Genomes and Metabolic Traits of Soil Microorganisms Enhanced by Organic Compost Amendment

Abstract:

Soil C storage impacts soil water retention through complex interactions between nutrient inputs, soil physicochemical properties, and soil microbiome. To elucidate the mechanistic basis of soil carbon storage, we are investigating the functional traits of soil microbial communities responding to different cropping practices using metagenomics. Our study is at Russell Ranch Sustainable Agriculture Facility and is part of the Century Experiment representing different crops and management systems that has been in place for over 20 years. We analyzed metagenomes from 64 soil samples from post-harvest sampling of the conventional, conventional plus cover-crop, and cover-crop plus organic compost-amended plots of rotational corn and tomato, and spanning soil depths up to 1m. 20 years of organic amendment enriched a variety of microbial taxa and functional genes across depths. In contrast, cover-crops had little effect relative to conventional systems on post-harvest microbial communities and their functional capacity at any depth. To date, we have reconstructed 121 MAGs spanning ten phyla. MAGS that were more frequent in surface depths included Thaumarchaeota (Nitrososphaera), various Actinobacteria, Aneromyxobacter and Xanthomonadaceae. Chloroflexi MAGs were exclusive to subsurface depths down to 60 cm. In the surface soils (0-30 cm), MAGs that were significantly enriched by the organic amendment included representatives of Nitrosphaera, Acidobacteriaceae, Gemmatimonas, Anaeromyxobacter and Sinobacteraceae. Subsurface soils down to 1 m were significantly enriched in MAGs representing Anaerolinea and Acidobacteria. These MAGs represent taxa, frequently detected in soil by taxonomic surveys but little is known about their functional importance. The majority of genes enriched by the organic amendment belonged to Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Proteobacteria and Thaumarchaeota. Organic amended soils were enriched in metabolic traits involved in the biosynthesis/breakdown of carbohydrates/lipids, nucleotides and amino acids, and energy production. Several microorganisms with C fixation pathways were enriched by organic amendment soils, indicating that stimulation of chemoautotrophic bacteria may further enhance C storage in subsurface soils.