Microbial diversity and functional potential of the Halobates melleus (Heteroptera: Gerridae) microbiome from the Red Sea coastline

Abstract

Background: Halobates, commonly known as sea skaters, are predatory Hemipterans uniquely adapted to tropical marine environments. Their ability to thrive in oligotrophic and environmentally extreme habitats, such as the open ocean surface and marine coastal areas, suggests the evolution of specialised adaptations, possibly including symbiotic associations with microorganisms that can support nutrition, niche adaptation, and stress resilience. To explore this hypothesis, we analysed the bacterial communities associated with Halobates melleus, a species inhabiting the Red Sea coastal mangroves in Saudi Arabia.

Results: Amplicon sequencing of the 16S rRNA gene and metagenomic analyses of composite body and gut samples from adult H. melleus revealed a population-level bacterial community dominated by Wolbachia and Spiroplasma, consistent with patterns observed in several terrestrial predatory insects. Members of Providencia and Swaminathania were also detected, along with other minor taxa that may represent transient environmental commensals. The identified bacteria encoded genes for the biosynthesis of essential vitamins and prosthetic groups, such as riboflavin and heme-compounds typically not synthesised de novo by insects-as well as amino acids, likely contributing to the host's nutritional requirements. Notably, the Wolbachia metagenome-assembled genome from H. melleus clustered within the supergroup B, showing high genetic similarity to strains from phylogenetically distant Dipteran and Lepidopteran hosts that nonetheless inhabit common ecological niches, i.e., mangrove and tropical environments. This extends the known ecological breadth of Wolbachia symbioses to marine insects, underscoring their evolutionary and environmental versatility.

Conclusion: Our findings highlight the potential nutritional and metabolic roles of the Halobates-associated bacterial microbiome, particularly members of the Wolbachia genus. This emphasises the importance of microbial symbionts in the ecological success and adaptation of marine insects, offering a perspective complementary to previously studied terrestrial insect microbiomes.

Keywords: Halobates; Wolbachia; Extreme environment; Marine insect; Metabolic potential; Metagenome; Microbiome; Symbiont.

Fig. 1

Sampling site and Halobates melleus individuals. (A) Satellite image of the mangroves near the King Abdullah monument at KAUST, Thuwal, Saudi Arabia. Orange icons represent the sampling sites. (B) Image of grey mangrove (Avicennia marina) stands where H. melleus are found (scale bar = 100 m). (C) Cluster of H. melleus; the zoomed-in inset shows individuals at different stages in a cluster. Activity and movement of insect clusters are shownin the Additional file Video S1. (D and E) Sampled individuals. (F) Separation of individuals by life stages and sex was conducted under a stereo microscope to distinguish and separate adult females and males (scale bar = 2 mm). (G) Representative image of dissected gut from adult individuals (scale bar = 1 mm)

Fig. 2

Microbiome composition and distribution of H. melleus. (A and C) Relative abundances of bacterial taxa associated with the body and gut based on (A) amplicon sequencing of the 16S rRNA gene and (C) the count of rplN gene from metagenome reads. Each taxon is organised by bacterial class and represented by average relative abundance within replicates of each sample; F denotes female, M denotes male, B denotes body, and G denotes gut. (B and D) Nonmetric multidimensional scaling (nMDS) ordination plot based on Bray–Curtis dissimilarity matrices. (B) nMDS of 16S rRNA gene amplicon sequencing data, showing separation between body (black), gut (yellow) samples, with symbols indicating females (squares) and males (triangles). (D) nMDS of metagenomic composite rplN sequence variants (rplN SVs) grouped at the lowest taxonomic ranking available (i.e., taxonomic clusters). Their positioning in the ordination space is based on their distribution across samples. Dot colour indicates the sample type in which rplN SVs were enriched: body-enriched (black), gut-enriched (yellow), and generalist/non-specific found in both sample types (grey). Taxonomic clusters matching the five representative metagenome-assembled genomes (MAGs, Fig. 3A and Table 1) are indicated with arrows

Fig. 3

Taxonomic identification and metabolic potential of bacterial MAGs associated with Halobates melleus. (A) Phylogenetic tree of high-quality (green) and medium-quality (orange) MAGs showing the closest related species identified by GTDB-Tk. (B) Heat map indicating the presence of complete pathway (blue) for the biosynthesis of amino acids, B vitamins, nucleotides, prosthetic groups, and CAZYmes. Incomplete pathways are reported in white. (C) Heat map of the presence of transporters for amino acids, B vitamins, nucleotides, prosthetic groups, and sugars. Shades of red colour indicate a higher number of genes per category, blues indicate fewer genes, and white indicates that the genes were not present

Fig. 4

Co-occurrence network of bacterial communities in H. melleus. Co-occurrence network based on statistically supported proportional associations among (A) ASVs (16S rRNA gene amplicon sequencing dataset) or (B) taxonomic clusters (rplN gene from metagenome dataset). Node colour represents the bacterial taxonomy of bacterial ASVs and rplN SVs. The node size is proportional to the number of connections formed. Black edges indicate significant (ρ-values, 5% FDR cutoff) positive relationships between nodes. Taxonomic clusters from rplN gene SVs corresponding to MAGs are labeled with their respective MAG codes (see Fig. 3A for details on taxonomic affiliations)

Fig. 5

Phylogenomic tree of Wolbachia strains. The phylogenomic relationships among Wolbachia strains were reconstructed throughmaximum likelihood (ML) analysis of the core genome alignment (see Methods), including 41 arthropod- and 10 nematode-associated strains. Nodes are supported by bootstrap values of 1 based on 1,000 replicates. Colour boxes indicate Wolbachia supergroups, coloured circles represent the host organisms, and the red arrow marks the MAG corresponding to Wolbachia of Halobates melleus (wHme)