More Like this

1. The Collaborative Policy Modeling Paradox: Perceptions of water quality modeling in the Chesapeake Bay Watershed

   https://doi.org/10.18174/sesmo.18677  

   Bitterman, Patrick; Webster, DG (February 2024, Socio-Environmental Systems Modelling)

   The Chesapeake Assessment Scenario Tool (CAST) serves multiple key functions in meeting nutrient reduction targets across the Chesapeake Bay Watershed (CBW) and is embedded in the water quality governance system. To investigate contested perspectives regarding the model, we interviewed 59 stakeholders engaged in model governance across the CBW. We recorded statements regarding the accuracy, legitimacy, and credibility of the model, influences on its use, and on challenges and opportunities. We found skepticism regarding the legitimacy of CAST, including suggestions its role facilitates a “paper process” of policy design and that past experience has greater influence on policy decisions than model predictions. However, despite its perceived shortcomings, CAST has been central in helping stakeholders in prioritizing mitigative activities. With respect to credibility, most respondents believe the model underestimates the effects of nutrient-reduction practices, thereby underestimating progress toward TMDL-related goals. Respondents also identified opportunities for model improvement, emphasizing co-benefits of conservation practices over and above nutrient reduction. Overall, our analysis demonstrates a Collaborative Policy Modeling Paradox: collaborative model development is necessary for effective policy modeling, but the political processes of collaborative model development can negatively impact perceptions of salience, credibility, and legitimacy. Although it is important to recognize this paradox, as it is linked to dissatisfaction with the models, our findings also point to areas where improvement has occurred and to future opportunities for development. 

   more » « less
2. Experimental N and P additions relieve stoichiometric constraints on organic matter flows through five stream food webs

   https://doi.org/10.1111/1365-2656.13197  

   Demi, Lee M.; Benstead, Jonathan P.; Rosemond, Amy D.; Maerz, John C.; Clay, ed., Natalie (April 2020, Journal of Animal Ecology)

   Abstract Human activities have dramatically altered global patterns of nitrogen (N) and phosphorus (P) availability. This pervasive nutrient pollution is changing basal resource quality in food webs, thereby affecting rates of biological productivity and the pathways of energy and material flow to higher trophic levels.Here, we investigate how the stoichiometric quality of basal resources modulates patterns of material flow through food webs by characterizing the effects of experimental N and P enrichment on the trophic basis of macroinvertebrate production and flows of dominant food resources to consumers in five detritus‐based stream food webs.After a pre‐treatment year, each stream received N and P at different concentrations for 2 years, resulting in a unique dissolved N:P ratio (target range from 128:1 to 2:1) for each stream. We combined estimates of secondary production and gut contents analysis to calculate rates of material flow from basal resources to macroinvertebrate consumers in all five streams, during all 3 years of study.Nutrient enrichment resulted in a 1.5× increase in basal resource flows to primary consumers, with the greatest increases from biofilms and wood. Flows of most basal resources were negatively related to resource C:P, indicating widespread P limitation in these detritus‐based food webs. Nutrient enrichment resulted in a greater proportion of leaf litter, the dominant resource flow‐pathway, being consumed by macroinvertebrates, with that proportion increasing with decreasing leaf litter C:P. However, the increase in efficiency with which basal resources were channelled into metazoan food webs was not propagated to macroinvertebrate predators, as flows of prey did not systematically increase following enrichment and were unrelated to basal resource flows.This study suggests that ongoing global increases in N and P supply will increase organic matter flows to metazoan food webs in detritus‐based ecosystems by reducing stoichiometric constraints at basal trophic levels. However, the extent to which those flows are propagated to the highest trophic levels likely depends on responses of individual prey taxa and their relative susceptibility to predation. 

   more » « less
3. Resource limitation of autotrophs and heterotrophs in boreal forest headwater streams

   https://doi.org/10.1086/722256  

   Weaver, Sophie A.; Jones, Jeremy B. (December 2022, Freshwater Science)

   Autotrophic and heterotrophic microbes in stream biofilms dominate biogeochemical cycling and rely on nutrient and energy resources for growth and productivity. In the boreal forest, variation in these resources can originate from permafrost distribution and controls competition for nutrients between stream autotrophs and heterotrophs. We investigated which resources control nutrient uptake and metabolism in headwater stream biofilms of subarctic Alaska, USA, and how resource availability affects competition for inorganic nutrients. We hypothesized that the competitive outcome between autotrophs and heterotrophs for inorganic nutrients would be dependent on availability of organic C, or inorganic nutrients (N and P). To test our hypotheses, we measured resource limitation at the patch and reach scales along a permafrost gradient in interior Alaska. At the patch scale, nutrient diffusing substrata revealed that, secondary to light, N and P were colimiting to autotrophic growth, whereas C was primarily limiting to heterotrophic respiration. In the presence of labile C, heterotrophs exhibited a larger response to nutrient enrichment and outcompeted autotrophs for inorganic nutrients. At the reach scale, light availability had the largest influence on nutrient uptake, but inorganic nutrients were also important. The positive response to increased nutrient and C availability at the patch scale suggests that the predicted increase in exports into fluvial networks with permafrost degradation will alter biofilm structure and function. Ultimately, biofilm communities will shift to more heterotroph-dominated patches if heterotrophs outcompete autotrophs for inorganic nutrients. As permafrost thaws and nutrients and organic C mobilize into streams, nutrient uptake dynamics and competition within biofilms will be altered, affecting nutrient use and export. 

   more » « less
4. An unconventional uptake rate objective function approach enhances applicability of genome-scale models for mammalian cells

   https://doi.org/10.1038/s41540-019-0103-6  

   Chen, Yiqun; McConnell, Brian O.; Gayatri Dhara, Venkata; Mukesh Naik, Harnish; Li, Chien-Ting; Antoniewicz, Maciek R.; Betenbaugh, Michael J. (July 2019, npj Systems Biology and Applications)

   Abstract Constraint-based modeling has been applied to analyze metabolism of numerous organisms via flux balance analysis and genome-scale metabolic models, including mammalian cells such as the Chinese hamster ovary (CHO) cells—the principal cell factory platform for therapeutic protein production. Unfortunately, the application of genome-scale model methodologies using the conventional biomass objective function is challenged by the presence of overly-restrictive constraints, including essential amino acid exchange fluxes that can lead to improper predictions of growth rates and intracellular flux distributions. In this study, these constraints are found to be reliably predicted by an “essential nutrient minimization” approach. After modifying these constraints with the predicted minimal uptake values, a series of unconventional objective functions are applied to minimize each individual non-essential nutrient uptake rate, revealing useful insights about metabolic exchange rates and flows across different cell lines and culture conditions. This unconventional uptake-rate objective functions (UOFs) approach is able to distinguish metabolic differences between three distinct CHO cell lines (CHO-K1, -DG44, and -S) not directly observed using the conventional biomass growth maximization solutions. Further, a comparison of model predictions with experimental data from literature correctly correlates with the specific CHO-DG44-derived cell line used experimentally, and the corresponding dual prices provide fruitful information concerning coupling relationships between nutrients. The UOFs approach is likely to be particularly suited for mammalian cells and other complex organisms which contain multiple distinct essential nutrient inputs, and may offer enhanced applicability for characterizing cell metabolism and physiology as well as media optimization and biomanufacturing control. 

   more » « less
5. Physiology, fast and slow: bacterial response to variable resource stoichiometry and dilution rate

   https://doi.org/10.1128/msystems.00770-24  

   Peoples, Logan M; Isanta-Navarro, Jana; Bras, Benedicta; Hand, Brian K; Rosenzweig, Frank; Elser, James J; Church, Matthew J (August 2024, mSystems)

   Schada_von_Borzyskowski, Lennart (Ed.)

   ABSTRACT Microorganisms grow despite imbalances in the availability of nutrients and energy. The biochemical and elemental adjustments that bacteria employ to sustain growth when these resources are suboptimal are not well understood. We assessed howPseudomonas putidaKT2440 adjusts its physiology at differing dilution rates (to approximate growth rates) in response to carbon (C), nitrogen (N), and phosphorus (P) stress using chemostats. Cellular elemental and biomolecular pools were variable in response to different limiting resources at a slow dilution rate of 0.12 h⁻¹, but these pools were more similar across treatments at a faster rate of 0.48 h⁻¹. At slow dilution rates, limitation by P and C appeared to alter cell growth efficiencies as reflected by changes in cellular C quotas and rates of oxygen consumption, both of which were highest under P- and lowest under C- stress. Underlying these phenotypic changes was differential gene expression of terminal oxidases used for ATP generation that allows for increased energy generation efficiency. In all treatments under fast dilution rates, KT2440 formed aggregates and biofilms, a physiological response that hindered an accurate assessment of growth rate, but which could serve as a mechanism that allows cells to remain in conditions where growth is favorable. Our findings highlight the ways that microorganisms dynamically adjust their physiology under different resource supply conditions, with distinct mechanisms depending on the limiting resource at slow growth and convergence toward an aggregative phenotype with similar compositions under conditions that attempt to force fast growth. IMPORTANCEAll organisms experience suboptimal growth conditions due to low nutrient and energy availability. Their ability to survive and reproduce under such conditions determines their evolutionary fitness. By imposing suboptimal resource ratios under different dilution rates on the model organismPseudomonas putidaKT2440, we show that this bacterium dynamically adjusts its elemental composition, morphology, pools of biomolecules, and levels of gene expression. By examining the ability of bacteria to respond to C:N:P imbalance, we can begin to understand how stoichiometric flexibility manifests at the cellular level and impacts the flow of energy and elements through ecosystems. 

   more » « less