Bacterial biota associated with the invasive insect pest Tuta absoluta (Meyrick)

Abstract

Tuta absoluta (the tomato pinworm) is an invasive insect pest with a highly damaging effect on tomatoes causing between 80 and 100% yield losses if left uncontrolled. Resistance to chemical pesticides have been reported in some T. absoluta populations. Insect microbiome plays an important role in the behavior, physiology, and survivability of their host. In a bid to explore and develop an alternative control method, the associated microbiome of this insect was studied. In this study, we unraveled the bacterial biota of T. absoluta larvae and adults by sequencing and analyzing the 16S rRNA V3-V4 gene regions using Illumina NovaSeq PE250. Out of 2,092,015 amplicon sequence variants (ASVs) recovered from 30 samples (15 larvae and 15 adults), 1,268,810 and 823,205 ASVs were obtained from the larvae and adults, respectively. A total of 433 bacterial genera were shared between the adults and larval samples while 264 and 139 genera were unique to the larvae and adults, respectively. Amplicon metagenomic analyses of the sequences showed the dominance of the phylum Proteobacteria in the adult samples while Firmicutes and Proteobacteria dominated in the larval samples. Linear discriminant analysis effect size (LEfSe) comparison revealed the genera Pseudomonas, Delftia and Ralstonia to be differentially enriched in the adult samples while Enterococcus, Enterobacter, Lactococcus, Klebsiella and Wiessella were differentially abundant in the larvae. The diversity indices showed that the bacterial communities were not different between the insect samples collected from different geographical regions. However, the bacterial communities significantly differed based on the sample type between larvae and adults. A co-occurrence network of significantly correlated taxa revealed a strong interaction between the microbial communities. The functional analysis of the microbiome using FAPROTAX showed that denitrification, arsenite oxidation, methylotrophy and methanotrophy as the active functional groups of the adult and larvae microbiomes. Our results have revealed the core taxonomic, functional, and interacting microbiota of T. absoluta and these indicate that the larvae and adults harbor a similar but transitory set of bacteria. The results provide a novel insight and a basis for exploring microbiome-based biocontrol strategy for this invasive insect pest as well as the ecological significance of some of the identified microbiota is discussed.

Figure 1

Rarefaction curves of the 30 samples.

Figure 2

Top 10 bacteria phyla from the adult and larval samples.

Figure 3

Top Abundant Bacterial species based on sample type ranging from 0 (least abundant) to 4 (most abundant).

Figure 4

LEfSe result based on differentially abundant taxa in the larvae as compared to that of the adult.

Figure 5

The Shared and Unique bacterial ASVs in each sample type.

Figure 6

Bacterial communities Alpha diversity indices- Observed, Chao1, Shannon and Simpson of the adult and larva samples of T. absoluta.

Figure 7

Principal co-ordinate analysis (PCoA) of the beta diversity of larval and adult samples beta diversity analyses by PERMANOVA at P < 0.01.

Figure 8

(A) Network analyses of the bacterial biota from adult samples. Each connection stands for a strong (Spearman's ρ > 0.7) and significant (P-value < 0.01) correlation. The size of each node is proportional to the number of its connections (degree). ASVs coloured by taxonomy. (B) Network analyses of the bacterial biota from larvae samples. Each connection stands for a strong (Spearman's ρ > 0.7) and significant (P-value < 0.01) correlation. The size of each node is proportional to the number of its connections (degree). ASVs coloured by taxonomy.

Figure 9

Abundance of the 20 predicted bacterial functions in the adult and larvae of T. absoluta as predicted by FAPROTAX.