Project description:The genome of Rhodothermus marinus DSM 4253 encodes six glycoside hydrolases (GH) classified under GH family 3 (GH3): RmBgl3A, RmBgl3B, RmBgl3C, RmXyl3A, RmXyl3B and RmNag3. The biochemical function, modelled 3D-structure, gene cluster and evolutionary relationships of each of these enzymes were studied. The six enzymes were clustered into three major evolutionary lineages of GH3: ?-N-acetyl-glucosaminidases, ?-1,4-glucosidases/?-xylosidases and macrolide ?-glucosidases. The RmNag3 with additional ?-lactamase domain clustered with the deepest rooted GH3-lineage of ?-N-acetyl-glucosaminidases and was active on acetyl-chitooligosaccharides. RmBgl3B displayed ?-1,4-glucosidase activity and was the only representative of the lineage clustered with macrolide ?-glucosidases from Actinomycetes. The ?-xylosidases, RmXyl3A and RmXyl3B, and the ?-glucosidases RmBgl3A and RmBgl3C clustered within the major ?-glucosidases/?-xylosidases evolutionary lineage. RmXyl3A and RmXyl3B showed ?-xylosidase activity with different specificities for para-nitrophenyl (pNP)-linked substrates and xylooligosaccharides. RmBgl3A displayed ?-1,4-glucosidase/?-xylosidase activity while RmBgl3C was active on pNP-?-Glc and ?-1,3-1,4-linked glucosyl disaccharides. Putative polysaccharide utilization gene clusters were also investigated for both R. marinus DSM 4253 and DSM 4252T (homolog strain). The analysis showed that in the homolog strain DSM 4252T Rmar_1080 (RmXyl3A) and Rmar_1081 (RmXyl3B) are parts of a putative polysaccharide utilization locus (PUL) for xylan utilization.
Project description:This work presents an evaluation of batch, fed-batch, and sequential batch cultivation techniques for production of R. marinus DSM 16675 and its exopolysaccharides (EPSs) and carotenoids in a bioreactor, using lysogeny broth (LB) and marine broth (MB), respectively, in both cases supplemented with 10 g/L maltose. Batch cultivation using LB supplemented with maltose (LB<sub>malt</sub>) resulted in higher cell density (OD<sub>620</sub>?=?6.6) than use of MB<sub>malt</sub> (OD<sub>620</sub>?=?1.7). Sequential batch cultivation increased the cell density threefold (OD<sub>620</sub>?=?20) in LB<sub>malt</sub> and eightfold (OD<sub>620</sub>?=?14) in MB<sub>malt</sub>. In both single and sequential batches, the production of carotenoids and EPSs using LB<sub>malt</sub> was detected in the exponential phase and stationary phase, respectively, while in MB<sub>malt</sub> formation of both products was detectable in both the exponential and stationary phases of the culture. Heteropolymeric EPSs were produced with an overall volumetric productivity (Q<sub>E</sub>) of 0.67 (mg/L h) in MB<sub>malt</sub> and the polymer contained xylose. In LB, Q<sub>E</sub> was lower (0.1 mg/L h) and xylose could not be detected in the composition of the produced EPSs. In conclusion, this study showed the importance of a process design and medium source for production of R. marinus DSM 16675 and its metabolites.
Project description:Rhodothermus marinus, a marine aerobic thermophile, was first isolated from an intertidal hot spring in Iceland. In recent years, the R. marinus strain PRI 493 has been genetically modified, which opens up possibilities for targeted metabolic engineering of the species, such as of the carotenoid biosynthetic pathway. In this study, the carotenoids of the R. marinus type-strain DSM 4252T , strain DSM 4253, and strain PRI 493 were characterized. Bioreactor cultivations were used for pressurized liquid extraction and analyzed by ultra-high performance supercritical fluid chromatography with diode array and quadropole time-of-flight mass spectrometry detection (UHPSFC-DAD-QTOF/MS). Salinixanthin, a carotenoid originally found in Salinibacter ruber and previously detected in strain DSM 4253, was identified in all three R. marinus strains, both in the hydroxylated and nonhydroxylated form. Furthermore, an additional and structurally distinct carotenoid was detected in the three strains. MS/MS fragmentation implied that the mass difference between salinixanthin and the novel carotenoid structure corresponded to the absence of a 4-keto group on the ß-ionone ring. The study confirmed the lack of carotenoids for the strain SB-71 (?trpB?purAcrtBI'::trpB) in which genes encoding two enzymes of the proposed pathway are partially deleted. Moreover, antioxidant capacity was detected in extracts of all the examined R. marinus strains and found to be 2-4 times lower for the knock-out strain SB-71. A gene cluster with 11 genes in two operons in the R. marinusDSM 4252T genome was identified and analyzed, in which several genes were matched with carotenoid biosynthetic pathway genes in other organisms.
Project description:We isolated Rhodothermus marinus strains AA2-13 and AA3-38 from Arima Onsen, a hot spring in Japan, and sequenced their genomes. The average nucleotide identity between their genomes was 99.2%, and that with the genome of R. marinus strain DSM 4252T (isolated from Iceland) was ?95.2%, suggesting close relationships among these strains.
Project description:Staphylothermus marinus Fiala and Stetter 1986 belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. S. marinus is a hyperthermophilic, sulfur-dependent, anaerobic heterotroph. Strain F1 was isolated from geothermally heated sediments at Vulcano, Italy, but S. marinus has also been isolated from a hydrothermal vent on the East Pacific Rise. We report the complete genome of S. marinus strain F1, the type strain of the species. This is the fifth reported complete genome sequence from the order Desulfurococcales.
Project description:Arcobacter species are often recovered from marine environments and are isolated from both seawater and shellfish. Arcobacter marinus was recovered from the homogenate of a sample containing surface seawater, seaweed, and a starfish. This study describes the whole-genome sequence of the A. marinus type strain JCM 15502 (= CL-S1T = KCCM 90072T).
Project description:Rhodothermus marinus Alfredsson et al. 1995 is the type species of the genus and is of phylogenetic interest because the Rhodothermaceae represent the deepest lineage in the phylum Bacteroidetes. R. marinus R-10(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from marine hot springs off the coast of Iceland. Strain R-10(T) is strictly aerobic and requires slightly halophilic conditions for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Rhodothermus, and only the second sequence from members of the family Rhodothermaceae. The 3,386,737 bp genome (including a 125 kb plasmid) with its 2914 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.