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Here we analyzed the innate fluorescence signature of single microbial cell, within both clonal and mixed populations of microorganisms. We found that even very similarly shaped cells differ noticeably in their autofluorescence features, and that the innate fluorescence signatures change dynamically with growth phases. We demonstrated that machine learning models can be trained with a dataset of single-cell innate fluorescence signatures to annotate cells according to their phenotypes and physiological status, for example distinguishing a wild type Aspergillus nidulans cells from its nitrogen metabolism mutant counterpart, and log phase cells from stationary phase cells in Pseudomonas putida . We developed a minimally invasive method (confo.
Some species belonging to Rhodococcus genus, such as R. opacus , R. jostii or R. wratislaviensis , are known to be oleaginous microorganisms, since they are able to accumulate more than 20% of triacylglycerols (TAG) of their cellular weight. Oleaginous rhodococci are promising microbial cell factories for the production of lipids to be used as fuels and chemicals. Cells could be engineered to create strains capable of producing high quantities of oils from industrial wastes and a variety of high-value lipids. The comprehensive understanding of carbon metabolism and its regulation will contribute to the design of a reliable process for bacterial oil production. Bacterial oleagenicity requires an integral configuration of metabolism and regul.
L-aspartate has been widely used in medicine and the food and chemical industries. In this study, Serratia marcescens maleate cis-trans isomerase (MaiA) and Escherichia coli aspartase (AspA) were coupled and coexpressed in an engineered E. coli strain in which the byproduct metabolic pathway was inactivated. The engineered E. coli strain containing the dual-enzyme system (pMA) was employed to bioproduce L-aspartate from maleate with a conversion of 98%. We optimized the activity ratio of double enzymes through ribosome binding site (RBS) regulation and molecular modification of MaiA, resulting in an engineered strain: pMA-RBS4-G27A/G171A. The conversion of L-aspartate biotransformed from maleate using the pMA-RBS4-G27A/G171A strain was almo.
Bacteria synthesize amino-acids according to their availability in the environment or within the host in the case of pathogens. We explored the regulation of the biosynthesis of branched-chain amino acids (BCAAs: L-Leucine, L-Valine and L-Isoleucine) in Vibrio alginolyticus , a marine fish and shellfish pathogen and an emerging opportunistic human pathogen. In this species, the ilvGMEDA operon encodes the main pathway for biosynthesis of BCAAs. Its upstream regulatory region shows no sequence similarity to the corresponding region in Escherichia coli or other Enterobacteriaceae and yet, we show that this operon is regulated by transcription attenuation. The translation of a BCAA rich peptide encoded upstream of the structural genes provides.
Knowledge in aquatic virology has been greatly improved by culture-independent methods, yet there is still a critical need for isolating novel phages to identify the large proportion of "unknowns" that dominate metagenomes and for detailed analyses of phage-host interactions.
In this study, we identified two P450 enzymes (CYP5150AP3 and CYP5150AN1) from Thanatephorus cucumeris NBRC 6298 by combination of transcriptome sequencing and heterologous expression in Pichia pastoris . The biotransformation of 11-deoxycortisol and testosterone by the Pichia pastoris whole cells co-expressing cyp5150ap3 and por genes demonstrated that the CYP5150AP3 enzyme possessed steroidal 7β-hydroxylase activities towards these substrates, and the regioselectivity was dependent on the structures of steroidal compounds. CYP5150AN1 catalyzed the 2β-hydroxylation of 11-deoxycortisol. It is interesting that they display different regioselectivity of hydroxylation from their isoenzyme, CYP5150AP2, which possesses 19- and 11β-hydroxylase ac.
The relationship between porcine gut microbiota composition and health is an important area of research, especially due to the need to find alternatives to antimicrobial use to manage disease in livestock production systems. Previous work has indicated that lower crude dietary protein levels can reduce the impacts of post-weaning colibacillosis (PWC), which is a porcine diarrheal disease caused by enterotoxigenic Escherichia coli (ETEC). Here, to explore the complex interactions between the gut microbiota, protein nutrition and ETEC exposure, the microbial compositions of both the ileal digesta and feces were analysed with and without ETEC exposure from pigs fed a low or high protein diet. As ETEC colonisation is mostly localised to the ile.
Earthworms are among the most primitive animals and are of fundamental importance to the turnover of organic matter in the terrestrial biosphere. These invertebrates ingest materials that are colonized by microbes, some of which are subject to disruption by the crop/gizzard or other lytic events during gut passage. Protein and RNA are dominant polymers of disrupted microbial cells, and these biopolymers facilitate robust fermentations by surviving ingested bacteria. To further resolve these fermentations, amino acids and ribose (as fermentable constituents of protein and RNA, respectively) were evaluated as potential drivers of fermentation in gut content of the model earthworm Lumbricus terrestris (taxa were examined with 16S rRNA-based an.
Anoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily slow rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities ( V max ) decreased with increasing sediment depth, although V max expressed on a per cell basis was approximately the same at all depths. Half-saturation constants ( K m ) decreased with depth, indicating peptidases that functioned more efficiently at low substrate c.
Plastics are widely used in our economy and each year, at least 350-400 million tons are being produced. Due to poor recycling and low circular use, millions of tons accumulate annually in terrestrial or marine environments. Today it has become clear that plastic causes adverse effects in all ecosystems and that microplastics are of particular concern to our health. Therefore, recent microbial research has addressed the question, if and to which extent microorganisms can degrade plastics in the environment. This review summarizes current knowledge on microbial plastic degradation. Enzymes available act mainly on the high molecular weight polymers of polyethylene terephthalate (PET) and ester-based polyurethane (PUR). Unfortunately, the best.
Large surface-to-volume ratios provide optimal nutrient uptake conditions for small microorganisms in oligotrophic habitats. The surface area can be increased with appendages. Here we describe chains of interconnecting vesicles protruding from cells of flavobacterium strain Hel3_A1_48 affiliating with Formosa and originating from coastal free-living bacterioplankton. The chains were up to 10 μm long and had vesicles emanating from the outer membrane with a single membrane and a size of 80-100 nm by 50-80 nm. Cells extruded membrane tubes in the exponential phase, whereas vesicle chains dominated on cells in the stationary growth phase. This formation is known as pearling, a physical morphogenic process in which membrane tubes protrude from
Viruses play important roles in regulating the abundance and composition of bacterial populations in aquatic ecosystems. The toxic bloom-forming cyanobacterium Microcystis aeruginosa is predicted to interact with diverse cyanoviruses, resulting in Microcystis population diversification. However, current knowledge of the genomes from these viruses and their infection programs are limited to Microcystis virus Ma-LMM01. Here, we performed a time-series sampling at a small pond in Japan during Microcystis bloom, and then investigated the genomic information and transcriptional dynamics of Microcystis -interacting viruses using metagenomic and metatranscriptomic approaches. We identified fifteen viral genomic fragments classified into three grou.
We investigated the putative effect on the growth and paramylon production of Euglena gracilis when co-cultivated with Vibrio natriegens . E. gracilis heterotrophically co-cultivated with V. natriegens displayed significant increases in biomass productivity and paramylon content. In addition, the effects of the bacterial inoculum density and interaction timing on the growth of E. gracilis were examined to determine the optimal conditions for the co-cultivation. With the optimal deployment of V. natriegens , biomass productivity and paramylon content were increased by more than 20% and 35%, respectively, compared to those in axenic E. gracilis . Interestingly, indole-3-acetic acid biosynthesized from V. natriegens was responsible for these e.
Members of the Chromobacterium genus includes opportunistic but often-fatal pathogens and soil saprophytes with highly versatile metabolic capabilities. In previous studies of Chromobacterium subtsugae (formerly C. violaceum ) strain CV017, we identified a resistance nodulation division (RND)-family efflux pump (CdeAB-OprM) that confers resistance to several antibiotics including the bactobolin antibiotic produced by the soil saprophyte Burkholderia thailandensis . Here, we show the cdeAB-oprM genes increase C. subtsugae survival in a laboratory competition model with B. thailandensis. We also demonstrate that adding sublethal bactobolin concentrations to the co-culture increases C. subtsugae survival, but this effect is not through CdeAB-O.
The objective of this study was to quantify the potential for hydrocarbon biodegradation in surface waters of three sites, representing geographic regions of major oil exploration (Beaufort Sea in the Arctic, northern Gulf of Mexico [GOM], and southern GOM), in a systematic experimental design that incorporated gradients in temperature and the availability of major nutrients.
The elongation growth of the mushroom stipe is a characteristic but not well-understood morphogenetic event of basidiomycetes. We found that extending native stipe cell walls of Coprinopsis cinerea were associated with the release of N -acetylglucosamine and chitinbiose and with chitinase activity. Two chitinases among all detected chitinases from C. cinerea , ChiE1 and ChiIII, reconstituted heat-inactivated stipe wall extension and released N -acetylglucosamine and chitinbiose. Interestingly, both ChiE1 and ChiIII hydrolyze insoluble crystalline chitin powder, while other C. cinerea chitinases do not, suggesting that crystalline chitin components of the stipe cell wall are the target of action for ChiE1 and ChiIII. ChiE1- or ChiIII-reconst.
Recent studies evaluating the community structures of microorganisms and macroorganisms have found greater diversity and rarity within micro-scale communities, compared to macro-scale communities. However, reproductive method has been a confounding factor in these comparisons; the microbes considered generally reproduce asexually, while the macroorganisms considered generally reproduce sexually. Sexual reproduction imposes the constraint of mate finding, which can have significant demographic consequences by depressing birth rates at low population sizes. First, I construct an island biogeography model to study the organization of ecological communities under neutral stochastic processes. Then, I examine theoretically how the effects of mat.
In polyextremophiles, i.e., microorganisms growing preferentially under multiple extremes, synergistic effects may allow growth when application of the same extremes alone would not. High hydrostatic pressure (HP) is rarely considered in studies of polyextremophiles, and its role in potentially enhancing tolerance to other extremes remains unclear. Here, we investigated the HP-temperature response in Clostridium paradoxum , a haloalkaliphilic moderately thermophilic endospore-forming bacterium, in the range of 50 to 70°C and 0.1 to 30 MPa. At ambient pressure, growth limits were extended from the previously reported 63°C to 70°C, defining C. paradoxum as an actual thermophile. Concomitant application of high HP and temperature compared to s.
Bacterial populations in long-term stationary-phase (LTSP) laboratory cultures can provide insights into physiological and genetic adaptations to low-energy conditions and population dynamics in natural environments. While overall population density remains stable, these communities are very dynamic and are characterized by the rapid emergence and succession of distinct mutants expressing the growth advantage in stationary phase (GASP) phenotype, which can reflect an increased capacity to withstand energy limitations and environmental stress. Here, we characterize the metabolic heat signatures and growth dynamics of GASP mutants within an evolving population using isothermal calorimetry. We aged Escherichia coli in anaerobic batch cultures

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