Biology subjects

Gorter de Vries, P. J.

Publications and source records attributed to Gorter de Vries, P. J..

4 recordsLinked to original sources

bioRxiv2026

Design and development of online pressure sensing for microbial batch cultivation

Gas production and consumption is a direct consequence of microbial activity in environmental and industrial settings. In closed batch cultivations, headspace pressure changes therefore give valuable insights into the microbial metabolism. For laboratory scale anaerobic batch cultivations, manual manometer measurements are routinely applied, as a simple and robust method, but it is labour intensive, causes disturbances in the headspace gas and temperature, leading to suboptimal growth, inhibition and noisy data. We built and tested an automated online pressure sensor for closed batch cultivations. It is designed for microbial cultivation and integrates with sterile and anaerobic cultivation workflows. The system uses an absolute pressure sensor (0-30 bar) mounted on a custom designed PCB, with a gas-tight needle mount. An ESP32 microcontroller logs pressure and temperature locally and generates a Wi-Fi access point for real-time visualization and direct CSV download through a local homepage. We detail hardware and software design decisions, assembly, and validation including long-term stability. Case studies demonstrate the applicability for: a multiphasic biogas kinetics during anaerobic digestion, capturing gas uptake dynamics and metabolic shifts during syngas fermentations and co-feeding experiments, and long-term robustness in a multi-year monitoring of a compressed-air system. More than 130 individual sensors have been deployed over 3 years in laboratories, at various academic and industrial settings. The platform provides reproducible, high-resolution pressure measurements that enable calculation of gas formation/consumption rates and improve experimental throughput without disturbing cultures. Design files, firmware, and example analysis scripts are openly available to support adoption and further development.

bioengineering↗

bioRxiv2026

Measure Catabolism: Real-time shifts in microbial metabolism through online pressure measurements

Microbial activity is often inferred from cell density measurements; however, biomass formation is merely an indirect, cumulative result of metabolism, known as anabolism. Microbial activity is more accurately indicated by energy conservation or catabolism. This is especially true under low or no-growth conditions, where anabolism remains constant, and shifts in catabolic fluxes go unnoticed with biomass measurements alone. In anaerobic and gas-based metabolic processes, net gas exchange is linked to energy conservation, and catabolism can then be quantified through headspace measurements. We introduce a sealed-vial, non-invasive workflow that uses high-resolution headspace pressure measurements to estimate gas exchange rates and catabolic reactions, enabling real-time visualisation of metabolic shifts throughout an entire batch cultivation cycle. The method was applied to carbon monoxide (CO) fermentations of three Clostridium autoethanogenum strains (JA1-1, LAbrini, and LAbrini_mut) cultivated in serum bottles. Two of them were indistinguishable by OD-derived max. Pressure-derived gas uptake rates resolved multiple exponential phases of gas consumption and identified specific shifts in the metabolism, consistent with transitions from mixotrophic to autotrophic growth. Small but significant differences in terminal headspace pressure were detected, providing an experimentally accessible end-state parameter for phenotypic characterisation that would be obscured by routine intrusive headspace sampling. Finally, pressure-derived catabolic rates further enabled estimates of relative product formation during the main autotrophic phase. The strains were successfully characterised and distinguished by identifying several exponential phases of gas consumption and their rates, as well as differences in the final absolute pressure threshold. This provided phenotypic characterisation and insights not obtainable from OD measurements alone. The work establishes a practical framework for catabolism-resolved microbial characterisation in sealed batch vials through high-resolution online pressure (gas exchange). The assumption that pressure measurements correlate with CO2 and catabolic rates is sensitive to solubility/buffering and temperature/vapour effects, but these limitations are addressable through controls and complementary analytics.

microbiology↗

bioRxiv2026

Mapping metabolic phases through online pressure and backscatter rates

Microbial metabolism can be represented as an energy-conserving process (catabolism) and a biomass-forming reaction (anabolism). Anabolism is traditionally measured through the turbidity of the culture, while catabolism is often assessed by the substrates consumed or the products formed. Standard measurements of biomass and products are intrusive and disrupt cultivation and headspace composition, potentially masking important analytical parameters and interactions. Online pressure and backscatter were combined in small-scale closed batch vials to obtain undisturbed real-time measurements of catabolic and anabolic rates, enabling mapping of metabolic phases throughout an entire batch cultivation cycle. The method identified discrete metabolic phases in yeast cultivation and thermophilic syngas fermentation. In nutrient-rich yeast cultivation, five metabolic phases were characterized, covering growth-associated and non-growth-associated gas formation. In a mixed community syngas fermentation, estimates of catabolic and anabolic rates distinguished early biomass increase from minimal net pressure change from two later gas-driven phases. An initial phase with a higher growth rate, linked to carboxydotrophy, followed by a phase with slightly lower growth and increased gas consumption, corresponding to hydrogenotrophic acetogenesis. The study demonstrates that a simple, affordable experimental setup with online pressure and backscatter measurements can be used to visualize phase-plane mapping of microbial metabolism. An additional advantage is the ability to detect sequential metabolic cascades in mixed microbial communities, which is not possible with gas-sparging bioreactor studies. Using a single simple batch culture, growth and maintenance data can be obtained, even when growth is low or absent, thereby yielding parameters applicable to phenotypic characterization and dynamic metabolic modelling.

microbiology↗

bioRxiv2023

Probing efficient microbial CO2 utilizationthrough metabolic and process modeling

Microbial gas fermentation is proving to be a promising technology to upcycle carbon-rich waste gasses into value-added biochemicals, though production yields of varied products are currently limited. Through the holistic pairing of process modeling with host agnostic black box metabolic modeling, here we investigate an efficient thermophilic CO2 upcycling process, based on acetogenic carbon utilization. From a process engineering perspective, higher temperatures were found to favor overall gas transfer rates, even with lower gas solubility, particularly for the more expensive and often limiting H2 gas. Metabolically, for growth coupled products, thermophilic production favors higher product yields as a result of a higher maintenance energy input. A process simulation for acetate production in a large-scale bubble column reactor predicts an optimal feed gas composition of approximately 9:1 mol H2 to mol CO2 and a process with higher production yields and rates at higher temperatures. To assess the expansion of the product portfolio beyond acetate, both a product volatility analysis and a metabolic pathway model were implemented. In-situ recovery of volatile products is shown to be within range for acetone but challenging due to the extensive evaporation of water, while the production of more valuable compounds is energetically unfavorable compared to acetate. We discuss alternative approaches to overcome these challenges to utilize acetogenic CO2 fixation for the production of a wider range of carbon negative chemicals.

bioengineering↗