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Katja Pulkkinen, Nina Pekkala, Roghaieh Ashrafi, Dorrit M Hämäläinen, Aloysius N Nkembeng, Anssi Lipponen, Teppo Hiltunen, Janne K Valkonen, Jouni Taskinen
Understanding ecological and epidemiological factors driving pathogen evolution in contemporary time scales is a major challenge in modern health management. Pathogens that replicate outside the hosts are subject to selection imposed by ambient environmental conditions. Increased nutrient levels could increase pathogen virulence by pre-adapting for efficient use of resources upon contact to a nutrient rich host or by favouring transmission of fast-growing virulent strains. We measured changes in virulence and competition in Flavobacterium columnare, a bacterial pathogen of freshwater fish, under high and low nutrient levels...
April 5, 2018: FEMS Microbiology Ecology
Jungeui Hong, Nathan Brandt, Farah Abdual-Rahman, Ally W H Yang, Timothy R Hughes, David Gresham
We studied adaptive evolution of gene expression using long-term experimental evolution of Saccharomyces cerevisiae in ammonium-limited chemostats. We found repeated selection for non-synonymous variation in the DNA binding domain of the transcriptional activator, GAT1, which functions with the repressor, DAL80 in an incoherent type-1 feedforward loop (I1-FFL) to control expression of the high affinity ammonium transporter gene, MEP2. Missense mutations in the DNA binding domain of GAT1 reduce its binding to the GATAA consensus sequence...
April 5, 2018: ELife
Pryce L Haddix, Robert M Q Shanks
Serratia marcescens is a gram-negative, facultatively-anaerobic bacterium and opportunistic pathogen which produces the red pigment prodigiosin. We employed both batch culture and chemostat growth methods to investigate prodigiosin function in the producing organism. Pigmentation correlated with an increased rate of ATP production during population lag phase. Results with a lacZ transcriptional fusion to the prodigiosin (pig) biosynthetic operon revealed that operon transcription is activated by low cellular levels of ATP at high cell density...
April 3, 2018: Archives of Microbiology
Regina L Radan, William P Cochlan
The toxigenic diatom Pseudo-nitzschia multiseries Hasle, isolated from the U.S. Pacific Northwest, was examined in unialgal laboratory cultures and in natural assemblages during shipboard experiments, to examine cellular growth and domoic acid (DA) production as a function of nitrogen (N) substrate and availability expected during bloom development and decline. Laboratory experiments utilizing batch cultures conducted at saturating (120 μmol photons m-2  s-1 ) photosynthetic photon flux density (PPFD), demonstrated that P...
March 2018: Harmful Algae
Vera Slomka, Esteban Rodriguez Herrero, Nico Boon, Kristel Bernaerts, Harsh M Trivedi, Carlo Daep, Marc Quirynen, Wim Teughels
BACKGROUND: Only recently the concept of prebiotics has been introduced in oral health. Few potential oral prebiotics have already been identified in dual species competition assays, showing a stimulatory effect on beneficial bacteria and by this suppressing the outgrowth of pathogenic species. This study aimed to validate the effect of previously identified potential prebiotic substrates on multispecies cultures by shifting the biofilm composition towards a more beneficial species dominated microbiota...
March 25, 2018: Journal of Periodontology
Oscar van Mastrigt, Marcel M A N Lommers, Yorick C de Vries, Tjakko Abee, Eddy J Smid
Lactic acid bacteria can carry multiple plasmids affecting their performance in dairy fermentations. The expression of plasmid-encoded genes and the activity of the corresponding proteins is severely affected by changes in the number of plasmid copies. We studied the impact of growth rate on dynamics of plasmid copy numbers at high growth rates in chemostat cultures and down to near-zero growth rates in retentostat cultures. Five plasmids of the dairy strain Lactococcus lactis FM03-V1 were selected which varied in size (3 to 39 kb), in replication mechanism (theta or rolling-circle) and in putative (dairy-associated) functions...
March 23, 2018: Applied and Environmental Microbiology
Jasmine M Bracher, Maarten D Verhoeven, H Wouter Wisselink, Barbara Crimi, Jeroen G Nijland, Arnold J M Driessen, Paul Klaassen, Antonius J A van Maris, Jean-Marc G Daran, Jack T Pronk
Background: l-Arabinose occurs at economically relevant levels in lignocellulosic hydrolysates. Its low-affinity uptake via the Saccharomyces cerevisiae Gal2 galactose transporter is inhibited by d-glucose. Especially at low concentrations of l-arabinose, uptake is an important rate-controlling step in the complete conversion of these feedstocks by engineered pentose-metabolizing S. cerevisiae strains. Results: Chemostat-based transcriptome analysis yielded 16 putative sugar transporter genes in the filamentous fungus Penicillium chrysogenum whose transcript levels were at least threefold higher in l-arabinose-limited cultures than in d-glucose-limited and ethanol-limited cultures...
2018: Biotechnology for Biofuels
Clement Aldebert, Bob W Kooi, David Nerini, Jean-Christophe Poggiale
Many current issues in ecology require predictions made by mathematical models, which are built on somewhat arbitrary choices. Their consequences are quantified by sensitivity analysis to quantify how changes in model parameters propagate into an uncertainty in model predictions. An extension called structural sensitivity analysis deals with changes in the mathematical description of complex processes like predation. Such processes are described at the population scale by a specific mathematical function taken among similar ones, a choice that can strongly drive model predictions...
March 14, 2018: Journal of Theoretical Biology
Diane Plouchart, Kim Milferstedt, Guillaume Guizard, Eric Latrille, Jérôme Hamelin
Continuous cultures in chemostats have proven their value in microbiology, microbial ecology, systems biology and bioprocess engineering, among others. In these systems, microbial growth and ecosystem performance can be quantified under stable and defined environmental conditions. This is essential when linking microbial diversity to ecosystem function. Here, a new system to test this link in anaerobic, methanogenic microbial communities is introduced. Rigorously replicated experiments or a suitable experimental design typically require operating several chemostats in parallel...
2018: PloS One
Kaspar Valgepea, Renato de Souza Pinto Lemgruber, Tanus Abdalla, Steve Binos, Nobuaki Takemori, Ayako Takemori, Yuki Tanaka, Ryan Tappel, Michael Köpke, Séan Dennis Simpson, Lars Keld Nielsen, Esteban Marcellin
Background: The global demand for affordable carbon has never been stronger, and there is an imperative in many industrial processes to use waste streams to make products. Gas-fermenting acetogens offer a potential solution and several commercial gas fermentation plants are currently under construction. As energy limits acetogen metabolism, supply of H2 should diminish substrate loss to CO2 and facilitate production of reduced and energy-intensive products. However, the effects of H2 supply on CO-grown acetogens have yet to be experimentally quantified under controlled growth conditions...
2018: Biotechnology for Biofuels
M Z Bieroza, A L Heathwaite, M Bechmann, K Kyllmar, P Jordan
Recent technological breakthroughs of optical sensors and analysers have enabled matching the water quality measurement interval to the time scales of stream flow changes and led to an improved understanding of spatially and temporally heterogeneous sources and delivery pathways for many solutes and particulates. This new ability to match the chemograph with the hydrograph has promoted renewed interest in the concentration-discharge (c-q) relationship and its value in characterizing catchment storage, time lags and legacy effects for both weathering products and anthropogenic pollutants...
February 27, 2018: Science of the Total Environment
V Rico-Caballero, Safa Almarzoky Abuhussain, Joseph L Kuti, David P Nicolau
Combination therapy is an attractive option for the treatment of multidrug resistant (MDR) Pseudomonas aeruginosa infections; however, limited data are available on combinations with ceftolozane/tazobactam (C/T). The in vitro pharmacodynamic chemostat model was employed to compare human simulated exposures of C/T 3g q8h alone or in combination with amikacin 25 mg/kg daily or colistin 360 mg daily against four MDR P. aeruginosa isolates. C/T alone resulted in 24 hour CFU changes of -0.02±0.21, -1.81±0.55, -1...
February 26, 2018: Antimicrobial Agents and Chemotherapy
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
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
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
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
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
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
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
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
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