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https://www.readbyqxmd.com/read/29218033/substrate-limited-and-unlimited-coastal-microbial-communities-show-different-metabolic-responses-with-regard-to-temperature
#1
Helmut Maske, Ramón Cajal-Medrano, Josué Villegas-Mendoza
Bacteria are the principal consumers of dissolved organic carbon (DOC) in the ocean and predation of bacteria makes organic carbon available to higher trophic levels. The efficiency with which bacteria convert the consumed carbon (C) into biomass (i.e., carbon growth efficiency, Y) determines their ecological as well as biogeochemical role in marine ecosystems. Yet, it is still unclear how changes in temperature will affect Y and, hence, the transfer of consumed C to higher trophic levels. Here, we experimentally investigated the effect of temperature on metabolic functions of coastal microbial communities inoculated in both nutrient-limited chemostats and nutrient-unlimited turbidostats...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29196124/combined-engineering-of-disaccharide-transport-and-phosphorolysis-for-enhanced-atp-yield-from-sucrose-fermentation-in-saccharomyces-cerevisiae
#2
Wesley Leoricy Marques, Robert Mans, Ryan K Henderson, Eko Roy Marella, Jolanda Ter Horst, Erik de Hulster, Bert Poolman, Jean-Marc Daran, Jack T Pronk, Andreas K Gombert, Antonius J A van Maris
Anaerobic industrial fermentation processes do not require aeration and intensive mixing and the accompanying cost savings are beneficial for production of chemicals and fuels. However, the free-energy conservation of fermentative pathways is often insufficient for the production and export of the desired compounds and/or for cellular growth and maintenance. To increase free-energy conservation during fermentation of the industrially relevant disaccharide sucrose by Saccharomyces cerevisiae, we first replaced the native yeast α-glucosidases by an intracellular sucrose phosphorylase from Leuconostoc mesenteroides (LmSPase)...
November 28, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29186812/biotechnological-applications-of-microbial-per-chlorate-reduction
#3
REVIEW
(no author information available yet)
While the microbial degradation of a chloroxyanion-based herbicide was first observed nearly ninety years ago, only recently have researchers elucidated the underlying mechanisms of perchlorate and chlorate [collectively, (per)chlorate] respiration. Although the obvious application of these metabolisms lies in the bioremediation and attenuation of (per)chlorate in contaminated environments, a diversity of alternative and innovative biotechnological applications has been proposed based on the unique metabolic abilities of dissimilatory (per)chlorate-reducing bacteria (DPRB)...
November 24, 2017: Microorganisms
https://www.readbyqxmd.com/read/29171840/what-intrinsic-and-extrinsic-factors-explain-the-stoichiometric-diversity-of-aquatic-heterotrophic-bacteria
#4
Casey M Godwin, James B Cotner
The elemental content of microbial communities is dependent upon the physiology of constituent populations, yet ecological stoichiometry has made slow progress toward identifying predictors of how species and strains change the elemental content of their biomass in response to the stoichiometry of elements in resources. We asked whether the elemental content of aquatic bacteria, especially flexibility in elemental content, could be predicted by their phylogeny, maximum growth rate or lake productivity. We examined 137 isolates using chemostats and found that strains differed substantially in how the carbon:nitrogen:phosphorus ratios (C:N:P) in their biomass responded to P-sufficient and P-limiting conditions...
November 24, 2017: ISME Journal
https://www.readbyqxmd.com/read/29161865/a-bacteriophage-model-based-on-crispr-cas-immune-system-in-a-chemostat
#5
Mengshi Shu, Rui Fu, Wendi Wang
Clustered regularly interspaced short palindromic repeats(CRISPRs) along with Cas proteins are a widespread immune system across bacteria and archaea. In this paper, a mathematical model in a chemostat is proposed to investigate the effect of CRISPR/Cas on the bacteriophage dynamics. It is shown that the introduction of CRISPR/Cas can induce a backward bifurcation and transcritical bifurcation. Numerical simulations reveal the coexistence of a stable infection-free equilibrium with an infection equilibrium, or a stable infection-free equilibrium with a stable periodic solution...
October 2017: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29160039/fine-tuning-the-p-pastoris-imt1026-genome-scale-metabolic-model-for-improved-prediction-of-growth-on-methanol-or-glycerol-as-sole-carbon-sources
#6
Màrius Tomàs-Gamisans, Pau Ferrer, Joan Albiol
The methylotrophic yeast Pichia pastoris (Komagataella spp.) is widely used as cell factory for recombinant protein production. In the past recent years, important breakthroughs in the systems-level quantitative analysis of its physiology have been achieved. This wealth of information has allowed the development of genome-scale metabolic models, which make new approaches possible for host cell and bioprocess engineering. Nevertheless, the predictive accuracy of the previous consensus model required to be upgraded and validated with new experimental data sets for P...
November 21, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/29145596/a-crispr-cas9-based-exploration-into-the-elusive-mechanism-for-lactate-export-in-saccharomyces-cerevisiae
#7
Robert Mans, Else-Jasmijn Hassing, Melanie Wijsman, Annabel Giezekamp, Jack T Pronk, Jean-Marc Daran, Antonius J A van Maris
CRISPR/Cas9-based genome editing allows rapid, simultaneous modification of multiple genetic loci in Saccharomyces cerevisiae. Here, this technique was used in a functional analysis study aimed at identifying the hitherto unknown mechanism of lactate export in this yeast. First, an S. cerevisiae strain was constructed with deletions in 25 genes encoding transport proteins, including the complete aqua(glycero)porin family and all known carboxylic-acid transporters. The 25-deletion strain was then transformed with an expression cassette for Lactobacillus casei lactate dehydrogenase (LcLDH)...
November 14, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/29131817/characterizing-steady-states-of-genome-scale-metabolic-networks-in-continuous-cell-cultures
#8
Jorge Fernandez-de-Cossio-Diaz, Kalet Leon, Roberto Mulet
In the continuous mode of cell culture, a constant flow carrying fresh media replaces culture fluid, cells, nutrients and secreted metabolites. Here we present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct accumulation. We provide a method to determine the steady states of this system that is tractable for metabolic networks of arbitrary complexity...
November 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29101089/comparison-of-the-metabolic-response-to-over-production-of-p-coumaric-acid-in-two-yeast-strains
#9
Angelica Rodriguez, Yun Chen, Sakda Khoomrung, Emre Özdemir, Irina Borodina, Jens Nielsen
The development of robust and efficient cell factories requires understanding of the metabolic changes triggered by the production of the targeted compound. Here we aimed to study how production of p-coumaric acid, a precursor of multiple secondary aromatic metabolites, influences the cellular metabolism of Saccharomyces cerevisiae. We evaluated the growth and p-coumaric acid production in batch and chemostat cultivations and analyzed the transcriptome and intracellular metabolome during steady state in low- and high-producers of p-coumaric acid in two strain backgrounds, S288c or CEN...
October 31, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29099858/effects-of-glucose-availability-in-lactobacillus-sakei-metabolic-change-and-regulation-of-the-proteome-and-transcriptome
#10
Anette McLeod, Ellen F Mosleth, Ida Rud, Filipe Branco Dos Santos, Lars Snipen, Kristian Hovde Liland, Lars Axelsson
Effects of glucose availability were investigated in Lactobacillus sakei strains 23K and LS25 cultivated in anaerobic, glucose-limited chemostats set at high (D = 0.357 h-1) and low (D = 0.045 h-1) dilution rates. We observed for both strains a shift from homolactic towards more mixed acid fermentation when comparing high to low growth rates. However, this change was more pronounced for LS25 than for 23K, where dominating products were lactate>formate>acetate≥ethanol at both conditions. A multivariate approach was used for analyzing proteome and transcriptome data from the bacterial cultures, where the predictive power of the omics data was used for identifying features that can explain the differences in the end-product profiles...
2017: PloS One
https://www.readbyqxmd.com/read/29076595/tuning-the-modular-paracoccus-denitrificans-respirome-to-adapt-from-aerobic-respiration-to-anaerobic-denitrification
#11
Georgios Giannopoulos, Matthew J Sullivan, Katherine Hartop, Gary Rowley, Andrew Gates, Nicholas J Watmough, D J Richardson
Bacterial denitrification is a respiratory process that is a major source and sink of the potent greenhouse gas nitrous oxide. Many denitrifying bacteria can adjust to life in both oxic and anoxic environments through differential expression of their respiromes in response to environmental signals such as oxygen, nitrate and nitric oxide. We used steady state oxic and anoxic chemostat cultures to demonstrate that the switch from aerobic to anaerobic metabolism is brought about by changes in the levels of expression of relatively few genes, but this is sufficient to adjust the configuration of the respirome to allow the organism to efficiently respire nitrate without the significant release of intermediates, such as nitrous oxide...
October 27, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29057884/dynamics-of-the-stochastic-chemostat-with-monod-haldane-response-function
#12
Liang Wang, Daqing Jiang, Gail S K Wolkowicz, Donal O'Regan
The stochastic chemostat model with Monod-Haldane response function is perturbed by environmental white noise. This model has a global positive solution. We demonstrate that there is a stationary distribution of the stochastic model and the system is ergodic under appropriate conditions, on the basis of Khasminskii's theory on ergodicity. Sufficient criteria for extinction of the microbial population in the stochastic system are established. These conditions depend strongly on the Brownian motion. We find that even small scale white noise can promote the survival of microorganism populations, while large scale noise can lead to extinction...
October 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29055584/nitrosomonas-europaea-adaptation-to-anoxic-oxic-cycling-insights-from-transcription-analysis-proteomics-and-metabolic-network-modeling
#13
Ran Yu, Octavio Perez-Garcia, Huijie Lu, Kartik Chandran
In suboxic or anoxic environments, nitrous oxide (N2O) can be produced by ammonia oxidizing bacteria (AOB) as a potent greenhouse gas. Although N2O producing inventory and pathways have been well-characterized using archetypal AOB, there is little known about their adaptive responses to oxic-anoxic cycling, which is a prevalent condition in soil, sediment, and wastewater treatment bioreactors. In this study, cellular responses of Nitrosomonas europaea 19718 to sustained anoxic-oxic cycling in a chemostat bioreactor were evaluated at transcriptomic, proteomic, and fluxomic levels...
February 15, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29054062/the-chemostat-metabolite-spectra-of-alkaline-mixed-culture-fermentation-under-mesophilic-thermophilic-and-extreme-thermophilic-conditions
#14
Kun Dai, Fang Zhang, Yan Zhang, Raymond Jianxiong Zeng
Alkaline mixed culture fermentation (MCF) is a promising technology for reducing organic waste and producing biochemicals. However, chemostat metabolite spectra that are necessary for constructing a model and analyzing factors are seldom reported. In the present study, the effects of pH on the metabolites distribution in mesophilic (35 °C), thermophilic (55 °C), and extreme-thermophilic (70 °C) alkaline MCF were demonstrated. A chemical oxygen demand balance above 80% was achieved, and the main metabolites included acetate, ethanol, propionate, lactate, and formate...
October 10, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29052015/stoichiometry-and-kinetics-of-single-and-mixed-substrate-uptake-in-aspergillus-niger
#15
Francisca Lameiras, Cor Ras, Angela Ten Pierick, Joseph J Heijnen, Walter M van Gulik
In its natural environment, the filamentous fungus Aspergillus niger grows on decaying fruits and plant material, thereby enzymatically degrading the lignocellulosic constituents (lignin, cellulose, hemicellulose, and pectin) into a mixture of mono- and oligosaccharides. To investigate the kinetics and stoichiometry of growth of this fungus on lignocellulosic sugars, we carried out batch cultivations on six representative monosaccharides (glucose, xylose, mannose, rhamnose, arabinose, and galacturonic acid) and a mixture of these...
October 19, 2017: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/29040817/potential-for-mcl-pha-production-from-nonanoic-and-azelaic-acids
#16
James Gillis, Kenton Ko, Juliana A Ramsay, Bruce A Ramsay
Greater than 65 % of canola and high oleic soy oil fatty acids is oleic acid, which is readily converted to nonanoic (NA) and azelaic (AzA) acids by ozonolysis. NA is an excellent substrate for medium-chain-length polyhydroxyalkanoate (mcl-PHA) production but AzA has few uses. Pseudomonas citronellolis DSM 50332 and Pseudomonas fluorescens ATCC 17400, both able to produce mcl-PHA from fatty acids and able to grow on AzA as the sole source of carbon and energy were assessed for the accumulation of mcl-PHA from AzA and NA...
October 17, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/29027144/erratum-to-quantitative-physiology-and-elemental-composition-of-kluyveromyces-lactis-cbs-2359-during-growth-on-glucose-at-different-specific-growth-rates
#17
Oscar Dias, Thiago O Basso, Isabel Rocha, Eugénio C Ferreira, Andreas K Gombert
In the original publication of the article, the below mentioned errors have appeared. The correct text is provided in this erratum, In the abstract section, the sentence "This dataset serve" should be replaced as "This dataset serves". Also, the reference "Basso TO, Gomes FS, Lopes ML, et al (2014) Homo- and heterofermentative lactobacilli differently affect sugarcane-based fuel ethanol fermentation. Antonie Van Leeuwenhoek 105:169-177. doi: 10.1007/s10482-013-0063-6 " should be replaced as "Basso TO, Dario MG, Tonso A, Stambuk BU, Gombert AK (2010) Insufficient uracil supply in fully aerobic chemostat cultures of Saccharomyces cerevisiae leads to respiro-fermentative metabolism and double nutrient-limitation...
October 12, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29024909/impact-of-phosphate-limitation-on-pha-production-in-a-feast-famine-process
#18
Emmanouela Korkakaki, Mark C M van Loosdrecht, Robbert Kleerebezem
Double-limitation systems have shown to induce polyhydroxyalkanoates (PHA) production in chemostat studies limited in e.g. carbon and phosphate. In this work the impact of double substrate limitation on the enrichment of a PHA producing community was studied in a sequencing batch process. Enrichments at different C/P concentration ratios in the influent were established and the effect on the PHA production capacity and the enrichment community structure was investigated. Experimental results demonstrated that when a double substrate limitation is imposed at a C/P ratio in the influent in a range of 150 (C-mol/mol), the P-content of the biomass and the specific substrate uptake rates decreased...
December 1, 2017: Water Research
https://www.readbyqxmd.com/read/29021488/aerobic-dechlorination-of-dichloromethane-using-biostimulation-agent-bd-c-in-continuous-and-batch-cultures-of-xanthobacter-autotrophicus-gj10
#19
Akifumi Hosoda, Yuta Isomura, Syungo Takeo, Takuho Onai, Kazutaka Takeuchi, Minoru Toda, Hiroto Tamura
It is important to construct microbiological treatment systems for organic solvent-contaminated water. We developed a continuous culture supplemented with a biostimulation agent named BD-C, which is formulated from canola oil, and Xanthobacter autotrophicus strain GJ10 for an aerobic dichloromethane (DCM)-dechlorinating microorganism. The continuous culture was a chemostat constructed using a 1 L screw-capped bottle containing artificial wastewater medium with 2.0 mM DCM and 1.0% (v/v) BD-C. The expression of genes for DCM metabolism in the dechlorinating aerobe was monitored and analyzed by reverse transcription-quantitative PCR...
October 11, 2017: Journal of Oleo Science
https://www.readbyqxmd.com/read/29016193/the-possible-emergence-of-life-and-differentiation-of-a-shallow-biosphere-on-irradiated-icy-worlds-the-example-of-europa
#20
Michael J Russell, Alison E Murray, Kevin P Hand
Irradiated ice-covered ocean worlds with rocky mafic mantles may provide the conditions needed to drive the emergence and maintenance of life. Alkaline hydrothermal springs-relieving the geophysical, thermal, and chemical disequilibria between oceans and tidally stressed crusts-could generate inorganic barriers to the otherwise uncontrolled and kinetically disfavored oxidation of hydrothermal hydrogen and methane. Ionic gradients imposed across these inorganic barriers, comprising iron oxyhydroxides and sulfides, could drive the hydrogenation of carbon dioxide and the oxidation of methane through thermodynamically favorable metabolic pathways leading to early life-forms...
October 10, 2017: Astrobiology
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