Metabarcoding of nematode communities associated with Ananas comosus L. (Pineapple)

Plant-parasitic nematodes are serious pests causing important crop losses worldwide. Hence, this study was conducted to determine the occurrence of plant-parasitic nematodes (PPNs) in healthy and unhealthy pineapple crops. To determine if the infestation is prevalent, a soil metabarcoding analysis was done. Six soil samples were obtained from the rhizospheres of Red Spanish pineapple farm in Mabitac, Laguna, Philippines. They were freeze-dried and brought to the laboratory for metagenomics analysis using Primers NemF and 18Sr2b. The results showed uncultured Eukaryotes (43.1%) nematodes (31.2%), Platyhelminthes (6.9%), Apicomplexa (6.5%), Annelida (5.0%), Rotifera (3.6%), Arthropoda (1.8%), Ascomycota (1%), unidentified (0.4%) and Basillariophyta, Cercozoa, Chytridiomycota, Mollusca and Mucoromycota with 0.1%. In total, 374,410 sequence reads were obtained and were clustered into 117 OTUs at 97% similarity. In assessing the nematode community structure, it yielded 26,565 nematodes; 5,315 nematodes were obtained from the rhizosphere of healthy samples, and 21,250 were from the unhealthy ones. The fungivore Apelenchus avenae (Bastian 1865) was the most prevalent (47.8% and 43.9%) in both locations. Other nematodes found on the plant rhizospheres were Rhabdolaimus aquaticus (de Man), Acrobeloides varius, Rotylenchulus reniformis (Linford and Oliveira, 1940), Aphelenchoidinae sp., Panagrolaimoidea sp., and two unidentified nematodes. The Basiria sp., Alaimus sp., and two other unidentified nematodes were the only ones found in the rhizosphere of unhealthy pineapple plants. Meanwhile, Mesocriconema onoense, Aphelenchoides sp., Ditylenchus gilanicus, and an unidentified nematode were found in the rhizosphere of healthy pineapple plants. Phylogenetic analyses of the nematode communities show that only Orders Rhabditida and Enoplida are associated with the crop and the Family Aphelenchoididae is distant from Rhabditida, thus, dividing the clade into three. The first clade consists of diverse nematode communities of fungivores, bacterivores, predators, and plant and insect parasites. The second clade consists of bacterivore nematodes found in moist environments, and the third clade comprises mainly Aphelenchoididae species, mostly plant parasites.