Loss and Gain of Gut Bacterial Phylotype Symbionts in Afrotropical Stingless Bee Species (Apidae: Meliponinae)

Abstract

Stingless bees (Apidae: Meliponini) are the most diverse group of corbiculate bees and are important managed and wild pollinators distributed in the tropical and subtropical regions of the globe. However, little is known about their associated beneficial microbes that play major roles in host nutrition, detoxification, growth, activation of immune responses, and protection against pathogens in their sister groups, honeybees and bumble bees. Here, we provide an initial characterization of the gut bacterial microbiota of eight stingless bee species from sub-Saharan Africa using 16S rRNA amplicon sequencing. Our findings revealed that Firmicutes, Actinobacteria, and Proteobacteria were the dominant and conserved phyla across the eight stingless bee species. Additionally, we found significant geographical and host intra-species-specific bacterial diversity. Notably, African strains showed significant phylogenetic clustering when compared with strains from other continents, and each stingless bee species has its own microbial composition with its own dominant bacterial genus. Our results suggest host selective mechanisms maintain distinct gut communities among sympatric species and thus constitute an important resource for future studies on bee health management and host-microbe co-evolution and adaptation.

Keywords: Acetobacteraceae; Bifidobacteriaceae; Dactylurina; Hypotrigona; Lactobacillaceae; Liotrigona; Meliponula.

Figure 1

Gut bacterial genera associated with eight stingless bee species in Kenya. (A) A bar plot representation of all the stingless bee gut bacterial genera with an overall abundance higher than 1%. All genera with abundances below 1% were categorized as “Others”. The phylogeny of Afrotropical stingless bees was based on [8]. (B,C) heatmap comprising of the ASVs from the five most abundant genera across the eight stingless bee species. ASV ID numbers (Table S1) are indicated at the top. Darker squares correspond to higher mean relative abundances for a given ASV in each bee species.

Figure 2

Alpha diversity estimates from the different stingless bee species. (A) Shannon diversity (p = 0.000038, H = 29.672), (B) Evenness diversity (p = 0.00005, H = 29.12), (C) Faith’s phylogenetic diversity (Faith’s PD) (p =0.00018, H = 24.888).

Figure 3

PCoA clustering using (A) Bray–Curtis PCoA, (B) Weighted UniFrac PCoA, (C) Unweighted UniFrac PCoA. The ellipse cluster indicate the distribution of the gut bacterial microbiota with respect to the different species of stingless bees (standard errors at 95% confidence).

Figure 4

Phylogenetic tree showing the relationships between Lactobacillaceae ASVs from this study and reference Lactobacillaceae sequences. Accession Number are indicated at the beginning of each name reported from [41,44,55,56,57,58], and bacterial strains are indicated in brackets. Only ASVs that represent more than 1% among Lactobacillaceae family per species were represented. Percentage greater than 1% of the relative abundance from total reads of each ASV are represented by color bars. Each color represents each stingless bee species using the same color code as in Figure 2 and Figure 3.

Figure 5

Phylogenetic tree showing the relationships between Bifidobacterium from stingless bees from Africa compared to other continents. Accession Number is indicated at the beginning of each name reported in [42,44,57,58,59,60,61,62]. Species from which the bacterial strain was reported and the country of origin (two letter code) are indicated in grey. Only ASVs that represent more than 1% among Bifidobacteriaceae family per species were represented. Percentage greater than 1% of the relative abundance from total reads of each ASV are represented by color bars. Each color represents each stingless bee species using the same color code as in Figure 2 and Figure 3.

Figure 6

Phylogenetic tree showing the relationships between Acetobacteraceae family from African stingless bees compared to other continents. Accession Number is indicated at the beginning of each name reported in [41,42,61,63,64,66,67,68]. Species from which the bacterial strain was reported and the country of origin (two letter code) are indicated in grey. Only ASVs that represent more than 1% among Acetobacteraceae family per species are represented. Percentage greater than 1% of the relative abundance from total reads of each ASV are represented by color bars. Each color represents each stingless bee species using the same color code as in Figure 2 and Figure 3.