Functional potential differences between <i>Firmicutes</i> and <i>Proteobacteria</i> in response to manure amendment in a reclaimed soil

Abstract

Manure amendment generally bolsters soil organisms but not all bacteria equally. To understand why different taxa respond differently, we used shotgun metagenomic approaches to profile functional potentials and correlate them with taxon abundances. A soil originally unproductive was reclaimed using commercial manure and finally became productive. The abundance of <i>Firmicutes</i> in the soil decreased, whereas that of <i>Bacteroidetes</i> and <i>Proteobacteria</i> increased after manure addition. Thirty-nine KEGG modules were significantly different across fertilizer treatments. These modules were mainly associated with the phosphoenolpyruvate-dependent phosphotransferase system (PTS), ATP-binding cassette (ABC) transporters, and two-component signal transduction systems. The <i>Proteobacteria</i> and <i>Firmicutes</i> mainly contributed to these modules. Correlation between the abundances of phyla and orthologs showed two distinctive patterns. One linked the <i>Firmicutes</i> to cell wall biosynthesis, PTS, and ABC transporters, and the other linked the <i>Betaproteobacteria</i>, <i>Bacteroidetes</i>, and <i>Verrucomicrobia</i> to lipopolysaccharide biosynthesis, bacterial motility, and carbon metabolism. Correlation between the abundances of phyla and Carbohydrate-Active Enzyme Database families also showed two distinctive patterns, one of them linking the <i>Betaproteobacteria</i>, <i>Bacteroidetes</i>, and <i>Verrucomicrobia</i> to very high abundances of glycosyltransferases and glycoside hydrolases. Overall, the <i>Proteobacteria</i> and <i>Firmicutes</i> were main drivers of functional potential differences across fertilizer treatments. The <i>Firmicutes</i> were enriched with genes associated with cell wall biosynthesis and membrane transports, while <i>Proteobacteria</i> with lipopolysaccharide biosynthesis and carbohydrate metabolism, which supports our hypothesis that the <i>Firmicutes</i> have a lower potential for utilizing manure-derived carbohydrates, while <i>Proteobacteria</i> have a higher potential. This explains why the <i>Proteobacteria</i> and <i>Firmicutes</i> responded to manure differently.