Microaerobic Lifestyle at Nanomolar O 2 Concentrations Mediated by Low-Affinity Terminal Oxidases in Abundant Soil Bacteria

Abstract

Low-oxygen habitats are widely distributed on Earth, ranging from the human intestine to soils. Microorganisms are assumed to have the capacity to respire low O 2 concentrations via high-affinity terminal oxidases. High-affinity terminal oxidases (TOs) are believed to permit microbial respiration at low oxygen (O 2 ) levels. Genes encoding such oxidases are widespread, and their existence in microbial genomes is taken as an indicator for microaerobic respiration. We combined respiratory kinetics determined via highly sensitive optical trace O 2 sensors, genomics, and transcriptomics to test the hypothesis that high-affinity TOs are a prerequisite to respire micro- and nanooxic concentrations of O 2 in environmentally relevant model soil organisms: acidobacteria. Members of the Acidobacteria harbor branched respiratory chains terminating in low-affinity ( caa 3 -type cytochrome c oxidases) as well as high-affinity ( cbb 3 -type cytochrome c oxidases and/or bd -type quinol oxidases) TOs, potentially enabling them to cope with varying O 2 concentrations. The measured apparent K m ( K m (app) ) values for O 2 of selected strains ranged from 37 to 288 nmol O 2 liter −1 , comparable to values previously assigned to low-affinity TOs. Surprisingly, we could not detect the expression of the conventional high-affinity TO ( cbb 3 type) at micro- and nanomolar O 2 concentrations but detected the expression of low-affinity TOs. To the best of our knowledge, this is the first observation of microaerobic respiration imparted by low-affinity TOs at O 2 concentrations as low as 1 nM. This challenges the standing hypothesis that a microaerobic lifestyle is exclusively imparted by the presence of high-affinity TOs. As low-affinity TOs are more efficient at generating ATP than high-affinity TOs, their utilization could provide a great benefit, even at low-nanomolar O 2 levels. Our findings highlight energy conservation strategies that could promote the success of Acidobacteria in soil but might also be important for as-yet-unrevealed microorganisms. IMPORTANCE Low-oxygen habitats are widely distributed on Earth, ranging from the human intestine to soils. Microorganisms are assumed to have the capacity to respire low O 2 concentrations via high-affinity terminal oxidases. By utilizing strains of a ubiquitous and abundant group of soil bacteria, the Acidobacteria , and combining respiration kinetics, genomics, and transcriptomics, we provide evidence that these microorganisms use the energetically more efficient low-affinity terminal oxidases to respire low-nanomolar O 2 concentrations. This questions the standing hypothesis that the ability to respire traces of O 2 stems solely from the activity of high-affinity terminal oxidases. We propose that this energetically efficient strategy extends into other, so-far-unrevealed microbial clades. Our findings also demonstrate that physiological predictions regarding the utilization of different O 2 concentrations based solely on the presence or absence of terminal oxidases in bacterial genomes can be misleading.