Community RNA-Seq: multi-kingdom responses to living versus decaying roots in soil

Erin E Nuccio,Nhu H Nguyen,Mary Firestone,Jennifer Pett-Ridge,Eoin Brodie,Jeremy Bougoure,Peter K Weber,Xavier Mayali,Ulisses Nunes Da Rocha

doi:10.1038/s43705-021-00059-3

Abstract

Roots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis (“community RNA-Seq”) and simultaneously assess the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in 13CO2-labeled microcosms amended with 15N-root litter to identify the preferences of rhizosphere organisms for root exudates (13C) versus decaying root biomass (15N) using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group’s more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving complex interactions, and our methodology can be used to track the trajectory of carbon through multi-kingdom soil food webs.

Highlights

Soil carbon is derived primarily from root inputs, both living and detrital [1,2,3,4], and the fluxes that control the size of the soil carbon pool are critical to the global carbon (C) cycle
While it is widely recognized that soil bacteria, fungi, and fauna are instrumental to decomposition [8], typically these groups are studied in isolation, and less is known about how the greater soil food web of bacteria, archaea, fungi, and microfauna responds to decomposing litter in the rhizosphere versus surrounding bulk soil
While it is widely recognized that soil bacteria, fungi, and fauna are instrumental to organic matter decomposition [8], typically these groups are studied in isolation, and less is known about how the greater soil food web interacts with and is shaped by the availability of different organic substrates

Summary

Introduction

Soil carbon is derived primarily from root inputs, both living and detrital [1,2,3,4], and the fluxes that control the size of the soil carbon pool are critical to the global carbon (C) cycle. While it is widely recognized that soil bacteria, fungi, and fauna are instrumental to decomposition [8], typically these groups are studied in isolation, and less is known about how the greater soil food web of bacteria, archaea, fungi, and microfauna responds to decomposing litter in the rhizosphere versus surrounding bulk soil. Microbial ecology surveys studying litter decomposition that use amplicon sequencing have primarily focused on bacteria or fungi, but decomposition is conducted by a broad array of organisms [9] including microfauna (here we use this umbrella term to include protists, nematodes, and other soil invertebrates

Methods

Results

Conclusion