Developmental stage-associated microbiota profile of the peach fruit fly, Bactrocera zonata (Diptera: Tephritidae) and their functional prediction using 16S rRNA gene metabarcoding sequencing

Abstract

The different developmental stage-associated microbiota of the peach fruit fly, Bactrocera zonata (Diptera: Tephritidae), was characterized using 16S rRNA gene (V3-V4 region) metabarcoding on the Illumina HiSeq platform. Taxonomically, at 97% similarity, there were total 16 bacterial phyla, comprising of 24 classes, 55 orders, 90 families and 134 genera. Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were the most abundant phyla with Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidia and Bacilli being the most abundant classes. The bacterial genus Enterobacter was dominant in the larval and adult stages and Pseudomonas in the pupal stage. A total of 2645 operational taxonomic units (OTUs) were identified, out of which 151 OTUs (core microbiota) were common among all the developmental stages of B. zonata. The genus Enterobacter, Klebsiella and Pantoea were dominant among the core microbiota. PICURSt analysis predicted that microbiota associated with B. zonata may be involved in membrane transport, carbohydrate metabolism, amino acid metabolism, replication and repair processes as well as in cellular processes and signalling. The microbiota that was shared by all the developmental stages of B. zonata in the present study could be targeted and the foundation for research on microbiota-based management of fruit flies.

Keywords: 16S rRNA gene; Bactrocera zonata; Management; Microbiota; Ontogeny.

Fig. 1

OTUs (Operational Taxonomic Units) analysis between different developmental stages of B. zonata at 97% similarity. a Venn diagram showing unique and shared OTUs, of which 151 OTUs shared between all developmental stages. b Percentage distribution of common shared OTUs (151 OTU) between all developmental stages at phylum level. BL1, BL3, BP and BF refers to first instar larvae, third instar larvae, pupa and adult female of Bactrocera zonata

Fig. 2

UPGMA clustering of B. zonata samples at different developmental stages according to community composition and structure with relative abundance of bacterial community at the phylum level. High-quality sequences obtained from different developmental stages were clustered in operational taxonomic units (OTUs) according to the open-reference method at a 97% of similarity. BL1, BL3, BP and BF refer to first instar larvae, third instar larvae, Pupa and Adult female of Bactrocera zonata

Fig. 3

Heat maps showing the relative abundances of 16S rRNA gene OTUs between different developmental stages, at family level. The colours indicate relative abundances ranging from green (lower abundances) to red (higher abundances) (indicated in a scale of − 1 to 1)

Fig. 4

Maximum likelihood tree constructed for phylogenetic analysis of most dominant taxa of bacterial community (on the basis of > 1% abundance of phylum in at least two developmental stages and present across all the developmental stage using 16S rRNA gene sequences) associated with the developmental stages of B. zonata. Bootstrap values were obtained from a search with 1000 replicates

Fig. 5

Predicted metabolic functions of bacterial communities associated with the different developmental stages of B. zonata. All of the predicted KEGG metabolic pathways are shown at the second hierarchical level and grouped by major functional categories