Scaling of plant chemotypic traits in Populus with potential desirable effects on soil microbial nitrogen cycle processes

Background/Question/Methods

Nitrogen fertilizer improves crop performance, but can increase agricultural energy consumption, negatively impact water quality, and promote the release of the greenhouse gas (GHG) nitrous oxide from agricultural soils. Some plant allelochemicals limit nitrifier activity in the soils through Biological Nitrification Inhibition (BNI), potentially reducing negative environmental aspects of N-fertilization. Our Bio-Scales project is using a genes-to-ecosystem approach to explore BNI of GWAS variants of the bioenergy crop Populus. These Populus genotypes produce variable amounts of allelochemicals that potentially impact nitrifying microorganisms, such as para-coumaric, ferulic and alpha-linolenic acids. We collected target plant genotypes with high and low expression levels for these secondary metabolites, as well as their associated rhizosphere and bulk soils, from two sites in Clatskanie and Corvallis Oregon in 2020. We analyzed replicate samples from 30 plant genotypes from the two sites through metagenomic sequencing of soil, rhizosphere and root microbiomes. We then used the FAMA Genome Profiling tool to identify changes in nitrogen-cycling gene abundance within the rhizosphere and bulk soil metagenomes. In addition, we are working to broadly associate patterns in plant metabolomics (analyses ongoing), soil/rhizosphere metagenomes, soil chemistry, nitrification and denitrification rates to identify the potential effects of these compounds through their host-microbiome-soil interactions.

Results/Conclusions

Nitrogen-cycling gene abundance and composition is both compartment and site specific, and the effects of both tree genotypic and chemotypic Populus traits scale differently across both sites. Across all nitrogen-cycle functions, gene composition in the rhizosphere metagenomes was significantly different than the bulk soil metagenomes. Normalized gene abundance in the rhizosphere metagenomes for functional genes associated with nitrate assimilatory reduction and nitrite assimilation, were significantly lower within the Clatskanie site than the Corvallis site and nitrification and denitrification rate potentials were significantly lower. Although metabolomic analyses of our root samples for target BNI compounds is ongoing, nitrogen-cycling gene abundance appears to also be altered under genotypes with predicted expression levels of BNI-related compounds available from prior leaf metabolomic datasets. Within the Clatskanie site, the gene abundance for both nitrate assimilatory reduction and nitrate assimilation is significantly lower in high expressing Populus chemotypes. Further, normalized gene abundance levels within both bulk soil and rhizosphere metagenomes are highly correlated with overall soil carbon, nitrogen, ammonium and nitrification rates. Through highly coordinated analyses of plant chemotypic traits, microbiome characterization, and their soil nitrogen cycle effects, the Bio-Scales project will identify key pathways and mechanisms through which gene functions may ultimately have ecosystem-scale consequences.