Amino Acid and Sugar Catabolism in the Marine Bacterium Phaeobacter inhibens DSM 17395 from an Energetic Viewpoint

Abstract

Growth energetics and metabolic efficiency contribute to the lifestyle and habitat imprint of microorganisms. Roseobacters constitute one of the most abundant and successful marine bacterioplankton groups. Here, we reflect on the energetics and metabolic efficiency of Phaeobacter inhibens DSM 17395, a versatile heterotrophic roseobacter. Fourteen different substrates (five sugars and nine amino acids) and their degradation pathways were assessed for energetic efficiencies based on catabolic ATP yields, calculated from net formed ATP and reducing equivalents. The latter were converted into ATP by employing the most divergent coupling ratios (i.e., ions per ATP) currently known for F1Fo ATP synthases in heterotrophic bacteria. The catabolic ATP yields of the pathways studied in P. inhibens differed ∼3-fold. The actual free energy costs for ATP synthesis were estimated at 81.6 kJ per mol ATP (3.3 ions per ATP) or 104.2 kJ per mol ATP (4.3 ions per ATP), yielding an average thermodynamic efficiency of ∼37.7% or ∼29.5%, respectively. Growth performance (rates, yields) and carbon assimilation efficiency were determined for P. inhibens growing in process-controlled bioreactors with 10 different single substrates (Glc, Man, N-acetylglucosamine [Nag], Phe, Trp, His, Lys, Thr, Val, or Leu) and with 2 defined substrate mixtures. The efficiencies of carbon assimilation into biomass ranged from ∼28% to 61%, with His/Trp and Thr/Leu yielding the lowest and highest levels. These efficiencies correlated with catabolic and ATP yields only to some extent. Substrate-specific metabolic demands and/or functions, as well as the compositions of the substrate mixtures, apparently affected the energetic costs of growth. These include energetic burdens associated with, e.g., slow growth, stress, and/or the production of tropodithietic acid. IMPORTANCE Heterotrophic members of the bacterioplankton serve the marine ecosystem by transforming organic matter, an activity that is governed by the bacterial growth efficiencies (BGEs) obtained under given environmental conditions. In marine ecology, the concept of BGE refers to the carbon assimilation efficiency within natural communities. The marine bacterium studied here, Phaeobacter inhibens DSM 17395, is a copiotrophic representative of the globally abundant Roseobacter group, and the 15 catabolic pathways investigated are widespread among these marine heterotrophs. Combining pathway-specific catabolic ATP yields with in-depth quantitative physiological data could (i) provide a new baseline for the study of growth energetics and efficiency in further Roseobacter group members and other copiotrophic marine bacteria in productive coastal ecosystems and (ii) contribute to a better understanding of the factors controlling BGE (including the additional energetic burden arising from widespread secondary-metabolite formation) based on laboratory studies with pure cultures.

Global Response of <b><i>Phaeobacter inhibens</i></b> DSM 17395 to Deletion of Its 262-kb Chromid Encoding Antibiotic Synthesis

“…Finally, the conspicuous enrichment of the exoproteome of the Δ262 mutant with a multitude of diverse proteins may hint at a profound difference in the membrane/cell envelope permeability between the wild type and the Δ262 mutant. While the wild type is the model system prima facie for system biology experiments with P. inhibens DSM 17395, several lines of evidence qualify the Δ262 mutant as a potentially more suitable alternative: (i) the observed overall metabolic congruence (except for transportome) between both genotypes, (ii) the recently reported influence of growth substrates on TDA formation in the wild type [Wünsch et al, 2019], (iii) the markedly better growth performance of the Δ262 mutant, and (iv) the avoidance of the multiple adverse effects of TDA with the Δ262 mutant.…”

The Formation of Refractory Dissolved Organic Nitrogen From Free Amino Acids in the Ocean

“…In contrast to Phe, the rapid remineralization of Ala-N to ammonium was likely due to the utilization of Ala-C. Pyruvate, an important precursor of citric acid cycle, is the direct product of Ala transamination (Drüppel et al, 2014). Thus, Ala may have been rapidly deaminated or transferred to pyruvate to fuel the growth of the microbial community (Drüppel et al, 2014;Wünsch et al, 2019). The higher yield of uncharacterizable DON from AVFA than single amino acids combined (Figure S3 in Supporting Information S1) suggests that peptide structure may have also played a role in the decomposition process.…”

“…This apparent decoupling suggested that the metabolic pathways of C and N differed. The C from labile organic substrate is likely used as energy source to fuel the growth of microbial community (e.g., Drüppel et al, 2014;Wünsch et al, 2019), and thus quickly remineralized into CO 2 (e.g., Lønborg et al, 2009;Ogawa et al, 2001).…”

Nanomolar Responsiveness of Marine <b><i>Phaeobacter inhibens</i></b> DSM 17395 toward Carbohydrates and Amino Acids

“…Deletion of this plasmid revealed its high energetic burden (∼50% of dissimilatory expenditure) and resulted in global responses revealing the functional interconnectivity of the replicons [Trautwein et al, 2016;Wünsch et al, 2020]. (iv) The metabolism of P. inhibens DSM 17395 was studied in our laboratory on the physiological/proteogenomic level with respect to differential substrate utilization from complex substrate mixtures [Zech et al, 2013], degradation networks, growth energetics, and metabolic efficiency for amino acids and carbohydrates [Drüppel et al, 2014;Wiegmann et al, 2014;Wünsch et al, 2019], as well as the stoichiometric constraints with respect to varying N/Pprovision [Trautwein et al, 2017] and a multifaceted strategy to secure external nitrogen [Trautwein et al, 2018].…”