Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil

Abstract

The functioning, health, and productivity of soil is intimately tied to a complex network of interactions, particularly in plant root-associated rhizosphere soil. We conducted a stable isotope-informed, genome-resolved metagenomic study to trace carbon from Avena fatua grown in a 13CO2 atmosphere into soil. We collected paired rhizosphere and non-rhizosphere soil at six and nine weeks of plant growth and extracted DNA that was then separated by density using gradient centrifugation. Thirty-two fractions from each sample were grouped by density, sequenced, assembled, and binned to generate 55 unique microbial genomes that were >70% complete. The complete 18S rRNA sequences of several micro-eukaryotic bacterivores and fungi were enriched in 13C. We generated several circularized bacteriophage (phage) genomes, some of which were the most labelled entities in the rhizosphere. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genomes for traits known to be used in interactions involving bacteria, micro-eukaryotes and plant roots and found that heavily isotopically-labeled bacteria have the ability to modulate plant signaling hormones, possess numerous plant pathogenicity factors, and produce toxins targeting micro-eukaryotes. Overall, 13C stable isotope-informed genome-resolved metagenomics revealed that very active bacteria often have the potential for strong interactions with plants and directly established that phage can be important agents of turnover of plant-derived carbon in soil.

The Functional Significance of Bacterial Predators

“…These results suggest that bacteria should be considered alongside eukaryotes and viruses as important predators in microbial food webs. Similarly, a recent metagenomic qSIP analysis using a 13 C-CO 2 tracer introduced via plant root exudates found that 13 C recovery in metagenomes associated with putative predator bacteria was comparable to the recovery in viruses and substantially higher than that in predatory eukaryotes (40). Slower growth might be expected if bacterial predators were inactive or dormant, as are many soil microorganisms (41).…”

Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches

“…In this study, we investigated the cooccurrence patterns of bacterial and fungal communities over space and time, using amplicon sequences of bacterial 16S and fungal internal transcribed spacer (ITS) rRNA genes, in soil samples from a greenhouse experiment that has previously yielded information on bacterial succession and cooccurrence patterns (47,48) as well as potential trophic interactions revealed by stableisotope-informed genome-resolved metagenomics (49). This experiment used soil from a California annual grassland and the annual grass Avena fatua, which is common and naturalized to the area from which the soil was collected.…”

The Functional Significance of Bacterial Predators

“…These results suggest that bacteria should be considered alongside eukaryotes and viruses as important predators in microbial food webs. Similarly, a recent metagenomic qSIP analysis using a 13 C-CO 2 tracer introduced via plant root exudates found that 13 C recovery in metagenomes associated with putative predator bacteria was comparable to the recovery in viruses and substantially higher than predatory eukaryotes (53). Slower growth might be expected if bacterial predators were inactive or dormant, as are many soil microorganisms (54).…”