Household arthropod- associated microbiota
We studied the microbiota composition associated with the arthropods captures and measured how they varied by arthropod’s family, season (month of sampling) and environments (urban/suburban).
The microbiota identified with the culture-based approach significantly differed among the arthropod families, and between environments, whereas it did not vary by season (Table 1A; Fig. 3A). We cultured and isolated bacteria from 84 pools (72.6%), whereas the remaining 31 pools (27.4%) did not harbour any culturable bacteria. Among the bacteria that could be cultured and taxonomically identified, Gram-positive cocci (including those strains not identifiable at family level) and Gram-positive rods were the most abundant (Fig. 3A, Table S2), followed byStaphylococcaceae (30.36%), Bacillaceae (10.71%) andMicrococcaceae (10.12%) (Fig. 3A, Table S2).Streptococcaceae and Enterococcaceae accounted for 9.52% and 8.33% of the taxonomically assigned sequences, respectively (Fig. 3A; Table S2). The remainder of the taxonomically assigned reads belonged to: Moraxellaceae (4.76%), Dysgonomonandaceae(4.17%), Rhodobacteraceae (4.17%), Yersiniaceae(4.17%), Erwiniaceae (2.98%), Carnobacteriaceae(1.79%), Clostridiaceae (1.79%), Brevibacteraceae(1.19%) and Microbacteriaceae (1.19%) (Fig. 3A, Table S2). Rare families accounting for 0.6% each of the total identified sequences were: Peptostreptococcaceae , Caryophanaceae ,Corynebacteriaceae , Dermabacteraceae ,Enterobacteriaceae , Neisseriaceae ,Pseudomonandaceae and Veillonellaceae (Table S2). A total of 192 isolates could not be identified at family level; they were Gram-positive cocci (49.48% of the unassigned sequences), Gram-positive rods (27.6%), Gram-negative rods (15.10%), Gram-negative cocci (6.77%), Gram-negative coccobacilli (0.52%) and Gram-negative filamentous bacteria (0.52%) (Table S2).
Gram-positive cocci and Gram-positive rods were found in all arthropods, except for Vespidae (Gram-positive cocci) and Blattidae (Gram-positive rods) (Fig. S1A). Even if few bacteria families were shared across the artropod’s families, each arthropod had a unique microbiota composition (Fig. S1A).
The microbiota identified with the metabarcoding approach significantly differed among arthropod families, season (sampling months) and environments (urban/suburban) (Fig. 3B; Table 1). The interaction term Arthropod Family*Season was also significant (Table 1). The metabarcoding approach identified 771 ASVs, taxonomically assigned to 15 phyla, 111 families and 249 genera of bacteria. Among the 10 most abundant families, Rickettsiaceae comprised 67.3 % of the identified families, followed by Anaplasmataceae (10.59%), unidentified family of the class Bacilli (3.59%),Proprionibacteriaceae (3.71%), Porphyromonadaceae(3.29%), Micrococcaceae (2.89%), Enterobacteriaceae(2.89%), Enterococcaceae (2.12%), Methylobacteriaceae(1.83%) and an unidentified family of the order Burkholderiales(1.78%) (Fig. 3B; Table S2). The metabarcoding approach revealed thatRickettsiaceae were common and abundant in the microbiota of all arthropod families, followed by Anaplasmataceae (Fig. S1B; Table S2). Bacilli were abundant in Tipulidae ; they were present in low abundance in 50% of the captured arthropods (Fig. S1B). Although the microbiota of the different arthropod families was dominated byRickettsiaceae , the relative abundance of other bacterial families was distinct among the arthropods (Fig. S1B, Table S2). For example, Enterobacteriaceae and Micrococcaceae made up 15.2 and 13.9%, respectively, of the Agelenidae microbiota, whereasEnterococcaceae (14.4%) were the second most abundant bacteria family in Blattidae (Fig. S1B; Table S2). The microbiota ofCalliphoridae was dominated by Porphyromonandaceae(70.7%), whereas Rickettsiaceae (8.3%) accounted for a small proportion of this microbiota (Fig. S1B).
We studied the change in community composition of the exogenous and endogenous microbiota separately in the arthropod captures between July and October 2019. We asked if changes in the endogenous and exogenous microbiota were explained by the arthropod family, the month of collection and their interaction terms. We also studied the correlation between the exogenous and endogenous microbiota communities with environmental variables. In the culture-based approach, the endogenous and exogenous microbial communities varied significantly by the arthropod families, whereas they did not differ significantly among seasons (month of collection; Fig. 4A; Table 2). Gram-positive cocci were abundant in both the endogenous and exogenous microbiota (Fig. 4A). Some bacteria families were only found in the exogenous microbiota (Staphylococcaceae , Peptostreptococcaceae ,Bacillaceae , Enterococcaceae , Rhodobacteraceae andErwiniaceae were isolated from the exoskeleton of the arthropods), whereas others were unique to the endogenous microbiota (Enterococcaceae , Erwiniaeae , Rhodobacteraceae ,Micrococcaceae , Carnobacteriaceae andStreptococcaceae ) (Fig. 4A). Some bacterial families were arthropod-specific: Staphylococcaceae were only found in the exogenous microbiota of Coccinellidae and Blattidae ;Rhodobacteraceae were only found in the endogenous microbiota of Blattidae and the exogenous microbiota of Gnaphosidae (Fig. 4A).Carnobacteriaceae and Streptococcaceae were only found in the Coccinellidae ’s endogenous microbiota (Fig. 4A).
The endogenous and exogenous microbiota identified with the metabarcoding approach were overall divergent and varied significantly by the arthropod family, whereas they did not differ significantly by the sampling month (Table 2). Rickettsiaceae were both common and abundant across the arthropods’ families (Fig. 4B). The exogenous microbiota was dominated by Rickettsiaceae, comprising 64.1% of the microbiota in Blattidae , 30.2% in Coccinellidae , 55.8% in Gnaphosidae spiders, 76.3% in Pholcidae and 34.4% of inTipulidae . The exogenous microbiota of Coccinellidae andTipulidae were the most diverse among the arthropods studied here. In addition to Rickettsiaceae , Coccinellidaeexogenous microbiota included Propionibacteriaceae (18.1%),Methylobacteriaceae (13.7%), Micrococcaceae (11.4%), andStreptococcaceae (9.4%) in relatively high abundance (Fig. 4B). The exogenous microbiota of Tipulidae comprisedEnterobacteriaceae (23.7%), Bacilli (16.9%),Planococcaceae (6.1%), Streptococcaceae (5%), in addition to Rickettsiaceae (Fig. 4B). The endogenous microbiota composition was arthropod-specific. For example, Enterococcaceaemade up 94% of the endogenous microbiota of Blattidae , whereas they were in low abundance (<1%) in other arthropods (Fig. 4B). Bacilli comprised 93% of the endogenous microbiota inTipulidae and 42% in Coccinellidae (Fig. 4B).Anaplasmataceae were present in low abundance in the endogenous microbiota of all arthropods and abundant (35%) in Gnaphosidae(Fig. 4B).
We used the Spearman correlation combined with the Shannon-Wiener index, which combines species richness and relative abundances, to establish associations between endogenous/exogenous bacterial communities and environmental variables: temperature, precipitation, humidity, and wind speed. Neither the endogenous nor the exogenous microbiota compositional changes were explained by significant covariation with the environmental variables (Table S3).