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Reduced diversity of gut microbiota in two Aedes mosquitoes species in areas of recent invasion

Aedes mosquitoes are considered highly successful global invasive species and vectors of several pathogens of relevance for public health. Their midgut’s microbiota can play an important role in affecting not only their vectorial competence but also their fitness, physiology, food digestion, metabolism, immunity and adaptation to new environmental conditions. Using high-throughput sequencing we compared the microbiota of Aedes albopictus collected in Italy with those reported in populations from France and Vietnam. We also analysed Aedes koreicus gut microbiota for the first time. We found remarkable individual difference along with common bacterial taxa in both species. Ae. albopictus collected in Italy had a lower richness and a different composition of microbiota in respect to specimens collected in France and Vietnam. It also showed a core microbiota formed mainly of bacteria of the genus Pseudomonas. Overall, the two Aedes species (Ae. albopictus and Ae. koreicus) collected in Italy, showed a large core microbiota with 75.98% of the identified Operational Taxonomic Units. Furthermore, Ae. albopictus had 2.5% prevalence of Wolbachia and 0.07% of Asaia spp, while Ae. koreicus had 14.42% of Asaia spp. and no Wolbachia. This study provides new informations on the spatial variation of the midgut bacterial communities in mosquitoes of medical relevance within areas of recent invasion and provide the basis for further studies aimed at assessing the effects of such variation on vectorial capacity for a range of pathogens.

The simplified microbiota structure in the Italian population was also confirmed by considering the number of unclassified reads (Fig. 1d), which is a measure of the fraction of the microbiota that is composed by organisms that are not present in the reference taxonomic databases. This fraction was much higher in the French and Vietnamese populations, suggesting the presence of a large fraction of not yet characterized organisms, compared to the Italian population. In particular, we found statistically significant differences in terms of unclassified reads at genus level (Fig. 1d) between Italy and France (Wilcoxon rank sum test, FDR corrected P-value = 6 × 10 −4 ), Italy and Vietnam (P = 8.7 × 10 −6 ) and France and Vietnam (P = 10 −3 ). In addition, the Italian population showed a significantly reduced α-diversity when compared to France and Vietnam both in terms of number of observed OTUs  Table S4).
To further investigate if the three different populations corresponded to clearly differentiated structure of the gut microbiota of Ae. albopictus, we computed the β-diversity of the samples using the unweighted Unifrac, weighted Unifrac and Bray-Curtis dissimilarity. A plot of the first two axes of the PCoA of the distances amongst the samples calculated using the weighted UniFrac distance showed three distinct clusters, corresponding to the Italian, French and Vietnamese samples (Fig. 2a).
This result is confirmed by the PCoA plots using the unweighted UniFrac distance and the Bray-Curtis dissimilarity (see Supplementary Figures S1 and S2). A permutational multivariate analysis of variance using distances (PERMANOVA) showed that the three different populations (Italian, French and Vietnamese) were significantly different (P < 10 −4 for the unweighted, weighted UniFrac distances and for Bray-Curtis dissimilarity, see also Fig. 2c). To confirm that the Italian population was clearly distinct from and less diverse than the French and Vietnamese ones, we compared the distributions of the distances within and between the three populations (Fig. 2b,c). Variability within Italy and France and within Italy and Vietnam was significantly different (P = 7.6 × 10 −7 and P = 3.3 × 10 −10 respectively, see Fig. 2b), but not within France and Vietnam (P = 0.96). Similarly, distances between countries highlighted the closeness between France and Vietnam, compared to Italy and France and Italy and Vietnam (P = 1.4 × 10 −5 P = 7.6 × 10 −13 respectively, Fig. 2c). We then examined which were the taxa differently distributed between Italy and France and Italy and Vietnam. As expected, we found that in most cases the difference between the Italian population and the others was due to taxa significantly more abundant in France and Vietnam than in Italy (P < 0.01, Wald significance test, Benjamini & Hochberg FDR correction, Fig. 2d,e for a summary at the class level, and Supplementary Tables S5 and S6). However, in Gamma-and Betaproteobacteria only a few OTUs were significantly more abundant in the Italian population, suggesting that the structure of the microbiota of these samples is the result of a general rearrangement of the relative abundances of the different species, rather than being just a simplified version of the French or Vietnamese ones.
Midgut microbiota of Ae. albopictus vs. Ae. koreicus. Ae. koreicus is a species very recently introduced in Italy. To investigate if stress factors due to the adaptation to an alien environment (which appears to be very strong in Ae. albopictus) dominated over the genetic differentiation of these two species in determining the structure of the midgut microbiota, we compared samples from the Italian populations of Ae. albopictus and Ae. koreicus. After rarefaction (without replacement) 2 153 OTUs were clustered into 9 Families and 12 Genus (Supplementary Tables S7-S9). Despite extensive variation between individuals of the same host species in the composition of their gut microbiota (Fig. 3), the comparison between Ae. albopictus and Ae. koreicus revealed a large shared core (75.98% of the reads), complemented by a smaller fraction specific to each of the two species. At Phylum level Proteobacteria and Firmicutes dominated the community (Supplementary Table S7). At Family level Pseudomonadaceae was the most abundant so far, followed by Rickettsiaceae, Oxalobacteraceae, Moraxellaceae, Enterobacteraceae, Xanthomonadaceae, Halomonadaceae, Acetobacteraceae and Comamodanaceae (Supplementary Table S8).
The core microbiota was largely composed by species of the genus Pseudomonas that alone accounted for an average of 64.63% and 63.38% of the reads in Ae. albopictus and in Ae. koreicus, respectively (core OTUs are  Supplementary Table S11). In 7 samples of Ae. koreicus there was a large contribution (up to the 14.42%) from an unidentified genus of the family Acetobacteraceae (see Supplementary Table S8). According to BLAST, the closest relative genus belonged to Asaia (97% percentual identity). We found that only 3 OTUs were specific to Ae. albopictus, corresponding to 9.81% of the total Ae. albopictus abundance (OTUs listed in Supplementary  Table S12), while no OTUs were specific to Ae. koreicus. Using indicator species analysis we confirmed the three OTUs specific to Ae. albopictus, additionally identifying 8 OTUs of Phylum Proteobacteria specific to Ae. albopictus, and three specific to Ae. koreicus (Supplementary Table S13). Two out of this three Ae. albopictus-specific OTUs were classified as belonging to the genus Wolbachia which resulted to be the dominant component in three samples from this species. No OTUs classified as Wolbachia were found in Ae. koreicus. In order to characterize more precisely the differences in the taxonomic composition of the samples from the two species, we identified all those OTUs with significant different relative abundance  (Wilcoxon rank-sum test P < 0.05, FDR corrected). In addition to the species-specific OTUs identified above, we obtained 7 relatively rare OTUs with relative abundances ranging from a few percent of the total microbiota to less than 10 −3 (Supplementary Table S14).

Discussion
Invasion by alien exotic mosquito species, such as Ae. albopictus and Ae. koreicus, is now occurring in an increasing number of european countries (see https://ecdc.europa.eu/en/disease-vectors/surveillance-and-disease-data/ mosquito-maps). These processes therefore enhance the probability of new diseases outbreak events within new areas. Therefore the needs is now to improve scientific knowledge on all the factors affecting mosquitoes vectorial capacity under a "pathobiome" approach 23 . Northern Italy is the only site in Europe where both Ae. albopictus and Ae. koreicus are considered established. Therefore, we took this unique opportunity to compare their gut microbiota not only for the potential health hazard they represent, but also because of the lack of knowledge on the midgut microbiota composition of Ae. koreicus. This latter species, although introduced in northern Italy few years ago 8 , is well established in an area of 3000 km 2 and its spreading is still ongoing 24 . The mosquito's gut microbiota composition varies as a result of complex interactions between environmental characteristics and developmental stages. Nonetheless the common characteristics of the habitat of Aedes spp. coupled with the high inter-individual diversity, makes it difficult to determine the geographic origin based on microbiota composition 19,25 . Moreover when alien species invade a new area they are usually less parasitised than native or well established species as seen within a previous study from Minard et al. showing that the midgut microbiota of the French tiger mosquitoes had a lower richness than the Vietnamese one 20 . This suggests that adaptation to a different environment had a profound impact on the resident intestinal microbiota of this species, with potential impacts on its biology, and consequently on its vector competence. According to these findings, our hypothesis was that if the differences were driven by the adaptation to a new environment, we should expect French and Italian populations to have similar richness, given the comparable macro climate (temperate), type of breeding sites (urban settlements and human-made containers) and introduction period (end of nineties-beginning of millennium). Surprisingly, we found that the degree of microbial diversity in the midgut microbiota of Italian female Ae. albopictus was lower not only compared with Vietnamese, but also with French ones, suggesting the existence of other population-specific factors. These could be either a particular condition of the Italian population, or a larger and continuous higher rate of introduction of new individuals in France, probably due to international commercial trades. The higher variability shown by French and Vietnamese samples compared to Italian ones, can also be linked to specific microclimatic features of the sampling sites, such as vegetation and naturality, but also to the type of hosts available. We tried to minimize or exclude most of the confounding factors, which could affect variability among populations (previous blood meal, type of habitat and seasonality). All the sampled wild adult female mosquitoes analyzed in these studies were unfed; however, no further molecular tests were performed to exclude previous blood meals. Although Aedes albopictus colonizes edges of forests and breed in natural habitats in its country of origin (tree holes, bamboo stumps, and bromeliads), this species has adapted well to suburban and urban environments with larvae now breeding in artificial containers such as tires, cemetery urns, and water storage tanks. All the mosquito samples were collected in urban and suburban environments, with the exception of one out of four sites in Vietnam. The year of collection was different for the Italian (2015, this study) and the French and Vietnamese samples ( 2012 20 ), but the season of collection was optimal for this species for all countries. To the best of our knowledge, there are no studies on the role of geographic location and year as factors affecting individual gut microbiota and we believe that such factors should be considered when comparing seasonality abundances or other ecological factors affecting population dynamic. In order to better assess the reasons of the differences among Ae. albopictus populations further comparisons with local mosquito species could be taken into account in the future. The genus Pseudomonas dominated the microbiota of the Italian samples similarly to what reported in wild females of other species such as Ae. aegypti in Brazil 26 , Culex pipiens in Belgium 27 , and in Anopheles stephensi and An. culicifacies in southern Iran 28,29 . The interaction of this bacteria with pathogens transmitted by mosquitoes was observed in the case of Anopheles and Plasmodium with both positive and negative effects 30,31 . Moreover it has been reported that the presence of Pseudomonas helps in facing the oxidative stress resulting from the catabolism of blood meal 32 which could cause a serious damage to insect cells. This bacteria has also been recently indicated as a good candidate to paratransgenesis since it grows in ordinary culture media and it is suitable for genetic transformation 27 .
The large core microbiota among the two Aedes species suggests a common environmental exposure in the breeding sites. In fact, the two mosquito species both share the same artificial habitats in urban settlements. Nonetheless, Ae. albopictus showed a higher richness and a different composition, as highlighted by αand β-diversity. This could be partly explained by the fact that Ae. albopictus colonized the area about 15 years before Ae. koreicus.
Along with Pseudomonadaceae, other bacterial families were identified in our Aedes samples (like Enterobacteriaceae, Acetobacteraceae, Rickettsiaceae and Moraxellaceae). These were already found in different species of mosquitoes collected from geographically distant locations, supporting the hypothesis that many components of the midgut are cosmopolitan, well established as commensals, and have an important role in insect life cycle [33][34][35][36][37][38] . The role of Enterobacteriaceae is considered important in the digestion of blood in hematophagous Diptera and is frequently recovered in female mosquitoes of various species [38][39][40][41] . Some species of this family could also be used for a paratransgenic approach; for example Enterobacter cloacae has been found to block the development of Plasmodium falciparum in An. gambiae and sporogonic development of P. vivax in An. albimanus 42,43 and to induce the expression of mosquito immune components in midgut of An. stephensi 44 . Other representatives from this family (genus Serratia) have a role in the suppression of the immune response of Ae. aegypti, therefore increasing its susceptibility to chikungunya and dengue viruses 45,46 .
A special attention should be focused on the contrasting presence of Wolbachia and members of the Acetobacteraceae family, most probably Asaia spp, in the two mosquito species. These two symbionts are the only bacteria known to be located in the reproductive organs of mosquito species, therefore vertically transmitted. The relationship between Wolbachia and mosquitoes is one of the most extensively studied among microbes harbored by insects 47-51 as it is commonly found in mosquitoes midgut (with the notable exception of Ae. aegypti 52 ), but also in somatic cells and gonads of Orthoptera 53 and Rhyncota, such as bedbugs 54 . The most known effects of Wolbachia presence is the cytoplasmatic incompatibility between infected males and uninfected females, and its ability to inhibit the horizontal transmission or reduce the vector competence of some mosquito-borne pathogens like Plasmodium spp., dengue, yellow fever, West Nile fever and chikungunya viruses 52,[55][56][57][58][59][60][61][62] . Once the vector potential of Ae. koreicus will be assessed, the lack of this endosymbiont could have important implications for the management of public health risk. Since the vectorial competence of Ae. koreicus for chikungunya virus was recently assessed by Ciocchetta et al. 63 more studies are now necessary to better assess the consequences of the lack of this endosymbiont on the enhancement of its vectorial capacity.
Asaia spp. is a group of acetic acid bacteria that can be found in different niches like nectar-bearing flowers. Recently, this genus has been reported to be stably associated with different mosquito species, often being the dominant microorganism of the mosquito microbiota. Asaia has been widely reported in lab-reared 64 , but also in wild caught Ae. albopictus species 41 and it seems to compete with Wolbachia in the ability to infect reproductive sites. Rossi et al. shown the infection of Asaia in the gut, but not in the reproductive organs of naturally infected Ae. albopictus and this was further confirmed by the absence of Asaia from the egg surface of this mosquito species 65 . Our findings reinforce the theory that mosquito-species naturally uninfected with Wolbachia (i.e. An. gambiae and An. stephensi 66 , Ae. aegypti 67 , Ae. koreicus (this study)) host Asaia spp. in various anatomical districts (midgut and ovary) and vice-versa, the occurrence of Asaia spp. in mosquitoes infected with Wolbachia is low. Most of the studies regarding the role of Asaia in mosquitoes, are related to several Anopheles species. In particular, it has been shown that Asaia spp. accelerates 68 or has a beneficial role 69 on larval development, with positive consequences on survivorship and competition with other mosquito species. In our study area, the two Aedes species overlap, therefore the presence of these bacteria needs to be further investigated. The consequences of microbiota composition in term of vector competence require more experimental studies since it has been previously assessed that the midgut bacteria play an important role in increasing or decreasing the vectorial capacity of the mosquito. Moreover it has been proven that vector-borne diseases can spread outside their endemic areas provided that the vector is present. An example are the chikungunya outbreaks in Italy in 2007 70 and 2017 71 . Northern Italy is experiencing a regular introduction of infected chikungunya and dengue viruses human cases every year, while West Nile and Usutu viruses are endemic [72][73][74] . The presence of a species such as Ae. koreicus which has better chances to survive to colder temperatures 24 , its proved competence in transmitting pathogenic viruses such as chikungunya and the lacks of Wolbachia which potentially inhibits the circulation of these viruses, enhances the chances of spreading of exotic pathogens.

Conclusions
In conclusion, the invasion of alien mosquito species into new areas challenges their gut microbiota in terms of reduction of richness and diversity, with possible consequences on the mosquito fitness and disease hazard. Local sampling conditions, though, could affect the gut microbiota composition and further research is necessary to investigate the effect of environmental factors on all developmental stages. With this study we provided an improvement of our knowledge of the highly diverse community of micro-organisms present in the midgut of two invasive mosquito species of public health concern.
Methods Samples collection. Mosquito collections were performed in July and August 2015 in the Autonomous Province of Trento (Trentino-Alto Adige region, Italy), which is an area of recent invasion by the two studied species. This territory covers an area of 6 200 km 2 with more than 70% lying above 1 000 m a.s.l. Only non-fed females were considered for the microbiota analysis. Thirty females belonging to the species Ae. albopictus and 30 to Ae. koreicus were included. Most of the specimens were collected by aspiration and CO2-baited BG sentinel traps, with the exception of 3 samples of Ae. koreicus which were captured by human landing technique. All the sampling sites were located in urban and suburban habitats. Mosquitoes were kept alive until the arrival in laboratory and then killed with a brief exposure to low temperature (−20°). Prior to dissection under stereomicroscope, specimens were identified to species level on the basis of morphological features 24,75 .
Midgut isolation and DNA extraction. Before dissection, mosquitoes were surface sterilized in ethanol 70% for few minutes and rinsed with sterile water for molecular analysis. A sterile drop of PBS (100 µl) was used on the slide to facilitate the extraction of midgut. Only mosquitoes without visible traces of blood in the midgut were chosen for the study. Sterilized instruments were used for each dissection while the stereomicroscope was frequently cleaned with absolute alcohol. Midguts were put in sterile tubes and incubated overnight with ATL buffer and proteinase K at 56 °C with a gentle shaking (Thermo-shaker Grant Bio) prior processing. DNA extraction was performed using the Qiamp DNA Investigator kit (Qiagen) protocol "tissues" following the manufacturer's protocol. Final elution volume was 25 µl (ATE buffer). DNA was quantified with fluorometer Qubit 2.0 (Invitrogen).   79 higher than 0.5% and shorter than 400 bp were discarded. Reads with less than 60% similarity to the Greengenes database (May 2013 version, clustered at 85% identity) 80 , were removed using VSEARCH version 1.9.5 81 . 6 101 971 high quality reads were clustered de novo at 97% identity using the "de novo greedy" Operational Taxonomic Unit (OTU) picking method implemented in MICCA. The representative sequences were classified using the consensus classifier 82 against the Greengenes database (May 2013 version) clustered at 97% identity. The sequences were aligned using the NAST 83 multiple sequence aligner and a phylogenetic tree was inferred using the FastTree software available in the MICCA pipeline. Downstream analyses were performed in R environment using the phyloseq 84 , vegan 85 and picante 86 libraries. Midgut samples were rarefied (without replacement) (see Supplementary Fig. 3S) at 90 000 reads per sample. A randomization sampling test was performed in order to rule out any bias in the taxonomic classification 87 (Supplementary Fig. 4S). The average proportion error was calculated as the relative difference between the relative abundance of each taxon in the whole library (i.e., with the maximum number of reads, 9,361,654) and in the random sample (20 random samples for each sample depth). As expected, the consistency of the estimations of taxa abundances grows as the sample depth increases.

Amplicon library preparation and sequencing.
Data analysis: Aedes albopictus and Aedes koreicus, V3-V4 hypervariable region. High Throughput Sequencing resulted in a total of 7 186 454 reads (after paired-end read alignment and merging). Pre-processing, filtering, clustering, taxonomic classification, multiple sequence alignment and phylogenetic tree inference was applied as for the V5-V6 samples. Samples were rarefied (without replacement) (see Supplementary  Fig. 5S) at 45 000 reads per sample and one sample with 11 416 reads was removed. The core microbiota of all samples is composed by OTUs seen more than 10 times in at least 50% of the samples in each species. The species specific microbiota is composed by OTUs seen more than 10 times in at least 50% of the samples in one species and in less than 5% of samples in the other. Indicator species analysis was performed using the R package indicspecies 88 . P-values were FDR corrected.

Bacterial community diversity.
To quantify the bacterial richness in each mosquito species three different α-diversity estimators were used: the number of observed OTUs, the Chao 1 estimator and the Shannon entropy.
To highlight the differences in the midgut microbiota of Ae. albopictus among countries and between Ae. koreicus and Ae. albopictus, we calculated the β-diversity using the unweighted and weighted Unifrac distances 89 and the Bray-Curtis (BC) dissimilarity 90 . Principal Coordinates Analysis (PCoA) was used to visualize differences between microbial communities in samples according to weighted and unweighted Unifrac measures and BC values. Statistical significance of the between-groups distances was assessed using PERMANOVA (Permutational Multivariate Analysis Of Variance Using Distance Matrices) 91 (with 9 999 permutations), implemented in the adonis function in the vegan R-package. We defined as 'core' the set of OTUs with at least 10 reads in at least 50% of the samples from each species, and as 'specific' the set of OTUs with at least 10 reads in at least 50% of the samples from one species, but absent from the other (i.e. present in less than 5% of the samples). OTUs lesser than 0.05%, in at least 20% of the samples were removed.

Data Availability
All data generated or analysed during this study are included in this published article (and its Supplementary Materials files).