The implications of microbial and substrate limitation for the fates of carbon in different organic soil horizon types of boreal forest ecosystems: a mechanistically based model analysis

He, Yujie; Zhuang, Qianlai; Harden, Jennifer W.; McGuire, A. D.; Fan, Zeng; Liu, Y.; Wickland, Kimberly P.

doi:10.5194/bg-11-4477-2014

Cited by 21 publications

(18 citation statements)

References 81 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The heterogeneous distribution of SOC and its bioavailability due to local physical protection and chemical recalcitrance (Six et al 2002), preferential and matrix transport of substrates due to pore connectivity and local moisture content (Hunt 2004;Liu et al 2015aLiu et al , 2014Steefel and Maher 2009), and nonuniform formation of microbial colonies and biofilms due to local substrate availability and predation inhibition (He et al 2014;Kakumanu et al 2013;Or et al 2007;Xu et al 2014) have been observed to affect the rate of heterotrophic respiration and its correlation with moisture content in soils (Franzluebbers 1999;Moyano et al 2012). Understanding the pore-scale physical and biochemical processes associated with these heterogeneous properties as well as their manifestations at large scales is crucial to reduce the uncertainty of predicting the relationship between HR rate and moisture content in soil systems.…”

Section: Introductionmentioning

confidence: 99%

Pore-scale investigation on the response of heterotrophic respiration to moisture conditions in heterogeneous soils

et al. 2016

View full text Add to dashboard Cite

The relationship between microbial respiration rate and soil moisture content is an important property for understanding and predicting soil organic carbon degradation, CO 2 production and emission, and their subsequent effects on climate change. This paper reports a pore-scale modeling study to investigate the response of heterotrophic respiration to moisture conditions in soils and to evaluate various factors that affect this response. X-ray computed tomography was used to derive soil pore structures, which were then used for pore-scale model investigation. The porescale results were then averaged to calculate the effective respiration rates as a function of water content in soils. The calculated effective respiration rate first increases and then decreases with increasing soil water content, showing a maximum respiration rate at water saturation degree of 0.75, which is consistent with field and laboratory observations. The relationship between the respiration rate and moisture content is affected by various factors, including pore-scale organic carbon bioavailability, the rate of oxygen delivery, soil pore structure and physical heterogeneity, soil clay content, and microbial drought resistivity. Overall, this study provides mechanistic insights into the soil respiration response to the change in moisture conditions, and reveals a complex relationship between heterotrophic microbial respiration rate and moisture content in soils that is affected by various hydrological, geophysical, and biochemical factors.

show abstract

Section: Introductionmentioning

confidence: 99%

Pore-scale investigation on the response of heterotrophic respiration to moisture conditions in heterogeneous soils

et al. 2016

View full text Add to dashboard Cite

show abstract

“…This has been manifested in a long list of microbial models that were published in the last few years (e.g., Schimel and Weintrub, 2003;Moorhead and Sinsabaugh, 2006;Allison et al, 2010;German et al, 2012;Wang et al, 2013;Wieder et al, 2013;Li et al, 2014;He et al, 2014;Riley et al, 2014;Xenakis and Williams, 2014;Tang and Riley, 2015;Sulman et al, 2014;Wieder et al, 2015). To build a microbial model, the substrate kinetics is fundamental as it describes the rate at which microbes would take up a substrate and represents the first step towards describing how microbes would decompose the soil organic matter.…”

Section: Introductionmentioning

confidence: 99%

On the relationships between the Michaelis–Menten kinetics, reverse Michaelis–Menten kinetics, equilibrium chemistry approximation kinetics, and quadratic kinetics

Tang

2015

Geosci. Model Dev.

View full text Add to dashboard Cite

Abstract. The Michaelis-Menten kinetics and the reverse Michaelis-Menten kinetics are two popular mathematical formulations used in many land biogeochemical models to describe how microbes and plants would respond to changes in substrate abundance. However, the criteria of when to use either of the two are often ambiguous. Here I show that these two kinetics are special approximations to the equilibrium chemistry approximation (ECA) kinetics, which is the first-order approximation to the quadratic kinetics that solves the equation of an enzyme-substrate complex exactly for a single-enzyme and single-substrate biogeochemical reaction with the law of mass action and the assumption of a quasi-steady state for the enzyme-substrate complex and that the product genesis from enzyme-substrate complex is much slower than the equilibration between enzymesubstrate complexes, substrates, and enzymes. In particular, I show that the derivation of the Michaelis-Menten kinetics does not consider the mass balance constraint of the substrate, and the reverse Michaelis-Menten kinetics does not consider the mass balance constraint of the enzyme, whereas both of these constraints are taken into account in deriving the equilibrium chemistry approximation kinetics. By benchmarking against predictions from the quadratic kinetics for a wide range of substrate and enzyme concentrations, the Michaelis-Menten kinetics was found to persistently underpredict the normalized sensitivity ∂ ln v/∂ ln k + 2 of the reaction velocity v with respect to the maximum product genesis rate k T , indicating that ECAbased models will be more calibratable if the modeled processes do obey the law of mass action. Since the equilibrium chemistry approximation kinetics includes advantages from both the Michaelis-Menten kinetics and the reverse Michaelis-Menten kinetics and it is applicable for almost the whole range of substrate and enzyme abundances, land biogeochemical modelers therefore no longer need to choose when to use the Michaelis-Menten kinetics or the reverse Michaelis-Menten kinetics. I expect that removing this choice ambiguity will make it easier to formulate more robust and consistent land biogeochemical models.

show abstract

“…Factors in addition to substrate quantity can limit heterotrophic metabolism (catabolism, anabolism, or both), including substrate quality (Jagadamma et al, 2014), mode and timing of substrate production (Carlson, 2002; Jiao et al, 2010), temperature (He et al, 2014), nutrient availability (Morita, 1997), and, in terms of the energy available from metabolic reactions, the redox environment (Brewer et al, 2014). We discuss these below.…”

Section: Discussionmentioning

confidence: 99%

Physiological Ecology of Microorganisms in Subglacial Lake Whillans

et al. 2016

View full text Add to dashboard Cite

Subglacial microbial habitats are widespread in glaciated regions of our planet. Some of these environments have been isolated from the atmosphere and from sunlight for many thousands of years. Consequently, ecosystem processes must rely on energy gained from the oxidation of inorganic substrates or detrital organic matter. Subglacial Lake Whillans (SLW) is one of more than 400 subglacial lakes known to exist under the Antarctic ice sheet; however, little is known about microbial physiology and energetics in these systems. When it was sampled through its 800 m thick ice cover in 2013, the SLW water column was shallow (~2 m deep), oxygenated, and possessed sufficient concentrations of C, N, and P substrates to support microbial growth. Here, we use a combination of physiological assays and models to assess the energetics of microbial life in SLW. In general, SLW microorganisms grew slowly in this energy-limited environment. Heterotrophic cellular carbon turnover times, calculated from 3H-thymidine and 3H-leucine incorporation rates, were long (60 to 500 days) while cellular doubling times averaged 196 days. Inferred growth rates (average ~0.006 d−1) obtained from the same incubations were at least an order of magnitude lower than those measured in Antarctic surface lakes and oligotrophic areas of the ocean. Low growth efficiency (8%) indicated that heterotrophic populations in SLW partition a majority of their carbon demand to cellular maintenance rather than growth. Chemoautotrophic CO2-fixation exceeded heterotrophic organic C-demand by a factor of ~1.5. Aerobic respiratory activity associated with heterotrophic and chemoautotrophic metabolism surpassed the estimated supply of oxygen to SLW, implying that microbial activity could deplete the oxygenated waters, resulting in anoxia. We used thermodynamic calculations to examine the biogeochemical and energetic consequences of environmentally imposed switching between aerobic and anaerobic metabolisms in the SLW water column. Heterotrophic metabolisms utilizing acetate and formate as electron donors yielded less energy than chemolithotrophic metabolisms when calculated in terms of energy density, which supports experimental results that showed chemoautotrophic activity in excess of heterotrophic activity. The microbial communities of subglacial lake ecosystems provide important natural laboratories to study the physiological and biogeochemical behavior of microorganisms inhabiting cold, dark environments.

show abstract

The implications of microbial and substrate limitation for the fates of carbon in different organic soil horizon types of boreal forest ecosystems: a mechanistically based model analysis

Cited by 21 publications

References 81 publications

Pore-scale investigation on the response of heterotrophic respiration to moisture conditions in heterogeneous soils

Pore-scale investigation on the response of heterotrophic respiration to moisture conditions in heterogeneous soils

On the relationships between the Michaelis–Menten kinetics, reverse Michaelis–Menten kinetics, equilibrium chemistry approximation kinetics, and quadratic kinetics

Physiological Ecology of Microorganisms in Subglacial Lake Whillans

Contact Info

Product

Resources

About