PS 6-77 - Linking soil biology and chemistry using knowledge of exometabolite substrate preferences

Monday, August 7, 2017
Exhibit Hall, Oregon Convention Center
Tami L. Swenson, Environmental Genomics and Systems Biology, Lawrence Berkeley National Lab, Berkeley, CA, Ulas Karaoz, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, Joel M. Swenson, Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, CA, Richard Baran, Thermo Fisher Scientific, San Jose, CA, Benjamin Bowen, Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA and Trent Northen, Joint Genome Institute, Walnut Creek, CA

The connections between soil metabolites and microbial community structure are not well-understood. The dramatic expansion of sequencing data provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microbes process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Understanding these dynamics are of particular interest in biocrust since these microbial ecosystems inhabit the surface of soils found in arid regions comprising more than 40% of Earth’s terrestrial surface and play a critical role in soil stabilization and nutrient cycling.

To facilitate correlation between soil microbes and metabolites, we focused on the cascade of microbial activity set in motion upon wetting of dry biocrust. At five timepoints following wetup and across four successional stages, soil water was collected and analyzed by normal-phase liquid chromatography/ mass spectrometry for metabolites and DNA was extracted and sequenced on the HiSeq sequencing platform. Ribosomal protein (L15) was used as a phylogenetic marker and sequences were compared to exometabolite-profiled isolates to determine relative abundance of isolate phylotypes in biocrust.


Biocrust wetting caused a dramatic shift in both microbial community structure and soil water metabolite profiles. Four dominant organisms in the biocrust were close phylotypes of the exometabolite-profiled isolates: a cyanobacterium (Microcoleus spp.), two firmicutes (Anoxybacillus sp. and Bacillus sp.) and an actinobacterium (Blastococcus sp.). Overall, soil metabolites displayed the expected directionality (positive or negative correlation) with isolate phylotype abundance. Specifically, 78% of the metabolites that were consumed by an isolate were negatively correlated with their phylotypes in situ and 73% of released metabolites were positively correlated.

Our results demonstrate that metabolite profiling, sequencing and exometabolomics can be successfully integrated to functionally link metagenomes and microbial community structure with environmental chemistry. Current efforts are now focused on continuing exometabolite profiling with additional biocrust isolates in order to be able combine bacteria into functional guilds based on substrate preferences. Continued analyses of their metagenomes may allow us to understand how exometabolite profiles relate to metabolic potential. Ultimately, these results are expected to further our understanding of the functions that link soil biology and chemistry.