Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Critical parameters and procedures for anaerobic cultivation of yeasts in bioreactors and anaerobic chambers.

ABSTRACT: All known facultatively fermentative yeasts require molecular oxygen for growth. Only in a small number of yeast species, these requirements can be circumvented by supplementation of known anaerobic growth factors such as nicotinate, sterols and unsaturated fatty acids. Biosynthetic oxygen requirements of yeasts are typically small and, unless extensive precautions are taken to minimize inadvertent entry of trace amounts of oxygen, easily go unnoticed in small-scale laboratory cultivation systems. This paper discusses critical points in the design of anaerobic yeast cultivation experiments in anaerobic chambers and laboratory bioreactors. Serial transfer or continuous cultivation to dilute growth factors present in anaerobically pre-grown inocula, systematic inclusion of control strains and minimizing the impact of oxygen diffusion through tubing are identified as key elements in experimental design. Basic protocols are presented for anaerobic-chamber and bioreactor experiments.

SUBMITTER: Mooiman C

PROVIDER: S-EPMC8216787 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Reliable cell retention of mammalian suspension cells in microfluidic cultivation chambers.

Project description:Microfluidic cultivation, with its high level of environmental control and spatio-temporal resolution of cellular behavior, is a well-established tool in today's microfluidics. Yet, reliable retention of (randomly) motile cells inside designated cultivation compartments still represents a limitation, which prohibits systematic single-cell growth studies. To overcome this obstacle, current approaches rely on complex multilayer chips or on-chip valves, which makes their application for a broad community of users infeasible. Here, we present an easy-to-implement cell retention concept to withhold cells inside microfluidic cultivation chambers. By introducing a blocking structure into a cultivation chamber's entrance and nearly closing it, cells can be manually pushed into the chamber during loading procedures but are unable to leave it autonomously in subsequent long-term cultivation. CFD simulations as well as trace substance experiments confirm sufficient nutrient supply within the chamber. Through preventing recurring cell loss, growth data obtained from Chinese hamster ovary cultivation on colony level perfectly match data determined from single-cell data, which eventually allows reliable high throughput studies of single-cell growth. Due to its transferability to other chamber-based approaches, we strongly believe that our concept is also applicable for a broad range of cellular taxis studies or analyses of directed migration in basic or biomedical research.

| S-EPMC9995442 | biostudies-literature

Zinc deprivation of methanol fed anaerobic granular sludge bioreactors.

Project description:The effect of omitting zinc from the influent of mesophilic (30 degrees C) methanol fed upflow anaerobic sludge bed (UASB) reactors, and latter zinc supplementation to the influent to counteract the deprivation, was investigated by coupling the UASB reactor performance to the microbial ecology of the bioreactor sludge. Limitation of the specific methanogenic activity (SMA) on methanol due to the absence of zinc from the influent developed after 137 days of operation. At that day, the SMA in medium with a complete trace metal solution except Zn was 3.4 g CH4-COD g VSS(-1) day(-1), compared to 4.2 g CH4-COD g VSS(-1) day(-1) in a medium with a complete (including zinc) trace metal solution. The methanol removal capacity during these 137 days was 99% and no volatile fatty acids accumulated. Two UASB reactors, inoculated with the zinc-deprived sludge, were operated to study restoration of the zinc limitation by zinc supplementation to the bioreactor influent. In a first reactor, no changes to the operational conditions were made. This resulted in methanol accumulation in the reactor effluent after 12 days of operation, which subsequently induced acetogenic activity 5 days after the methanol accumulation started. Methanogenesis could not be recovered by the continuous addition of 0.5 microM ZnCl2 to the reactor for 13 days. In the second reactor, 0.5 microM ZnCl2 was added from its start-up. Although the reactor stayed 10 days longer methanogenically than the reactor operated without zinc, methanol accumulation was observed in this reactor (up to 1.1 g COD-MeOH L(-1)) as well. This study shows that zinc limitation can induce failure of methanol fed UASB reactors due to acidification, which cannot be restored by resuming the continuous supply of the deprived metal.

| S-EPMC2668640 | biostudies-other

Enhanced Biogas Production from Nanoscale Zero Valent Iron-Amended Anaerobic Bioreactors.

Project description:Addition of nanoscale zero valent iron (NZVI) to anaerobic batch reactors to enhance methanogenic activity is described. Two NZVI systems were tested: a commercially available NZVI (cNZVI) slurry and a freshly synthesized NZVI (sNZVI) suspension that was prepared immediately before addition to the reactors. In both systems, the addition of NZVI increased pH and decreased oxidation/reduction potential compared with unamended control reactors. Biodegradation of a model brewery wastewater was enhanced as indicated by an increase in chemical oxygen demand removal with both sNZVI and cNZVI amendments at all concentrations tested (1.25-5.0 g Fe/L). Methane production increased for all NZVI-amended bioreactors, with a maximum increase of 28% achieved on the addition of 2.5 and 5.0 g/L cNZVI. Addition of bulk zero-valent iron resulted in only a 5% increase in methane, indicating the advantage of using the nanoscale particles. NZVI amendments further improved produced biogas by decreasing the amount of CO2 released from the bioreactor by approximately 58%. Overall, addition of cNZVI proved more beneficial than the sNZVI at equal iron concentrations, due to decreased colloidal stability and larger effective particle size of sNZVI. Although some have reported cytotoxicity of NZVI to anaerobic microorganisms, work presented here suggests that NZVI of a certain particle size and reactivity can serve as an amendment to anaerobic digesters to enhance degradation and increase the value of the produced biogas, yielding a more energy-efficient anaerobic method for wastewater treatment.

| S-EPMC4545702 | biostudies-literature

Anaerobic carbon-limited retentostat cultivation of Lactobacillus plantarum WCFS1

2010-01-01 | GSE18340 | GEO

Arrested anaerobic digestion bioreactors

Project description:Unlocking the Potential of Mixed-Microbial Fermentation for Enhancing Carbonaceous Resource Recovery from Organic "Wastes"

| PRJNA953645 | ENA

Sludge from anaerobic bioreactors

Project description:Sludge from anaerobic bioreactors Metagenome

| PRJNA814683 | ENA

Divergent evolution of pyrimidine biosynthesis between anaerobic and aerobic yeasts.

Project description:A cDNA encoding the dihydroorotate dehydrogenase (DHOdehase; EC 1.3.3.1) of the yeast Schizosaccharomyces pombe was isolated by functional complementation in Saccharomyces cerevisiae. A divergent subcellular compartmentation of the DHOdehase of each yeast was shown. The DHOdehase from Sch. pombe was localized in the mitochondria whereas its homolog from S. cerevisiae was found to be cytosolic. The heterologous expression of the Sch. pombe enzyme in S. cerevisiae allowed us to demonstrate that the Sch. pombe DHOdehase activity requires the integrity of the mitochondrial electron transport chain. Indeed, the presence of a mutation inactivating cytochrome b abolished the complementation of a S. cerevisiae ura1 mutant by the corresponding Sch. pombe gene. By contrast, in vitro studies have revealed that the DHOdehase of S. cerevisiae uses fumarate as terminal electron acceptor. These results are discussed in relation to the anaerobic growth competence of the two yeasts and to the fermentative processes they use.

| S-EPMC50045 | biostudies-other

Dynamic Membrane Formation in Anaerobic Dynamic Membrane Bioreactors: Role of Extracellular Polymeric Substances.

Project description:Dynamic membrane (DM) formation in dynamic membrane bioreactors plays an important role in achieving efficient solid-liquid separation. In order to study the contribution of extracellular polymeric substances (EPS) to DM formation in anaerobic dynamic membrane bioreactor (AnDMBR) processes, EPS extraction from and re-addition to bulk sludge were carried out in short-term filtration tests. DM formation behaviors could be well simulated by cake filtration model, and sludge with EPS re-addition showed the highest resistance coefficient, followed by sludge after EPS extraction. The DM layers exhibited a higher resistance and a lower porosity for the sludge sample after EPS extraction and for the sludge with EPS re-addition. Particle size of sludge flocs decreased after EPS extraction, and changed little with EPS re-addition, which was confirmed by interaction energy analysis. Further investigations by confocal laser scanning microscopy (CLSM) analysis and batch tests suggested that the removal of in-situ EPS stimulated release of soluble EPS, and re-added EPS were present as soluble EPS rather than bound EPS, which thus improved the formation of DM. The present work revealed the role of EPS in anaerobic DM formation, and could facilitate the operation of AnDMBR processes.

| S-EPMC4593540 | biostudies-literature

Mimicked Mixing-Induced Heterogeneities of Industrial Bioreactors Stimulate Long-Lasting Adaption Programs in Ethanol-Producing Yeasts.

Project description:Commercial-scale bioreactors create an unnatural environment for microbes from an evolutionary point of view. Mixing insufficiencies expose individual cells to fluctuating nutrient concentrations on a second-to-minute scale while transcriptional and translational capacities limit the microbial adaptation time from minutes to hours. This mismatch carries the risk of inadequate adaptation effects, especially considering that nutrients are available at optimal concentrations on average. Consequently, industrial bioprocesses that strive to maintain microbes in a phenotypic sweet spot, during lab-scale development, might suffer performance losses when said adaptive misconfigurations arise during scale-up. Here, we investigated the influence of fluctuating glucose availability on the gene-expression profile in the industrial yeast Ethanol Red™. The stimulus-response experiment introduced 2 min glucose depletion phases to cells growing under glucose limitation in a chemostat. Even though Ethanol Red™ displayed robust growth and productivity, a single 2 min depletion of glucose transiently triggered the environmental stress response. Furthermore, a new growth phenotype with an increased ribosome portfolio emerged after complete adaptation to recurring glucose shortages. The results of this study serve a twofold purpose. First, it highlights the necessity to consider the large-scale environment already at the experimental development stage, even when process-related stressors are moderate. Second, it allowed the deduction of strain engineering guidelines to optimize the genetic background of large-scale production hosts.

| S-EPMC10218636 | biostudies-literature

Anaerobic carbon-limited retentostat cultivation of Lactobacillus plantarum WCFS1

Project description:Lactobacillus plantarum WCFS1 was grown under anaerobic carbon-limited conditions in a chemostat with complete biomass retention (retentostat). In this cultivation system, the biomass concentration progressively increases while the dilution rate is kept constant, resulting in decreased specific susbtrate availibility, and hence, a progressive decrease in the specific growth rate. During the progressive transition from growth to virtually no growth, the global changes occurring at the level of metabolism and gene expression were studied using a genome-scale metabolic model and DNA microarrays. Four different time-points are compared, corresponding to 4 different specific growth rates, and hence, 4 different ratios of energy used for maintenance and growth. The samples taken at the start of retentostat cultivation serves as a a reference sample, to which the three other samples (taken after 3 days, 17 days, and 31 days under retentostat conditions) are compared. No biological replicates: all samples were taken from the same retentostat fermentation.

2010-05-16 | E-GEOD-18340 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data