Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

Cervin Guyomar,Christophe Mougel,Jean-Christophe Simon,Emmanuelle Jousselin,Claire Lemaitre,Fabrice Legeai

doi:10.1186/s40168-018-0562-9

Abstract

BackgroundMost metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact.ResultsWe present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host.ConclusionsWe present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.

Highlights

Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism
Most of the microbiome diversity is captured by the mapping approach On average, 90% of the reads were assigned by mapping to the pea aphid nuclear or mitochondrial genomes
Presence and absence of symbionts as inferred from read depth was in agreement with the results of PCR diagnostic tests conducted for individual samples [42], and the few mismatches observed in the previous study were corrected by the choice of more appropriate reference sequences for Rickettsia sp., R. viridis, and Spiroplasma sp

Summary

Introduction

Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The pea aphid is a model system for the study of insect-bacteria symbiosis It is organized in a complex of biotypes, each adapted to specific host plants. A prerequisite to understand the functional, ecological, and evolutionary implications of host-microbiota associations for holobionts is to evaluate the extent and partitioning of diversity at different scales involving individuals and populations of holobionts. This can be obtained from (i) a full inventory of the microbial entities associated with the host, including transient low abundant symbionts and (ii) a fine characterization of the genomic diversity of microbial partners both within and between individual hosts from different populations. Inter-individual host diversity is often ignored when pooling together several individuals, or underestimated by insufficient sampling in the population, and intra-host variability is rarely considered, but these two levels are essential to infer the evolutionary dynamics of host microbiota interactions [12] and to better link microbiota diversity with associated phenotypic changes in the host [13]

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