Metagenomic ecosystem monitoring of soft scale insects and mealybug communities

Soft scale insects and mealybugs are phloem-feeding Hemipterans that are considered major pests in agriculture and horticulture throughout the world. However, correct taxonomic identification in the field can be difficult, making it hard for growers to implement control strategies. In viticulture, soft scale insects are a major issue due to their ability to secrete honeydew, which facilitates the development of sooty mould, and their propensity for being transmission vectors of several viral diseases of grapevine. To facilitate the rapid identification and quantification of vineyard-associated insects a metagenomic-based bioinformatic pipeline (MitoMonitor) was developed for generalised ecosystem monitoring, which automated the assembly and classification of insect mitochondrial genomes from shotgun sequencing data using the Barcode of Life Database API. The proof-of-concept application of MitoMonitor on metagenomic data obtained from eight samples from South Australian vineyards led to the identification of Parthenolecanium corni (European fruit scale)—which was thought to be absent in Australian vineyards—as the dominant coccoid species across the samples, with less frequent, and also lower abundance of Pseudococcus viburni (obscure mealybug) and Pseudo. longispinus (long-tailed mealybug). In addition, parisitoidism by Coccophagus scutellaris (Aphelinidae) wasps was also detected. The discovery of Parth. corni as a member of scale communities in these samples has significant implications for the development of effective control strategies for this important group of pests in affected areas.