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https://www.readbyqxmd.com/read/29469946/genome-variations-of-evolved-escherichia-coli-et8-with-a-rhodopsin-based-phototrophic-metabolism
#1
Hyun Aaron Kim, Hyun Ju Kim, Min Ju Lee, Jihoon Park, Ah Reum Choi, Haeyoung Jeong, Kwang-Hwan Jung, Pil Kim, Sang Jun Lee
We reported that the phototrophic metabolism via plasmid-originated Gloeobacter rhodopsin(GR)-expression is improved in Escherichia coli ET5 harboring pKJ606-GR by a genomic point mutation (dgcQC1082A ) encoding a transmembrane cell signaling protein (Microb. Cell Fact. 16:111, 2017). Another evolved descendant was isolated from the chemostat, and the genome variation of the strain named ET8 harboring pKJ606-GR was investigated in this study. Whole genome sequencing analysis identified a single point mutation (C3831976A) located in the non-coding upstream region of kdtA and an IS4 insertional mutation at galUG706 without any mutations in the plasmid...
February 22, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29457693/growth-yield-and-selection-of-nosz-clade-ii-types-in-a-continuous-enrichment-culture-of-n-2-o-respiring-bacteria
#2
Monica Conthe, Lea Wittorf, J Gijs Kuenen, Robbert Kleerebezem, Sara Hallin, Mark C M van Loosdrecht
Nitrous oxide (N2 O) reducing microorganisms may be key in the mitigation of N2 O emissions from managed ecosystems. However, there is still no clear understanding of the physiological and bioenergetic implications of microorganisms possessing either of the two N2 O reductase genes (nosZ), clade I and the more recently described clade II type nosZ. It has been suggested that organisms with nosZ clade II have higher growth yields and a lower affinity constant (Ks ) for N2 O. We compared N2 O reducing communities with different nosZI/nosZII ratios selected in chemostat enrichment cultures, inoculated with activated sludge, fed with N2 O as a sole electron acceptor and growth limiting factor, and acetate as electron donor...
February 19, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29453803/competition-for-nutrients-and-light-testing-advances-in-resource-competition-with-a-natural-phytoplankton-community
#3
Amanda Burson, Maayke Stomp, Emma Greenwell, Julia Grosse, Jef Huisman
A key challenge in ecology is to understand how nutrients and light affect the biodiversity and community structure of phytoplankton and plant communities. According to resource competition models, ratios of limiting nutrients are major determinants of the species composition. At high nutrient levels, however, species interactions may shift to competition for light, which might make nutrient ratios less relevant. The "nutrient-load hypothesis" merges these two perspectives, by extending the classic model of competition for two nutrients to include competition for light...
February 17, 2018: Ecology
https://www.readbyqxmd.com/read/29416562/optimizing-anaerobic-growth-rate-and-fermentation-kinetics-in-saccharomyces-cerevisiae-strains-expressing-calvin-cycle-enzymes-for-improved-ethanol-yield
#4
Ioannis Papapetridis, Maaike Goudriaan, María Vázquez Vitali, Nikita A de Keijzer, Marcel van den Broek, Antonius J A van Maris, Jack T Pronk
Background: Reduction or elimination of by-product formation is of immediate economic relevance in fermentation processes for industrial bioethanol production with the yeast Saccharomyces cerevisiae. Anaerobic cultures of wild-type S. cerevisiae require formation of glycerol to maintain the intracellular NADH/NAD+ balance. Previously, functional expression of the Calvin-cycle enzymes ribulose-1,5-bisphosphate carboxylase (RuBisCO) and phosphoribulokinase (PRK) in S. cerevisiae was shown to enable reoxidation of NADH with CO2 as electron acceptor...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29415113/supply-and-transport-limitations-on-phosphorus-losses-from-agricultural-fields-in-the-lower-great-lakes-region-canada
#5
Janina M Plach, Merrin L Macrae, Genevieve A Ali, Richard R Brunke, Michael C English, Gabrielle Ferguson, W Vito Lam, Tatianna M Lozier, Kevin McKague, Ivan P O'Halloran, Gilian Opolko, Christopher J Van Esbroeck
Phosphorus (P) mobilization in agricultural landscapes is regulated by both hydrologic (transport) and biogeochemical (supply) processes interacting within soils; however, the dominance of these controls can vary spatially and temporally. In this study, we analyzed a 5-yr dataset of stormflow events across nine agricultural fields in the lower Great Lakes region of Ontario, Canada, to determine if edge-of-field surface runoff and tile drainage losses (total and dissolved reactive P) were limited by transport mechanisms or P supply...
January 2018: Journal of Environmental Quality
https://www.readbyqxmd.com/read/29401445/simulating-genetic-circuits-in-bacterial-populations-with-growth-heterogeneity
#6
Anjan Roy, Stefan Klumpp
We computationally study genetic circuits in bacterial populations with heterogeneities in the growth rate. To that end, we present a stochastic simulation method for gene circuits in populations of cells and propose an efficient implementation that we call the "Next Family Method". Within this approach, we implement different population setups, specifically Chemostat-type growth and growth in an ideal Mother Machine and show that the population structure and its statistics are different for the different setups whenever there is growth heterogeneity...
January 23, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29393582/substrate-and-electron-donor-limitation-induce-phenotypic-heterogeneity-in-different-metabolic-activities-in-a-green-sulphur-bacterium
#7
M Zimmermann, S Escrig, G Lavik, M M M Kuypers, A Meibom, M Ackermann, F Schreiber
Populations of genetically identical cells can display marked variation in phenotypic traits; such variation is termed phenotypic heterogeneity. Here we investigate the effect of substrate and electron donor limitation on phenotypic heterogeneity in N2 and CO2 fixation in the green sulphur bacterium Chlorobium phaeobacteroides. We grew populations in chemostats and batch cultures and used stable isotope labelling combined with nanometer-scale secondary ion mass spectrometry (NanoSIMS) to quantify phenotypic heterogeneity...
February 2, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29383456/continuous-culture-techniques-as-simulators-for-standard-cells-jacques-monod-s-aron-novick-s-and-leo-szilard-s-quantitative-approach-to-microbiology
#8
Gabriele Gramelsberger
Continuous culture techniques were developed in the early twentieth century to replace cumbersome studies of cell growth in batch cultures. In contrast to batch cultures, they constituted an open concept, as cells are forced to proliferate by adding new medium while cell suspension is constantly removed. During the 1940s and 1950s new devices have been designed-called "automatic syringe mechanism," "turbidostat," "chemostat," "bactogen," and "microbial auxanometer"-which allowed increasingly accurate quantitative measurements of bacterial growth...
January 30, 2018: History and Philosophy of the Life Sciences
https://www.readbyqxmd.com/read/29357936/the-effect-of-metabolic-stress-on-genome-stability-of-a-synthetic-biology-chassis-escherichia-coli-k12-strain
#9
Jillian M Couto, Anne McGarrity, Julie Russell, William T Sloan
BACKGROUND: Synthetic organism-based biotechnologies are increasingly being proposed for environmental applications, such as in situ sensing. Typically, the novel function of these organisms is delivered by compiling genetic fragments in the genome of a chassis organism. To behave predictably, these chassis are designed with reduced genomes that minimize biological complexity. However, in these proposed applications it is expected that even when contained within a device, organisms will be exposed to fluctuating, often stressful, conditions and it is not clear whether their genomes will retain stability...
January 22, 2018: Microbial Cell Factories
https://www.readbyqxmd.com/read/29357933/metabolic-flux-analysis-and-the-nad-p-h-nad-p-ratios-in-chemostat-cultures-of-azotobacter-vinelandii
#10
Andres García, Pau Ferrer, Joan Albiol, Tania Castillo, Daniel Segura, Carlos Peña
BACKGROUND: Azotobacter vinelandii is a bacterium that produces alginate and polyhydroxybutyrate (P3HB); however, the role of NAD(P)H/NAD(P)+ ratios on the metabolic fluxes through biosynthesis pathways of these biopolymers remains unknown. The aim of this study was to evaluate the NAD(P)H/NAD(P) + ratios and the metabolic fluxes involved in alginate and P3HB biosynthesis, under oxygen-limiting and non-limiting oxygen conditions. RESULTS: The results reveal that changes in the oxygen availability have an important effect on the metabolic fluxes and intracellular NADPH/NADP+ ratio, showing that at the lowest OTR (2...
January 22, 2018: Microbial Cell Factories
https://www.readbyqxmd.com/read/29327471/exploring-microbial-n2-o-reduction-a-continuous-enrichment-in-nitrogen-free-medium
#11
Monica Conthe, J Gijs Kuenen, Robbert Kleerebezem, Mark C M van Loosdrecht
N2 O is a potent greenhouse gas, but also a potent electron acceptor. In search of thermodynamically favorable - yet undescribed - metabolic pathways involving N2 O reduction, we set up a continuous microbial enrichment, inoculated with activated sludge, fed with N2 O as the sole electron acceptor and acetate as an electron donor. A nitrogen-free mineral medium was used with the intention of creating a selective pressure towards organisms that would use N2 O directly as source of nitrogen for cell synthesis...
January 12, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29289014/responses-and-recovery-assessment-of-continuously-cultured-nitrosomonas-europaea-under-chronic-zno-nanoparticle-stress-effects-of-dissolved-oxygen
#12
Junkang Wu, Yan Chang, Huan Gao, Geyu Liang, Ran Yu, Zhen Ding
Although the antibacterial performances of emerging nanoparticles (NPs) have been extensively explored in the nitrifying systems, the impacts of dissolved oxygen (DO) levels on their bio-toxicities to the nitrifiers and the impaired cells' recovery potentials have seldom been addressed yet. In this study, the physiological and transcriptional responses of the typical ammonia oxidizers - Nitrosomonas europaea in a chemostat to the chronic ZnO NP exposure under different DO conditions were investigated. The results indicated that the cells in steady-growth state in the chemostat were more persevering than batch cultured ones to resist ZnO NP stress despite the dose-dependent NP inhibitory effects were observed...
December 13, 2017: Chemosphere
https://www.readbyqxmd.com/read/29261671/tragedy-of-the-commons-in-the-chemostat
#13
Martin Schuster, Eric Foxall, David Finch, Hal Smith, Patrick De Leenheer
We present a proof of principle for the phenomenon of the tragedy of the commons that is at the center of many theories on the evolution of cooperation. Whereas the tragedy is commonly set in a game theoretical context, and attributed to an underlying Prisoner's Dilemma, we take an alternative approach based on basic mechanistic principles of species growth that does not rely on the specification of payoffs which may be difficult to determine in practice. We establish the tragedy in the context of a general chemostat model with two species, the cooperator and the cheater...
2017: PloS One
https://www.readbyqxmd.com/read/29239113/detection-of-novel-syntrophic-acetate-oxidizing-bacteria-from-biogas-processes-by-continuous-acetate-enrichment-approaches
#14
Maria Westerholm, Bettina Müller, Abhijeet Singh, Oskar Karlsson Lindsjö, Anna Schnürer
To enrich syntrophic acetate-oxidizing bacteria (SAOB), duplicate chemostats were inoculated with sludge from syntrophic acetate oxidation (SAO)-dominated systems and continuously supplied with acetate (0.4 or 7.5 g l-1 ) at high-ammonia levels. The chemostats were operated under mesophilic (37°C) or thermophilic (52°C) temperature for about six hydraulic retention times (HRT 28 days) and were sampled over time. Irrespective of temperature, a methane content of 64-69% and effluent acetate level of 0.4-1...
December 14, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/29235714/formate-hydrogenlyase-and-formate-secretion-ameliorate-h2-inhibition-in-the-hyperthermophilic-archaeon-thermococcus-paralvinellae
#15
Begüm D Topçuoğlu, Cem Meydan, Roberto Orellana, James F Holden
Some hyperthermophilic heterotrophs in the genus Thermococcus produce H2 in the absence of S° and have up to seven hydrogenases, but their combined physiological roles are unclear. Here, we show which hydrogenases in Thermococcus paralvinellae are affected by added H2 during growth without S°. Growth rates and steady-state cell concentrations decreased while formate production rates increased when T. paralvinallae was grown in a chemostat with 65 µM of added H2(aq) . Differential gene expression analysis using RNA-Seq showed consistent expression of six hydrogenase operons with and without added H2 ...
December 13, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29218033/substrate-limited-and-unlimited-coastal-microbial-communities-show-different-metabolic-responses-with-regard-to-temperature
#16
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
#17
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
#18
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
#19
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
#20
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
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