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Near Full-Length 16S Rrna Gene Next-Generation Sequencing Deutscher et al. Microbiome (2018) 6:85 https://doi.org/10.1186/s40168-018-0463-y RESEARCH Open Access Near full-length 16S rRNA gene next- generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae Ania T. Deutscher1,2*, Catherine M. Burke4, Aaron E. Darling3, Markus Riegler5, Olivia L. Reynolds1,2 and Toni A. Chapman1 Abstract Background: Gut microbiota affects tephritid (Diptera: Tephritidae) fruit fly development, physiology, behavior, and thus the quality of flies mass-reared for the sterile insect technique (SIT), a target-specific, sustainable, environmentally benign form of pest management. The Queensland fruit fly, Bactrocera tryoni (Tephritidae), is a significant horticultural pest in Australia and can be managed with SIT. Little is known about the impacts that laboratory-adaptation (domestication) and mass-rearing have on the tephritid larval gut microbiome. Read lengths of previous fruit fly next-generation sequencing (NGS) studies have limited the resolution of microbiome studies, and the diversity within populations is often overlooked. In this study, we used a new near full-length (> 1300 nt) 16S rRNA gene amplicon NGS approach to characterize gut bacterial communities of individual B. tryoni larvae from two field populations (developing in peaches) and three domesticated populations (mass- or laboratory-reared on artificial diets). Results: Near full-length 16S rRNA gene sequences were obtained for 56 B. tryoni larvae. OTU clustering at 99% similarity revealed that gut bacterial diversity was low and significantly lower in domesticated larvae. Bacteria commonly associated with fruit (Acetobacteraceae, Enterobacteriaceae,andLeuconostocaceae)weredetectedinwild larvae, but were largely absent from domesticated larvae. However, Asaia, an acetic acid bacterium not frequently detected within adult tephritid species, was detected in larvae of both wild and domesticated populations (55 out of 56 larval gut samples). Larvae from the same single peach shared a similar gut bacterial profile, whereas larvae from different peaches collected from the same tree had different gut bacterial profiles. Clustering of the Asaia near full- length sequences at 100% similarity showed that the wild flies from different locations had different Asaia strains. Conclusions: Variation in the gut bacterial communities of B. tryoni larvae depends on diet, domestication, and horizontal acquisition. Bacterial variation in wild larvae suggests that more than one bacterial species can perform the same functional role; however, Asaia could be an important gut bacterium in larvae and warrants further study. A greater understanding of the functions of the bacteria detected in larvae could lead to increased fly quality and performance as part of the SIT. Keywords: Diptera, Tephritidae, Bactrocera tryoni, Sterile insect technique, Host–microbe interactions, Insect–microbe interactions, Illumina, Microbiota, Microbial symbiont, Acetic acid bacteria * Correspondence: [email protected] Olivia L. Reynolds and Toni A. Chapman are joint senior authors. 1Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia 2Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia Full list of author information is available at the end of the article © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Deutscher et al. Microbiome (2018) 6:85 Page 2 of 22 Background Ceratitis capitata (Tephritidae) used in SIT programs Globally, some of the most economically damaging significantly reduced fly developmental time (egg to horticultural pests are fruit flies of the family Tephriti- pupae and egg to adult), but not at the expense of fly dae (Diptera). In Australia, the Queensland fruit fly, quality [20]. It also increased pupal weight, longevity, Bactrocera tryoni (Tephritidae), is a significant economic morphometric traits (greater head width, abdomen, and pest that causes losses due to damage of horticultural thorax length), mating competitiveness under laboratory produce, while also restricting domestic and inter- conditions, and spermatozoa storage in females [21]. national market access [1]. Bactrocera tryoni is highly Therefore, addition of probiotic bacteria may be a means polyphagous, with females ovipositing and larvae devel- of restoring or improving gut bacteria to positively influ- oping in a large range of host fruits and fruiting vegeta- ence fly production and performance. bles [2–4]. The larvae and bacteria introduced into the To appreciate how insect–microbe interactions can fruit during oviposition cause the fruit to rapidly decay impact the quality and competitiveness of mass-reared [5]. Although B. tryoni originated from tropical and sub- B. tryoni for SIT programs, it is necessary to determine tropical regions of Australia, its range has expanded fur- how the gut bacterial diversity and community compos- ther down the east coast of Australia with increasing ition of laboratory- and mass-reared B. tryoni differs to detections further inland. It is now established in New that of wild flies. Knowledge of the diversity within pop- South Wales and Victoria, apart from the Greater ulations is also required to identify “core” bacteria and Sunraysia Pest-Free Area [6]. Outbreaks also occur infre- provide context to the differences in gut microbial quently in South Australia and Western Australia [6, 7]. communities between populations. Previously, next- Severe restrictions or withdrawal of two of the most ef- generation sequencing (NGS) was employed to identify fective agrochemicals against B. tryoni, fenthion and di- the microbiome of adult domesticated and wild B. tryoni methoate, requires alternative control options to be populations on a 454 pyrosequencing platform [19]. The available to growers [8, 9]. The sterile insect technique study, by Morrow et al. (2015), detected shifts in the (SIT) is a species-specific, sustainable, environmentally types of bacteria present and their relative abundance benign pest management strategy that involves mass- between laboratory-reared flies and their wild counter- rearing of the target insects. The insects are irradiated to parts, but only analyzed the bacterial communities of render them sterile prior to release in the field, where whole adult female flies and did not look at the diversity the sterile males copulate with wild females of the target in larvae and between individuals within populations. pest population and are unable to produce viable off- Pooling of samples and analysis of only a small number spring [10]. Over time and with repeated releases of ster- of sample pools, as well as the NGS of short amplicons, ile flies, the pest population is suppressed or may be limited the ability to characterize the relative abundance eradicated within the release area. of taxa and the identification of core bacteria across B. The quality and performance of the released sterile in- tryoni individuals. sects are critical to the cost efficiency and efficacy of SIT Very few “core” bacterial species have been identified programs. By impacting on host nutrition, physiology, in tephritids. Unculturable “Candidatus Erwinia daci- metabolism, and immunity, gut microbiota can pro- cola” is an important symbiont of olive fly, Bactrocera foundly influence various aspects of insect health, fit- oleae (Tephritidae), in field populations, as it helps the ness, and behavior [11, 12]. As a result, changes in gut larvae overcome plant chemical defense mechanisms microbiota associated with fruit fly domestication, mass- and develop in unripe olives [14]. Acetobacter tropicalis rearing, and sterilization are also likely to impact the was reported as highly prevalent and part of the “core” quality of fruit flies produced for SIT programs. microbiota of B. oleae in one study [22], but was not de- Fruit flies reared under artificial conditions are no lon- tected in other recent studies [14, 23]. Identifying other ger exposed to the microorganisms present in their nat- important, possible “core” symbionts of fruit flies has ural environment. In addition, artificial larval diets been limited due to studies not reporting on bacterial typically contain antimicrobials and have a low pH to community variation within fruit fly populations as a re- control bacterial and fungal contamination [13]. Conse- sult of analyzing either only a single sample, pooling quently, laboratory- or mass-reared adult fruit flies (in- samples, or only a very small total number of individual cluding Drosophila) are reported to have decreased gut samples from a limited number of populations. At a microbial diversity and density compared to wild flies higher level, Enterobacteriaceae are found in the major- [14–16]. Shifts in bacterial
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