Transcription of protease and chitinase genes provides a window onto macromolecular organic nitrogen decomposition in soil
AbstractNitrogen is a common limiting nutrient in soil in part because most N is present as macromolecular organic compounds, not directly available to plants. The microbial community present in soil near roots (rhizosphere) is in many ways analogous to the human gut microbiome, transforming nutrients present in organic substrates to forms available to plants through extracellular enzymes. Many recent studies have focused on the genetic potential for nitrogen cycling by bacteria in the
... re, and on measuring inorganic N pools and fluxes. Between those two bodies of knowledge, there is scarce information on functionality of macromolecular nitrogen decomposing bacteria and fungi and how it relates to life stages of the plant. This is particularly important as many soil bacteria identified in community composition studies can be inactive or not viable. Here we use a time-series of metatranscriptomes from rhizosphere and bulk soil bacteria and fungi to follow extracellular protease and chitinase expression during rhizosphere aging. In addition, we explore the effect of adding plant litter as a source of macromolecular carbon and nitrogen. Expression of extracellular proteases increased over time in the absence of litter, more so in the presence of roots, whereas the dominant chitinase (chit1) was upregulated with exposure to litter. Structural groups of proteases were surprisingly dominated by serineproteases, possibly due to the importance of betaproteobacteria and actinobacteria in this grassland soil. Extracellular proteases of betaprotebacterial origin were more highly expressed in the presence of roots, whereas deltaroteobacteria and fungi responded to the presence of litter. We found functional guilds specializing in decomposition of proteins in the rhizosphere, detritusphere and in the vicinity of aging roots. We also identify a guild that appears to specialize in protein decomposition in the presence of roots and litter and increases its activity in aging rhizosphere, which may imply that this guild targets rhizodeposits or the senescing root itself as a protein source. Different temporal patterns of guilds imply that rather than functional redundancy, microbial decomposers operate within distinct niches.