Diversity of Bacterial Communities in the Intestinal Tracts of Two Geographically Distant Populations of Bactrocera dorsalis (Diptera: Tephritidae)

Significant variations of bacterial communities among the developmental stages of Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae)

The yellow stemborer, Scirpophaga incertulas, is a monophagous pest of rice, attacking the crop from its vegetative to reproductive stages. Microorganisms are crucial in influencing the insect's life cycle, evolution, and ecology, presenting an avenue for understanding and improving management strategies. Present research employed advanced next-generation sequencing technology to investigate the microbiota of S. incertulas, a previously unexplored area for developmental stage associated microbial diversity. The study used 16 S rRNA V3-V4 region amplicon sequencing to determine the diversity of bacteria associated with different developmental stages of S. incertulas. Taxonomically, bacterial communities were classified into 25 phyla, encompassing 46 classes, 101 orders, 197 families, and 364 genera. The major phyla identified were Proteobacteria (39%), Firmicutes (39%), Actinobacteria (11%), and Bacteroidetes (7%), with Proteobacteria being the most predominant across all developmental stages except the larval stage, where Firmicutes took precedence. Moraxellaceae, Bacillaceae, Xanthomonadaceae, Sphingobacteriaceae, and Flavobacteriaceae were predominant families across all the developmental stages. However, in the egg and adult stages, the abundance of Bacillaceae was notably lower, whereas Prevotellaceae found significantly higher in adult stages. Dominant genera across all stages included Acinetobacter, Bacillus, Lactobacillus, Enterococcus, and Pseudomonas. The result showed that the highest number of Operational Taxonomic Units (OTUs) were in the larval stage (426 OTUs), the lowest in adults (251 OTUs), and the egg stage (254 OTUs). This suggests that the microbiota may play a role in the growth and development of S. incertulas. The predicted functional assessment of the associated S. incertulas microbiota revealed that the microbiota primarily participated in metabolic pathways, secondary metabolite biosynthesis, energy metabolism, signaling, and cellular processes. Our findings shed light on the significant variations in the microbial community and their predicted functions present in S. incertulas across developmental stages. The present study findings will help in developing novel microbiota-based management strategies.

Unveiling biogeographic patterns in the worldwide distributed Ceratitis capitata (medfly) using populations genomics and microbiome composition

Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean medfly, Ceratitis capitata, is one of the most damaging representatives of a group of rapidly expanding species in the Tephritidae family, due to their wide host range and high invasiveness potential. Here, we used restriction site-associated DNA sequencing (RADseq) to investigate the population genomic structure and phylogeographic history of medflies collected from six sampling sites, including Africa (South Africa), the Mediterranean (Spain, Greece), Latin America (Guatemala, Brazil) and Australia. A total of 1,907 single nucleotide polymorphisms (SNPs) were used to identify two genetic clusters separating native and introduced ranges, consistent with previous findings. In the introduced range, all individuals were assigned to one genetic cluster except for those in Brazil, which showed introgression of an additional genetic cluster that also appeared in South Africa, and which could not be previously identified using microsatellite markers. Moreover, we assessed the microbial composition variations in medfly populations from selected sampling sites using amplicon sequencing of the 16S ribosomal RNA (V4 region). Microbiome composition and structure were highly similar across geographic regions and host plants, and only the Brazilian specimens showed increased diversity levels and a unique composition of its microbiome compared to other sampling sites. The unique SNP patterns and microbiome features in the Brazilian specimens could point to a direct migration route from Africa with subsequent adaptation of the microbiota to the specific conditions present in Brazil. These findings significantly improve our understanding of the evolutionary history of the global medfly invasions and their adaptation to newly colonised environments.

Analysis of the Gut Bacterial Community of Wild Larvae of Anastrepha fraterculus sp. 1: Effect of Host Fruit, Environment, and Prominent Stable Associations of the Genera Wolbachia, Tatumella, and Enterobacter

The genus Anastrepha (Diptera Tephritidae) includes some of the most important fruit fly pests in the Americas. Here, we studied the gut bacterial community of 3rd instar larvae of Anastrepha fraterculus sp. 1 through Next Generation Sequencing (lllumina) of the V3-V4 hypervariable region within the 16S rRNA gene. Gut bacterial communities were compared between host species (guava and peach), and geographical origins (Concordia and Horco Molle in Argentina) representing distinct ecological scenarios. In addition, we explored the effect of spatial scale by comparing the samples collected from different trees within each geographic origin and host species. We also addressed the effect of fruit size on bacterial diversity. The gut bacterial community was affected both by host species and geographic origin. At smaller spatial scales, the gut bacterial profile differed among trees of the same species and location at least in one host-location combination. There was no effect of fruit size on the larval gut bacteriome. Operational Taxonomic Units (OTUs) assigned to Wolbachia, Tatumella and Enterobacter were identified in all samples examined, which suggest potential, non-transient symbioses. Better knowledge on the larval gut bacteriome contributes valuable information to develop sustainable control strategies against A. fraterculus targeting key symbionts as the Achilles' heel to control this important fruit fly pest.

Metagenomic Survey of the Highly Polyphagous Anastrepha ludens Developing in Ancestral and Exotic Hosts Reveals the Lack of a Stable Microbiota in Larvae and the Strong Influence of Metamorphosis on Adult Gut Microbiota

We studied the microbiota of a highly polyphagous insect, Anastrepha ludens (Diptera: Tephritidae), developing in six of its hosts, including two ancestral (Casimiroa edulis and C. greggii), three exotic (Mangifera indica cv. Ataulfo, Prunus persica cv. Criollo, and Citrus x aurantium) and one occasional host (Capsicum pubescens cv. Manzano), that is only used when extreme drought conditions limit fruiting by the common hosts. One of the exotic hosts (“criollo” peach) is rife with polyphenols and the occasional host with capsaicinoids exerting high fitness costs on the larvae. We pursued the following questions: (1) How is the microbial composition of the larval food related to the composition of the larval and adult microbiota, and what does this tell us about transience and stability of this species’ gut microbiota? (2) How does metamorphosis affect the adult microbiota? We surveyed the microbiota of the pulp of each host fruit, as well as the gut microbiota of larvae and adult flies and found that the gut of A. ludens larvae lacks a stable microbiota, since it was invariably associated with the composition of the pulp microbiota of the host plant species studied and was also different from the microbiota of adult flies indicating that metamorphosis filters out much of the microbiota present in larvae. The microbiota of adult males and females was similar between them, independent of host plant and was dominated by bacteria within the Enterobacteriaceae. We found that in the case of the “toxic” occasional host C. pubescens the microbiota is enriched in potentially deleterious genera that were much less abundant in the other hosts. In contrast, the pulp of the ancestral host C. edulis is enriched in several bacterial groups that can be beneficial for larval development. We also report for the first time the presence of bacteria within the Arcobacteraceae family in the gut microbiota of A. ludens stemming from C. edulis. Based on our findings, we conclude that changes in the food-associated microbiota dictate major changes in the larval microbiota, suggesting that most larval gut microbiota is originated from the food.

The composition of bacteria in gut and beebread of stingless bees (Apidae: Meliponini) from tropics Yunnan, China

Stingless bees are the main pollinators in tropical and subtropical regions. However, there are only a few studies on the structure and composition of bacteria in the gut and beebread of stingless bees, especially in China. To address this shortage of information, we characterized the microbiota of three common species of stingless bees (Lepidotrigona terminata, Lepidotrigona ventralis and Tetragonula pagdeni) and beebread samples of T. pagdeni. The results showed that the gut of stingless bees contained a set of dominant bacteria, including Acetobacter-like, Snodgrassella, Lactobacillus, Psychrobacter, Pseudomonas, Bifidobacterium and other species. The gut microbiota structures of the three stingless bees were different, and the abundances of bacterial species in the gut varied between communities of the same bee species. The reasons for this are manifold and may include food preference, age and genetic differences. In addition, the abundances of Lactobacillus, Carnimonas, Escherichia-Shigella, Acinetobacter and other species were high in the beebread of stingless bees. In conclusion, our findings reveal the bacteria composition and structure of the gut and beebread of stingless bees in China and deepen our understanding of the dominant bacteria of the gut and beebread of stingless bees.

New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

High Taxonomic and Functional Diversity of Bacterial Communities Associated with Melon Fly, Zeugodacus cucurbitae (Diptera: Tephritidae)

The next generation sequencing (NGS) approach has facilitated the investigations of gut microbiota with high throughput and resolution. The present study was focused on the taxonomic and functional characterization of bacterial community associated with different developmental stages of melon fly, Zeugodacus cucurbitae using 16S ribosomal RNA (rRNA) gene amplicons metagenomics. Z. cucurbitae is considered an invasive and most staid polyphagous pest of cucurbitaceous and other related crops. The taxonomic analysis of highly variable V3-V4 region of bacterial 16S rRNA gene sequencing indicated that the bacterial community associated with Z. cucurbitae consists of a total of 23 bacterial phyla (including unclassified and unassigned bacteria), comprising 32 classes, 69 orders, 99 families and 130 genera. Proteobacteria, Firmicutes, Actinobacteria and Tenericutes were dominant phyla of which family, Enterobacteriaceae was the most abundant in the larval and adult female stages, whereas Mycoplasmataceae was the dominant in the pupal stage. In larval stages of Z. cucurbitae, genus Providencia and Comamonas were the most abundant. However, genus Candidatus-Bacilloplasma and Klebsiella were the most dominant in pupae and adult females of Z. cucurbitae, respectively. PICRUSt analysis conducted for prediction of metabolic activities revealed that associated microbiota were involved in membrane transport, carbohydrate metabolism, amino acid metabolism, energy metabolism, replication and repair processes as well as cellular processes and signalling. The higher number of OTUs was annotated for phosphoglycerate mutase and transketolase in adult females followed by larval stages, which may support the digestive function of the microbiota in larvae and adult females. Our findings provide insights about the high variation in microbiota across developmental stages and basis for microbiota-based management strategies of fruit flies.

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

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.

Differential abundance and core members of the bacterial community associated with wild male Zeugodacus cucurbitae fruit flies (Insecta: Tephritidae) from three geographical regions of Southeast Asia

Zeugodacus cucurbitae (Coquillet) is one of the most significant and widespread tephritid pest species of agricultural crops. This study reports the bacterial communities associated with Z. cucurbitae from three geographical regions in Southeast Asia (Thailand, Peninsular Malaysia, and Sarawak). The bacterial microbiota were investigated by targeted 16S rRNA gene (V3-V4 region) sequencing using the Illumina Mi-Seq platform. At 97% similarity and filtering at 0.001%, there were seven bacterial phyla and unassigned bacteria, comprising 11 classes, 23 orders, 39 families and 67 genera. The bacterial diversity and richness varied within and among the samples from the three geographical regions. Five phyla were detected for the Sarawak sample, and six each for the Thailand and Peninsular Malaysia samples. Four phyla-Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria-were represented in all the fruit fly specimens, forming the core members of the bacterial community. Proteobacteria was the predominant phylum, followed by Bacteroidetes, Firmicutes, and Actinobacteria. Fifty-three genera were represented in the Thailand sample, 56 in the Peninsular Malaysia sample, and 55 in the Sarawak sample. Forty-two genera were present in all the three geographical regions. The predominant core members were order Enterobacteriales (Proeteobacteria), and family Enterobacteriaceae (Enterobacteriales). Klebsiella (Enterobacteriaceae) was the predominant genus and K. oxytoca the predominant species with all specimens having > 10% relative abundance. The results indicate the presence of a great diversity as well as core members of the bacterial community associated with different populations of Z. cucurbitae.