With the rapid development of single-cell technologies, the mechanisms underlying viral infections and the interactions between hosts and viruses are starting to be explored at the single-cell level. The foot-and-mouth-disease (FMD) virus (FMDV) causes an acute and persistent infection that can result in the break-out of FMD, which can have serious effects on animal husbandry. Single-cell techniques have emerged as powerful approaches to analyze virus infection at the resolution of individual cells. In this review, the existing single-cell studies examining FMDV will be systematically summarized, and the central themes of these studies will be presented. Copyright © 2020 Wang, Xin, Zheng and Shen.Persistence of infection despite extensive chemotherapy with antibiotics displaying low MICs is a hallmark of lung disease caused by Mycobacterium abscessus (Mab). Thus, the classical MIC assay is a poor predictor of clinical outcome. Discovery of more efficacious antibiotics requires more predictive in vitro potency assays. As a mycobacterium, Mab is an obligate aerobe and a chemo-organo-heterotroph – it requires oxygen and organic carbon sources for growth. However, bacteria growing in patients can encounter micro-environmental conditions that are different from aerated nutrient-rich broth used to grow planktonic cultures for MIC assays. These in vivo conditions may include oxygen and nutrient limitation which should arrest growth. Furthermore, Mab was shown to grow as biofilms in vivo. Here, we show Mab Bamboo, a clinical isolate we use for Mab drug discovery, can survive oxygen deprivation and nutrient starvation for extended periods of time in non-replicating states and developed an in vitro model where the bacterium grows as biofilm. Using these culture models, we show that non-replicating or biofilm-growing bacteria display tolerance to clinically used anti-Mab antibiotics, consistent with the observed persistence of infection in patients. To demonstrate the utility of the developed „persister” assays for drug discovery, we determined the effect of novel agents targeting membrane functions against these physiological forms of the bacterium and find that these compounds show „anti-persister” activity. In conclusion, we developed in vitro „persister” assays to fill an assay gap in Mab drug discovery compound progression and to enable identification of novel lead compounds showing „anti-persister” activity. Copyright © 2020 Yam, Alvarez, Go and Dick.Bioremediation of crude oil contaminated environments is an economical, low-maintenance, environmentally friendly technology and has attracted increasing attention in recent years. In the present study, two efficient crude oil degrading bacteria strains were isolated from soils contaminated with crude oil. Phylogenetic analysis suggested they belonged to genus Bacillus, and were designated as Bacillus cereus T-04 and Bacillus halotolerans 1-1. The crude oil depletion of each strain under different conditions was tested. The optimum conditions for both strains’ oil degradation was pH 7, 15-20 g/L NaCl concentration, and 5-15 g/L original oil concentration. The crude oil depletion rate could reach to 60-80% after 20 days of treatment. The crude oil bioremediation simulation tests revealed that the bioremediation promoted the depletion of crude oil to a large extent. The inoculum group with inorganic medium showed the highest crude oil depletion (97.5%) while the crude oil depletion of control group was only 26.6% after 180 days of treatment. High-throughput sequencing was used to monitor the changes of microbial community using different treatments. In all groups, Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla. After contaminated with crude oil, the relative abundance of phylum Actinobacteria was dramatically increased and occupied 81.8%. Meanwhile although strains of Bacillus were added in the bioaugmentation groups, the relative abundance of genus Bacillus was not the most abundant genus at the end of simulation tests. The crude oil contamination dramatically decreased the soil microbial diversity and bioremediation could not recover the microbial community in the short term. Copyright © 2020 Deng, Jiang, Chen, Gao and Liu.In order to improve the thermostability of lipases derived from Rhizopus chinensis, we identified lipase (Lipr27RCL) mutagenesis sites that were associated with enhanced flexibility based upon B-factor analysis and multiple sequence alignment. We found that two mutated isoforms (Lipr27RCL-K64N and Lipr27RCL-K68T) exhibited enhanced thermostability and improved residual activity, with respective thermal activity retention values of 37.88% and 48.20% following a 2 h treatment at 50°C relative to wild type Lipr27RCL. In addition, these Lipr27RCL-K64N and Lipr27RCL-K68T isoforms exhibited 2.4- and 3.0-fold increases in enzymatic half-life following a 90 min incubation at 60°C. Together these results indicate that novel mutant lipases with enhanced thermostability useful for industrial applications can be predicted based upon B-factor analysis and constructed via site-directed mutagenesis. Copyright © 2020 Jiang, Zhang, Tang, Xu, Wang, Qian, He, Zhao, Wu, Mu, Ding, Zhang, Huang and Han.Extracellular polymeric substances (EPS) play an important role in diatom physiology and carbon biogeochemical cycling in marine ecosystems. Both the composition and yield of EPS in diatom cells can vary with environmental changes. However, information on intracellular pathways and controls of both biochemical and genetic of EPS is limited. Further, how such changes would affect their critical ecological roles in marine systems is also unclear. Here, we evaluated the physiological characteristics, EPS yields, EPS compositions, and gene expression levels of Phaeodactylum tricornutum under elevated pCO2 levels. Genes and pathways related to EPS metabolism in P. tricornutum were identified. Carbohydrate yields in different EPS fractions increased with elevated pCO2 exposure. Although the proportions of monosaccharide sugars among total sugars did not change, higher abundances of uronic acid were observed under high pCO2 conditions, suggesting the alterations of EPS composition. Elevated pCO2 increased PSII light energy conversion efficiency and carbon sequestration efficiency. The up-regulation of most genes involved in carbon fixation pathways led to increased growth and EPS release. RNA-Seq analysis revealed a number of genes and divergent alleles related to EPS production that were up-regulated by elevated pCO2 levels. Nucleotide diphosphate (NDP)-sugar activation and accelerated glycosylation could be responsible for more EPS responding to environmental signals. Further, NDP-sugar transporters exhibited increased expression levels, suggesting roles in EPS over-production. Overall, these results provide critical data for understanding the mechanisms of EPS production in diatoms and evaluating the metabolic plasticity of these organisms in response to environmental changes. Copyright © 2020 Zhang, Tang, Yang, Zhang and Zhang.Escherichia coli carrying bla CTX-M- 1 mediating resistance to extended-spectrum cephalosporins was recently described as a new genotype in Norwegian broiler production. The aim of this study was to characterize these isolates (n = 31) in order to determine whether the emergence of the genotype was caused by clonal expansion or horizontal dissemination of bla CTX-M- 1-carrying plasmids. All included isolates were subjected to whole genome sequencing. Plasmid transferability was determined by conjugation, and plasmid replicons in the transconjugants were described using PCR-based replicon typing. Plasmid sizes were determined using S1 nuclease digestion. Plasmids in a subset of strains were reconstructed and compared to plasmids from broiler production in other European countries. The isolates belonged to nine different sequence types (STs), with the largest group being ST57 (n = 12). The vast majority of bla CTX-M- 1-carrying plasmids were conjugative. All transconjugants were positive for the IncI1-Iγ replic.With the emergence of multidrug-resistant and extensively drug-resistant bacterial pathogens, phage therapy and other alternative or additional therapeutic modalities are receiving resurgent attention. One of the major obstacles in developing effective phage therapies is the evolution of phage resistance in the bacterial host. When Pseudomonas aeruginosa was infected with a phage that uses O-antigen as receptor, phage resistances typically achieved through changing or loss of O-antigen structure. In this study, we showed that dsRNA phage phiYY uses core lipopolysaccharide as receptor and therefore efficiently kills the O-antigen deletion mutants. Furthermore, by phage training, we obtained PaoP5-m1, a derivative of dsDNA phage PaoP5, which is able to infect mutants with truncated O-antigen. We then generated a cocktail by mixing phiYY and PaoP5-m1 with additional three wide host range P. aeruginosa phages. The phage cocktail was effective against a diverse selection of clinical isolates of P. aeruginosa, and in the short-term constrained the appearance of the phage-resistant mutants that had beleaguered the effectiveness of single phage. Resistance to the 5-phage cocktail emerges after several days, and requires mutations in both wzy and migA Thus, this study provides an alternative strategy for designing phage cocktail and phage therapy. Copyright © 2020 Yang, Shen, Zhong, Chen, He, Baker, Xiong, Jin, Wang, Hu and Le.An extreme halophilic archaeon, strain SGH1, is a novel microorganism isolated from endolithic microbial communities colonizing halites at Salar Grande, Atacama Desert, in northern Chile. Our study provides structural, biochemical, genomic, and physiological information on this new isolate living at the edge of the physical and chemical extremes at the Atacama Desert. SGH1 is a Gram-negative, red-pigmented, non-motile unicellular coccoid organism. Under the transmission electron microscope, strain SGH1 showed an abundant electro-dense material surrounding electron-lucent globular structures resembling gas vacuoles. Strain SGH1 showed a 16S rRNA gene sequence with a close phylogenetic relationship to the extreme halophilic archaea Haloterrigena turkmenica and Haloterrigena salina and has been denominated Haloterrigena sp. strain SGH1. Strain SGH1 grew at 20-40°C (optimum 37°C), at salinities between 15 and 30% (w/v) NaCl (optimum 25%) and growth was improved by addition of 50 mM KCl and 0.5% w/v casamino acids-carotene. Both, plasma membrane integrity and mitochondrial membrane potential measurements under acute 18-h assays showed that purified BR isomers were non-toxic to cultured human THP-1 cells. Copyright © 2020 Flores, Hoyos, Venegas, Galetovic´, Zúñiga, Fábrega, Paredes, Salazar-Ardiles, Vilo, Ascaso, Wierzchos, Souza-Egipsy, Araya, Batista-García and Gómez-Silva.Because of the remarkable efficacy in treating mycobacterial infections, rifamycin and its derivatives are still first-line antimycobacterial drugs. It has been intensely studied to increase rifamycin yield from Amycolatopsis mediterranei, and nitrate is found to provide a stable and remarkable stimulating effect on the rifamycin production, a phenomenon known as „nitrate-stimulating effect (NSE)”. Although the NSE has been widely used for the industrial production of rifamycin, its detailed molecular mechanism remains ill-defined. And our previous study has established that the global nitrogen regulator GlnR may participate in the NSE, but the underlying mechanism is still enigmatic. Here, we demonstrate that GlnR directly controls rifamycin biosynthesis in A. mediterranei and thus plays an essential role in the NSE. Firstly, GlnR specifically binds to the upstream region of rifZ, which leads us to uncover that rifZ has its own promoter. As RifZ is a pathway-specific activator for the whole rif cluster, GlnR indirectly upregulates the whole rif cluster transcription by directly activating the rifZ expression.