Comparative Microbiomics of Tephritid Frugivorous Pests (Diptera: Tephritidae) From the Field: A Tale of High Variability Across and Within Species

Abstract

The family Tephritidae includes some of the most notorious insect pests of agricultural and horticultural crops in tropical and subtropical regions. Despite the interest in the study of their gut microbiome, our present knowledge is largely based on the analysis of laboratory strains. In this study, we present a first comparative analysis of the gut microbiome profiles of field populations of ten African and Mediterranean tephritid pests. For each species, third instar larvae were sampled from different locations and host fruits and compared using 16S rRNA amplicon sequencing and a multi-factorial sampling design. We observed considerable variation in gut microbiome diversity and composition both between and within fruit fly species. A "core" microbiome, shared across all targeted species, could only be identified at most at family level (Enterobacteriaceae). At genus level only a few bacterial genera (Klebsiella, Enterobacter, and Bacillus) were present in most, but not all, samples, with high variability in their relative abundance. Higher relative abundances were found for seven bacterial genera in five of the fruit fly species considered. These were Erwinia in Bactrocera oleae, Lactococcus in B. zonata, Providencia in Ceratitis flexuosa, Klebsiella, and Rahnella in C. podocarpi and Acetobacter and Serratia in C. rosa. With the possible exception of C. capitata and B. dorsalis (the two most polyphagous species considered) we could not detect obvious relationships between fruit fly dietary breadth and microbiome diversity or abundance patterns. Similarly, our results did not suggest straightforward differences between the microbiome profiles of species belonging to Ceratitis and the closely related Bactrocera/Zeugodacus. These results provide a first comparative analysis of the gut microbiomes of field populations of multiple economically relevant tephritids and provide base line information for future studies that will further investigate the possible functional role of the observed associations.

New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

“…The diet of adult flies mainly includes plant exudates, honeydew and bird droppings scattered on leaves and fruits [58], while larvae develop in cucurbits [23]. This difference in dietary habits is reflected in the distinct microbial communities between developmental stages of the fly, especially between larval and adult stages [50,59]. However, regarding larvae, their microbiome did not seem significantly affected by different host plants [50].…”

“…Results suggest that the composition of the bacterial communities was significantly associated to the origin of the population. Changes in the structure of microbial communities among populations with different geographic distributions have been recorded in other Z. cucurbitae populations [ 16 , 50 ], but also in other fly species or insects [ 18 , 19 , 51 , 52 , 53 ]. Seasonal changes in climate conditions may shift the composition of the insect microbiome [ 54 ].…”

“…This difference in dietary habits is reflected in the distinct microbial communities between developmental stages of the fly, especially between larval and adult stages [ 50 , 59 ]. However, regarding larvae, their microbiome did not seem significantly affected by different host plants [ 50 ]. In our case, since samples were collected with traps placed in orchards with various cucurbit crops, it was difficult to assess the specific adult diet or larval host, and therefore their impact on the identified bacterial communities.…”

Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

“…Six out of 10 currently recognized Providencia species, namely P. rettgeri, P. stuartii, P. alcalifaciens, P. rustigianii, P. heimbachae and P. huaxiensis [ 1 ], were isolated from clinical samples [ 2 – 4 ] and comprise opportunistic human pathogens typically causing diarrhea [ 5 – 7 ] and urinary tract infections [ 8 ] that are often clinically complicated by multidrug resistance of the pathogen [ 9 – 12 ]. Moreover, bacteria assigned to the recognized Providencia species P. vermicola, P. rettgeri, P. alcalifaciens, P. sneebia, and P. burhodogranariaea [ 1 ] together with the recently proposed new species P. entomophila [ 13 ] have been found associated with or pathogenic to insects as honeybees [ 14 ], house and blow flies [ 15 , 16 ], the fly-parasitic wasp Nasonia vitripennis [ 17 ], and a diverse range of fruit flies [ 13 , 18 – 23 ].…”

Entomobacter blattae gen. nov., sp. nov., a new member of the Acetobacteraceae isolated from the gut of the cockroach Gromphadorhina portentosa

“…These results suggest that amplicon sequencing targeting the 16S rRNA V3–V4 regions, which is commonly used to examine the diversity of bacteria in a particular niche, may assign the genus Acetobacter to bacteria taxonomically closer to G55GP T . The genus Acetobacter is often identified by V3–V4 amplicon sequencing in insect guts, including beetles [41], fruit flies [42] and moths [43]. Although some fruit flies do actually harbour Acetobacter [44], it may well be that other insects carry bacteria more closely related to G55GP T .…”