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The multicellular communities of microorganisms known as biofilms are of high significance in agricultural setting, yet it is largely unknown about the biofilm formed by nitrogen-fixing bacteria. Here we report the biofilm formation by Pseudomonas stutzeri A1501, a free-living rhizospheric bacterium, capable of fixing nitrogen under microaerobic and nitrogen-limiting conditions. P. stutzeri A1501 tended to form biofilm in minimal media, especially under nitrogen depletion condition. Under such growth condition, the biofilms formed at the air–liquid interface (termed as pellicles) and the colony biofilms on agar plates exhibited nitrogenase activity in air. The two kinds of biofilms both contained large ovoid shape ‘cells’ that were multiple living bacteria embedded in a sac of extracellular polymeric substances (EPSs). We proposed to name such large ‘cells’ as A1501 cyst. Our results suggest that the EPS, especially exopolysaccharides enabled the encased bacteria to fix nitrogen while grown under aerobic condition. The formation of A1501 cysts was reversible in response to the changes of carbon or nitrogen source status. A1501 cyst formation depended on nitrogen-limiting signaling and the presence of sufficient carbon sources, yet was independent of an active nitrogenase. The pellicles formed by Azospirillum brasilense, another free-living nitrogen-fixing rhizobacterium, which also exhibited nitrogenase activity and contained the large EPS-encapsuled A1501 cyst-like ‘cells’. Our data imply that free-living nitrogen-fixing bacteria could convert the easy-used carbon sources to exopolysaccharides in order to enable nitrogen fixation in a natural aerobic environment.The ISME Journal advance online publication, 24 March 2017; doi:10.1038/ismej.2017.30. © 2017 International Society for Microbial Ecology


Baldrian P.,CAS Institute of Microbiology
FEMS Microbiology Reviews | Year: 2017

Globally, forests represent highly productive ecosystems that act as carbon sinks where soil organic matter is formed from residuals after biomass decomposition as well as from rhizodeposited carbon. Forests exhibit a high level of spatial heterogeneity and the importance of trees, the dominant primary producers, for their structure and functioning. Fungi, bacteria and archaea inhabit various forest habitats: foliage, the wood of living trees, the bark surface, ground vegetation, roots and the rhizosphere, litter, soil, deadwood, rock surfaces, invertebrates, wetlands or the atmosphere, each of which has its own specific features, such as nutrient availability or temporal dynamicy and specific drivers that affect microbial abundance, the level of dominance of bacteria or fungi as well as the composition of their communities. However, several microorganisms, and in particular fungi, inhabit or even connect multiple habitats, and most ecosystem processes affect multiple habitats. Forests are dynamic on a broad temporal scale with processes ranging from short-term events over seasonal ecosystem dynamics to long-term stand development after disturbances such as fires or insect outbreaks. The understanding of these processes can be only achieved by the exploration of the complex 'ecosystem microbiome' and its functioning using focused, integrative microbiological and ecological research performed across multiple habitats. © FEMS 2016. All rights reserved.


Provided are engineered Escherichia coli for producing 1,5-pentanediamine by whole-cell catalysis and an application thereof. The engineered bacterium is engineered bacterium, for whole-cell catalysis of 1,5-pentanediamine, constructed by over-expressing a lysine decarboxylase gene cadA and meanwhile moderately expressing a lysine-pentanediamine reverse transport protein gene cadB in an Escherichia coli B derivative strain. Also provided is a method for producing 1,5-pentanediamine by catalysis using the engineered bacterium.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: KBBE.2012.3.2-01 | Award Amount: 13.29M | Year: 2012

The PharmaSea project focuses on obstacles in marine biodiscovery research, development and commercialization and brings together a broad interdisciplinary team of academic and industry researchers and specialists to address and overcome these. The partners are ideally placed to demonstrate how to widen the bottlenecks and increase the flow of ideas and products derived from the marine microbiome towards a greater number of successes in a larger number of application areas. Despite the tremendous potential of marine biodiscovery, exploitation, particularly at a commercial scale, has been hampered by a number of constraints. These relate to access (physical and legal), genetics of the organisms, compound isolation, structure elucidation, early reliable validation of biological activity and best mechanisms of flow-through into exploitation. PharmaSea will solve these chronic bottlenecks by developing essential actions beyond the state of the art and linking them with best practice and appropriate pragmatic approaches. The robust pipeline structure established within PharmaSea will process a wide genetic basis including marine microbial strain collections held by partners and new strain collections from extreme environments (deep, cold and hot vent habitats) to produce new products with desirable characteristics for development by the SME partners in three accessible market sectors, health (infection, inflammation, CNS diseases), personal care and nutrition. The global aim of PharmaSea is to produce two compounds at larger scale and advance them to pre-clinical evaluation. To address relevant challenges in marine biodiscovery related to policy and legal issues, PharmaSea will bring together practitioners, legal experts, policy advisors/makers and other stakeholders, focusing on the feasibility of harmonising, aligning and complementing current legal frameworks with recommendations and ready to use solutions tailored to marine biodiscovery.


Patent
University of Tokyo, Nihon University, CAS Institute of Microbiology, Toray Industries Inc, Japan National Institute of Infectious Diseases and Tokyo Metropolitan Institute of Medical Science | Date: 2013-01-30

An objective of this invention is to provide an HCV strain with a high capacity for virus production in a cell culture system. This invention provides a nucleic acid encoding a polyprotein precursor of the hepatitis C virus JFH1 strain having one or more amino acid substitutions, wherein the polyprotein precursor comprises at least substitution of glutamine at position 862 with arginine, as determined with reference to the amino acid sequence as shown in SEQ ID NO: 2 in the Sequence Listing.


The immunosuppressive drug cyclosporin A (CsA) has inhibitory effects on the replication of several viruses. The antiviral effects are through targeting the interaction between viral proteins and host factor cyclophilin A (CypA). CypA has been identified to interact with influenza A virus M1 protein and impair the early stage of the viral life cycle. In order to identify the effect of CsA on influenza virus replication, a CypA-depleted 293T cell line, which was named as 293T/CypA-, was constructed. The cytopathic effect (CPE) assay and the growth curve results indicated that CsA specifically suppressed the influenza A virus replication in a dose-dependent manner. CsA treatment had no effect on the viral genome replication and transcription but selectively suppressed the viral proteins expression. Further studies indicated that CsA could impair the nuclear export of viral mRNA in the absence of CypA. In addition, the antiviral activity of CsA was independent of calcineurin signaling. Finally, CsA could enhance the binding between CypA and M1. The above results suggested that CsA inhibited the replication of influenza A virus through CypA-dependent and -independent pathways.


Huang G.,CAS Institute of Microbiology
Virulence | Year: 2012

The human commensal fungus Candida albicans can cause not only superficial infections, but also life-threatening disease in immunocompromised individuals. C. albicans can grow in several morphological forms. The ability to switch between different phenotypic forms has been thought to contribute to its virulence. The yeast-filamentous growth transition and white-opaque switching represent two typical morphological switching systems, which have been intensively studied in C. albicans. The interplay between environmental factors and genes determines the morphology of C. albicans. This review focuses on the regulation of phenotypic changes in this pathogenic organism by external environmental cues and internal genes. ©2012 Landes Bioscience.


The present application discloses recombinant bacteria producing L-amino acid(s) its construction method and the method of producing L-amino acid(s). The recombinant bacteria producing L-amino acid(s) according to the present invention has reduced expression of the glucose-6-phosphate isomerase Pgi and improved expression of the glucose-6-phosphate dehydrogenase Zwf-OpcA than the starting bacteria, wherein: said starting bacterium is a bacterial strain which can accumulate target amino acid(s). During fermenting and culturing the recombinant bacteria according to the present invention, it is observed that the effect of improving yield can be additive and the yield of L-amino acid(s) is improved obviously. The strategy of combinational modification according to the present invention develops a new method of improving the yield of L-amino acid(s) and hence it can be applied to produce L-amino acid(s) through bacterial fermentation.


The present application discloses recombinant bacteria producing L-amino acid(s) its construction method and the method of producing L-amino acid(s). The recombinant bacteria producing L-amino acid(s) according to the present invention has reduced expression of the glucose-6-phosphate isomerase Pgi and improved expression of the glucose-6-phosphate dehydrogenase Zwf-OpcA than the starting bacteria, wherein: said starting bacterium is a bacterial strain which can accumulate target amino acid(s). During fermenting and culturing the recombinant bacteria according to the present invention, it is observed that the effect of improving yield can be additive and the yield of L-amino acid(s) is improved obviously. The strategy of combinational modification according to the present invention develops a new method of improving the yield of L-amino acid(s) and hence it can be applied to produce L-amino acid(s) through bacterialfermentation.


The present invention discloses a method for introducing an exogenous DNA by overcoming the restriction modification barrier of the target bacterium. The method provided in the present invention comprises the steps of 1) co-expressing all DNA-methyltransferase-encoding genes in the genome of the target bacterium in E. coli in which the restriction modification system thereof has been deleted to obtain a recombinant bacterium A; 2) introducing an exogenous DNA molecule into the recombinant bacterium A for in vivo modification so as to obtain a methylation-modified exogenous DNA molecule; 3) introducing the methylation-modified exogenous DNA molecule into the target bacterium. The experiments of the invention have demonstrated that the invention has a high transformation efficiency compared to prior methods for enabling genetic manipulation by overcoming the restriction modification barrier of the bacterium.

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