Comparative gene expression on a co-culture of anaerobic ammonium and sulfur-oxidizing bacteria under ammonium and nitrate limitation

Comparing the expression of genes under different growth conditions can provide valuable insight into the response of a microorganism to changing environmental conditions. To elucidate the effect of nitrate- and ammonium-limiting conditions on anammox bacteria and autotrophic denitrifiers we subjected a previously described co-culture of a sulfide-dependent denitrifier and anammox bacteria to differential limitations and compared the short-term changes in the transcriptome of the key players to those under standard conditions. Under ammonium-limiting conditions 762 genes of Scalindua sp. were either up- or downregulated representing about 15% of the total predicted genes. As ammonium was an essential substrate its low concentrations led to the downregulation of genes involved in energy conservation, transcription, translation, protein biosynthesis, cell division and carbon fixation. The ammonium transporting genes (amtB) were significantly upregulated (7-128-fold) under ammonium limitation. The two encoded focA-like formate/nitrite transporters were also upregulated (5-10-fold), replacing the nirC-like scal00416 as the most highly expressed nitrite transporter. Also genes involved in the formation of flagella were highly upregulated under ammonium limitation to ensure motility under unfavorable conditions. Nitrate limitation did not have the same effect as differential expression of only 228 genes (4.6%) could be observed. Sedimenticola sp. differentially expressed 742 genes under nitrate limitation, which represents 17% of all its genes. The most significant changes were the downregulation of genes making up the membrane-bound nitrate reductase complex, genes involved in sulfur metabolism as well as energy conservation and central metabolism. For Sedimenticola sp., ammonium limitation resulted in the up- or downregulation of 331 genes, including the upregulation of ammonium transporter genes and genes encoding nitrogen assimilation enzymes. This study presents the first insights into the interaction of anammox bacteria and its denitrifying partner at the molecular level by studying gene expression changes in response to ammonium and nitrate.