I urval från Stockholms universitets publikationsdatabas
Carbon supply–consumption balance in plant roots: effects of carbon use efficiency and root anatomical plasticity
2022. Tino Colombi, Arjun Chakrawal, Anke Marianne Herrmann. New Phytologist 233 (4), 1542-1547Artikel
Energetic scaling in microbial growth
2021. Salvatore Calabrese (et al.). Proceedings of the National Academy of Sciences of the United States of America 118 (47)Artikel
Microbial growth is a clear example of organization and structure arising in nonequilibrium conditions. Due to the complexity of the microbial metabolic network, elucidating the fundamental principles governing microbial growth remains a challenge. Here, we present a systematic analysis of microbial growth thermodynamics, leveraging an extensive dataset on energy-limited monoculture growth. A consistent thermodynamic framework based on reaction stoichiometry allows us to quantify how much of the available energy microbes can efficiently convert into new biomass while dissipating the remaining energy into the environment and producing entropy. We show that dissipation mechanisms can be linked to the electron donor uptake rate, a fact leading to the central result that the thermodynamic efficiency is related to the electron donor uptake rate by the scaling law eta proportional to M-1/2 ED and to the growth yield by eta proportional to Y4/5. These findings allow us to rederive the Pirt equation from a thermodynamic perspective, providing a means to compute its coefficients, as well as a deeper understanding of the relationship between growth rate and yield. Our results provide rather general insights into the relation between mass and energy conversion in microbial growth with potentially wide application, especially in ecology and biotechnology.
Modeling Microbial Adaptations to Nutrient Limitation During Litter Decomposition
2021. Stefano Manzoni (et al.). Frontiers in Forests and Global Change 4Artikel
Microbial decomposers face large stoichiometric imbalances when feeding on nutrient-poor plant residues. To meet the challenges of nutrient limitation, microorganisms might: (i) allocate less carbon (C) to growth vs. respiration or excretion (i.e., flexible C-use efficiency, CUE), (ii) produce extracellular enzymes to target compounds that supply the most limiting element, (iii) modify their cellular composition according to the external nutrient availability, and (iv) preferentially retain nutrients at senescence. These four resource use modes can have different consequences on the litter C and nitrogen (N) dynamics-modes that selectively remove C from the system can reduce C storage in soil, whereas modes that delay C mineralization and increase internal N recycling could promote storage of C and N. Since we do not know which modes are dominant in litter decomposers, we cannot predict the fate of C and N released from plant residues, in particular under conditions of microbial nutrient limitation. To address this question, we developed a process-based model of litter decomposition in which these four resource use modes were implemented. We then parameterized the model using similar to 80 litter decomposition datasets spanning a broad range of litter qualities. The calibrated model variants were able to capture most of the variability in litter C, N, and lignin fractions during decomposition regardless of which modes were included. This suggests that different modes can lead to similar litter decomposition trajectories (thanks to the multiple alternative resource acquisition pathways), and that identification of dominant modes is not possible using standard litter decomposition data (an equifinality problem). Our results thus point to the need of exploring microbial adaptations to nutrient limitation with empirical estimates of microbial traits and to develop models flexible enough to consider a range of hypothesized microbial responses.
Leveraging energy flows to quantify microbial traits in soils
2021. Arjun Chakrawal, Anke M. Herrmann, Stefano Manzoni. Soil Biology and Biochemistry 155Artikel
Heat dissipation from organic matter decomposition is a well-recognized proxy for microbial activity in soils, but only a few modeling studies have used heat signals to quantify microbial traits such as maximum substrate uptake rate, specific growth rate, mortality rate, and growth efficiency. In this contribution, a hierarchy of coupled mass-energy balance models is proposed to estimate microbial traits encoded in model parameters using heat dissipation and respiration data from glucose induced microbial activity. Moreover, the models are used to explain the observed variability in calorespirometric ratios (CR)-the ratio of heat dissipation to respiration rate. We parametrized four model variants using heat dissipation and respiration rates measured in an isothermal calorimeter during the lag-phase only or during the whole growth-phase. The four variants are referred to as: (i) complex physiological model, (ii) simplified physiological model, (iii) lag-phase model, and (iv) growth-phase model. Model parameters were determined using three combinations of data: A) only the heat dissipation rate, B) only the respiration rate, and C) both heat dissipation and respiration rates. We assumed that the 'best' parameter estimates were those obtained when using all the data (i.e., option C). All model variants were able to fit the observed heat dissipation and respiration rates. The parameters estimated using only heat dissipation data were similar to the 'best' estimates compared to using only respiration rate data, suggesting that the observed heat dissipation rate can be used to constrain microbial models and estimate microbial traits. However, the observed variability in CR was not well captured by some model variants such as the simplified physiological model, in contrast to the lag- and growth-phase model that predicted CR well. This suggests that CR can be used to scrutinize how well metabolic processes are represented in decomposition models.