Journal: Microbial cell factories

Article Title: Adaptive laboratory evolution of Rhodococcus rhodochrous DSM6263 for chlorophenol degradation under hypersaline condition.

doi: 10.1186/s12934-023-02227-7

Figure Lengend Snippet: Fig. 1 The cell growth of R. rhodochrous DSM6263 and CP-8 in M65 medium. (a) the growth curve of cells in medium without NaCl addition, and (b) the growth curve of cells in medium with 8% NaCl addition. All the experiments were performed in triplicate and data shown are mean ± SD. Some deriva tions were too small to be shown

Article Snippet: Adaptive laboratory evolution to increase salt tolerance Rhodococcus rhodochrous DSM6263 was purchased from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ).

Techniques:

Journal: Microbial cell factories

Article Title: Adaptive laboratory evolution of Rhodococcus rhodochrous DSM6263 for chlorophenol degradation under hypersaline condition.

doi: 10.1186/s12934-023-02227-7

Figure Lengend Snippet: Fig. 4 The intracellular concentrations of cAMP in parent strain DSM6263 and evolved strain CP-8 under conditions of 0% and 8% NaCl, respective ly. All the experiments were performed in triplicate and data shown are mean ± SD.

Article Snippet: Adaptive laboratory evolution to increase salt tolerance Rhodococcus rhodochrous DSM6263 was purchased from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ).

Techniques:

Journal: Microbial Cell Factories

Article Title: Adaptive laboratory evolution of Rhodococcus rhodochrous DSM6263 for chlorophenol degradation under hypersaline condition

doi: 10.1186/s12934-023-02227-7

Figure Lengend Snippet: The cell growth of R. rhodochrous DSM6263 and CP-8 in M65 medium. (a) the growth curve of cells in medium without NaCl addition, and (b) the growth curve of cells in medium with 8% NaCl addition. All the experiments were performed in triplicate and data shown are mean ± SD. Some derivations were too small to be shown

Article Snippet: Rhodococcus rhodochrous DSM6263 , Wild type strains , Purchased from DSMZ.

Techniques:

Journal: Microbial Cell Factories

Article Title: Adaptive laboratory evolution of Rhodococcus rhodochrous DSM6263 for chlorophenol degradation under hypersaline condition

doi: 10.1186/s12934-023-02227-7

Figure Lengend Snippet: The intracellular concentrations of cAMP in parent strain DSM6263 and evolved strain CP-8 under conditions of 0% and 8% NaCl, respectively. All the experiments were performed in triplicate and data shown are mean ± SD.

Article Snippet: Rhodococcus rhodochrous DSM6263 , Wild type strains , Purchased from DSMZ.

Techniques:

Journal: Microbial Cell Factories

Article Title: Adaptive laboratory evolution of Rhodococcus rhodochrous DSM6263 for chlorophenol degradation under hypersaline condition

doi: 10.1186/s12934-023-02227-7

Figure Lengend Snippet: SNP analysis of point mutation genes between strains DSM6263 and CP-8

Article Snippet: Rhodococcus rhodochrous DSM6263 , Wild type strains , Purchased from DSMZ.

Techniques: Mutagenesis

Journal: Microbial Cell Factories

Article Title: Adaptive laboratory evolution of Rhodococcus rhodochrous DSM6263 for chlorophenol degradation under hypersaline condition

doi: 10.1186/s12934-023-02227-7

Figure Lengend Snippet: Strains and plasmids used in this study

Article Snippet: Rhodococcus rhodochrous DSM6263 , Wild type strains , Purchased from DSMZ.

Techniques: Expressing, Generated

Journal: bioRxiv

Article Title: Membrane adaptation in the hyperthermophilic archaeon Pyrococcus furiosus relies upon a novel strategy involving glycerol monoalkyl glycerol tetraether lipids

doi: 10.1101/2021.11.17.468962

Figure Lengend Snippet: P. furiosus DSM3638 was grown under optimal conditions (TRM at 3 % w/v NaCl and pH 6.8 with 10 g L -1 elemental sulfur) at different temperatures (80, 85, 90, 98, and 103 °C). 98 °C represents the optimal growth temperature. Error bars represent the standard deviation calculated on three biological replicates. * indicates temperatures with significantly different core lipid compositions. (A) Total core lipid compositions under each temperature. (B) Influence of the temperature on GDGT relative proportions. GDGT (dark purple) corresponds to the summed GDGT, regardless of the cyclopentane ring content. (C) Influence of the temperature on GMGT relative proportions. GMGT (dark red) corresponds to the summed GMGT, regardless of the cyclopentane ring content. (D) Influence of the temperature on DGD relative abundance. (E) Influence of the temperature on GTGT0 relative abundance. (F) Temperature dependence of the ring index (RI) for all tetraethers (GDGT, GTGT, and GMGT), GDGT and GMGT (RI ± standard deviation). (G) Temperature dependence of the GMGT/GDGT ratio.

Article Snippet: Pyrococcus furiosus strain DSM3638 was purchased from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ, Braunschweig, Germany).

Techniques: Standard Deviation

Journal: bioRxiv

Article Title: Membrane adaptation in the hyperthermophilic archaeon Pyrococcus furiosus relies upon a novel strategy involving glycerol monoalkyl glycerol tetraether lipids

doi: 10.1101/2021.11.17.468962

Figure Lengend Snippet: P. furiosus DSM3638 was grown under optimal conditions (TRM at 3 % w/v NaCl and 98 °C with 10 g L -1 elemental sulfur) at different pH (5.5, 5.6, 5.9, 6.2, 6.4 and 6.6). pH 6.6 represents the optimal growth pH. Error bars represent the standard deviation calculated on three biological replicates. * indicates pH with significantly different core lipid compositions. (A) Total core lipid compositions under each pH. (B) Influence of the pH on GDGT relative proportions. GDGT (dark purple) corresponds to the summed GDGT, regardless of the cyclopentane ring content. (C) Influence of the pH on GMGT relative proportions. GMGT (dark red) corresponds to the summed GMGT, regardless of the cyclopentane ring content. (D) Influence of the pH on DGD relative abundance. (E) Influence of the pH on GTGT0 relative abundance. (F) pH dependence of the ring index (RI) for all tetraethers (GDGT, GTGT, and GMGT), GDGT and GMGT (RI ± standard deviation). (G) pH dependence of the GMGT/GDGT ratio.

Article Snippet: Pyrococcus furiosus strain DSM3638 was purchased from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ, Braunschweig, Germany).

Techniques: Standard Deviation

Journal: bioRxiv

Article Title: Membrane adaptation in the hyperthermophilic archaeon Pyrococcus furiosus relies upon a novel strategy involving glycerol monoalkyl glycerol tetraether lipids

doi: 10.1101/2021.11.17.468962

Figure Lengend Snippet: P. furiosus DSM3638 was grown under optimal conditions (TRM at 98 °C and pH 6.8 with 10 g L -1 elemental sulfur) at different salinities (1, 2, 3 and 4 % w/v NaCl). 3 % NaCl represents the optimal growth salinity. Error bars represent the standard deviation calculated on three biological replicates. * indicates % NaCl with significantly different core lipid compositions. (A) Total core lipid compositions under each % NaCl. (B) Influence of the salinity on GDGT relative proportions. GDGT (dark purple) corresponds to the summed GDGT, regardless of the cyclopentane ring content. (C) Influence of the salinity on GMGT relative proportions. GMGT (dark red) corresponds to the summed GMGT, regardless of the cyclopentane ring content. (D) Influence of the salinity on DGD relative abundance. (E) Influence of the salinity on GTGT0 relative abundance. (F) Salinity dependence of the ring index (RI) for all tetraethers (GDGT, GTGT, and GMGT), GDGT and GMGT (RI ± standard deviation). (G) Salinity dependence of the GMGT/GDGT ratio.

Article Snippet: Pyrococcus furiosus strain DSM3638 was purchased from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ, Braunschweig, Germany).

Techniques: Standard Deviation

Journal: bioRxiv

Article Title: Membrane adaptation in the hyperthermophilic archaeon Pyrococcus furiosus relies upon a novel strategy involving glycerol monoalkyl glycerol tetraether lipids

doi: 10.1101/2021.11.17.468962

Figure Lengend Snippet: P. furiosus DSM3638 was grown under optimal conditions (at 98 °C, pH 6.8 and 3 % w/v NaCl with 10 g L 1 elemental sulfur) in DC and TRM media. TRM represents the optimal growth condition. For details on media compositions, refer to the Method section. Error bars represent the standard deviation calculated on three biological replicates. (A) Total core lipid compositions under each medium condition. (B) Influence of the growth medium on GDGT relative proportions. GDGT (dark purple) corresponds to the summed GDGT, regardless of the cyclopentane ring content. (C) Influence of the growth medium on GMGT relative proportions. GMGT (dark red) corresponds to the summed GMGT, regardless of the cyclopentane ring content. (D) Influence of the growth medium on DGD relative abundance. (E) Influence of the growth medium on GTGT0 relative abundance. (F) Growth medium dependence of the ring index (RI) for all tetraethers (GDGT, GTGT, and GMGT), GDGT, GTGT and GMGT (RI ± standard deviation). (G) Growth medium dependence of the GMGT/GDGT ratio.

Article Snippet: Pyrococcus furiosus strain DSM3638 was purchased from the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ, Braunschweig, Germany).

Techniques: Standard Deviation

Journal: Applied Microbiology and Biotechnology

Article Title: A new Rhodococcus aetherivorans strain isolated from lubricant-contaminated soil as a prospective phenol-biodegrading agent

doi: 10.1007/s00253-020-10385-6

Figure Lengend Snippet: Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showing the relationship between strain UCM Ac-602 (*) and type strains of representative Rhodococcus species. The scale bars represent 5 substitutions per 1000 nucleotide positions. T is the type strain. GenBank accession numbers are given in parentheses

Article Snippet: Type strains of Rhodococcus rhodochrous UCM Ac-744 (= DSMZ 43241) and Rhodococcus ruber UCM Ac-745 (= DSMZ 43338) were obtained from the UCM to use as reference Rhodococcus species.

Techniques:

Journal: Applied Microbiology and Biotechnology

Article Title: A new Rhodococcus aetherivorans strain isolated from lubricant-contaminated soil as a prospective phenol-biodegrading agent

doi: 10.1007/s00253-020-10385-6

Figure Lengend Snippet: Phenol biodegradation rates exhibited by R . aetherivorans UCM Ac-602 at different phenol concentrations: [1a] freely-suspended cells and [1b] vermiculite-immobilized cells. The error bars indicate standard error of the mean ( n = 3), and when not shown were less than the symbol dimensions. The data obtained in this study were compared to biodegradation rate values from the literature as follows: [2] mixed microbial culture (Dey and Mukherjee ); [3] Pseudomonas sp. SA01 (Mollaei et al. ), [4] R . rhodochrous No21 (Przybulewska et al. ), [5] Rhodococcus sp. UKMP-5M (Suhaila et al. ), [6] Acinetobacter sp. (Khleifat ), [7] R . opacus PD630 (Yoneda et al. ), [8] P . aeruginosa SPD 10 (Shweta and Dhandayuthapani ), [9] Rhodococcus sp. AQ5NOL 2 KCTC 11961BP (Arif et al. ), [10] Acinetobacter sp. (Adav et al. ), [11] P . pseudomallei NIGB 3 B (Afzal et al. )

Article Snippet: Type strains of Rhodococcus rhodochrous UCM Ac-744 (= DSMZ 43241) and Rhodococcus ruber UCM Ac-745 (= DSMZ 43338) were obtained from the UCM to use as reference Rhodococcus species.

Techniques:

Journal: Applied Microbiology and Biotechnology

Article Title: A new Rhodococcus aetherivorans strain isolated from lubricant-contaminated soil as a prospective phenol-biodegrading agent

doi: 10.1007/s00253-020-10385-6

Figure Lengend Snippet: Rhodococcus spp. and other bacteria able to degrade high phenol concentrations (> 1000 mg L −1 ) in batch culture

Article Snippet: Type strains of Rhodococcus rhodochrous UCM Ac-744 (= DSMZ 43241) and Rhodococcus ruber UCM Ac-745 (= DSMZ 43338) were obtained from the UCM to use as reference Rhodococcus species.

Techniques: Bacteria, Isolation, Concentration Assay