Ontology highlight
ABSTRACT:
PROVIDER: PRJNA418244 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.
2021-04-06 | MTBLS2021 | MetaboLights
Project description:L-Arabinose occurs at economically relevant levels in lignocellulosic hydrolysates. Especially at low concentrations of L-arabinose, its uptake via the Gal2 galactose transporter is an important rate-controlling step in the complete conversion of these feedstocks by engineered, pentose-metabolizing Saccharomyces cerevisiae strains. Chemostat-based transcriptome analysis yielded 16 putative sugar transporter genes in the filamentous fungus Penicillium chrysogenum whose transcript levels were at least three-fold higher in L-arabinose-limited cultures than in glucose-limited and ethanol-limited cultures. Of five genes that showed an over 30-fold higher transcript level in arabinose-grown cultures, only one (Pc20g01790) restored growth on L-arabinose upon expression in an engineered L-arabinose-fermenting S. cerevisiae strain in which GAL2 had been deleted. Sugar-transport assays indicated that Pc20g01790this transporter, designated as PcAraT, encodes functions as a high-affinity (Km = 0.13 mM) L-arabinose-proton symporter that does not transport xylose or glucose. An L-arabinose-metabolizing S. cerevisiae strain co-expressing Pc20g01790PcAraT and GAL2 showed lower residual substrate concentrations in L-arabinose-limited chemostat cultures (4 mg L-1) than a congenic strain in which L-arabinose import exclusively depended on Gal2 (1.8 g L-1). Inhibition of L-arabinose transport by these sugars was less pronounced than observed with Gal2. A hexose-phosphorylation-deficient, L-arabinose-metabolizing S. cerevisiae strain expressing PcAraT Pc20g0190 grew on 20 g L-1 L-arabinose in the presence of 20 g L-1 glucose, which completely inhibited growth on L-arabinose of a congenic strain dependent on L-arabinose transport via Gal2. Its high affinity and specificity for L-L-arabinose, combined with limited sensitivity to inhibition by glucose and D-D-xylose make PcAraT/ Pc20g01790 a valuable transporter gene for application in metabolic engineering strategies aimed at engineering S. cerevisiae strains for efficient conversion of lignocellulosic hydrolysates.
2017-10-03 | GSE104491 | GEO
Project description:Lignocellulosic biomass is composed of three major biopolymers: cellulose, hemicellulose and lignin. Although lignin has long been considered a waste product in biomass conversion efforts, its utilization has since been identified as critical to the economic viability of second-generation biofuel production. There is thus increasing interest in finding enzymes and enzyme cocktails which can efficiently deconstruct both the cellulose/hemicellulose and lignin components of lignocellulosic biomass. Analytical tools capable of quickly detecting both glycan and lignin deconstruction could are needed to support the development and characterization of efficient enzymes/enzyme cocktails.
2021-09-09 | PXD020215 | Pride
Project description:Creating Saccharomyces yeasts capable of efficient fermentation of pentoses such as xylose remains a key challenge in the production of ethanol from lignocellulosic biomass. Metabolic engineering of industrial Saccharomyces cerevisiae strains has yielded xylose-fermenting strains, but these strains have not yet achieved industrial viability due largely to xylose fermentation being prohibitively slower than that of glucose. Recently, it has been shown that naturally occurring xylose-utilizing Saccharomyces species exist. Uncovering the genetic architecture of such strains will shed further light on xylose metabolism, suggesting additional engineering approaches or possibly even the development of xylose-fermenting yeasts that are not genetically modified. We previously identified a hybrid yeast strain, the genome of which is largely Saccharomyces uvarum, which has the ability to grow on xylose as the sole carbon source. Despite the sterility of this hybrid strain, we were able to develop novel methods to genetically characterize its xylose utilization phenotype, using bulk segregant analysis in conjunction with high-throughput sequencing. We found that its growth in xylose is governed by at least two genetic loci: one of the loci maps to a known xylose-pathway gene, a novel allele of the aldo-keto reductase gene GRE3, while a second locus maps to an allele of APJ1, a chaperonin gene not previously connected to xylose metabolism. Our work demonstrates that the power of sequencing combined with bulk segregant analysis can also be applied to a non-genetically-tractable hybrid strain that contains a complex, polygenic trait, and it identifies new avenues for metabolic engineering as well as for construction of non-genetically modified xylose-fermenting strains.
2012-07-19 | GSE35528 | GEO
Project description:Draft genomes of syntroph and methanogen populations from methanogenic wastewater-treating bioreactor granular sludge metagenome
| PRJNA310790 | ENA
Project description:The physiology of ethanologenic Escherichia coli grown anaerobically in alkaline-pretreated plant hydrolysates is not well studied. To gain insight into how E. coli responds to such hydrolysates, we studied an E. coli K-12 ethanologen fermenting a hydrolysate prepared from corn stover pre-treated by ammonia fiber expansion. Despite the high sugar content (~6% glucose, 3% xylose) and relatively low toxicity of this hydrolysate, E. coli ceased growth long before glucose was depleted. Nevertheless, the cells remained metabolically active and continued conversion of glucose to ethanol until all glucose was consumed. Gene expression profiling revealed complex and changing patterns of metabolic physiology and cellular stress responses throughout the different stages of growth. During the exponential and transition phases of growth, high cell maintenance and stress response costs were mitigated, in part, by free amino acids available in the hydrolysate media. However, after the majority of amino acids were depleted from the media cells entered stationary phase and ATP derived from glucose fermentation was consumed entirely by the demands of cell maintenance in the hydrolysate. Comparative gene expression profiling and metabolic modeling of the ethanologen suggested that the high energetic cost of mitigating osmotic, lignotoxin and ethanol stress collectively limits growth, sugar utilization rates and ethanol yields in alkaline-pretreated lignocellulosic hydrolysates. 38 samples in total. 24 samples were derived from biological replicate fermentations of alkaline-pretreated cornstover hydrolysate (12 datapoint time-series per fermentation). The remaining samples were obtained from fermentations conducted in defined media (Glucose Minimal Media (GMM, n=7), Synthetic Hydrolysate media (SynH, n=7)).
2012-06-17 | E-GEOD-35049 | biostudies-arrayexpress
Project description:The conversion of sugars in lignocellulosic hydrolysates to bioethanol represents an industrially relevant system for understanding microbial physiology associated with production of bio-based fuels and chemicals. To this end we have developed a new version of synthetic hydrolysate (SynH) modeled on highly concentrated 9% AFEX-pretreated cornstove hydrolysate (ACSH) with and without lignocellulose-derived inhibitors (LDIs) added, termed SynH3 and SynH3- respectively. We profiled the cellular responses of xylose-utilizing Z. mobilis 2032 grown in both SynH3- and SynH3 via collection and analysis of multiple omics-based data (multiomics) including transcriptomics, proteomics, and metabolomics. Our study was focused on answering the following two questions. First, how does Z. mobilis respond to LDIs in SynH3 and how does this compare to our previous studies with E. coli in 6% ACSH SynH? Second, what is the potential cause for the poor xylose conversion in the presence of LDIs? Addressing these questions will provide critical information for engineering of Z. mobilis strains with improved productivities in lignocellulosic hydrolysates.
2019-10-25 | GSE135718 | GEO