Improved method for enumerating sulfate-reducing bacteria using optical density

Bernardez, L. A.; Lima, L. R. P. de Andrade

doi:10.1016/j.mex.2015.04.006

Cited by 27 publications

(19 citation statements)

References 5 publications

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“…The latter was assumed to be an equal biomass distribution among constituting species. To estimate this distribution, total biomass concentration in C-mol l −1 was approximated from the experimental OD (at 600 nm) measurements at the start of the experiment (electronic supplementary material, table S4) and using a previously calibrated relationship between OD and biomass using sulfate-reducing bacteria ( predominantly Desulfovibrio vulgaris) [38]; ln(DW) = 5.12 • OD600 -4.987, where DW is the dry weight of the cells in g l −1 . We converted the resulting DW value to 1 C mol −1 by dividing it by the molecular weight of the generic molecule used to represent biomass (C 1 H 1.8 O 0.5 N 0.2 , [27]); 24.6 g.C mol −1 .…”

Section: Numerical Simulationsmentioning

confidence: 99%

Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

Delattre

Chen

Wade

et al. 2020

J. R. Soc. Interface.

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Microbial communities are complex dynamical systems harbouring many species interacting together to implement higher-level functions. Among these higher-level functions, conversion of organic matter into simpler building blocks by microbial communities underpins biogeochemical cycles and animal and plant nutrition, and is exploited in biotechnology. A prerequisite to predicting the dynamics and stability of community-mediated metabolic conversions is the development and calibration of appropriate mathematical models. Here, we present a generic, extendable thermodynamic model for community dynamics and calibrate a key parameter of this thermodynamic model, the minimum energy requirement associated with growth-supporting metabolic pathways, using experimental population dynamics data from synthetic communities composed of a sulfate reducer and two methanogens. Our findings show that accounting for thermodynamics is necessary in capturing the experimental population dynamics of these synthetic communities that feature relevant species using low energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis (in the range of −30 kJ mol −1 ) and elaborate on previous estimates of lactate fermentation by sulfate reducers (in the range of −30 to −17 kJ mol −1 depending on the culture conditions). The open-source nature of the developed model and demonstration of its use for estimating a key thermodynamic parameter should facilitate further thermodynamic modelling of microbial communities.

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Section: Numerical Simulationsmentioning

confidence: 99%

Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

Delattre

Chen

Wade

et al. 2020

J. R. Soc. Interface.

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“…The initial optical density (OD) recorded for this experiment was approximately 0.025 (da Silva et al, 2013). No calibration to other units was performed by these authors and few exist in the literature for Desulfovibrio strains, but Bernardez and de Andrade Lima (2015) suggested a conversion of: dry weight (mg) = exp (5.12 OD–4.987), which gives an approximate initial bacterial concentration for this experiment of 7.76 mg L –1 . Although the conditions under which this conversion was derived differ from the experiment of da Silva et al (2013), this estimate compares well to that of our model.…”

Section: Resultsmentioning

confidence: 95%

A Mathematical Model for the Hydrogenotrophic Metabolism of Sulphate-Reducing Bacteria

et al. 2019

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Sulphate-reducing bacteria (SRB) are studied across a range of scientific fields due to their characteristic ability to metabolise sulphate and produce hydrogen sulphide, which can lead to significant consequences for human activities. Importantly, they are members of the human gastrointestinal microbial population, contributing to the metabolism of dietary and host secreted molecules found in this environment. The role of the microbiota in host digestion is well studied, but the full role of SRB in this process has not been established. Moreover, from a human health perspective, SRB have been implicated in a number of functional gastrointestinal disorders such as Irritable Bowel Syndrome and the development of colorectal cancer. To assist with the study of SRB, we present a mathematical model for the growth and metabolism of the well-studied SRB, Desulfovibrio vulgaris in a closed system. Previous attempts to model SRB have resulted in complex or highly specific models that are not easily adapted to the study of SRB in different environments, such as the gastrointestinal tract. We propose a simpler, Monod-based model that allows for easy alteration of both key parameter values and the governing equations to enable model adaptation. To prevent any incorrect assumptions about the nature of SRB metabolic pathways, we structure the model to consider only the concentrations of initial and final metabolites in a pathway, which circumvents the current uncertainty around hydrogen cycling by SRB. We parameterise our model using experiments with varied initial substrate conditions, obtaining parameter values that compare well with experimental estimates in the literature. We then validate our model against four independent experiments involving D. vulgaris with further variations to substrate availability. Further use of the model will be possible in a number of settings, notably as part of larger models studying the metabolic interactions between SRB and other hydrogenotrophic microbes in the human gastrointestinal tract and how this relates to functional disorders.

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“…The protocol for acid-amended OD (aaOD) growth estimation was modified from Bernardez and De Andrade Lima [1] which details the use of relatively large culture volumes (45 mL) to estimate microbial biomass from OD readings following the dissolution of iron precipitates using HCl. We have adapted this method to a high throughput microtiter plate approach that is more time efficient, does not require cell washing steps and, due the incorporation of smaller aliquot volumes (180 μL), allows for collection of higher resolution time series data (Supplementary Table S1).…”

Section: Methods Detailsmentioning

confidence: 99%

An efficient, cost-effective method for determining the growth rate of sulfate-reducing bacteria using spectrophotometry

2019

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Improved method for enumerating sulfate-reducing bacteria using optical density

Abstract: Graphical abstract

Cited by 27 publications

References 5 publications

Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

A Mathematical Model for the Hydrogenotrophic Metabolism of Sulphate-Reducing Bacteria

An efficient, cost-effective method for determining the growth rate of sulfate-reducing bacteria using spectrophotometry

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