A new mathematical model to explore microbial processes and their constraints in phytoplankton colonies and sinking marine aggregates

Moradi, Nasrollah; Liu, Bo; Iversen, Morten Hvitfeldt; Kuypers, Marcel M. M.; Ploug, Helle

doi:10.1126/sciadv.aat1991

Cited by 21 publications

(27 citation statements)

References 38 publications

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“…Applications of the Michaelis-Menten equation are ubiquitous [e.g., see Table 1 in Wong et al (2018)], and scaling up the associated processes is a common concern in heterogeneous systems. For example, microbe-driven element cycling in marine systems faces a similar problem of heterogeneity (e.g., Follows et al 2007;Ward et al 2014;Moradi et al 2018), and we speculate that an application of the ECA equation (not necessarily the exact same parameter meaning) could help address this challenge. In forest systems, a landscape mosaic of forest gaps at differing stages (Shugart 1984) could benefit from a similar application of the ECA equation in a different form.…”

Section: Broder Implications For Developing Soil Biogeochemical Modelsmentioning

confidence: 84%

Emergent properties of organic matter decomposition by soil enzymes

Wang

Allison

2019

Soil Biology and Biochemistry

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Plant residues and soil organic matter are predominantly decomposed by exoenzymes. Many soil carbon models now represent enzymatic decomposition, but the mathematical formulation of this process has been debated over the last 15 years. Some models apply the traditional "forward" Michaelis-Menten equation to represent enzyme kinetics, whereas others apply the "reverse" Michaelis-Menten equation, which assumes that kinetic rates saturate at high enzyme concentrations. Recently the equilibrium chemistry approximation (ECA) has been proposed as an alternative to both Michaelis-Menten formulations. However, because of methodological limitations, in-situ enzyme kinetics-especially in the context of soil system heterogeneity-have been difficult to verify experimentally. Therefore, the overarching goal of our study was to evaluate different enzyme kinetic formulations using model-based evidence at microbial to ecosystem scales. We used a spatially explicit individual-and trait-based microbial model, DEMENT, to circumvent methodological challenges. Although DEMENT assumes forward Michaelis-Menten kinetics at local scales, at the grid scale we found saturating relationships between degradation rate and both substrate concentrations and enzyme concentrations that fit the forward and reverse Michaelis-Menten equations, respectively, at specific successional stages during decomposition. Although forward and reverse Michaelis-Menten equations emerged under some conditions, only the ECA adequately represented decay rates emerging from the spatial-temporal variation in substrate and enzyme concentrations throughout the decomposition process. Our results support a more widespread adoption of the ECA equation in soil biogeochemical modelling at ecosystem scales.

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Section: Broder Implications For Developing Soil Biogeochemical Modelsmentioning

confidence: 84%

Emergent properties of organic matter decomposition by soil enzymes

Wang

Allison

2019

Soil Biology and Biochemistry

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“…Concentration profiles and distribution fields of oxygen, ammonium and nitrate were simulated for colonies and single trichomes, using a recently developed advection-diffusion-reaction model [52]. This model is applicable to simulate small-scale fluxes of gases and nutrients in porous phytoplankton colonies, whose chemical microenvironments are driven by diffusive and advective mass transfer, as well as by metabolic activities.…”

Section: Numerical Modelling: Concentrations Of Oxygen Ammonium and mentioning

confidence: 99%

“…To solve Eq. 1 numerically in the computational domain, we used the lattice Boltzmann method [52,57]. A detailed description of this method, including underlying assumptions, boundary conditions and input parameters, is included in the supplementary material (Text S3, Fig.…”

Section: Numerical Modelling: Concentrations Of Oxygen Ammonium and mentioning

confidence: 99%

Distinct nitrogen cycling and steep chemical gradients in Trichodesmium colonies

et al. 2019

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Trichodesmium is an important dinitrogen (N 2 )-fixing cyanobacterium in marine ecosystems. Recent nucleic acid analyses indicate that Trichodesmium colonies with their diverse epibionts support various nitrogen (N) transformations beyond N 2 fixation. However, rates of these transformations and concentration gradients of N compounds in Trichodesmium colonies remain largely unresolved. We combined isotope-tracer incubations, micro-profiling and numeric modelling to explore carbon fixation, N cycling processes as well as oxygen, ammonium and nitrate concentration gradients in individual fieldsampled Trichodesmium colonies. Colonies were net-autotrophic, with carbon and N 2 fixation occurring mostly during the day. Ten percent of the fixed N was released as ammonium after 12-h incubations. Nitrification was not detectable but nitrate consumption was high when nitrate was added. The consumed nitrate was partly reduced to ammonium, while denitrification was insignificant. Thus, the potential N transformation network was characterised by fixed N gain and recycling processes rather than denitrification. Oxygen concentrations within colonies were~60-200% air-saturation. Moreover, our modelling predicted steep concentration gradients, with up to 6-fold higher ammonium concentrations, and nitrate depletion in the colony centre compared to the ambient seawater. These gradients created a chemically heterogeneous microenvironment, presumably facilitating diverse microbial metabolisms in millimetre-sized Trichodesmium colonies.

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“…Additionally, we are only just beginning to be able to model biological processes and distributions of solutes, such as oxygen, carbon dioxide and dissolved organic matter, within sinking permeable aggregates with different internal structure and porosities, i.e. marine snow (Moradi et al, 2018).…”

Section: (E) Settling Tubementioning

confidence: 99%

Sinking Organic Particles in the Ocean—Flux Estimates From in situ Optical Devices

et al. 2020

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Optical particle measurements are emerging as an important technique for understanding the ocean carbon cycle, including contributions to estimates of their downward flux, which sequesters carbon dioxide (CO 2) in the deep sea. Optical instruments can be used from ships or installed on autonomous platforms, delivering much greater spatial and temporal coverage of particles in the mesopelagic zone of the ocean than traditional techniques, such as sediment traps. Technologies to image particles have advanced greatly over the last two decades, but the quantitative translation of these immense datasets into biogeochemical properties remains a challenge. In particular, advances are needed to enable the optimal translation of imaged objects into carbon content and sinking velocities. In addition, different devices often measure different optical properties, leading to difficulties in comparing results. Here we provide a practical overview of the challenges and potential of using these instruments, as a step toward improvement and expansion of their applications. Keywords: sinking particle fluxes, sinking velocities, carbon content, size, image processing, automated classification, in situ optical particle measurements, biological carbon pump * Different magnifications available. Quoted details are for the magnification that is most suitable for marine snow.

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A new mathematical model to explore microbial processes and their constraints in phytoplankton colonies and sinking marine aggregates

Abstract: New mathematical model explains physical-biological coupling of processes occurring within sinking aggregates in the ocean.

Cited by 21 publications

References 38 publications

Emergent properties of organic matter decomposition by soil enzymes

Emergent properties of organic matter decomposition by soil enzymes

Distinct nitrogen cycling and steep chemical gradients in Trichodesmium colonies

Sinking Organic Particles in the Ocean—Flux Estimates From in situ Optical Devices

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