Differences of heterotrophic ¹³CO₂ assimilation by Pseudomonas knackmussii strain B13 and Rhodococcus opacus 1CP and potential impact on biomarker stable isotope probing

Abstract

Motivated by the finding that Pseudomonas knackmussii B13 but not Rhodococcus opacus 1CP grows in the absence of externally provided CO(2), we investigated the assimilation of (13)CO(2) into active cells cultivated with non-labelled glucose as sole energy substrate. (13)C found in the bulk biomass indicated a substantial but different CO(2) assimilation by Pseudomonas and Rhodococcus, respectively (3500 per thousand and 2600 per thousand). Cellular fatty acids were labelled from -15 per thousand to 470 per thousand and amino acids from 500 per thousand to 24,000 per thousand demonstrating clear differences between various compound classes. 'You are what you eat plus 1 per thousand' is therefore only valid for the average bulk C without specific isotope signature deviation of the external CO(2) or carbonates. Odd-numbered and 10-methyl fatty acids, which are much more abundant in Rhodococcus or other Gram-positive bacteria, were up to fivefold higher enriched in (13)C relative to the Pseudomonas fatty acids. A high-level growth-phase-independent, labelling of the oxaloacetate-derived amino acids indicated heterotrophic CO(2) fixation by anaplerotic reactions known to replenish the tricarboxylic acid cycle. Although both strains assimilate CO(2) via similar general pathways, Rhodococcus depends to a much higher extent on carboxylations reactions with external CO(2) owing to the formation of odd-numbered fatty acids. As a general consequence, heterotrophic fixation of CO(2) should be taken into account in investigations of degradation experiments using isotope tracer compounds.

Tracking heavy water (D 2 O) incorporation for identifying and sorting active microbial cells

“…Microbiologists have tested fluorescent probes and stains to quantify cellular rRNA or its precursors (18,19) and membrane potential (20) as activity measures, but cellular rRNA levels often do not correlate with activity (21) and membrane potential stains perform differently with different cell types (22). Recently, heterotrophic 14 CO 2 fixation was used to infer the general activity of heterotrophic microbes semiquantitatively (23), but the extent of heterotrophic CO 2 fixation can vary widely between different species and also depends on the heterotrophic substrate used for growth (24)(25)(26)(27). In addition, fluorescence-based methods have been developed for measuring single-cell biosynthesis of macromolecules (28)(29)(30), but the generalizability and usability of these new methods, which rely on the addition of substrates with modified functional groups, are still either largely untested in complex ecosystems or have known biases across different species.…”

“…CO 2 fixation was used to infer the general activity of heterotrophic microbes semiquantitatively (23), but the extent of heterotrophic CO 2 fixation can vary widely between different species and also depends on the heterotrophic substrate used for growth (24)(25)(26)(27). In addition, fluorescence-based methods have been developed for measuring single-cell biosynthesis of macromolecules (28-30), but the generalizability and usability of these new methods, which rely on the addition of substrates with modified functional groups, are still either largely untested in complex ecosystems or have known biases across different species.…”

Autotrophic fixation of geogenic CO<sub>2</sub> by microorganisms contributes to soil organic matter formation and alters isotope signatures in a wetland mofette

“…Autotrophic acetogenic organisms, using the Wood-Ljungdahl pathway for CO 2 fixation, are important groups in wetland and forest soils (Küsel and Drake, 1995;Ye et al, 2014). In addition, many heterotrophic soil microorganisms fix CO 2 in order to maintain their metabolic cycle by anaplerotic reactions, either to form new sugars for cell wall synthesis or to excrete organic acids for nutrient mobilization (Feisthauer et al, 2008;Miltner et al, 2005;Santruckova et al, 2005). Global estimates of microbial CO 2 fixation in soils range between 0.9 and 5.4 PgC yr −1 (Yuan et al, 2012).…”

High bicarbonate assimilation in the dark by Arctic bacteria

“…However, its use as a proxy for bacterial heterotrophic production was ruled out due to the large uncertainty in the ratio of inorganic C fixed to total C assimilated (Overbeck and Daley, 1973). The importance of CO 2 assimilation varies with the type of organic substrate used for growth (Romanenko, 1964;Sorokin, 1966), the metabolic state of the organisms (Overbeck, 1979) and even between different bacterial species, which incorporate CO 2 to replenish distinct biomass components (Feisthauer et al, 2008). Interestingly, the proteorhodopsin-containing flavobacterium Polaribacter sp.…”