# Shotgun Metagenome Analysis of Two Schizaphis graminum Biotypes over Time With and Without Carried Cereal Yellow Dwarf Virus

## TL;DR

This study analyzed the microbes in greenbug aphids over time, finding that their microbial communities changed significantly, especially as the wheat host declined.

## Contribution

A novel RNA-seq approach was used to track microbial changes in greenbug aphids with and without a virus over time.

## Key findings

- Microbial communities in greenbugs shifted significantly from early to late stages, with a decline in fecal-like bacteria.
- The aphid endosymbiont Buchnera aphidicola was less dominant than expected, accounting for less than 25% of read counts.
- The late microbial community likely responded to starvation as the wheat host deteriorated from aphid feeding.

## Abstract

The greenbug aphid is one of the leading pests of wheat and sorghum in the United States. Messenger RNA was used to inventory the microorganisms in two forms of greenbugs, each with and without a wheat virus, over 20 days. Many of the most common bacteria were similar to those in human feces, while an important aphid-specific bacterium was not as dominant as usually seen in aphids. The overall microbial population declined by 50% from day 5 to day 20, led by a decline in the typical fecal organisms. The greenbug genotype and wheat virus affected the microorganisms less than the collection date. This study adds to basic knowledge about microbes in aphids and the methods used to census these microbes.

The greenbug aphid (Schizaphis graminum (Rondani)) is a major pest of wheat and an important vector of wheat viruses. An RNA-seq study was conducted to investigate the microbial effects of two greenbug genotypes, the presence or absence of cereal yellow dwarf virus, and the condition of the wheat host over a 20-day time course of unrestricted greenbug feeding. Messenger RNA reads were mapped to ca. 47,000 bacterial, 1218 archaeal, 14,165 viral, 571 fungal, and 94 protozoan reference or representative genomes, plus greenbug itself and its wheat host. Taxon counts were analyzed with QIIME2 and DESeq2. Distinct early (days 1 through 10) and late (days 15 and 20) communities differed in the abundance of typical enteric genera (Shigella, Escherichia, Citrobacter), which declined in the late community, while the ratio of microbial to greenbug read counts declined 50% and diversity measures increased. The nearly universal aphid endosymbiont, Buchnera aphidicola, accounted for less than 25% of the read counts in both communities. There were 302 differentially expressed (populated) genera with respect to early and late dates, while 25 genera differed between the greenbug genotypes and nine differed between carrier and virus-free greenbugs. The late community was likely responding to starvation as the wheat host succumbed to aphid feeding. Our results add to basic knowledge about aphid microbiomes and offer an attractive alternative method to assess insect microbiomes.