| 1. |
- Castelnuovo, Gianluca, et al.
(author)
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What Is the Role of the Placebo Effect for Pain Relief in Neurorehabilitation? : Clinical Implications From the Italian Consensus Conference on Pain in Neurorehabilitation
- 2018
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In: Frontiers in Neurology. - : Frontiers Media SA. - 1664-2295. ; 9
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Research review (peer-reviewed)abstract
- Background: It is increasingly acknowledged that the outcomes of medical treatments are influenced by the context of the clinical encounter through the mechanisms of the placebo effect. The phenomenon of placebo analgesia might be exploited to maximize the efficacy of neurorehabilitation treatments. Since its intensity varies across neurological disorders, the Italian Consensus Conference on Pain in Neurorehabilitation (ICCP) summarized the studies on this field to provide guidance on its use.Methods: A review of the existing reviews and meta-analyses was performed to assess the magnitude of the placebo effect in disorders that may undergo neurorehabilitation treatment. The search was performed on Pubmed using placebo, pain, and the names of neurological disorders as keywords. Methodological quality was assessed using a pre-existing checklist. Data about the magnitude of the placebo effect were extracted from the included reviews and were commented in a narrative form.Results: 11 articles were included in this review. Placebo treatments showed weak effects in central neuropathic pain (pain reduction from 0.44 to 0.66 on a 0-10 scale) and moderate effects in postherpetic neuralgia (1.16), in diabetic peripheral neuropathy (1.45), and in pain associated to HIV (1.82). Moderate effects were also found on pain due to fibromyalgia and migraine; only weak short-term effects were found in complex regional pain syndrome. Confounding variables might have influenced these results.Clinical implications: These estimates should be interpreted with caution, but underscore that the placebo effect can be exploited in neurorehabilitation programs. It is not necessary to conceal its use from the patient. Knowledge of placebo mechanisms can be used to shape the doctor-patient relationship, to reduce the use of analgesic drugs and to train the patient to become an active agent of the therapy.
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| 2. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 3. |
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| 4. |
- Abs, Elsa, et al.
(author)
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Microbial evolution—An under-appreciated driver of soil carbon cycling
- 2024
-
In: Global Change Biology. - 1354-1013 .- 1365-2486. ; 30:4
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Journal article (peer-reviewed)abstract
- Although substantial advances in predicting the ecological impacts of global change have been made, predictions of the evolutionary impacts have lagged behind. In soil ecosystems, microbes act as the primary energetic drivers of carbon cycling; however, microbes are also capable of evolving on timescales comparable to rates of global change. Given the importance of soil ecosystems in global carbon cycling, we assess the potential impact of microbial evolution on carbon-climate feedbacks in this system. We begin by reviewing the current state of knowledge concerning microbial evolution in response to global change and its specific effect on soil carbon dynamics. Through this integration, we synthesize a roadmap detailing how to integrate microbial evolution into ecosystem biogeochemical models. Specifically, we highlight the importance of microscale mechanistic soil carbon models, including choosing an appropriate evolutionary model (e.g., adaptive dynamics, quantitative genetics), validating model predictions with ‘omics’ and experimental data, scaling microbial adaptations to ecosystem level processes, and validating with ecosystem-scale measurements. The proposed steps will require significant investment of scientific resources and might require 10–20 years to be fully implemented. However, through the application of multi-scale integrated approaches, we will advance the integration of microbial evolution into predictive understanding of ecosystems, providing clarity on its role and impact within the broader context of environmental change.
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| 5. |
- Alavaisha, Edmond, et al.
(author)
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Different agricultural practices affect soil carbon, nitrogen and phosphorous in Kilombero -Tanzania
- 2019
-
In: Journal of Environmental Management. - : Elsevier BV. - 0301-4797 .- 1095-8630. ; 234, s. 159-166
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Journal article (peer-reviewed)abstract
- Converting natural and semi-natural vegetation to agriculture is currently the most significant land use change at global scale. This conversion leads to changes in soil nutrients and increased CO2 emissions. However, knowledge of how soil organic carbon and nutrients change under various farming management is still limited, especially for small scale farming systems. This study evaluated the effects of different farming systems on soil organic carbon (SOC), total nitrogen (TN) and total phosphorous (TP) in subsistence farming at Kilombero, Tanzania. We applied an in-situ experimental setup, comparing maize and rice farming with and without irrigation and difference in fertilizers, with replicated soil sampling at five soil depths to a depth of 60 cm. The results show that irrigation had a positive effect on profile-averaged concentrations of SOC and TN, while fertilization had a positive effect on TN. Higher concentrations and stocks of TN were found in maize field soils compered to rice fields. In the vertical profile, irrigation and fertilization had positive effects on concentrations of SOC and TN of top soil layers, and the interaction between irrigation and fertilization extended the effect to deeper soil layers. Our results indicate that moderate irrigation and fertilization can help to improve carbon storage and nutrient availability (TN) in small-scale farming soils in Africa.
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| 6. |
- Baker, Paul A., et al.
(author)
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The emerging field of geogenomics : Constraining geological problems with genetic data
- 2014
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In: Earth-Science Reviews. - : Elsevier BV. - 0012-8252 .- 1872-6828. ; 135, s. 38-47
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Journal article (peer-reviewed)abstract
- The development of a genomics-derived discipline within geology is timely, as a result of major advances in acquiring and processing geologically relevant genetic data. This paper articulates the emerging field of geogenomics, which involves the use of large-scale genetic data to constrain geological hypotheses. The paper introduces geogenomics and discusses how hypotheses can be addressed through collaboration between geologists and evolutionary biologists. As an example, geogenomic methods are applied to evaluate competing hypotheses regarding the timing of the Andean uplift, the closure of the Isthmus of Panama, the onset of trans-Amazon drainage, and Quaternary climate variation in the Neotropics.
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| 7. |
- Baskaran, Preetisri, et al.
(author)
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Modelling the influence of ectomycorrhizal decomposition on plant nutrition and soil carbon sequestration in boreal forest ecosystems
- 2017
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In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 213:3, s. 1452-1465
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Journal article (peer-reviewed)abstract
- Tree growth in boreal forests is limited by nitrogen (N) availability. Most boreal forest trees form symbiotic associations with ectomycorrhizal (ECM) fungi, which improve the uptake of inorganic N and also have the capacity to decompose soil organic matter (SOM) and to mobilize organic N (ECM decomposition'). To study the effects of ECM decomposition' on ecosystem carbon (C) and N balances, we performed a sensitivity analysis on a model of C and N flows between plants, SOM, saprotrophs, ECM fungi, and inorganic N stores. The analysis indicates that C and N balances were sensitive to model parameters regulating ECM biomass and decomposition. Under low N availability, the optimal C allocation to ECM fungi, above which the symbiosis switches from mutualism to parasitism, increases with increasing relative involvement of ECM fungi in SOM decomposition. Under low N conditions, increased ECM organic N mining promotes tree growth but decreases soil C storage, leading to a negative correlation between C stores above- and below-ground. The interplay between plant production and soil C storage is sensitive to the partitioning of decomposition between ECM fungi and saprotrophs. Better understanding of interactions between functional guilds of soil fungi may significantly improve predictions of ecosystem responses to environmental change.
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| 8. |
- Bassiouni, Maoya, et al.
(author)
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Optimal plant water use strategies explain soil moisture variability
- 2023
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In: Advances in Water Resources. - : Elsevier BV. - 0309-1708 .- 1872-9657. ; 173
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Journal article (peer-reviewed)abstract
- Plant responses to water stress influence water and carbon cycles and can lead to feedbacks on climate yet characterizing these responses at ecosystem levels remains uncertain. Quantifying ecosystem-level water use strategies is complex due to challenges of upscaling plant traits and disentangling confounding environmental factors, ultimately limiting our ability to understand and anticipate global change in ecosystem dynamics and ecohydrological fluxes. We reduce the dimensionality of this problem and quantify plant water use strategies by combining plant traits with soil and climate variables into parameter groups that synthesize key eco-physiological tradeoffs. Using a parsimonious soil water balance framework, we explore variations in plant water uptake capacity, water stress responses, and water use performance via these non-dimensional parameter groups. The group characterizing the synchronization of plant water transport and atmospheric water demand emerges as the primary axis of variation in water use strategies and interacts with the group representing plant hydraulic risk tolerance, especially in arid conditions when plant water transport is limiting. Next, we show that specific plant water use strategies maximize plant water uptake (leading to carbon gain benefits) weighted by risks of water stress (leading to higher costs of water use). A model-data comparison demonstrates that these ecohydrologically optimal parameter groups capture observed soil moisture variability in 40 ecosystems and beyond aridity, rainfall frequency is an important environmental control for plant water use strategies. The emerging parsimonious link between ecohydrological performance and non-dimensional parameters provides a tractable representation of plant water use strategies, relevant to parameterize global models while accounting for ecological and evolutionary constraints on the water cycle.
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| 9. |
- Beyer, Friderike, et al.
(author)
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Relationship between foliar δ13C and sapwood area indicates different water use patterns across 236 Salix genotypes
- 2018
-
In: Trees. - : Springer Science and Business Media LLC. - 0931-1890 .- 1432-2285. ; 32:6, s. 1737-1750
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Journal article (peer-reviewed)abstract
- The relationship between leaf δ13C and plant size (represented by e.g. total leaf area) has been used to analyze different water use patterns of plants. However, the total leaf area (TLA) is difficult to assess in trees. Our aims were to (i) identify a feasible predictor for TLA; (ii) estimate the effects of TLA on leaf-level δ13C and δ18O values; and (iii) evaluate whether the relationship between leaf-level δ13C and a TLA proxy can be used to discriminate between different water use patterns. Various leaf and shoot traits of up to 236 Salix genotypes field-grown in Sweden and Italy were assessed and analyzed. Accumulated shoot diameter and sapwood area (SA) calculated from it were the best predictors for TLA. The SA was significantly correlated with foliar δ13C, but not δ18O values in some genotypes. The effects of SA on foliar δ13C values varied significantly among genotypes, and the foliar δ13C–SA relationship could be used to discriminate between different water use patterns across 236 Salix genotypes. Our results demonstrate a great variability of water use patterns across taxonomically closely related plants, and may also have implications for Salix pre-breeding and selection for different drought conditions.
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| 10. |
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| 11. |
- Brangarí, Albert C., et al.
(author)
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A soil microbial model to analyze decoupled microbial growth and respiration during soil drying and rewetting
- 2020
-
In: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 148
-
Journal article (peer-reviewed)abstract
- Soils are continuously exposed to cycles of drying and rewetting (D/RW), which drive pronounced fluctuations in soil carbon (C) fluxes. These C dynamics are characterized by a decoupled behavior between microbial biomass synthesis (growth) and CO2 production (respiration). In general, respiration rates peak shortly after RW and subsequently decrease, while the growth peaks lag several hours behind. Despite the significance of these dynamics for the soil C budget and the global C cycle, this feature has so far been overlooked in biogeochemical models and the underlying mechanisms are still unclear. We present a new process-based soil microbial model that incorporates a wide range of physical, chemical and biological mechanisms thought to affect D/RW responses. Results show that the model is able to capture the respiration dynamics in soils exposed to repeated cycles of D/RW, and also to single events in which moisture was kept constant after RW. In addition, the model reproduces, for the first time, the responses of microbial growth to D/RW. We have identified the C accumulation during dry periods, the drought-legacy effect on the synthesis of new biomass, and osmoregulation as the strongest candidate mechanisms to explain these C dynamics. The model outputs are further compared to earlier process-based models, highlighting the advances generated by the new model. This work thus represents a step towards unravelling the microbial responses to drought and rainfall events, with implications for our understanding of C cycle and C sequestration in soils.
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| 12. |
- Brangari, Albert C., et al.
(author)
-
Ecological and soil hydraulic implications of microbial responses to stress - A modeling analysis
- 2018
-
In: Advances in Water Resources. - : Elsevier BV. - 0309-1708 .- 1872-9657. ; 116, s. 178-194
-
Journal article (peer-reviewed)abstract
- A better understanding of microbial dynamics in porous media may lead to improvements in the design and management of a number of technological applications, ranging from the degradation of contaminants to the optimization of agricultural systems. To this aim, there is a recognized need for predicting the proliferation of soil microbial biomass (often organized in biofilms) under different environments and stresses. We present a general multi-compartment model to account for physiological responses that have been extensively reported in the literature. The model is used as an explorative tool to elucidate the ecological and soil hydraulic consequences of microbial responses, including the production of extracellular polymeric substances (EPS), the induction of cells into dormancy, and the allocation and reuse of resources between biofilm compartments. The mechanistic model is equipped with indicators allowing the microorganisms to monitor environmental and biological factors and react according to the current stress pressures. The feedbacks of biofilm accumulation on the soil water retention are also described. Model runs simulating different degrees of substrate and water shortage show that adaptive responses to the intensity and type of stress provide a clear benefit to microbial colonies. Results also demonstrate that the model may effectively predict qualitative patterns in microbial dynamics supported by empirical evidence, thereby improving our understanding of the effects of pore-scale physiological mechanisms on the soil macroscale phenomena.
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| 13. |
- Brangarí, Albert C., et al.
(author)
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The mechanisms underpinning microbial resilience to drying and rewetting - A model analysis
- 2021
-
In: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 162
-
Journal article (peer-reviewed)abstract
- Soil moisture is one of the most important factors controlling the activity and diversity of soil microorganisms. Soils exposed to pronounced cycles of drying and rewetting (D/RW) exhibit disconnected patterns in microbial growth and respiration at RW. These patterns differ depending on the preceding soil moisture history, leading to contrasting amounts of carbon retained in the soil as biomass versus that respired as CO2. The mechanisms underlying these microbially-induced dynamics are still unclear. In this work, we used the process-based soil microbial model EcoSMMARTS to offer candidate explanations for: i) how soil moisture can shape the structure of microbial communities, ii) how soil moisture history affects the responses during D/RW, iii) what microbial mechanisms control the shape, intensity and duration of these responses, and iv) what carbon sources sustain the increased biogeochemical rates after RW. We first evaluated the response to D/RW in bacterial communities previously exposed to two different stress histories (‘moderate’ vs ‘severe’ soil moisture regimes). We found that both the history of soil moisture and the harshness of the dry period preceding the rewetting shaped the structure and physiology of microbial communities. The characteristics of these communities determined the harshness experienced and the nature of the responses to RW obtained. Modelled communities exposed to extended severe conditions showed a resilient response to D/RW, whereas those exposed to moderate environments exhibited a more sensitive response. We then interchanged the soil moisture regimes and found that the progressive adaptation of microbial physiology and structure to new environmental conditions resulted in a switch in the response patterns. These microbial changes also determined the contribution of biomass synthesis, osmoregulation, mineralization by cell residues, and disruption of soil aggregates to CO2 emissions.
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| 14. |
- Buendía, Corina, et al.
(author)
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Evaluating the effect of nutrient redistribution by animals on the phosphorus cycle of lowland Amazonia
- 2018
-
In: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 15:1, s. 279-295
-
Journal article (peer-reviewed)abstract
- Phosphorus (P) availability decreases with soil age and potentially limits the productivity of ecosystems growing on old and weathered soils. Despite growing on ancient soils, ecosystems of lowland Amazonia are highly productive and are among the most biodiverse on Earth. P eroded and weathered in the Andes is transported by the rivers and deposited in floodplains of the lowland Amazon basin creating hotspots of P fertility. We hypothesize that animals feeding on vegetation and detritus in these hotspots may redistribute P to P-depleted areas, thus contributing to dissipate the P gradient across the landscape. Using a mathematical model, we show that animal-driven spatial redistribution of P from rivers to land and from seasonally flooded to terra firme (upland) ecosystems may sustain the P cycle of Amazonian lowlands. Our results show how P imported to land by terrestrial piscivores in combination with spatial redistribution of herbivores and detritivores can significantly enhance the P content in terra firme ecosystems, thereby highlighting the importance of food webs for the biogeochemical cycling of Amazonia.
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| 15. |
- Butler, Orpheus M., et al.
(author)
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Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients
- 2023
-
In: The ISME Journal. - 1751-7362 .- 1751-7370. ; 17:12, s. 2259-2269
-
Journal article (peer-reviewed)abstract
- Many microorganisms synthesise carbon (C)-rich compounds under resource deprivation. Such compounds likely serve as intracellular C-storage pools that sustain the activities of microorganisms growing on stoichiometrically imbalanced substrates, making them potentially vital to the function of ecosystems on infertile soils. We examined the dynamics and drivers of three putative C-storage compounds (neutral lipid fatty acids [NLFAs], polyhydroxybutyrate [PHB], and trehalose) across a natural gradient of soil fertility in eastern Australia. Together, NLFAs, PHB, and trehalose corresponded to 8.5–40% of microbial C and 0.06–0.6% of soil organic C. When scaled to “structural” microbial biomass (indexed by polar lipid fatty acids; PLFAs), NLFA and PHB allocation was 2–3-times greater in infertile soils derived from ironstone and sandstone than in comparatively fertile basalt- and shale-derived soils. PHB allocation was positively correlated with belowground biological phosphorus (P)-demand, while NLFA allocation was positively correlated with fungal PLFA : bacterial PLFA ratios. A complementary incubation revealed positive responses of respiration, storage, and fungal PLFAs to glucose, while bacterial PLFAs responded positively to PO43-. By comparing these results to a model of microbial C-allocation, we reason that NLFA primarily served the “reserve” storage mode for C-limited taxa (i.e., fungi), while the variable portion of PHB likely served as “surplus” C-storage for P-limited bacteria. Thus, our findings reveal a convergence of community-level processes (i.e., changes in taxonomic composition that underpin reserve-mode storage dynamics) and intracellular mechanisms (e.g., physiological plasticity of surplus-mode storage) that drives strong, predictable community-level microbial C-storage dynamics across gradients of soil fertility and substrate stoichiometry.
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| 16. |
- Calabrese, Salvatore, et al.
(author)
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Energetic scaling in microbial growth
- 2021
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 118:47
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Journal article (peer-reviewed)abstract
- 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.
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| 17. |
- Capek, Petr, et al.
(author)
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Drivers of phosphorus limitation across soil microbial communities
- 2016
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In: Functional Ecology. - : Wiley. - 0269-8463 .- 1365-2435. ; 30:10, s. 1705-1713
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Journal article (peer-reviewed)abstract
- Nutrient limitation of soil microbial communities controls the rates of plant litter and soil organic matter decomposition and nutrient mineralization, and as such, it is central to soil and ecosystem models. According to ecological stoichiometry theory, when the carbon (C)-to-nutrient (E) ratio of resources used by a microbial community is higher than a critical ratio (C:E-CR), that nutrient is limiting. The C-to-phosphorus (P) critical ratio (C:P-CR) that determines P limitation is largely unknown for soils, and thus, it is the subject of our study. Our results show that the C:P-CR in widely different soils ranges from 266 to 4651 or from 209 to 7407 when accounting for 95% confidence intervals. Using constant or narrowly fluctuating C:P-CR in ecosystem models is therefore inaccurate. The C:P-CR cannot be simply predicted from microbial community C:P or available soil P. C:P-CR was only related to relative abundance of phospholipid fatty acids, which reflects microbial community structure and physiology. Our data suggest complex controls over microbial community C:P-CR. We further propose that using P storage compounds that allow the microbial community to temporarily buffer variability in available P can represent a widely adopted strategies across soils.
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| 18. |
- Capek, P. T., et al.
(author)
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A plant-microbe interaction framework explaining nutrient effects on primary production
- 2018
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In: Nature Ecology & Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 2:10, s. 1588-1596
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Journal article (peer-reviewed)abstract
- In most terrestrial ecosystems, plant growth is limited by nitrogen and phosphorus. Adding either nutrient to soil usually affects primary production, but their effects can be positive or negative. Here we provide a general stoichiometric framework for interpreting these contrasting effects. First, we identify nitrogen and phosphorus limitations on plants and soil microorganisms using their respective nitrogen to phosphorus critical ratios. Second, we use these ratios to show how soil microorganisms mediate the response of primary production to limiting and non-limiting nutrient addition along a wide gradient of soil nutrient availability. Using a meta-analysis of 51 factorial nitrogen-phosphorus fertilization experiments conducted across multiple ecosystems, we demonstrate that the response of primary production to nitrogen and phosphorus additions is accurately predicted by our stoichiometric framework. The only pattern that could not be predicted by our original framework suggests that nitrogen has not only a structural function in growing organisms, but also a key role in promoting plant and microbial nutrient acquisition. We conclude that this stoichiometric framework offers the most parsimonious way to interpret contrasting and, until now, unresolved responses of primary production to nutrient addition in terrestrial ecosystems.
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| 19. |
- Chakrawal, Arjun, et al.
(author)
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Dynamic upscaling of decomposition kinetics for carbon cycling models
- 2020
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In: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 13:3, s. 1399-1429
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Journal article (peer-reviewed)abstract
- The distribution of organic substrates and microorganisms in soils is spatially heterogeneous at the microscale. Most soil carbon cycling models do not account for this microscale heterogeneity, which may affect predictions of carbon (C) fluxes and stocks. In this study, we hypothesize that the mean respiration rate (R) over bar at the soil core scale (i) is affected by the microscale spatial heterogeneity of substrate and microorganisms and (ii) depends upon the degree of this heterogeneity. To theoretically assess the effect of spatial heterogeneities on (R) over bar, we contrast heterogeneous conditions with isolated patches of substrate and microorganisms versus spatially homogeneous conditions equivalent to those assumed in most soil C models. Moreover, we distinguish between biophysical heterogeneity, defined as the nonuniform spatial distribution of substrate and microorganisms, and full heterogeneity, defined as the nonuniform spatial distribution of substrate quality (or accessibility) in addition to biophysical heterogeneity. Four common formulations for decomposition kinetics (linear, multiplicative, Michaelis-Menten, and inverse Michaelis-Menten) are considered in a coupled substrate-microbial biomass model valid at the microscale. We start with a 2-D domain characterized by a heterogeneous substrate distribution and numerically simulate organic matter dynamics in each cell in the domain. To interpret the mean behavior of this spatially explicit system, we propose an analytical scale transition approach in which microscale heterogeneities affect (R) over bar through the second-order spatial moments (spatial variances and covariances). The model assuming homogeneous conditions was not able to capture the mean behavior of the heterogeneous system because the second-order moments cause (R) over bar to be higher or lower than in the homogeneous system, depending on the sign of these moments. This effect of spatial heterogeneities appears in the upscaled nonlinear decomposition formulations, whereas the upscaled linear decomposition model deviates from homogeneous conditions only when substrate quality is heterogeneous. Thus, this study highlights the inadequacy of applying at the macroscale the same decomposition formulations valid at the microscale and proposes a scale transition approach as a way forward to capture microscale dynamics in core-scale models.
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| 20. |
- Chakrawal, Arjun, 1992-, et al.
(author)
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Interacting Bioenergetic and Stoichiometric Controls on Microbial Growth
- 2022
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In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 13
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Journal article (peer-reviewed)abstract
- Microorganisms function as open systems that exchange matter and energy with their surrounding environment. Even though mass (carbon and nutrients) and energy exchanges are tightly linked, there is a lack of integrated approaches that combine these fluxes and explore how they jointly impact microbial growth. Such links are essential to predicting how the growth rate of microorganisms varies, especially when the stoichiometry of carbon- (C) and nitrogen (N)-uptake is not balanced. Here, we present a theoretical framework to quantify the microbial growth rate for conditions of C-, N-, and energy-(co-) limitations. We use this framework to show how the C:N ratio and the degree of reduction of the organic matter (OM), which is also the electron donor, availability of electron acceptors (EAs), and the different sources of N together control the microbial growth rate under C, nutrient, and energy-limited conditions. We show that the growth rate peaks at intermediate values of the degree of reduction of OM under oxic and C-limited conditions, but not under N-limited conditions. Under oxic conditions and with N-poor OM, the growth rate is higher when the inorganic N (NInorg)-source is ammonium compared to nitrate due to the additional energetic cost involved in nitrate reduction. Under anoxic conditions, when nitrate is both EA and NInorg-source, the growth rates of denitrifiers and microbes performing the dissimilatory nitrate reduction to ammonia (DNRA) are determined by both OM degree of reduction and nitrate-availability. Consistent with the data, DNRA is predicted to foster growth under extreme nitrate-limitation and with a reduced OM, whereas denitrifiers are favored as nitrate becomes more available and in the presence of oxidized OM. Furthermore, the growth rate is reduced when catabolism is coupled to low energy yielding EAs (e.g., sulfate) because of the low carbon use efficiency (CUE). However, the low CUE also decreases the nutrient demand for growth, thereby reducing N-limitation. We conclude that bioenergetics provides a useful conceptual framework for explaining growth rates under different metabolisms and multiple resource-limitations.
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| 21. |
- Chakrawal, Arjun, et al.
(author)
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Leveraging energy flows to quantify microbial traits in soils
- 2021
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In: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 155
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Journal article (peer-reviewed)abstract
- 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.
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| 22. |
- Chakrawal, Arjun, 1992-, et al.
(author)
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Modelling optimal ligninolytic activity during plant litter decomposition
- 2024
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In: New Phytologist. - 0028-646X .- 1469-8137.
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Journal article (peer-reviewed)abstract
- A large fraction of plant litter comprises recalcitrant aromatic compounds (lignin and other phenolics). Quantifying the fate of aromatic compounds is difficult, because oxidative degradation of aromatic carbon (C) is a costly but necessary endeavor for microorganisms, and we do not know when gains from the decomposition of aromatic C outweigh energetic costs.To evaluate these tradeoffs, we developed a litter decomposition model in which the aromatic C decomposition rate is optimized dynamically to maximize microbial growth for the given costs of maintaining ligninolytic activity. We tested model performance against > 200 litter decomposition datasets collected from published literature and assessed the effects of climate and litter chemistry on litter decomposition.The model predicted a time-varying ligninolytic oxidation rate, which was used to calculate the lag time before the decomposition of aromatic C is initiated. Warmer conditions increased decomposition rates, shortened the lag time of aromatic C oxidation, and improved microbial C-use efficiency by decreasing the costs of oxidation. Moreover, a higher initial content of aromatic C promoted an earlier start of aromatic C decomposition under any climate.With this contribution, we highlight the application of eco-evolutionary approaches based on optimized microbial life strategies as an alternative parametrization scheme for litter decomposition models.
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| 23. |
- Chakrawal, Arjun, 1992-
(author)
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Novel approaches in modeling of soil carbon : Upscaling theories and energetics
- 2021
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Doctoral thesis (other academic/artistic)abstract
- Soils contain more carbon (C) than terrestrial (above ground) and atmospheric carbon combined. Mismanagement of soil C could lead to increased greenhouse gas emissions, whereas practices leading to increased C storage would help mitigate climate change while improving soil fertility and ecological functions. At the center of these complex feedbacks, soil microorganisms play a pivotal role in the cycling of C and nutrients, and thus in soil-climate interactions. However, this role is not fully understood; therefore, developing new methods for studying their dynamics is essential for an understanding of bio-physicochemical processes leading to mineralization or stabilization of soil organic matter (SOM).Current soil C cycling models lack a robust upscaling approach that links SOM decomposition from process (μm) to observation scale (cm to km). Moreover, these models often neglect energy fluxes from microbial metabolism, which may provide additional constraints in model parameterization and alternative observable quantities such as heat dissipation rate to study decomposition processes. In this doctoral work, I investigated two aspects of microbial processes and their consequences for SOM dynamics: 1) use of energetics to constrain SOM dynamics by explicitly accounting for thermodynamics of microbial growth, and 2) spatial constraints at microscale resulting from the non-uniform distribution of microorganisms and substrates.In the first part of the thesis, I developed a general mass and energy balance framework for the uptake of added substrates and native SOM. This framework provided the theoretical underpinnings for understanding variations in the calorespirometric ratios—the ratio of rates of heat dissipation to CO2 production—a useful metric used as a proxy for microbial carbon-use efficiency (CUE). Moreover, in a follow-up work, I extended this mass-energy framework to describe dynamic (time-varying) conditions, which was used to interpret rates of heat and CO2 evolution from different soils amended with glucose. The dynamic mass-energy framework was also used as a tool for data-model integration and estimation of microbial functional traits, such as their CUE and maximum substrate uptake rates. In the second part of the thesis, I linked the micro and macroscale dynamics of decomposition using scale transition theory. The findings of this study were further validated from laboratory experiments, in which spatial heterogeneity in the added substrate was manipulated.Results from the first part show that the calorespirometric ratios can be used to identify active metabolic pathways and to estimate CUE. Further, the heat dissipation rate can be used as a reliable complement or alternative to mass fluxes such as respiration rates for estimating microbial traits and constraining model parameters. In the second part, I show that the co-location of microorganisms and substrates increased, and separation decreased the microbial activity measured as heat dissipation from the incubation experiment. These results were in line with the expectation from the scale transition theory. In summary, this work provides novel approaches for studying soil C cycling and explicitly highlights a way forward to address two fundamental issues in microbial decomposition—the role of spatial heterogeneities and of energetic constraints on microbial metabolisms.
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| 24. |
- Chakrawal, Arjun, et al.
(author)
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Quantifying Microbial Metabolism in Soils Using Calorespirometry — A Bioenergetics Perspective
- 2020
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In: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 148
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Journal article (peer-reviewed)abstract
- Microbial carbon use efficiency (CUE) measures the partitioning between anabolic and catabolic processes. While most work on CUE has been based on carbon (C) mass flows, the roles of organic C energy contents and microbial energy demand on CUE have been rarely considered. Thus, a bioenergetics perspective could provide new insights on how microorganisms utilize C and ultimately allow evaluating their role in C stabilization in soils. Recently, the calorespirometric ratio (CR)— the ratio of heat dissipation and respiration— has been used to characterize the efficiency of microbial growth in soils. Here, we formulate a coupled mass and energy balance model for microbial growth and provide a generalized relationship between CUE and CR. In the model, we consider two types of organic C in soils: an added substrate (e.g., glucose) and the native soil organic matter (SOM), to also account for priming effects. Furthermore, we consider both aerobic and fermentation metabolic pathways. We use this model as a framework to generalize previous formulations and generate hypotheses on the expected variations in CR as a function of substrate quality, metabolic pathways, and microbial traits (specifically CUE). In turn, the same equations can be used to estimate CUE from measured CR. Our results confirm previous findings on CR and show that without microbial growth, CR depends only on the rates of the different metabolic pathways, while CR is also a function of the growth yields for these metabolic pathways when microbial growth occurs. Under strictly aerobic conditions, CUE increases with increasing CR for substrates with a higher degree of reduction than that of the microbial biomass, while CUE decreases with increasing CR for substrates with a lower degree of reduction than the microbial biomass. When aerobic reactions and fermentation occur simultaneously, the relation between CUE and CR is mediated by (i) the degree of reduction of the substrates, (ii) the rates and growth yields of all metabolic pathways, and (iii) the contribution of SOM priming to microbial growth. Using the proposed framework, calorespirometry can be used to evaluate CUE and the role of different metabolic pathways in soil systems.
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| 25. |
- Clemenzi, Ilaria, et al.
(author)
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Annual water balance and hydrological trends in the glacierised Tarfala Catchment, Sweden
- 2023
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In: Journal of Hydrology. - 0022-1694 .- 1879-2707. ; 626
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Journal article (peer-reviewed)abstract
- Quantifying components of the hydrological cycle in glacierised catchments is important for the assessment of the temporal distribution, quantity and quality of water resources available to downstream regions, especially under a changing climate. However, this assessment requires long time series of observations, which are typically unavailable for remote catchments, such as those in mountainous areas. In this study, we leverage a unique ∼40 year time series of hydrological data recorded in the subarctic glacierised Tarfala catchment (Sweden) to explore temporal trends in the components of the catchment water balance (precipitation, runoff, change in storage, and evaporation), and to assess if water balance residuals are associated with specific hydro-climatic conditions. No significant temporal trends were found in precipitation and storage changes of the glacierised area, but significant increases were found in evaporation and summer discharge (in part attributed to glacier volume losses). The annual water balance could not be perfectly closed, and water losses were on average 112 mm y−1 larger than the water inputs over the study period. Among the water balance components, discharge contributed most to the total water balance uncertainty, and storage surplus due to antecedent meteorological conditions could explain why water losses in specific years exceeded the uncertainty bounds. It is therefore essential to consider legacy effects from previous years when applying water balance calculations in mountainous and/or glacierised catchments.
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