Metagenomic analysis reveals changes of the Drosophila suzukii microbiota in the newly colonized regions

Abstract

The spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a highly polyphagous pest of a wide variety of wild or cultivated berry and stone fruit. Originating from Southeast Asia, it has recently invaded a wide range of regions in Europe and North America. It is well known that insect microbiotas may significantly influence several aspects of the host biology and play an important role in invasive species introduction into new areas. However, in spite of the great economic importance of D. suzukii, a limited attention has been given so far to its microbiota. In this study, we present the first in-depth characterization of gut bacterial diversity from field (native and invasive range) and lab-reared populations of this insect. The gut bacterial communities of field insects were dominated, regardless of their origin, by 2 families of the phylum Proteobacteria: Acetobacteraceae and Enterobacteriaceae, while Firmicutes, mainly represented by the family Staphylococcaceae, prevailed in lab-reared population. Locality was the most significant factor in shaping the microbiota of wild flies. Moreover, a negative correlation between diversity and abundance of Enterobacteriaceae and the time elapsed since the establishment of D. suzukii in a new region was observed. Altogether our results indicate that habitat, food resources as well as the colonization phase of a new region contribute to shape the bacterial communities of the invasive species which, in turn, by evolving more quickly, could influence host adaptation in a new environment.

Nutrient-Dependent Impact of Microbes onDrosophila suzukiiDevelopment

“…The major bacteria identified in our sequencing data belonged to the families Comamonadaceae , Enterococcaceae , Lactobacillaceae , Leuconostocaceae , and Pseudomonadaceae , which were also detected previously in D. suzukii ( 32 , 33 ) and other Drosophila species ( 16 , 18 , 37 – 39 ). The fungi/yeasts isolated in this study were Candida , Hanseniaspora , Pichia , and Saccharomycetes sp., which are known to be prevalent in D. suzukii in the field, as well as in other Drosophila species ( 30 , 40 , 59 ).…”

“…Although associations with some higher taxonomic categories (such as Enterobacteriaceae , Acetobacteraceae , and Staphylococcaceae ) were repeatedly found in multiple studies, different populations harbored differing genera and species. For instance, among the members of the family Enterobacteriaceae , the dominant bacteria were Tatumella in a study by Chandler et al ( 31 ), Enterobacter and Lonsdalea in a study by Martinez-Sañudo et al ( 32 ), and Dickeya in our present study ( Fig. 2C ).…”

“…2C ). D. suzukii was reported to harbor different Acetobacteraceae species in different studies ( 31 – 33 ), but Acetobacteraceae species were not prevalent in our own sequencing results. A similar situation has been documented in D. melanogaster , where Acetobacteraceae species were present in one study ( 38 ) but absent in another ( 16 ).…”

“…The most abundant bacteria detected in wild D. suzukii flies were Lactobacillus , Leuconostoc , Lactococcus , Comamonadaceae , and Enterobacteriaceae ( Fig. 2C ), which were also prevalent in other Drosophila surveys ( 32 , 37 , 38 ). In laboratory-raised flies, the most abundant bacteria are Enterococcaceae ( 39 ), which corresponded to roughly 87% of the sequencing reads ( Fig.…”

“…Our study, along with several other reports on the bacterial community of D. suzukii ( 31 – 33 ), attempted to identify a core microbiota for D. suzukii . However, given the considerable amount of variation found among such investigations, we could not find a strictly defined core of bacterial species that are always associated with D. suzukii .…”