Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae

Assessing the impact of diet formulation and age on targeted bacterial establishment in laboratory and mass-reared Mediterranean fruit fly using full-length 16S rRNA sequencing

Insect gut microbiota play important roles in host health and interactions with the environment. In laboratory and mass-reared insects, gut microbiomes can differ in composition and function compared to wild conspecifics. For fruit flies, such as the Mediterranean fruit fly (medfly; Ceratitis capitata), these changes can influence male performance and behavior. Overall, understanding factors that influence the ability of bacteria to establish in hosts is important for the establishment of lost or novel microbiota in mass-reared insects. The goal of this study was to evaluate how host age and diet-inoculation method influenced bacterial establishment in laboratory and mass-reared medflies. We used an Enterobacter strain with antibiotic resistance and coupled it with full-length PacBio Kinnex 16S rRNA sequencing to track the establishment of the specific isolates under different adult dietary conditions. We also used two longstanding reared lines of medfly in our study. Our results identified that diet had a strong interaction with age. The target bacterial isolate was detected in medfly when inoculated with liquid diet regardless of age, but those fed a slurry-based diet and a separate water source had less establishment. This was consistent for both fly rearing lines used in the study. 16S rRNA sequencing corroborated the establishment of the specific strain but also revealed some species/strain-level variation of Enterobacter sequences associated with the flies. Additionally, our study illustrates that long-read 16S rRNA sequencing may afford improved characterization of species- and strain-level distribution of Enterobacteriaceae in insects.

IMPORTANCE

Insects form intimate relationships with gut microorganisms that can help facilitate several important roles. The goal of our study was to evaluate factors that influence microbial establishment in lines of the Mediterranean fruit fly (medfly), an important pest species worldwide. Mass-reared insects for the sterile insect technique often possess gut microbiomes that substantially differ from wild flies, which can impact their performance in pest control contexts. Here, we show that liquid-based formulations can be utilized to manipulate the gut microbiota of mass-reared medflies. Furthermore, using near full-length 16S rRNA metabarcoding sequencing, we uncovered strain-level diversity that was not immediately obvious using other approaches. This is a notable finding, as it suggests that full-length 16S rRNA approaches can have marked improvements for some taxa compared to fewer hypervariable regions at approximately the same cost. Our results provide new avenues for exploring and interrogating medfly-microbiome interactions.

The Role of Gut Microbiota in Shaping Immune Responses in Tephritidae Fruit Fly and Prospective Implications for Management

The interaction of microbial communities with host immunity has become one of the most explored research areas with significant implications for pest control strategies. It has been found that the gut microbiota plays substantial roles in immune response regulation and host-gut microbiome symbiosis, as well as in pathogen resistance and overall fitness in Tephritidae fruit flies that are major pests of agricultural importance. In this review, we discuss the modulation of immune responses of Tephritidae fruit flies by the gut microbiota with particular emphasis on the general interactions between microbiota and the immune system. These interactions help to unravel new horizons of pest management. Regulating gut microbiota modifies the performance of biological control agents and SIT and allows the creation of microbial therapies that affect the vital physiological functions of fruit flies. Besides, deploying microbes that can modulate the immune response and using microbial-derived signals provide an eco-friendly and more sustainable way of eradicating chemical pesticides and making farming systems less susceptible to climatic variability. This paper reviews various aspects of the possibility of using gut microbiota for changing the approach to Integrated Pest Management (IPM) programs that would improve methods of controlling Tephritidae fruit fly populations more ecologically.

Effects of Gut Bacteria on the Fitness of Rice Leaf Folder Cnaphalocrocis medinalis

The rice leaf folder Cnaphalocrocis medinalis is an important migratory pest in Asia. Although this pest possesses diverse bacterial communities in its gut, functions of these bacteria in modulating host fitness, including development durations, pupal weight, adult longevity, and fecundity, remain unknown. We isolated gut bacteria from field-collected C. medinalis larvae using a culture-dependent method and identified 15 bacterial isolates. Six of the isolates (Klebsiella aerogenes, Klebsiella pneumoniae, Enterobacter ludwigii, Enterobacter asburiae, Pantoea dispersa, and Pantoea ananatis) were newly discovered in C. medinalis. When larvae were orally inoculated with individual bacterial isolates, 15 isolates showed varying degrees of effects on C. medinalis fitness. Importantly, we found that 10 bacterial isolates induced significant larval mortality. Specifically, the inoculation of Pseudomonas mosselii, P. dispersa, Chryseobacterium culicis, P. ananatis, and Myroides odoratus caused high mortality ranging from 40.0% to 56.7%. However, reducing the entire gut bacterial community with antibiotic treatment negatively impacted C. medinalis fitness, while the reinoculation of a bacterial community to antibiotic-treated larvae recovered some of the adverse effects. In particular, control and bacterial community-inoculated C. medinalis laid approximately 37.6% more eggs than antibiotic-treated C. medinalis. This suggests that these bacteria affect their hosts differently when they are together as compared to alone. Our results reveal that C. medinalis harbors gut bacteria capable of both mutualistic and pathogenic interactions, suggesting their potential as biocontrol agents and indicating that targeting the gut bacterial community could be an effective strategy for controlling C. medinalis infestations.

Advancements in the Impact of Insect Gut Microbiota on Host Feeding Behaviors

With the application and development of high-throughput sequencing technology, the structure and function of insect gut microbiota have been analysed, which lays a foundation for further exploring the intricate relationships between gut microbiota and host feeding behaviour. The microbial community in the insect gut, as an important ecological factor, affects the host's food selection and nutritional metabolic processes through various mechanisms, which play a key role in population dynamics and ecosystems. The implications of these interactions are profound, affecting agricultural practices, biodiversity, and the broader environment, such as pollination and pest control. In-depth exploration of the molecular mechanism of the interaction between gut microbiota and hosts contributes to the grasp of insect biology and evolution and offers novel avenues for manipulating insect behaviour for practical applications in agriculture and environmental management. This paper focuses on the possible mechanisms of insect gut microbiota regulating host feeding behaviour. It inspires further research on the interaction between gut microbiota and insects affecting host behaviour.

Resistance to preservatives and the viable but non-culturable state formation of Asaia lannensis in flavored syrups

Food security is a crucial issue that has caused extensive concern, and the use of food flavors has become prevalent over time. we used the molecular biological techniques, preservative susceptibility testing, viable but non-culturable (VBNC) state induction testing, and a transcriptome analysis to examine the bacterial contamination of favored syrup and identify the causes and develop effective control measures. The results showed that Asaia lannensis WLS1-1 is a microorganism that can spoil food and is a member of the acetic acid bacteria families. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) tests showed that WLS1-1 was susceptible to potassium sorbate (PS), sodium benzoate (SB), and sodium sulffte (SS) at pH 4.0. It revealed a progressive increase in resistance to these preservatives at increasing pH values. WLS1-1 was resistant to PS, SB and SS with an MIC of 4.0, 2.0 and 0.5  g/L at pH 5.0, respectively. The MIC values exceed the maximum permissible concentrations that can be added. The induction test of the VBNC state demonstrated that WLS1-1 lost its ability to grow after 321 days of PS induction, 229  days of SB induction and 52  days of SS induction combined with low temperature at 4°C. Additionally, laser confocal microscopy and a propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) assay showed that WLS1-1 was still alive after VBNC formation. There were 7.192 ± 0.081 (PS), 5.416 ± 0.149 (SB) and 2.837 ± 0.134 (SS) log10(CFU/mL) of viable bacteria. An analysis of the transcriptome data suggests that Asaia lannensis can enter the VBNC state by regulating oxidative stress and decreasing protein synthesis and metabolic activity in response to low temperature and preservatives. The relative resistance of Asaia lannensis to preservatives and the induction of the VBNC state by preservatives are the primary factors that contribute to the contamination of favored syrup by this bacterium. To our knowledge, this study represents the first evidence of the ability of Asaia lannensis to enter the VBNC state and provides a theoretical foundation for the control of organisms with similar types of activity.

Exploring the gut microbiota in patients with pre-diabetes and treatment naïve diabetes type 2 - a pilot study

BACKGROUND

Compared to their healthy counterparts, patients with type 2 diabetes (T2D) can exhibit an altered gut microbiota composition, correlated with detrimental outcomes, including reduced insulin sensitivity, dyslipidemia, and increased markers of inflammation. However, a typical T2D microbiota profile is not established. The aim of this pilot study was to explore the gut microbiota and bacteria associated with prediabetes (pre-T2D) patients, and treatment naïve T2D patients, compared to healthy subjects.

METHODS

Fecal samples were collected from patients and healthy subjects (from Norway). The bacterial genomic DNA was extracted, and the microbiota analyzed utilizing the bacterial 16S rRNA gene. To secure a broad coverage of potential T2D associated bacteria, two technologies were used: The GA-map® 131-plex, utilizing 131 DNA probes complementary to pre-selected bacterial targets (covering the 16S regions V3-V9), and the LUMI-Seq™ platform, a full-length 16S sequencing technology (V1-V9). Variations in the gut microbiota between groups were explored using multivariate methods, differential bacterial abundance was estimated, and microbiota signatures discriminating the groups were assessed using classification models.

RESULTS

In total, 24 pre-T2D patients, 18 T2D patients, and 52 healthy subjects were recruited. From the LUMI-Seq™ analysis, 10 and 9 bacterial taxa were differentially abundant between pre-T2D and healthy, and T2D and healthy, respectively. From the GA-map® 131-plex analysis, 10 bacterial markers were differentially abundant when comparing pre-T2D and healthy. Several of the bacteria were short-chain fatty acid (SCFA) producers or typical opportunistic bacteria. Bacteria with similar function or associated properties also contributed to the separation of pre-T2D and T2D from healthy as found by classification models. However, limited overlap was found for specific bacterial genera and species.

CONCLUSIONS

This pilot study revealed that differences in the abundance of SCFA producing bacteria, and an increase in typical opportunistic bacteria, may contribute to the variations in the microbiota separating the pre-T2D and T2D patients from healthy subjects. However, further efforts in investigating the relationship between gut microbiota, diabetes, and associated factors such as BMI, are needed for developing specific diabetes microbiota signatures.

Comparison of gut bacterial communities of Hyphantriacunea Drury (Lepidoptera, Arctiidae), based on 16S rRNA full-length sequencing

There are a large number of microorganisms in the gut of insects, which form a symbiotic relationship with the host during the long-term co-evolution process and have a significant impact on the host's nutrition, physiology, development, immunity, stress tolerance and other aspects. However, the composition of the gut microbes of Hyphantriacunea remains unclear. In order to investigate the difference and diversity of intestinal microbiota of H.cunea larvae feeding on different host plants, we used PacBio sequencing technology for the first time to sequence the 16S rRNA full-length gene of the intestinal microbiota of H.cunea. The species classification, β diversity and function of intestinal microflora of the 5th instar larvae of four species of H.cunea feeding on apricot, plum, redbud and Chinese ash were analysed. The results showed that a total of nine phyla and 65 genera were identified by PacBio sequencing, amongst which Firmicutes was the dominant phylum and Enterococcus was the dominant genus, with an average relative abundance of 59.29% and 52.16%, respectively. PERMANOVA analysis and cluster heat map showed that the intestinal microbiomes of H.cunea larvae, fed on different hosts, were significantly different. LEfSe analysis confirmed the effect of host diet on intestinal community structure and PICRUSt2 analysis showed that most of the predictive functions were closely related to material transport and synthetic, metabolic and cellular processes. The results of this study laid a foundation for revealing the interaction between the intestinal microorganisms of H.cunea and its hosts and provided ideas for exploring new green prevention and control strategies of H.cunea.

Bacterial Community Survey of Wolbachia-Infected Parthenogenetic Parasitoid Trichogramma pretiosum (Hymenoptera: Trichogrammatidae) Treated with Antibiotics and High Temperature

Wolbachia has been shown to induce thelytokous parthenogenesis in Trichogramma species, which have been widely used as biological control agents around the world. Little is known about the changes of bacterial community after restoring arrhenotokous or bisexual reproduction in the T. pretiosum. Here, we investigate the emergence of males of T. pretiosum through curing experiments (antibiotics and high temperature), crossing experiments, and high-throughput 16S ribosomal RNA sequencing (rRNA-seq). The results of curing experiments showed that both antibiotics and high temperatures could cause the thelytokous T. pretiosum to produce male offspring. Wolbachia was dominant in the thelytokous T. pretiosum bacterial community with 99.01% relative abundance. With the relative abundance of Wolbachia being depleted by antibiotics, the diversity and relative content of other endosymbiotic bacteria increased, and the reproductive mode reverted from thelytoky to arrhenotoky in T. pretiosum. Although antibiotics did not eliminate Wolbachia in T. pretiosum, sulfadiazine showed an advantage in restoring entirely arrhenotokous and successive bisexual reproduction. This study was the first to demonstrate the bacterial communities in parthenogenetic Trichogramma before and after antibiotics or high-temperature treatment. Our findings supported the hypothesis that Wolbachia titer-dependence drives a reproduction switch in T. pretiosum between thelytoky and arrhenotoky.

Microbial diversity in stingless bee gut is linked to host wing size and influenced by the environment

Stingless bees are important social corbiculate bees, fulfilling critical pollination roles in many ecosystems. However, their gut microbiota, particularly the fungal communities associated with them, remains inadequately characterised. This knowledge gap hinders our understanding of bee gut microbiomes and their impacts on the host fitness. We collected 121 samples from two species, Tetragonula carbonaria and Austroplebeia australis across 1200 km of eastern Australia. We characterised their gut microbiomes and investigated potential correlations between bee gut microbiomes and various geographical and morphological factors. We found their core microbiomes consisted of the abundant bacterial taxa Snodgrassella, Lactobacillus and Acetobacteraceae, and the fungal taxa Didymellaceae, Monocilium mucidum and Aureobasidium pullulans, but variances of their abundances among samples were large. Furthermore, gut bacterial richness of T. carbonaria was positively correlated to host forewing length, an established correlate to body size and fitness indicator in insects relating to flight capacity. This result indicates that larger body size/longer foraging distance of bees could associate with greater microbial diversity in gut. Additionally, both host species identity and management approach significantly influenced gut microbial diversity and composition, and similarity between colonies for both species decreased as the geographic distance between them increased. We also quantified the total bacterial and fungal abundance of the samples using qPCR analyses and found that bacterial abundance was higher in T. carbonaria compared to A. australis, and fungi were either lowly abundant or below the threshold of detection for both species. Overall, our study provides novel understanding of stingless bee gut microbiomes over a large geographic span and reveals that gut fungal communities likely not play an important role in host functions due to their low abundances.

Symbiotic Microorganisms and Their Different Association Types in Aquatic and Semiaquatic Bugs

True bugs (Hemiptera, suborder Heteroptera) constitute the largest suborder of nonholometabolous insects and occupy a wide range of habitats various from terrestrial to semiaquatic to aquatic niches. The transition and occupation of these diverse habitats impose various challenges to true bugs, including access to oxygen for the aquatic species and plant defense for the terrestrial phytophagans. Although numerous studies have demonstrated that microorganisms can provide multiple benefits to terrestrial host insects, a systematic study with comprehensive higher taxa sampling that represents aquatic and semiaquatic habitats is still lacking. To explore the role of symbiotic microorganisms in true bug adaptations, 204 samples belonging to all seven infraorders of Heteroptera were investigated, representing approximately 85% of its superfamilies and almost all known habitats. The symbiotic microbial communities of these insects were analyzed based on the full-length amplicons of the bacterial 16S rRNA gene and fungal ITS region. Bacterial communities varied among hosts inhabiting terrestrial, semiaquatic, and aquatic habitats, while fungal communities were more related to the geographical distribution of the hosts. Interestingly, co-occurrence networks showed that species inhabiting similar habitats shared symbiotic microorganism association types. Moreover, functional prediction analyses showed that the symbiotic bacterial community of aquatic species displayed richer amino acid and lipid metabolism pathways, while plant-feeding true bugs benefited more from the symbiont-provided xenobiotics biodegradation pathway. These results deepened the recognition that symbiotic microorganisms were likely to help heteropterans occupy diverse ecological habitats and provided a reference framework for further studies on how microorganisms affect host insects living in various habitats. IMPORTANCE Symbiotic bacteria and fungi generally colonize insects and provide various benefits for hosts. Although numerous studies have investigated symbionts in terrestrial plant-feeding insects, explorations of symbiotic bacterial and fungal communities in aquatic and semiaquatic insects are rare. In this study, the symbiotic microorganisms of 204 aquatic, semiaquatic, and terrestrial true bugs were explored. This comprehensive taxon sampling covers ~85% of the superfamilies of true bugs and most insect habitats. Analyses of the diversity of symbionts demonstrated that the symbiotic microbial diversities of true bugs were mainly affected by host habitats. Co-occurrence networks showed that true bugs inhabiting similar habitats shared symbiotic microbial association types. These correlations between symbionts and hosts together with the functions of bacterial communities indicated that symbiotic microbial communities may help true bugs adapt to (semi)aquatic habitats.

Fruit fly phylogeny imprints bacterial gut microbiota

One promising avenue for reconciling the goals of crop production and ecosystem preservation consists in the manipulation of beneficial biotic interactions, such as between insects and microbes. Insect gut microbiota can affect host fitness by contributing to development, host immunity, nutrition, or behavior. However, the determinants of gut microbiota composition and structure, including host phylogeny and host ecology, remain poorly known. Here, we used a well-studied community of eight sympatric fruit fly species to test the contributions of fly phylogeny, fly specialization, and fly sampling environment on the composition and structure of bacterial gut microbiota. Comprising both specialists and generalists, these species belong to five genera from to two tribes of the Tephritidae family. For each fly species, one field and one laboratory samples were studied. Bacterial inventories to the genus level were produced using 16S metabarcoding with the Oxford Nanopore Technology. Sample bacterial compositions were analyzed with recent network-based clustering techniques. Whereas gut microbiota were dominated by the Enterobacteriaceae family in all samples, microbial profiles varied across samples, mainly in relation to fly identity and sampling environment. Alpha diversity varied across samples and was higher in the Dacinae tribe than in the Ceratitinae tribe. Network analyses allowed grouping samples according to their microbial profiles. The resulting groups were very congruent with fly phylogeny, with a significant modulation of sampling environment, and with a very low impact of fly specialization. Such a strong imprint of host phylogeny in sympatric fly species, some of which share much of their host plants, suggests important control of fruit flies on their gut microbiota through vertical transmission and/or intense filtering of environmental bacteria.

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.

Dynamics of the Queensland Fruit Fly Microbiome through the Transition from Nature to an Established Laboratory Colony

The transition from nature to laboratory or mass rearing can impose significant physiological and evolutionary impact on insects. The Queensland fruit fly (also known as ‘Qfly’), Bactrocera tryoni (Froggatt) (Diptera: Tephritidae), is a serious economic pest that presents major challenges for horticulture industries in Australia. The sterile insect technique (SIT) is being developed to manage outbreaks in regions that remain free of Qfly and to suppress populations in regions where this species is endemic. The biology of Qfly is intimately connected to its microbiome. Therefore, changes in the microbiome that occur through domestication have implications for SIT. There are numerous studies of the microbiome in Qfly larvae and adults, but there is little information on how the microbiome changes as Qfly laboratory colonies are established. In this study, high-throughput Illumina sequencing was used to assess the Qfly microbiome in colonies reared from wild larvae, collected from fruit, for five generations, on a gel-based larval diet. Beta diversity analysis showed that the bacterial communities from Generation 5 (G5) clustered separately from earlier generations. At the genus level, bacterial communities were significantly different between the generations and mostly altered at G5. However, communities were found similar at phyla to family taxonomic levels. We observed high abundance of Morganella and Burkholderia at the genus level in the larval and pupal stages respectively at G5, but these were not detected in earlier generations. Overall, our findings demonstrate that the domestication process strongly affects the Qfly microbiome and prompts questions about the functional relationship between the Qfly and its microbiome, as well as implications for the performance of insects that have been domesticated and mass-reared for SIT programs.

Evaluation of Sample Preservation Approaches for Better Insect Microbiome Research According to Next-Generation and Third-Generation Sequencing

The microbial communities associated with insects play critical roles in many physiological functions such as digestion, nutrition, and defense. Meanwhile, with the development of sequencing technology, more and more studies begin to focus on broader biodiversity of insects and the corresponding mechanisms of insect microbial symbiosis, which need longer time collecting in the field. However, few studies have evaluated the effect of insect microbiome sample preservation approaches especially in different time durations or have assessed whether these approaches are appropriate for both next-generation sequencing (NGS) and third-generation sequencing (TGS) technologies. Here, we used Tessaratoma papillosa (Hemiptera: Tessaratomidae), an important litchi pest, as the model insect and adopted two sequencing technologies to evaluate the effect of four different preservation approaches (cetyltrimethylammonium bromide (CTAB), ethanol, air dried, and RNAlater). We found the samples treated by air dried method, which entomologists adopted for morphological observation and classical taxonomy, would get worse soon. RNAlater as the most expensive approaches for insect microbiome sample preservation did not suit for field works longer than 1 month. We recommended CTAB and ethanol as better preservatives in longer time field work for their effectiveness and low cost. Comparing with the full-length 16S rRNA gene sequenced by TGS, the V4 region of 16S rRNA gene sequenced by NGS has a lower resolution trait and may misestimate the composition of microbial communities. Our results provided recommendations for suitable preservation approaches applied to insect microbiome studies based on two sequencing technologies, which can help researchers properly preserve samples in field works.

Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution

The advent of NGS-based methods has been profoundly transforming entomological research. Through continual development and improvement of different methods and sequencing platforms, NGS has promoted mass elucidation of partial or whole genetic materials associated with beneficial insects, pests (of agriculture, forestry and animal, and human health), and species of conservation concern, helping to unravel ecological and evolutionary mechanisms and characterizing survival, trophic interactions, and dispersal. It is shifting the scale of biodiversity and environmental analyses from individuals and biodiversity indicator species to the large-scale study of communities and ecosystems using bulk samples of species or a mixed "soup" of environmental DNA. As the NGS-based methods have become more affordable, complexity demystified, and specificity and sensitivity proven, their use in entomological research has spread widely. This article presents several examples on how NGS-based methods have been used in entomology to provide incentives to apply them when appropriate and to open our minds to the expected advances in entomology that are yet to come.

Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology

Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example, by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities, such as rapid molecular diagnostics and direct RNA sequencing, and both Pacific Biosciences (PacBio) and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long-read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.

Facility-specific 'house' microbiome ensures the maintenance of functional microbial communities into coffee beans fermentation: implications for source tracking

This work aimed at studying the unconfirmed hypothesis predicting the existence of a connection between coffee farm microbiome and the resulting spontaneous fermentation process. Using Illumina-based amplicon sequencing, 360 prokaryotes and 397 eukaryotes were identified from coffee fruits and leaves, over-ripe fruits, water used for coffee de-pulping, depulped coffee beans, soil, and temporal fermentation samples at an experimental farm in Honduras. Coffee fruits and leaves were mainly associated with high incidence of Enterobacteriaceae, Pseudomonas, Colletotrichum, and Cladosporium. The proportion of Enterobacteriaceae was increased when leaves and fruits were collected on the ground compared to those from the coffee tree. Coffee farm soil showed the richest microbial diversity with marked presence of Bacillus. Following the fermentation process, microorganisms present in depulped coffee beans (Leuconostoc, Gluconobater, Pichia, Hanseniaspora, and Candida) represented more than 90% of the total microbial community, which produced lactic acid, ethanol, and several volatile compounds. The community ecology connections described in this study showed that coffee fruit provides beneficial microorganisms for the fermentation process. Enterobacteria, Colletotrichum, and other microbial groups present in leaves, fruit surface, over-ripe fruits, and soil may transfer unwanted aromas to coffee beans, so they should be avoided from having access to the fermentation tank.

Canopy distribution and microclimate preferences of sterile and wild Queensland fruit flies

Insects tend to live within well-defined habitats, and at smaller scales can have distinct microhabitat preferences. These preferences are important, but often overlooked, in applications of the sterile insect technique. Different microhabitat preferences of sterile and wild insects may reflect differences in environmental tolerance and may lead to spatial separation in the field, both of which may reduce the control program efficiency. In this study, we compared the diurnal microhabitat distributions of mass-reared (fertile and sterile) and wild Queensland fruit flies, Bactrocera tryoni (Froggatt) (Diptera: Tephritidae). Flies were individually tagged and released into field cages containing citrus trees. We recorded their locations in the canopies (height from ground, distance from canopy center), behavior (resting, grooming, walking, feeding), and the abiotic conditions on occupied leaves (temperature, humidity, light intensity) throughout the day. Flies from all groups moved lower in the canopy when temperature and light intensity were high, and humidity was low; lower canopy regions provided shelter from these conditions. Fertile and sterile mass-reared flies of both sexes were generally lower in the canopies than wild flies. Flies generally fed from the top sides of leaves that were lower in the canopy, suggesting food sources in these locations. Our observations suggest that mass-reared and wild B. tryoni occupy different locations in tree canopies, which could indicate different tolerances to environmental extremes and may result in spatial separation of sterile and wild flies when assessed at a landscape scale.

Amplicon sequencing detects mutations associated with pyrethroid resistance in Bemisia tabaci (Hemiptera: Aleyrodidae)

BACKGROUND

Bemisia tabaci (Gennadius) is a major damaging agricultural pest that exhibits high resistance to pyrethroid insecticides. L925I (TTA to ATA) and T929V (ACT to GTT) mutations in the para-type voltage-gated sodium channel (VGSC) are associated with resistance of B. tabaci to pyrethroids. Amplicon sequencing is a reliable and highly efficient method to detect the frequency of mutations linked with insecticide resistance.

RESULTS

Similar frequencies of L925I and T929V mutations were obtained by amplicon sequencing and Sanger sequencing (L925I: 0.3548 vs 0.3619; T929V: 0.6140 vs 0.6381) with overlap of 95% confidence interval in the SX population of B. tabaci. In five populations of B. tabaci from China, the maximum and minimum frequencies of the two mutations were found in the LN (L925I: 0.1126; T929V: 0.8834) and JS (L925I: 0.8776; T929V: 0.1166) populations by amplicon sequencing. However, there was no significant difference in frequencies between the L925I and T929V mutations. The sum frequency of L925I and T929V exceeded 0.9688 in all populations. In addition, a combining mutation, L925 + T929V (L925I and T929V located in same allele), was found in five populations by amplicon sequencing even though its highest frequency was only 0.0157.

CONCLUSION

We established an efficient approach for detecting frequency of mutation by amplicon sequencing. The frequencies of L925I and T929V in VGSC associated with pyrethroid resistance were detected in this study, which could provide foundational data for resistance management of B. tabaci. © 2021 Society of Chemical Industry.

Interkingdom Gut Microbiome and Resistome of the Cockroach Blattella germanica

Cockroaches are intriguing animals with two coexisting symbiotic systems, an endosymbiont in the fat body, involved in nitrogen metabolism, and a gut microbiome whose diversity, complexity, role, and developmental dynamics have not been fully elucidated. In this work, we present a metagenomic approach to study Blattella germanica populations not treated, treated with kanamycin, and recovered after treatment, both naturally and by adding feces to the diet, with the aim of better understanding the structure and function of its gut microbiome along the development as well as the characterization of its resistome.IMPORTANCE For the first time, we analyze the interkingdom hindgut microbiome of this species, including bacteria, fungi, archaea, and viruses. Network analysis reveals putative cooperation between core bacteria that could be key for ecosystem equilibrium. We also show how antibiotic treatments alter microbiota diversity and function, while both features are restored after one untreated generation. Combining data from B. germanica treated with three antibiotics, we have characterized this species' resistome. It includes genes involved in resistance to several broad-spectrum antibiotics frequently used in the clinic. The presence of genetic elements involved in DNA mobilization indicates that they can be transferred among microbiota partners. Therefore, cockroaches can be considered reservoirs of antibiotic resistance genes (ARGs) and potential transmission vectors.

Differences in the intestinal microbiota between insecticide-resistant and -sensitive Aedes albopictus based on full-length 16S rRNA sequencing

The intestinal symbiotic bacteria of Aedes albopictus play a potential role in host resistance to insecticides. In this study, we sequenced the full‐length of 16S rRNA and analyzed the differences in the intestinal microbiota between deltamethrin‐resistant and ‐sensitive Ae. albopictus. Symbiotic bacteria were cultured and analyzed using six types of culture media in aerobic and anaerobic environments. We found significant differences in the diversity and abundance of the intestinal microbiota of the two strains of Ae. albopictus. The symbiotic bacteria cultured in vitro were found to be mainly facultative anaerobes. The cultured bacteria such as Serratia oryzae and Acinetobacter junii may function to promote the development of insecticide resistance. This work indicates that intestinal bacteria may contribute to the enhancement of insecticide resistance of Ae. albopictus It also highlights the analytical advantage of full‐length 16S rRNA sequencing to study the intestinal microbiota of mosquitoes.

Domestication Shapes the Community Structure and Functional Metagenomic Content of the Yak Fecal Microbiota

Domestication is a key factor of genetic variation; however, the mechanism by which domestication alters gut microbiota is poorly understood. Here, to explore the variation in the structure, function, rapidly evolved genes (REGs), and enzyme profiles of cellulase and hemicellulose in fecal microbiota, we studied the fecal microbiota in wild, half-blood, and domestic yaks based on 16S rDNA sequencing, shotgun-metagenomic sequencing, and the measurement of short-chain-fatty-acids (SCFAs) concentration. Results indicated that wild and half-blood yaks harbored an increased abundance of the phylum Firmicutes and reduced abundance of the genus Akkermansia, which are both associated with efficient energy harvesting. The gut microbial diversity decreased in domestic yaks. The results of the shotgun-metagenomic sequencing showed that the wild yak harbored an increased abundance of microbial pathways that play crucial roles in digestion and growth of the host, whereas the domestic yak harbored an increased abundance of methane-metabolism-related pathways. Wild yaks had enriched amounts of REGs in energy and carbohydrate metabolism pathways, and possessed a significantly increased abundance of cellulases and endohemicellulases in the glycoside hydrolase family compared to domestic yaks. The concentrations of acetic, propionic, n-butyric, i-butyric, n-valeric, and i-valeric acid were highest in wild yaks. Our study displayed the domestic effect on the phenotype of composition, function in gut microbiota, and SCFAs associated with gut microbiota, which had a closely association with the growth performance of the livestock. These findings may enlighten the researchers to construct more links between economic characteristics and gut microbiota, and develop new commercial strains in livestock based on the biotechnology of gut microbiota.

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.

Vertically Transmitted Gut Bacteria and Nutrition Influence the Immunity and Fitness of Bactrocera dorsalis Larvae

Symbiotic bacterial communities that colonize the digestive tract of tephritid fruit flies interact with nutrient intake to improve the flies' fitness and immunity. Some bacterial species consistently inhabit the tephritid guts and are transmitted to the next generation vertically. These species contribute significantly to some aspects of their host's physiology. In the current study, we examined the role of four vertically transmitted bacteria (Citrobacter, Enterobacter, Klebsiella, and Providencia) on the fitness parameters and immunity of Bactrocera dorsalis larvae that were fed a nutritionally manipulated diet. For this purpose, eggs were collected from axenic, gnotobiotic, and symbiotic adult flies, and larvae were reared on four types of diets in which carbohydrate and/or protein contents were reduced and then compared with larvae raised on a control diet. The diet and bacterial interactions significantly affected the fitness and immunity of B. dorsalis. Larvae of axenic flies grew slower and displayed weaker immune-based responses (PO activity, antibacterial activity, survival) than larvae of gnotobiotic and symbiotic flies. Overall, larvae reared on the low-protein diet grew slower than those reared on the control or low-carbohydrate diets. Survival, PO activity, and antibacterial activity were significantly lower in the hemolymph of larvae reared on low-protein diets. Our results also revealed that the levels of hemolymph protein, glucose, trehalose, and triglyceride in larvae from axenic flies were significantly lower than those in larvae of the symbiotic group after they fed on most of the tested diets. These results strongly infer that diet and vertically transmitted bacteria are both essential contributors to the fitness and immunity of B. dorsalis.

Fruit host-dependent fungal communities in the microbiome of wild Queensland fruit fly larvae

Bactrocera tryoni (Froggatt), the Queensland fruit fly (Qfly), is a highly polyphagous tephritid fly that is widespread in Eastern Australia. Qfly physiology is closely linked with its fungal associates, with particular relationship between Qfly nutrition and yeast or yeast-like fungi. Despite animal-associated fungi typically occurring in multi-species communities, Qfly studies have predominately involved the culture and characterisation of single fungal isolates. Further, only two studies have investigated the fungal communities associated with Qfly, and both have used culture-dependant techniques that overlook non-culturable fungi and hence under-represent, and provide a biased interpretation of, the overall fungal community. In order to explore a potentially hidden fungal diversity and complexity within the Qfly mycobiome, we used culture-independent, high-throughput Illumina sequencing techniques to comprehensively, and holistically characterized the fungal community of Qfly larvae and overcome the culture bias. We collected larvae from a range of fruit hosts along the east coast of Australia, and all had a mycobiome dominated by ascomycetes. The most abundant fungal taxa belonged to the genera Pichia (43%), Candida (20%), Hanseniaspora (10%), Zygosaccharomyces (11%) and Penicillium (7%). We also characterized the fungal communities of fruit hosts, and found a strong degree of overlap between larvae and fruit host communities, suggesting that these communities are intimately inter-connected. Our data suggests that larval fungal communities are acquired from surrounding fruit flesh. It is likely that the physiological benefits of Qfly exposure to fungal communities is primarily due to consumption of these fungi, not through syntrophy/symbiosis between fungi and insect ‘host’.

Antibiotic exposure perturbs the bacterial community in the small brown planthopper Laodelphax striatellus

Bacteria symbionts in herbivores play an important role in host biology and ecology, and are affected by environmental factors such as temperature, diet, habitat, antibiotics and so on. However, the effects of antibiotics on the microbiome of the small brown planthopper Laodelphax striatellus (SBPH) remain unclear. Here, we studied the effects of tetracycline on the diversity and composition of bacterial colonies in different tissues of SBPH using high throughput sequencing of 16S ribosomal RNA amplicons. Our results show that Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria were most abundant in SBPH, and the genera Asaia and Wolbachia were most abundant in all body parts of SBPH. Antibiotic treatment had persistent effects on the composition of the SBPH microbiome. Tetracycline depleted the population of Firmicutes, Bacteroidetes, Tenericutes and Fusobacteria, and nearly 100% eliminated Wolbachia, Bacteroides and Abiotrophia in SBPH. Together, these results suggest that antibiotic exposure affects the bacteria symbionts of different body parts in SBPH and will facilitate future studies of the bacterial symbionts of arthropod hosts.

Artificial Larval Diet Mediates the Microbiome of Queensland Fruit Fly

Larval diets used for artificial rearing can have a significant effect on insect biology. The Queensland fruit fly (aka "Qfly"), Bactrocera tryoni (Froggatt) (Diptera: Tephritidae), is one of the greatest challenges for fruit growers in Australia. The sterile insect technique (SIT) is being developed to manage outbreaks in regions that remain free of Qfly and to reduce populations in regions where this species is endemic. Factory scale rearing is essential for SIT; however, artificial larval diets are known to affect the microbiome of Qfly, which may then affect fly performance. In this study, high-throughput Illumina sequencing was used to assess the Qfly microbiome in colonies reared, for five generations from nature, on two common artificial diets (carrot and gel). At generation five (G5), the microbiome was assessed in larvae, pupae, adult males and adult females and standard fly quality control parameters were assessed together with additional performance measures of mating propensity and survival under nutritional stress. At the genus level, bacterial communities were significantly different between the colonies reared on the two larval diets. However, communities converged at Phyla to family taxonomic levels. Bacterial genera of Morganella, Citrobacter, Providencia, and Burkholderia were highly abundant in all developmental stages of Qfly reared on the gel diet, when compared to the carrot diet. Despite abundance of these genera, a greater percentage of egg hatching, heavier pupal weight and a higher percentage of fliers were found in the Qfly reared on the gel diet. Mating propensity and survival under nutritional stress was similar for adult Qfly that had been reared on the two larval diets. Overall, our findings demonstrate that the artificial larval diet strongly influences the microbiome and quality control measures of Qfly, with likely downstream effects on performance of flies released in SIT programs.

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.

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

The family Tephritidae includes some of the most notorious insect pests of agricultural and horticultural crops in tropical and sub-tropical 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.

Wild bacterial probiotics fed to larvae of mass-reared Queensland fruit fly [Bactrocera tryoni (Froggatt)] do not impact long-term survival, mate selection, or locomotor activity

Queensland fruit fly [Bactrocera tryoni (Froggatt), Diptera, Tephritidae] is the most devastating insect pest impacting Australian horticulture. The Sterile Insect Technique (SIT) is an important component of tephritid pest management programs. However, mass-rearing and irradiation (to render insects sterile) may reduce the fitness and performance of the insect, including the ability of sterile males to successfully compete for wild females. Manipulation of the gut microbiome, including the supplementation with bacterial probiotics shows promise for enhancing the quality of mass-reared sterile flies, however there are fewer published studies targeting the larval stage. In this study, we supplemented the larval stage of mass-reared B. tryoni with bacterial probiotics. We tested several individual bacteria that had been previously isolated and characterized from the gut of wild B. tryoni larvae including Asaia sp., Enterobacter sp., Lactobacillus sp., Leuconostoc sp. We also tested a consortium of all four of these bacterial isolates. The fitness parameters tested included adult survival in field cages, laboratory mate selection of bacteria supplemented males by bacteria nonsupplemented females, and laboratory locomotor activity of adult flies. None of the bacterial probiotic treatments in the current study was significantly different to the control for field survival, mate selection or locomotor activity of adult B. tryoni, which agree with some of the other studies regarding bacterial probiotics fed to the larval stage of tephritids. Future work is needed to determine if feeding the same, and/or other probiotics to adults, as opposed to larvae can positively impact survival, mating performance, mating competitiveness and locomotor activity of B. tryoni. The bacterial group(s) and function of bacterial species that increase fitness and competitiveness is also of interest to tephritid mass-rearing programs.

Microbiome of the Queensland Fruit Fly through Metamorphosis

Bactrocera tryoni (Froggatt) (Queensland fruit fly, or “Qfly”) is a highly polyphagous tephritid fruit fly and a serious economic pest in Australia. Qfly biology is intimately linked to the bacteria and fungi of its microbiome. While there are numerous studies of the microbiome in larvae and adults, the transition of the microbiome through the pupal stage remains unknown. To address this knowledge gap, we used high-throughput Next-Generation Sequencing (NGS) to examine microbial communities at each developmental stage in the Qfly life cycle, targeting the bacterial 16S rRNA and fungal ITS regions. We found that microbial communities were similar at the larval and pupal stage and were also similar between adult males and females, yet there were marked differences between the larval and adult stages. Specific bacterial and fungal taxa are present in the larvae and adults (fed hydrolyzed yeast with sugar) which is likely related to differences in nutritional biology of these life stages. We observed a significant abundance of the Acetobacteraceae at the family level, both in the larval and pupal stages. Conversely, Enterobacteriaceae was highly abundant (>80%) only in the adults. The majority of fungal taxa present in Qfly were yeasts or yeast-like fungi. In addition to elucidating changes in the microbiome through developmental stages, this study characterizes the Qfly microbiome present at the establishment of laboratory colonies as they enter the domestication process.

Role of plants in the transmission of Asaia sp., which potentially inhibit the Plasmodium sporogenic cycle in Anopheles mosquitoes

Biological control against malaria and its transmission is currently a considerable challenge. Plant-associated bacteria of the genus Asaia are frequently found in nectarivorous arthropods, they thought to have a natural indirect action on the development of plasmodium in mosquitoes. However, virtually nothing is known about its natural cycle. Here, we show the role of nectar-producing plants in the hosting and dissemination of Asaia. We isolated Asaia strains from wild mosquitoes and flowers in Senegal and demonstrated the transmission of the bacteria from infected mosquitoes to sterile flowers and then to 26.6% of noninfected mosquitoes through nectar feeding. Thus, nectar-producing plants may naturally acquire Asaia and then colonize Anopheles mosquitoes through food-borne contamination. Finally, Asaia may play an indirect role in the reduction in the vectorial capacity of Anopheles mosquitoes in a natural environment (due to Plasmodium-antagonistic capacities of Asaia) and be used in the development of tools for Asaia-based paratransgenetic malaria control.

Diet and irradiation effects on the bacterial community composition and structure in the gut of domesticated teneral and mature Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae)

BACKGROUND

Mass-rearing, domestication and gamma irradiation of tephritid fruit flies used in sterile insect technique (SIT) programmes can negatively impact fly quality and performance. Symbiotic bacteria supplied as probiotics to mass-reared fruit flies may help to overcome some of these issues. However, the effects of tephritid ontogeny, sex, diet and irradiation on their microbiota are not well known.

RESULTS

We have used next-generation sequencing to characterise the bacterial community composition and structure within Queensland fruit fly, Bactrocera tryoni (Froggatt), by generating 16S rRNA gene amplicon libraries derived from the guts of 58 individual teneral and mature, female and male, sterile and fertile adult flies reared on artificial larval diets in a laboratory or mass-rearing environment, and fed either a full adult diet (i.e. sugar and yeast hydrolysate) or a sugar only adult diet. Overall, the amplicon sequence read volume in tenerals was low and smaller than in mature adult flies. Operational taxonomic units (OTUs), belonging to the families Enterobacteriaceae (8 OTUs) and Acetobacteraceae (1 OTU) were most prevalent. Enterobacteriaceae dominated laboratory-reared tenerals from a colony fed a carrot-based larval diet, while Acetobacteraceae dominated mass-reared tenerals from a production facility colony fed a lucerne chaff based larval diet. As adult flies matured, Enterobacteriaceae became dominant irrespective of larval origin. The inclusion of yeast in the adult diet strengthened this shift away from Acetobacteraceae towards Enterobacteriaceae. Interestingly, irradiation increased 16S rRNA gene sequence read volume.

CONCLUSIONS

Our findings suggest that bacterial populations in fruit flies experience significant bottlenecks during metamorphosis. Gut bacteria in teneral flies were less abundant and less diverse, and impacted by colony origin. In contrast, mature adult flies had selectively increased abundances for some gut bacteria, or acquired these bacteria from the adult diet and environment. Furthermore, irradiation augmented bacterial abundance in mature flies. This implies that either some gut bacteria were compensating for damage caused by irradiation or irradiated flies had lost their ability to regulate bacterial load. Our findings suggest that the adult stage prior to sexual maturity may be ideal to target for probiotic manipulation of fly microbiota to increase fly performance in SIT programmes.

Enterobacter sp. AA26 gut symbiont as a protein source for Mediterranean fruit fly mass-rearing and sterile insect technique applications

Background

Insect species have established sophisticated symbiotic associations with diverse groups of microorganisms including bacteria which have been shown to affect several aspects of their biology, physiology, ecology and evolution. In addition, recent studies have shown that insect symbionts, including those localized in the gastrointestinal tract, can be exploited for the enhancement of sterile insect technique (SIT) applications against major insect pests such as the Mediterranean fruit fly (medfly) Ceratitis capitata. We previously showed that Enterobacter sp. AA26 can be used as probiotic supplement in medfly larval diet improving the productivity and accelerating the development of the VIENNA 8 genetic sexing strain (GSS), which is currently used in large scale operational SIT programs worldwide.

Results

Enterobacter sp. AA26 was an adequate nutritional source for C. capitata larvae, comprising an effective substitute for brewer’s yeast. Incorporating inactive bacterial cells in the larval diet conferred a number of substantial beneficial effects on medfly biology. The consumption of bacteria-based diet (either as full or partial yeast replacement) resulted in decreased immature stages mortality, accelerated immature development, increased pupal weight, and elongated the survival under stress conditions. Moreover, neither the partial nor the complete replacement of yeast with Enterobacter sp. AA26 had significant impact on adult sex ratio, females’ fecundity, adults’ flight ability and males’ mating competitiveness. The absence of both yeast and Enterobacter sp. AA26 (deprivation of protein source and possible other important nutrients) from the larval diet detrimentally affected the larval development, survival and elongated the immature developmental duration.

Conclusions

Enterobacter sp. AA26 dry biomass can fully replace the brewer’s yeast as a protein source in medfly larval diet without any effect on the productivity and the biological quality of reared medfly of VIENNA 8 GSS as assessed by the FAO/IAEA/USDA standard quality control tests. We discuss this finding in the context of mass-rearing and SIT applications.

Bacterial communities in the gut of wild and mass-reared Zeugodacus cucurbitae and Bactrocera dorsalis revealed by metagenomic sequencing

BACKGROUND

Insect pests belonging to genus Bactrocera sp. (Diptera: Tephritidae) pose major biotic stress on various fruits and vegetable crops around the world. Zeugodacus and Bactrocera sp. are associated with diverse bacterial communities which play an important role in the fitness of sterile insects. The wild populations of melon fly, Zeugodacus cucurbitae (Coquillett) and Oriental fruit fly, Bactrocera dorsalis (Hendel) were collected from pumpkin and mango fields, respectively. The laboratory populations of Z. cucurbitae and B. dorsalis were mass-reared on bottle gourd and sweet banana, respectively. Bacterial communities present in the gut of wild and mass-reared mature (~ 12 days old) and newly emerged (< 1 h after emergence) male and female adults of Z. cucurbitae and B. dorsalis were assessed. We used Illumina HiSeq next-generation sequencing of 16S rRNA gene to profile the gut bacterial communities of wild and mass-reared mature and newly emerged Z. cucurbitae and B. dorsalis adults.

RESULTS

We found diverse bacterial composition in the gut of wild and mass-reared Z. cucurbitae (ZC) and B. dorsalis (BD) with varied relative abundance. Few taxonomic groups were common to both the species. The most dominant phyla in all samples of Z. cucurbitae and B. dorsalis adults were Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The phylum Proteobacteria occurred more in wild Z. cucurbitae (~ 87.72%) and B. dorsalis (~ 83.87%) as compared to mass-reared Z. cucurbitae (64.15%) and B. dorsalis (~ 80.96%). Higher relative abundance of Phylum Firmicutes was observed in mass-reared fruit fly than wild adults. Cyanobacteria/Chloroplast and Actinobacteria were also present with very low relative abundance in both wild as well as mass-reared melon fly and Oriental fruit fly. Enterobacteriaceae (61.21%) was dominant family in the gut of both wild and mass-reared adults. Providencia and Lactococcus were dominant genera with varied relative abundance in wild as well as in mass-reared mature and newly emerged fruit fly adults of both species. Some of the genera like Morganella and Serratia were only detected in mass-reared mature and newly emerged Z. cucurbitae and B. dorsalis adults. Principal Coordinate Analysis (PCoA) showed that fruit fly adult samples were grouped based on species and age of the adults while no grouping was observed on the basis of sex of the adult fruit fly.

CONCLUSIONS

The gut bacterial communities associated with wild and mass-reared mature and newly emerged adults of Z. cucurbitae and B. dorsalis showed variation that depends on species and age of the insects. Understanding the gut microbiota of wild and mass-reared Z. cucurbitae and B. dorsalis using high throughput technology will help to illustrate microbial diversity and this information could be used to develop efficient mass-rearing protocols for successful implementation of sterile insect technique (SIT).

Tephritid-microbial interactions to enhance fruit fly performance in sterile insect technique programs

BACKGROUND

The Sterile Insect Technique (SIT) is being applied for the management of economically important pest fruit flies (Diptera: Tephritidae) in a number of countries worldwide. The success and cost effectiveness of SIT depends upon the ability of mass-reared sterilized male insects to successfully copulate with conspecific wild fertile females when released in the field.

METHODS

We conducted a critical analysis of the literature about the tephritid gut microbiome including the advancement of methods for the identification and characterization of microbiota, particularly next generation sequencing, the impacts of irradiation (to induce sterility of flies) and fruit fly rearing, and the use of probiotics to manipulate the fruit fly gut microbiota.

RESULTS

Domestication, mass-rearing, irradiation and handling, as required in SIT, may change the structure of the fruit flies' gut microbial community compared to that of wild flies under field conditions. Gut microbiota of tephritids are important in their hosts' development, performance and physiology. Knowledge of how mass-rearing and associated changes of the microbial community impact the functional role of the bacteria and host biology is limited. Probiotics offer potential to encourage a gut microbial community that limits pathogens, and improves the quality of fruit flies.

CONCLUSIONS

Advances in technologies used to identify and characterize the gut microbiota will continue to expand our understanding of tephritid gut microbial diversity and community composition. Knowledge about the functions of gut microbes will increase through the use of gnotobiotic models, genome sequencing, metagenomics, metatranscriptomics, metabolomics and metaproteomics. The use of probiotics, or manipulation of the gut microbiota, offers significant opportunities to enhance the production of high quality, performing fruit flies in operational SIT programs.

A walk on the wild side: gut bacteria fed to mass-reared larvae of Queensland fruit fly [Bactrocera tryoni (Froggatt)] influence development

BACKGROUND

The Queensland fruit fly, Bactrocera tryoni (Froggatt) (Diptera, Tephritidae) is the most significant insect pest of Australian horticulture. Bactrocera tryoni is controlled using a range of tools including the Sterile Insect Technique (SIT). Mass-rearing and irradiation of pupae in SIT can reduce the fitness and quality of the released sterile insects. Studies have also showed reduced microbial gut diversity in domesticated versus wild tephritids.

RESULTS

Transmission electron microscopy confirmed the presence of the bacterial isolates in the mid-gut of mass-reared larvae, and plate counts from individual larval guts showed increased numbers of bacteria in supplemented larvae. Several developmental and fitness parameters were tested including larval development time (egg-hatch to pupation), pupal weight, emergence, flight ability, sex-ratio, and time to adult eclosion (egg-hatch to adult eclosion). Enterobacter sp. and Asaia sp. shortened larval development time, while this was delayed by Lactobacillus sp., Leuconostoc sp. and a blend of all four bacteria. The mean time from egg hatch to adult eclosion was significantly reduced by Leuconostoc sp. and the blend for males and females, indicating that the individual bacterium and consortium affect flies differently depending on the life stage (larval or pupal). There was no impact of bacterial supplemented larvae on pupal weight, emergence, flight ability, or sex ratio.

CONCLUSIONS

Our findings show that bacteria fed to the larval stage of B. tryoni can impart fitness advantages, but the selection of probiotic strains (individual or a consortium) is key, as each have varying effects on the host. Bacteria added to the larval diet particularly Leuconostoc sp. and the blend have the capacity to reduce costs and increase the number of flies produced in mass-rearing facilities by reducing time to adult eclosion by 1.3 and 0.8 mean days for males, and 1.2 and 0.8 mean days for females.

Impact of Sample Preservation and Manipulation on Insect Gut Microbiome Profiling. A Test Case With Fruit Flies (Diptera, Tephritidae)

High-throughput sequencing (HTS) techniques are of great value for the investigation of microbial communities, and have been extensively used to study the gut microbiome. While most studies focus on the human gut, many others have investigated insects. However, because of the rapid spread of HTS techniques, a lot of variation exists in the protocols for sample preparation. In the present study, we investigated the impact of two widely adopted sample-processing procedures preceding library preparation, i.e., preservation of insect tissue in 70% ethanol (EtOH) and sample dissection. We used the fruit fly Ceratitis capitata (Diptera: Tephritidae) as a model organism and set up two experiments, one comparing the effects of sample manipulation and preservation across life stages and the other across fruit samples from different sources. The results of this study showed no major effects of dissection on the outcome of HTS. However, EtOH preservation did have effects on the recovered gut microbiome, the main effect being a significant reduction of the dominant genus, Providencia, in EtOH-preserved samples. Less abundant bacterial groups were also affected resulting in altered microbial profiles obtained from samples preserved in 70% EtOH. These results have important implications for the planning of future studies and when comparing studies that used different sample preparation protocols.

Next-Generation Sequencing reveals relationship between the larval microbiome and food substrate in the polyphagous Queensland fruit fly

Insects typically host substantial microbial communities (the ‘microbiome’) that can serve as a vital source of nutrients and also acts as a modulator of immune function. While recent studies have shown that diet is an important influence on the gut microbiome, very little is known about the dynamics underpinning microbial acquisition from natural food sources. Here, we addressed this gap by comparing the microbiome of larvae of the polyphagous fruit fly Bactrocera tryoni (‘Queensland fruit fly’) that were collected from five different fruit types (sapodilla [from two different localities], hog plum, pomegranate, green apple, and quince) from North-east to South-east Australia. Using Next-Generation Sequencing on the Illumina MiSeq platform, we addressed two questions: (1) what bacterial communities are available to B. tryoni larvae from different host fruit; and (2) how does the microbiome vary between B. tryoni larvae and its host fruit? The abundant bacterial taxa were similar for B. tryoni larvae from different fruit despite significant differences in the overall microbial community compositions. Our study suggests that the bacterial community structure of B. tryoni larvae is related less to the host fruit (diet) microbiome and more to vertical transfer of the microbiome during egg laying. Our findings also suggest that geographic location may play a quite limited role in structuring of larval microbiomes. This is the first study to use Next-Generation Sequencing to analyze the microbiome of B. tryoni larvae together with the host fruit, an approach that has enabled greatly increased resolution of relationships between the insect’s microbiome and that of the surrounding host tissues.

Taxonomy, Diet, and Developmental Stage Contribute to the Structuring of Gut-Associated Bacterial Communities in Tephritid Pest Species

Insect-symbiont interactions are receiving much attention in the last years. Symbiotic communities have been found to influence a variety of parameters regarding their host physiology and fitness. Gut symbiotic communities can be dynamic, changing through time and developmental stage. Whether these changes represent real differential needs and preferential relationships has not been addressed yet. In this study, we characterized the structure of symbiotic communities of five laboratory populations that represent five Tephritidae species that are targets for pest control management through the sterile insect technique (SIT), namely Bactrocera oleae, Anastrepha grandis, Anastrepha ludens, and two morphotypes of Anastrepha fraterculus (sp.1 and the Andean lineage). These populations are under artificial or semi artificial rearing conditions and their characterization was performed for different developmental stages and age. Our results demonstrate the presence of a symbiotic community comprising mainly from different Enterobacteriaceae genera. These communities are dynamic across developmental stages, although not highly variable, and appear to have a species-specific profile. Additional factors may contribute to the observed structuring, including diet, rearing practices, and the degree of domestication. Comparison of these results with those derived from natural populations could shed light to changes occurring in the symbiotic level during domestication of Tephritidae populations. Further studies will elucidate whether the changes are associated with modification of the behavior in laboratory strains and assess their effects in the quality of the mass rearing insects. This could be beneficial for improving environmentally friendly, species-specific, pest control methods, such as the SIT.

Biodiversity and dynamics of cyanobacterial communities during blooms in temperate lake (Harsha Lake, Ohio, USA)

Cyanobacterial blooms are intensifying global ecological hazards. The fine structure and dynamics of bloom community are critical to understanding bloom development but little understood. Here, the questions whether dominant bloomers have high diversity and whether dominant OTUs (operational taxonomical units) compete with one another were addressed. 16S rRNA gene amplicons from an annual bloom at five locations in Harsha Lake (Ohio, USA) showed cyanobacteria were the dominant phylum, and co-existing major bacterial phyla included Proteobacteria, Bacteroidetes, Actinoacteria, and Verrucomicrobia. On the genus level, the initial dominance by Dolichospermum in June yielded to Planktothrix in July, which were replaced by Microcystis and Cylindrospermopsis in August throughout the bloom. Based on the number of verified unique OTUs (a within-genus biodiversity metric), dominant genera tended to have high within-genus diversity. For example, Dolichospermum had 57 unique OTUs, Planktothrix had 36, Microcystis had 12, and Cylindrospermopsis had 4 unique OTUs. Interestingly, these different OTUs showed different dynamics and association with other OTUs. First, no between-OTU competitions were observed during the bloom cycle, and dominant OTUs were abundant throughout the bloom. Such biodiversity of OTUs and their dynamics were verified in Microcystis aeruginosa with two microcystin synthetase genes (mcyA and mcyG): the relative abundance of both genes varied during the bloom based on quantitative PCR. Two Dolichospermum circinale OTUs and one P. rubescens OTU were most abundant and persistently present throughout the entire bloom. Second, these OTUs differed in the OTUs they were associated with. Third, these OTUs tended to have different levels of association with the environmental factors, even they belonged to the same genera. These findings suggest the structure and dynamics of a cyanobacterial bloom community is complex, with only few OTUs dominating the bloom. Thus, high-resolution molecular characterization will be necessary to understand bloom development.

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

The oriental fruit fly, Bactrocera dorsalis (Hendel), is one of the most destructive agricultural pests and hosts diverse intestinal bacterial communities. We used 16S rRNA gene sequencing to investigate the microbial communities associated with the intestines of females and males from two B. dorsalis populations collected from Hainan and Guizhou Provinces of China. A total of 260,615 high-quality 16S rRNA gene reads with an average length of 253 bp were obtained. Highly diverse bacterial communities were observed across individuals, with communities containing between 691 and 1,262 bacterial operational taxonomic units. In addition, 37 bacterial phyla, 65 classes, 130 orders, 198 families, 201 genera, and 70 annotated species were identified, wherein the Proteobacteria were the most dominant phylum among all of the libraries, followed by the Firmicutes and Bacteroidetes. Bacterial community composition varied by host sex and geographic location of the populations. Female gut communities comprised fewer bacterial families than males, and females had lower relative abundances of 33 of the 35 most abundant families. In addition, female gut communities harbored greater abundances of Enterobacteriaceae than males. The Hainan population gut communities contained fewer bacterial families than those of the Guizhou populations. However, 5 of the 35 most abundant families were more abundant in communities from the Hainan population than those of the Guizhou population. The results of this study help us better understand the importance of symbiotic bacteria in B. dorsalis and provide a foundation for assessing the use of gut microorganisms as bio-control agents for these serious pests.

The Composition of Midgut Bacteria in Aedes aegypti (Diptera: Culicidae) That Are Naturally Susceptible or Refractory to Dengue Viruses

The composition, abundance, and diversity of midgut bacteria in mosquitoes can influence pathogen transmission. We used 16S rRNA microbiome profiling to survey midgut microbial diversity in pooled samples of laboratory colonized dengue-refractory, Cali-MIB, and dengue-susceptible, Cali-S Aedes aegypti (Linnaeus). The 16S rRNA sequences from the sugar-fed midguts of adult females clustered to 63 amplicon sequence variants (ASVs), primarily from Proteobacteria, Firmicutes, Flavobacteria, and Actinobacteria. An average of five ASVs dominated the midguts, and most ASVs were present in both Cali-MIB and Cali-S midguts. No differences in abundance were noted at any phylogenetic level (Phylum, Class, Order, Family, Genus) by analysis of composition of microbiome (w = 0). No community diversity metrics were significantly different between refractory and susceptible mosquitoes. These data suggest that phenotypic differences in the susceptibility to dengue virus between Cali-MIB and Cali-S are not likely due to major differences in midgut bacterial communities.

First insight into microbiome profile of fungivorous thrips Hoplothrips carpathicus (Insecta: Thysanoptera) at different developmental stages: molecular evidence of Wolbachia endosymbiosis

Insects' exoskeleton, gut, hemocoel, and cells are colonized by various microorganisms that often play important roles in their host life. Moreover, insects are frequently infected by vertically transmitted symbionts that can manipulate their reproduction. The aims of this study were the characterization of bacterial communities of four developmental stages of the fungivorous species Hoplothrips carpathicus (Thysanoptera: Phlaeothripidae), verification of the presence of Wolbachia, in silico prediction of metabolic potentials of the microorganisms, and sequencing its mitochondrial COI barcode. Taxonomy-based analysis indicated that the bacterial community of H. carpathicus contained 21 bacterial phyla. The most abundant phyla were Proteobacteria, Actinobacteria, Bacterioidetes and Firmicutes, and the most abundant classes were Alphaproteobacteria, Actinobacteria, Gammaproteobacteria and Betaproteobacteria, with different proportions in the total share. For pupa and imago (adult) the most abundant genus was Wolbachia, which comprised 69.95% and 56.11% of total bacterial population respectively. Moreover, similarity analysis of bacterial communities showed that changes in microbiome composition are congruent with the successive stages of H. carpathicus development. PICRUSt analysis predicted that each bacterial community should be rich in genes involved in membrane transport, amino acid metabolism, carbohydrate metabolism, replication and repair processes.