorata (L.), Acrocarpus fraxinifolius, Azadirachta indica (A. Juss.), Cordia ecalyculata (Vell), Calophyllum brasiliense (Cambess.) and Poecilanthe parviflora (Benth)], and 97 in areas with fruit [Litchi chinensis (Sonn.), Macadamia integrifolia (Maiden & Betche), Citrus reticulata (L.), Prunus persica (L.), Prunus sp., Psidium guajava (L.), Mangifera indica (L.), Citrus sinensis (L.), Citrus sp., Rubus idaeus (L.), Musa spp. and Coffea arabica (L.)]. In addition, four samples were collected in native forest, one in a pasture and 42 in plowed soil areas, totaling 201 samples.

A zero to 25 cm deep soil sample was taken per sampling point and placed in 2L labeled plastic bags, stored in a Styrofoam box and transferred to the laboratory. The geographical coordinates of each sample were obtained with Garmin GPS device Etrex Vista H 2.8. Nematodes were isolated in the laboratory using fifth instar Galleria mellonella Linnaeus (Lepidoptera: Pyralidae) larvae. Briefly, each soil sample was packed into a 250 mL a glass vial with five G. mellonella larvae. These vials were covered and stored without light at 25 ± 2 °C. After three to seven days, dead G. mellonella showing nematode infection symptoms were removed, rinsed in distilled water and transferred to White traps34. The infective juveniles (IJs) were again inoculated in G. mellonella larvae for multiplication. Five G. mellonella larvae were used in a Petri dish (9 cm diameter) containing two moistened paper filters with 1.5 mL of solution with 100 JIs/larvae, for each nematode species. The samples were covered with PVC plastic and stored at 25 ± 2 °C and RH > 80%35. After three days, dead larvae were transferred to a White trap34 at 25 ± 2 °C for seven and 15 days. The IJs that left the G. mellonella carcasses were collected with distilled water every two days and stored at 18 °C. The nematode samples were named FCA 01 to 14 and stored in the Entomopathogenic Nematode Bank of the Nematology Laboratory at FCA/UNESP. Vials contained 1 M NaCl solution and were frozen at −80 °C until DNA extraction and EPN identification.

PCR

Genomic DNA was obtained for each population (FCA 01 to 14) from three individuals of each EPN, extracted using Lysis Buffer Holterman [(HLB) (800 μg proteinase K/ml, β-mercaptoethanol 1% (v/v), 0.2 M NaCl and 0.2 M Tris HCl pH 8)]36. A total of 25 μL of HLB was diluted in 25 μL of ultrapure water totaling 50 μL in a 0.2 mL Eppendorff tube. A drop of this solution (5 μL) was placed on a glass slide, where the nematodes were individually cut into three parts and placed in the same 0.2 mL tube. The 45 μL of remaining solution was used to wash the slide and added to the tube with the sectioned nematode. Samples were submitted to PCR at 65 °C for 2 h, 99 °C for five minutes and stored at −20 °C37. The universal primers D2A (5′-CAAGTACCGTGAGGGAAAGTTG-3′) and D3B (5′TCGGAAGGAACCAGCTACT A-3′) were used to amplify the D2/D3 expansion segment of 28S rDNA by PCR38. A total of 12.5 μL of Gotaq Hot Start (Promega, São Paulo State, Brazil), with the reagents necessary for reaction: 5 U/μL Taq, 100 mM of each NTP and 25 mM MgCl2, 9.5 μL of nuclease free water (Promega), and 1 μL of each primer [10 mM] and 1 μL of cDNA from each representative population of target and non-target species, totaling 25 μL per reaction was submitted to pCR at 94 °C for seven minutes; followed by 35 cycles at 94 °C for 60 seconds, 55 °C for 60 seconds, 72 °C for 60 seconds; and 72 °C for 10 minutes39. Five μL of PCR product was used for electrophoresis in TAE buffer40 on 1% agarose gel, stained with ethidium bromide (0.02 mg/mL), visualized and photographed under UV light. The result of the amplification was compared to the molecular weight marker VIII.

The amplified fragments of D2/D3 expansion 28S rDNA were sequenced with the Big Dye Terminator kit (Applied Biosystems)41. A reagent mix containing 2 μL Big Dye, 3.2 mmol sense primers, 3.0 μL of amplified product containing 400 ng DNA and 2.0 mL of water was prepared for the product end of the PCR reaction. The reaction for sequencing was carried out according to manufacturer’s instructions (Applied Biosystems) with further purification of the amplified product by precipitation with isopropanol. Samples were denatured at 95 °C for three minutes and electrophoresis performed in an ABI Prism 377 DNA Sequencer unit (Applied Biosystems).

The sequences were aligned and compared to nucleotide polymorphism identification with the aid of BioEdit Aligment Sequence Editor Program. The EPN population sequences were compared with other nematode species in the database (GenBank, http://www.ncbi.nlm.nih.gov) for identification based on genetic similarity.

For phylogenetic analysis, the multiple alignments between the sequences of the region D2/D3 of the different isolates were edited manually with BioEdit Sequence Aligment program when phylogenetically uninformative columns were excluded from the analyses. Phylogenetic analyses were inferred using the Maximum Likelihood method based on the Kimura 2-parameter model42, considered the best fitting model for sequence evolution determined using the BIC scores (Bayesian Information Criterion) implemented in 6 MEGA program42. Initial trees for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (4 categories (+G, parameter = 2.3432)). The model variation rate allowed for some sites to be evolutionarily invariable ([+I], 19.1558% sites). The tree was drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 48 nucleotide sequences, including 16 obtained in the present study (FCA01 to FCA16) and 32 from the GenBank. All positions containing gaps and missing data were eliminated. A total of 292 positions was obtained in the final dataset. Trees were sampled at intervals of 1000 generations and Caenorhabditis elegans (Brenner) was selected as outgroup. Evolutionary analyses were conducted in 6 MEGA program42.

Results

The nematodes obtained from White traps were inoculated in new G. mellonela larvae, which demonstrates parasitism by the isolated entomopathogen. EPNs were found in 16 soil samples, corresponding to 8% of 201 samples. Seven (35%) of 20 samples from forest plantation areas had nematodes (FCA 04, FCA 05, FCA 06, FCA 07, FCA 08, FCA 10 and FCA 15). In annual crops, three (8.1%) out of 37 samples had nematodes: isolated FCA 11, detected in sandy soil in irrigated rice in Botucatu, São Paulo State, Brazil and isolates FCA 16 and FCA 03 in soybean crops in clay soils in Palotina, Paraná State, Brazil. Among 97 samples taken from orchards, six (6.2%) were positive for EPNs, FCA 12 isolates grown in sandy soils with wild raspberry, FCA 13 in citrus soil and FCA 14 in mango soil in São Manuel, São Paulo, Brazil. FCA 01 and FCA 02 isolates were also found in clay soil with citrus in Botucatu, São Paulo State, Brazil (Fig. 1). EPN samples were not found in plowed soil, native forest and pasture areas.

Figure 1: Geographical distribution of the sampling sites (x) in São Paulo and Paraná States, Brazil.
figure 1

EPNs positive samples (.) (ESC.: 1: 10000). AutoCAD SP2 (2015) [vJ.210.0.0]. http://www.Autodesk.com.br/products/autocad/overview.

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Amplification of D2/D3 expansion 28S rDNA gene of EPN isolates produced 590 bp fragments, whose sequences were deposited in the GenBank under the accession codes KRO11843 and KRO11858 (Fig. 2). The technique of DNA barcode sequences showed that the expansion D2/D3 28S rDNA gene of FCA 07 were identical to H. amazonensis (EU099036). The sequences of isolates FCA 01, FCA 04, FCA 06, FCA 08, FCA 15 and FCA 16 were identical to the Metarhabditis rainai (EU195966). The sequences of FCA 02, FCA 03 and FCA 05 isolates were identical to Oscheius tipulae (Lam & Webster, 1971) (EU195969). FCA 09, FCA 10, FCA 11, FCA 12, FCA 13 and FCA 14 isolates were observed (99–100%) with Steinernema rarum (AF331905). However, these isolates formed two groups that had three polymorphisms between them. One group with FCA 09, FCA 11 and FCA 12 isolates were similar to each other, but different in 3 bp from the group comprising FCA 10, FCA 13 and FCA 14 isolates. The phylogenetic tree (Fig. 2) obtained from the 48 aligned sequences of the D2/D3 expansion 28S rDNA genes in EPNs showed four distinct groups, H. amazonensis (FCA 07), S. rarum (FCA 09, FCA 10, FCA 11, FCA 12, FCA 13 and FCA 14), M. rainai (FCA 01, FCA 04, FCA 06, FCA 08, FCA 15 and FCA 16) and O. tipulae (FCA 02, FCA 03 and FCA 05).

Figure 2: Phylogenetic tree showing the relationship between the entomopathogenic nematodes isolated (in bold) and their similarity with those from the GenBank based on expansion D2/D3 sequences 28S rDNA region.
figure 2

Caenorhabditis elegans was used as outgroup.

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Heterorhabditis amazonensis was found in clay soil with P. parviflora in Garça, São Paulo State, Brazil; S. rarum in clay soil with Eucalyptus sp. and C. reticulata in Botucatu, São Paulo State, Brazil and in sandy soil with R. idaeus (FCA 12) and C. reticulata (FCA 13) and M. indica (FCA 14) in São Manuel, São Paulo State, Brazil.

Metarhabditis rainai was detected in clay soils cultivated with A. fraxinifolius, C. odorata, C. brasiliense and C. ecalyculata, in Garça, São Paulo State, Brazil and in those with C. reticulata, in Botucatu, São Paulo State, Brazil. Oscheius tipulae was found in soils with A. indica and C. reticulata in Botucatu, São Paulo State, Brazil and in clay soils cultivated with G. max, in Palotina, Paraná State. Brazil (Table 1).

Table 1 Code (Code), species, sampling site (Site), soil type (S), crops, geographical coordinates (coordinates) and collection date (date) of entomopathogenic nematodes (species) in soils with annual, fruit and forest plantation crops in Brazil (2010 to 2013).
Full size table

Discussion

Nematology surveys with G. mellonella baiting technique are useful to detect Steinernematidae and Heterorhabditidae species as well as other rhabditids. The molecular technique used was adequate to identify nematode isolates, enabling knowledge of its biodiversity and contributing to the detection of new isolates that may be used in biological control programs of insect pests.

The sequence of D2/D3 expansion 28S rDNA gene analysis by DNA barcode technique was useful for the diagnosis of H. amazonensis, S. rarum, M. rainai and O. tipulae. The phylogenetic tree obtained from the 48 aligned sequences of the expansion D2/D3 EPNs with four distinct groups support the molecular identification of these nematodes isolated from soil samples. This technique has been used to diagnose plant and animal parasites and entomopathogenic nematodes with accurate and reliable results, such as one Pratylenchus penetrans (Cobb) specimen in potato41, Bursaphelenchus fungivorus (Franklin & Hooper) in coconut fiber43, M. rainai (Carta & Osbrink) in soil cultivated with soybean44 and Metarhabditis blumi (Sudhaus) parasitizing the ear canal of cattle45.

The finding of H. amazonensis and S. rarum in seven (3.5%) of the 201 soil samples, shows the reduced occurrence of these organisms in Brazil compared to surveys in Western Canada (20%)46, Argentina (13.2%)47 and Spain (23.3%)48. However, the prevalence of 3.5%, of these species, is similar to surveys in Turkey (2%, 9.1%)25,49, Azores Archipelago, Portugal (3.9%)19 and Minas Gerais state, Brazil (9%)29. The absence of EPNs in plowed soil areas suggests inadequate conditions for nematode survival, but zero EPN detection in the natural forest was unexpected and may be due the low soil samples collected in this area. This result may also indicate the need for a higher number of samples taken at different soil depths. The species habitat and soil type affected EPNs recovery25,50. Our samples with nematodes were obtained from, clay (75%) and sandy (25%) soils, indicating the mobility and survival of EPNs in soils rich in sand, but S. rarum occurred in clay (FCA 09 and FCA 10) and sandy (FCA, 11, 12, 13 and 14) soils. Many EPNs positive samples (89.65%) were obtained in acid soils in Nepal51. Six EPNs were found in soils with PH < 4, which is uncommon, but this has also been reported in Belgium52. Steinernema spp. are widespread in different regions and niches, whereas Heterorhabditis spp. are common in forest and river banks53. Heterorhabditis and Steinernema species were found in Sandy soils with pH < 6, whereas representatives of Heterorhabditis, mainly in Sandy soils with pH > 6 were found on nine islands of Açores19.

Steinernema rarum detection in sandy soil with Rubus edaeus, Mangifera indica and Oryza sativa crops and clay soils with Citrus sp. and Eucalyptus sp. demonstrates the habitat diversity of this nematode, which has been detected in Olea europea L. crops in Argentina54, Carya illinoinensis orchards (Wangenh.) in Mississippi and Louisiana State, USA28 and in sandy soils with annual and forest cultures in China55. In Brazil, this nematode was detected in soils with Nicotiana tabacum L., Triticum aestivum L., Glycine max and in native vegetation56. Steinernema rarum showed desiccation tolerance and freezing intolerance57, features that may be related to its adaptation to Brazilian soils. This species has shown promise in biological control programs against Antonomus grandis Boheman (Coleoptera: Curculionidae) and Spodoptera frugiperda J.E. Smith (Lepidoptera: Noctuidae)27. Metarhabditis rainai detection in fruit orchards, annual crops and forest areas shows the broad habitat diversity of this nematode. This species was reported in Glycine max crop in Araras, São Paulo State, Brazil44. Other species, such as Metarhabditis blumi, are considered entomopathogenic and associated with the bacteria Alcaligenes faecalis Castellani & Chalmers, Flavobacterium sp. (Bernardet & Grimont) and Providencia vermicola (Somvanshi), which killed G. mellonella larvae58. Other genera, besides Heterorhabditis and Steinernema may feed on and kill insects44. Rhabditidae nematodes are usually bacteriophages, found in insect carrions59. However, M. rainai was described from specimens isolated from the Oscheios tipulae termite gut60 detected in soil samples and may parasitize insects and was also found to be associated with Tipula paludosa Meigen (Diptera: Tipulidae) larvae61. This nematode has been frequently isolated in soil samples from around the world, enabling species population62. Oscheius genus (Rhabditidae) includes free-living, vertebrate and invertebrate parasitic species63, such as Oscheios chongmingensis (Zhang), considered a facultative entomopathogenic nematode64. The bacteria symbiosis with this genus species is similar to that of Steinernematidae and Heterorhabditidae65.

EPNs identified in agricultural areas in Brazil were Heterorhabditis amazonensis, Metarhabditis rainai, Oscheios tipulae and Steinernema rarum. These species should be considered a pest biocontrol agent.

Additional Information

How to cite this article: de Brida, A. L. et al. Entomopathogenic nematodes in agricultural areas in Brazil. Sci. Rep. 7, 45254; doi: 10.1038/srep45254 (2017).

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