Pathway-level analysis suggests a maintenance-oriented transcriptional response of the ammonia-oxidizing bacterium Nitrosospira sp. NT to acidic pH

Abstract

Acidic environments impose energetic constraints on ammonia-oxidizing bacteria (AOB), although some acid-tolerant lineages remain capable of ammonia oxidation at low pH. The transcriptional responses of acid-tolerant AOB to low-pH conditions remain poorly resolved. Here, we characterized the pathway-level response of Nitrosospira sp. NT by integrating a reconstructed metagenome-assembled genome with comparative metatranscriptomic data from cultures incubated for 24 h at pH 5.0 or pH 8.0. Transcript abundance was not uniformly reduced among the metabolic pathways examined at pH 5.0. Genes associated with the Calvin–Benson–Bassham cycle, the oxidative tricarboxylic acid cycle, nucleotide and deoxyribonucleotide biosynthesis, glycogen metabolism, and septal peptidoglycan synthesis generally showed lower transcript abundance, indicating reduced expression of pathways linked to biomass production and cell proliferation. By contrast, transcripts associated with selected oxidative pentose phosphate pathway enzymes, cell-envelope homeostasis, membrane-protein quality control, c-di-GMP-associated surface functions, stored-iron mobilization, and c-type cytochrome maturation showed comparable or higher transcript abundance. Iron-dependent cofactor pathways also responded differently: transcripts related to bacterioferritin-associated iron mobilization and Ccm-dependent cytochrome c maturation were higher, whereas those involved in heme a/o synthesis and SUF-mediated Fe–S cluster assembly were lower. Collectively, these patterns support a maintenance-oriented transcriptional model in which transcripts associated with cellular integrity, redox support, envelope homeostasis, and intracellular iron reutilization were relatively more abundant than those associated with biomass accumulation at pH 5.0. This study provides a pathway-level framework for understanding the transcriptional response of acid-tolerant AOB to acidic conditions.