PS 26-103
Community level physiological profiling of diverse soil environments reveals functional diversity but taxonomic homogeneity within aerobic, single carbon source enrichments

Tuesday, August 12, 2014
Exhibit Hall, Sacramento Convention Center
Theodore M. Flynn, Computation Institute, University of Chicago and Argonne National Laboratory, Chicago, IL
Jason C. Koval, Biosciences Division, Argonne National Laboratory, Argonne, IL
Stephanie M. Moormann, Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL
Sarah M. Owens, Computation Institute, Earth Microbiome Project (http://www.earthmicrobiome.org), University of Chicago and Argonne National Laboratory, Argonne, IL
Sarah L. O'Brien, Bioscience Division, Argonne National Laboratory, Argonne, IL
Edward J. O'Loughlin, Biosciences Division, Argonne National Laboratory, Argonne, IL
Kenneth M. Kemner, Biosciences Division, Argonne National Laboratory, Argonne, IL
Dionysios A. Antonopoulos, Biosciences Division, Argonne National Laboratory, Argonne, IL
Background/Question/Methods

Community level physiological profiling (CLPP) is a commonly used tool in environmental microbiology that utilizes a 96-well microtiter plate containing a variety of carbon substrates for differentiating microbial communities based on their functional capabilities. Each well on the plate contains a single carbon substrate from one of several categories (e.g. amino acids, carbohydrates, or phenolic compounds) as well as the redox indicator dye tetrazolium violet. Microbial respiration causes an irreversible reaction that transforms the initially-colorless dye into a vivid purple. The broad functional diversity of a community can then be inferred from the pattern of “active” purple wells on the microtiter plate.


We used CLPP to characterize the functional diversity of forest soil, prairie soil, and a freshwater wetland sediment. In addition to characterizing their functional capabilities with CLPP, we also created microbial community profiles of both the initial soil as well as the communities enriched within each well of the microtiter plate. DNA was extracted from sampled wells using the MOBIO PowerSoil DNA Isolation kit followed by targeted PCR amplification and sequencing of the V4 region of the 16S rRNA genes using the Illumina MiSeq platform.

Results/Conclusions

Analysis of 16S rRNA inventories showed that prior to enrichment, forest and prairie soils were more similar to one another than with the wetland sediment, whereas CLPP (based on well-color development) revealed the “functional diversity” of prairie soil and wetland sediment was more similar to each other than to the forest soil. Analysis of the enriched community within each well indicated that active enrichments were almost universally dominated by the genus Pseudomonas, despite these organisms representing <1% of the original inocula. While the rapid growth of Pseudomonas under aerobic conditions is unsurprising, the functional diversity represented by the patterns of positive wells is. Within the forest and prairie soil, at least 89% of the microbial community within each active well was comprised of Pseudomonas. A similar pattern was observed in the wetland sediment enrichments, although the sequences most closely related to the family Aeromonadaceae (Proteobacteria) dominated active wells where mannitol or cellobiose was the sole carbon source. These results provide a molecular-based description of sub-community composition partitioned by CLPP and the promotion of fast-growing community members under aerobic conditions. We are interested in exploring the impact of media components (alternate electron acceptors), more complex substrates, and spatial segregation.