The capacity to fix nitrogen is widely distributed in phyla of Bacteria and Archaea but has long been considered to be absent from the Pseudomonas genus. We report here the complete genome sequencing of nitrogen-fixing root-associated Pseudomonas stutzeri A1501. The genome consists of a single circular chromosome with 4,567,418 bp. Comparative genomics revealed that, among 4,146 protein-encoding genes, 1,977 have orthologs in each of the five other Pseudomonas representative species sequenced to date. The genome contains genes involved in broad utilization of carbon sources, nitrogen fixation, denitrification, degradation of aromatic compounds, biosynthesis of polyhydroxybutyrate, multiple pathways of protection against environmental stress, and other functions that presumably give A1501 an advantage in root colonization. Genetic information on synthesis, maturation, and functioning of nitrogenase is clustered in a 49-kb island, suggesting that this property was acquired by lateral gene transfer. New genes required for the nitrogen fixation process have been identified within the nif island. The genome sequence offers the genetic basis for further study of the evolution of the nitrogen fixation property and identification of rhizosphere competence traits required in the interaction with host plants; moreover, it opens up new perspectives for wider application of root-associated diazotrophs in sustainable agriculture.

Fermentation has been used for ages as a safe technique for food preservation, and it uses minimal resources. Fermentation is related to a wide range of catabolic biochemical procedures in both eukaryotes and prokaryotes. Yeasts are eukaryotes; they can use oxygen while also having the ability to live without oxygen. The lactate fermentation process consists of glycolysis and some alternative steps. A review of the literature was done using keywords in main indexing systems, including PubMed/MEDLINE, Scopus, the search engine of the Institute for Scientific Web of Science and Google Scholar. The keywords reviewed were fermentation technologies, protein mass expression, health benefits of functional foods, microbial fermentation technology, anaerobic respiration, fermentation in eukaryotes, fermentation in prokaryotes, solid state fermentation and submerged fermentation. This research was carried out to highlight the importance of fermentation technology and to introduce and survey the technology and its relationship with functional foods. Research progress in the area of protein factory-microbial fermentation technology was also investigated and inspected.

Globally, about 20% of cultivated land is now affected by salinity. Salt tolerance is a trait of importance to all crops in saline soils. Previous efforts to improve salt tolerance in crop plants have met with only limited success. Bacteria of the genus Deinococcus are known for their ability to survive highly stressful conditions, and therefore possess a unique pool of genes conferring extreme resistance. In Deinococcus radiodurans, the irrE gene encodes a global regulator responsible for extreme radioresistance. Using plate assays, we showed that IrrE protected E. coli cells against salt shock and other abiotic stresses such as oxidative, osmotic and thermal shocks. Comparative proteomic analysis revealed that IrrE functions as a switch to regulate different sets of proteins such as stress responsive proteins, protein kinases, glycerol-degrading enzymes, detoxification proteins, and growth-related proteins in E. coli. We also used quantitative RT-PCR to investigate expression of nine selected stress-responsive genes in transgenic and wild-type Brassica napus plants. Transgenic B. napus plants expressing the IrrE protein can tolerate 350 mM NaCl, a concentration that inhibits the growth of almost all crop plants. Expression of IrrE, a global regulator for extreme radiation resistance in D. radiodurans, confers significantly enhanced salt tolerance in both E. coli and B. napus. We thus propose that the irrE gene might be used as a potentially promising transgene to improve abiotic stress tolerances in crop plants.

The desert is an excellent model for studying evolution under extreme environments. We present here the complete genome and ultraviolet (UV) radiation-induced transcriptome of Deinococcus gobiensis I-0, which was isolated from the cold Gobi desert and shows higher tolerance to gamma radiation and UV light than all other known microorganisms. Nearly half of the genes in the genome encode proteins of unknown function, suggesting that the extreme resistance phenotype may be attributed to unknown genes and pathways. D. gobiensis also contains a surprisingly large number of horizontally acquired genes and predicted mobile elements of different classes, which is indicative of adaptation to extreme environments through genomic plasticity. High-resolution RNA-Seq transcriptome analyses indicated that 30 regulatory proteins, including several well-known regulators and uncharacterized protein kinases, and 13 noncoding RNAs were induced immediately after UV irradiation. Particularly interesting is the UV irradiation induction of the phrB and recB genes involved in photoreactivation and recombinational repair, respectively. These proteins likely include key players in the immediate global transcriptional response to UV irradiation. Our results help to explain the exceptional ability of D. gobiensis to withstand environmental extremes of the Gobi desert, and highlight the metabolic features of this organism that have biotechnological potential.

Significance: The biological nitrogen fixation process responsible for the reduction of atmospheric nitrogen to ammonia represents the primary source of nitrogen supporting extant life. We have identified a novel noncoding RNA (ncRNA) in the Pseudomonas stutzeri core genome, called NfiS, that is involved in the stress response and controls the expression of genes located in a genomic nitrogen-fixing ( nif ) island. NfiS was found to optimize nitrogen fixation by the direct posttranscriptional regulation of nitrogenase gene nifK mRNA. The acquisition of the nif island and the recruitment of NfiS by nifK mRNA are evolutionary events that seem to contribute to fine-tuned regulation of nitrogenase activity in P. stutzeri . This study provides a new regulatory pathway, mediated by an ncRNA for optimal nitrogen fixation, that may operate in other diazotrophs.