RT Journal Article
SR Electronic
T1 Selective carbon sources influence the end-products of microbial nitrate respiration
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 829143
DO 10.1101/829143
A1 Hans K. Carlson
A1 Lauren M. Lui
A1 Morgan N. Price
A1 Alexey E. Kazakov
A1 Alex V. Carr
A1 Jennifer V. Kuehl
A1 Trenton K. Owens
A1 Torben Nielsen
A1 Adam P. Arkin
A1 Adam M. Deutschbauer
YR 2019
UL http://biorxiv.org/content/early/2019/11/04/829143.abstract
AB Respiratory and catabolic pathways are differentially distributed in microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end-products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end-products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content and function.