Journal: ACS Applied Polymer Materials

Article Title: 3D-Bioprinted Marine Bacteria for the Degradation of Polyhydroxybutyrate Bioplastics

doi: 10.1021/acsapm.5c03370

Figure Lengend Snippet: Growth and PHB degradation of marine bacteria. (A) Growth curves of Bacillus sp. NRRL B-14911 (dark green), C. testosteroni (light green), Marinobacter sp. NK-1 (light brown), and Microbulbifer sp. SOL66 (dark brown) cultured in Marine Broth at 30 °C. (B) Degradation of PHB by the marine bacteria species was determined by growing bacterial colonies on Marine Broth-agar plates containing PHB powder and measuring the radii of the clear zones of depolymerized PHB formed around the colonies after 7 days ( n = 8). **** P ≤ 0.0001 by one-way ANOVA statistical analysis.

Article Snippet: The bacteria strains used in this study are Bacillus sp. NRRL B-14911 , (Agricultural Research Service Culture Collection, United States Department of Agriculture), Comamonas testosteroni (ATCC 11996), Marinobacter sp. NK-1 (ATCC 700491), Microbulbifer sp. SOL66 (ATCC 70072), and Escherichia coli BL21 (ATCC BAA-1025).

Techniques: Bacteria, Cell Culture

Journal: Applied and Environmental Microbiology

Article Title: Multispecies Diesel Fuel Biodegradation and Niche Formation Are Ignited by Pioneer Hydrocarbon-Utilizing Proteobacteria in a Soil Bacterial Consortium

doi: 10.1128/AEM.02268-20

Figure Lengend Snippet: Phylogenetic characterization for the major bacterial genera detected from the consortium

Article Snippet: TABLE 1 Bacterial genus MAG 16S rRNA gene assembled from metagenomic reads Genome size (bp) Genome completeness (%) Contamination (%) Closest bacterial genome (ANI [%]) Length (bp) Identical 16S rRNA gene amplicon Closest bacterial strain (NCBI accession no. [% homology]) Closest bacterial isolate from the consortium (% homology) Pseudomonas 6,686,507 99.07 0.60 Pseudomonas aeruginosa DSM 500071 (99.43) 1,536 OTU-1 Pseudomonas aeruginosa DSM 500071 ( CP012001 [100]) KK6 (100) Sphingobium 4,974,394 99.89 1.65 Sphingobium barthaii KK22 (99.98) 1,485 OTU-2 Sphingobium barthaii KK22 ( NR_137223 [100]) KK22 (100) Ochrobactrum 4,842,250 96.96 0.43 Ochrobactrum anthropi ATCC 49188 (97.50) 1,481 OTU-3 Ochrobactrum anthropi ATCC 49188 ( CP000758 [100]) Achromobacter 6,329,203 96.26 0.99 Achromobacter insolitus DSM 23807 (99.03) 1,511 OTU-4 Achromobacter denitrificans PR1 ( CP020917 [100]) KK8 (99.18) Achromobacter insolitus DSM 23807 ( CP019325 [99.67]) Cupriavidus 7,560,176 96.44 0.69 Cupriavidus necator N-1 (99.41) 1,530 OTU-5 Cupriavidus necator N-1 ( CP002877 [100]) KK10 (99.51) Parvibaculum 3,950,696 99.57 0.87 Parvibaculum lavamentivorans DS-1 (80.62) 1,486 OTU-6 Parvibaculum lavamentivorans DS-1 ( CP000774 [95.37]) Olivibacter 1,520 OTU-7 Olivibacter jilunii 14-2A ( NR_109321 [99.46]) Dokdonella 1,491 OTU-9 Dokdonella ginsengisoli Gsoil 191 ( NR_041369 [100]) Rhodanobacter 1,503 OTU-10 Rhodanobacter rhizosphaerae CR164 ( NR_156938 [100]) Open in a separate window Phylogenetic characterization for the major bacterial genera detected from the consortium.

Techniques: Amplification

Journal: Applied and Environmental Microbiology

Article Title: Multispecies Diesel Fuel Biodegradation and Niche Formation Are Ignited by Pioneer Hydrocarbon-Utilizing Proteobacteria in a Soil Bacterial Consortium

doi: 10.1128/AEM.02268-20

Figure Lengend Snippet: Numbers of aromatic hydrocarbon- and alkane-degrading genes harbored in the major bacterial MAGs detected in the consortium

Article Snippet: TABLE 1 Bacterial genus MAG 16S rRNA gene assembled from metagenomic reads Genome size (bp) Genome completeness (%) Contamination (%) Closest bacterial genome (ANI [%]) Length (bp) Identical 16S rRNA gene amplicon Closest bacterial strain (NCBI accession no. [% homology]) Closest bacterial isolate from the consortium (% homology) Pseudomonas 6,686,507 99.07 0.60 Pseudomonas aeruginosa DSM 500071 (99.43) 1,536 OTU-1 Pseudomonas aeruginosa DSM 500071 ( CP012001 [100]) KK6 (100) Sphingobium 4,974,394 99.89 1.65 Sphingobium barthaii KK22 (99.98) 1,485 OTU-2 Sphingobium barthaii KK22 ( NR_137223 [100]) KK22 (100) Ochrobactrum 4,842,250 96.96 0.43 Ochrobactrum anthropi ATCC 49188 (97.50) 1,481 OTU-3 Ochrobactrum anthropi ATCC 49188 ( CP000758 [100]) Achromobacter 6,329,203 96.26 0.99 Achromobacter insolitus DSM 23807 (99.03) 1,511 OTU-4 Achromobacter denitrificans PR1 ( CP020917 [100]) KK8 (99.18) Achromobacter insolitus DSM 23807 ( CP019325 [99.67]) Cupriavidus 7,560,176 96.44 0.69 Cupriavidus necator N-1 (99.41) 1,530 OTU-5 Cupriavidus necator N-1 ( CP002877 [100]) KK10 (99.51) Parvibaculum 3,950,696 99.57 0.87 Parvibaculum lavamentivorans DS-1 (80.62) 1,486 OTU-6 Parvibaculum lavamentivorans DS-1 ( CP000774 [95.37]) Olivibacter 1,520 OTU-7 Olivibacter jilunii 14-2A ( NR_109321 [99.46]) Dokdonella 1,491 OTU-9 Dokdonella ginsengisoli Gsoil 191 ( NR_041369 [100]) Rhodanobacter 1,503 OTU-10 Rhodanobacter rhizosphaerae CR164 ( NR_156938 [100]) Open in a separate window Phylogenetic characterization for the major bacterial genera detected from the consortium.

Techniques:

Journal: Applied and Environmental Microbiology

Article Title: Multispecies Diesel Fuel Biodegradation and Niche Formation Are Ignited by Pioneer Hydrocarbon-Utilizing Proteobacteria in a Soil Bacterial Consortium

doi: 10.1128/AEM.02268-20

Figure Lengend Snippet: Distributions of key aromatic hydrocarbon degradation genes harbored in six high-quality MAGs for Sphingobium, Pseudomonas, Ochrobactrum, Achromobacter, Cupriavidus, and Parvibaculum spp. reconstructed from the consortium grown on diesel fuel. Arrows labeled as different colors indicate functional genes found in each MAG. (Step 1) Initial biotransformation step of phenanthrene, naphthalene, and toluene by class A ARHDs. (Step 2) Transformation of 3,4-dihydroxyphenanthrene and 1,2-dihydroxynaphthalene via extradiol ring cleavage pathways. (Step 3) Decarboxylation of 1-hydroxy-2-naphthoic acid and salicylic acid. (Step 4) Transformation of 1,2-dihydroxynaphthalene via intradiol ring cleavage pathway. (Step 5) Methyl-monooxygenation of toluene. (Step 6) Ring-monooxygenation of toluene. (Step 7) Transformation of benzoic acid to catechol. (Step 8) Transformation of phthalic acid to protocatechuic acid. (Step 9) Transformation of salicylic acid to gentisic acid. (Step 10) Degradation of gentisic acid. (Steps 11 and 12) Degradation of catechol via intradiol or extradiol ring cleavage pathways. (Step 13) Degradation of protocatechuic acid.

Article Snippet: TABLE 1 Bacterial genus MAG 16S rRNA gene assembled from metagenomic reads Genome size (bp) Genome completeness (%) Contamination (%) Closest bacterial genome (ANI [%]) Length (bp) Identical 16S rRNA gene amplicon Closest bacterial strain (NCBI accession no. [% homology]) Closest bacterial isolate from the consortium (% homology) Pseudomonas 6,686,507 99.07 0.60 Pseudomonas aeruginosa DSM 500071 (99.43) 1,536 OTU-1 Pseudomonas aeruginosa DSM 500071 ( CP012001 [100]) KK6 (100) Sphingobium 4,974,394 99.89 1.65 Sphingobium barthaii KK22 (99.98) 1,485 OTU-2 Sphingobium barthaii KK22 ( NR_137223 [100]) KK22 (100) Ochrobactrum 4,842,250 96.96 0.43 Ochrobactrum anthropi ATCC 49188 (97.50) 1,481 OTU-3 Ochrobactrum anthropi ATCC 49188 ( CP000758 [100]) Achromobacter 6,329,203 96.26 0.99 Achromobacter insolitus DSM 23807 (99.03) 1,511 OTU-4 Achromobacter denitrificans PR1 ( CP020917 [100]) KK8 (99.18) Achromobacter insolitus DSM 23807 ( CP019325 [99.67]) Cupriavidus 7,560,176 96.44 0.69 Cupriavidus necator N-1 (99.41) 1,530 OTU-5 Cupriavidus necator N-1 ( CP002877 [100]) KK10 (99.51) Parvibaculum 3,950,696 99.57 0.87 Parvibaculum lavamentivorans DS-1 (80.62) 1,486 OTU-6 Parvibaculum lavamentivorans DS-1 ( CP000774 [95.37]) Olivibacter 1,520 OTU-7 Olivibacter jilunii 14-2A ( NR_109321 [99.46]) Dokdonella 1,491 OTU-9 Dokdonella ginsengisoli Gsoil 191 ( NR_041369 [100]) Rhodanobacter 1,503 OTU-10 Rhodanobacter rhizosphaerae CR164 ( NR_156938 [100]) Open in a separate window Phylogenetic characterization for the major bacterial genera detected from the consortium.

Techniques: Labeling, Functional Assay, Transformation Assay

Journal: Applied and Environmental Microbiology

Article Title: Multispecies Diesel Fuel Biodegradation and Niche Formation Are Ignited by Pioneer Hydrocarbon-Utilizing Proteobacteria in a Soil Bacterial Consortium

doi: 10.1128/AEM.02268-20

Figure Lengend Snippet: Summary of the growth test results of bacterial isolates obtained from the consortium

Article Snippet: TABLE 1 Bacterial genus MAG 16S rRNA gene assembled from metagenomic reads Genome size (bp) Genome completeness (%) Contamination (%) Closest bacterial genome (ANI [%]) Length (bp) Identical 16S rRNA gene amplicon Closest bacterial strain (NCBI accession no. [% homology]) Closest bacterial isolate from the consortium (% homology) Pseudomonas 6,686,507 99.07 0.60 Pseudomonas aeruginosa DSM 500071 (99.43) 1,536 OTU-1 Pseudomonas aeruginosa DSM 500071 ( CP012001 [100]) KK6 (100) Sphingobium 4,974,394 99.89 1.65 Sphingobium barthaii KK22 (99.98) 1,485 OTU-2 Sphingobium barthaii KK22 ( NR_137223 [100]) KK22 (100) Ochrobactrum 4,842,250 96.96 0.43 Ochrobactrum anthropi ATCC 49188 (97.50) 1,481 OTU-3 Ochrobactrum anthropi ATCC 49188 ( CP000758 [100]) Achromobacter 6,329,203 96.26 0.99 Achromobacter insolitus DSM 23807 (99.03) 1,511 OTU-4 Achromobacter denitrificans PR1 ( CP020917 [100]) KK8 (99.18) Achromobacter insolitus DSM 23807 ( CP019325 [99.67]) Cupriavidus 7,560,176 96.44 0.69 Cupriavidus necator N-1 (99.41) 1,530 OTU-5 Cupriavidus necator N-1 ( CP002877 [100]) KK10 (99.51) Parvibaculum 3,950,696 99.57 0.87 Parvibaculum lavamentivorans DS-1 (80.62) 1,486 OTU-6 Parvibaculum lavamentivorans DS-1 ( CP000774 [95.37]) Olivibacter 1,520 OTU-7 Olivibacter jilunii 14-2A ( NR_109321 [99.46]) Dokdonella 1,491 OTU-9 Dokdonella ginsengisoli Gsoil 191 ( NR_041369 [100]) Rhodanobacter 1,503 OTU-10 Rhodanobacter rhizosphaerae CR164 ( NR_156938 [100]) Open in a separate window Phylogenetic characterization for the major bacterial genera detected from the consortium.

Techniques:

Journal: Applied and Environmental Microbiology

Article Title: Multispecies Diesel Fuel Biodegradation and Niche Formation Are Ignited by Pioneer Hydrocarbon-Utilizing Proteobacteria in a Soil Bacterial Consortium

doi: 10.1128/AEM.02268-20

Figure Lengend Snippet: Hypothetical model of multispecies bacterial diesel fuel biodegradation by the consortium. Hydrophobic oil droplets are first colonized by the pioneer aromatic and alkane hydrocarbon-degrading bacteria, Sphingobium and Pseudomonas, which initiate biotransformation of complex hydrocarbons by forming biofilms. The hydrocarbon biotransformation products and secondary metabolites such as biofilm matrices produced by the pioneers, which have relatively higher bioavailability, are thus utilized by other bacterial cocolonizers. These cocolonizers mainly consisted of Ochrobactrum, Achromobacter, and Cupriavidus, and their coexistence may enhance further biofilm formation and accelerate hydrocarbon biodegradation. Another major bacterial genus, Parvibaculum, was potentially responsible for biodegradation of short- and middle-chain-length alkanes and/or biphenyl-related compounds.

Article Snippet: TABLE 1 Bacterial genus MAG 16S rRNA gene assembled from metagenomic reads Genome size (bp) Genome completeness (%) Contamination (%) Closest bacterial genome (ANI [%]) Length (bp) Identical 16S rRNA gene amplicon Closest bacterial strain (NCBI accession no. [% homology]) Closest bacterial isolate from the consortium (% homology) Pseudomonas 6,686,507 99.07 0.60 Pseudomonas aeruginosa DSM 500071 (99.43) 1,536 OTU-1 Pseudomonas aeruginosa DSM 500071 ( CP012001 [100]) KK6 (100) Sphingobium 4,974,394 99.89 1.65 Sphingobium barthaii KK22 (99.98) 1,485 OTU-2 Sphingobium barthaii KK22 ( NR_137223 [100]) KK22 (100) Ochrobactrum 4,842,250 96.96 0.43 Ochrobactrum anthropi ATCC 49188 (97.50) 1,481 OTU-3 Ochrobactrum anthropi ATCC 49188 ( CP000758 [100]) Achromobacter 6,329,203 96.26 0.99 Achromobacter insolitus DSM 23807 (99.03) 1,511 OTU-4 Achromobacter denitrificans PR1 ( CP020917 [100]) KK8 (99.18) Achromobacter insolitus DSM 23807 ( CP019325 [99.67]) Cupriavidus 7,560,176 96.44 0.69 Cupriavidus necator N-1 (99.41) 1,530 OTU-5 Cupriavidus necator N-1 ( CP002877 [100]) KK10 (99.51) Parvibaculum 3,950,696 99.57 0.87 Parvibaculum lavamentivorans DS-1 (80.62) 1,486 OTU-6 Parvibaculum lavamentivorans DS-1 ( CP000774 [95.37]) Olivibacter 1,520 OTU-7 Olivibacter jilunii 14-2A ( NR_109321 [99.46]) Dokdonella 1,491 OTU-9 Dokdonella ginsengisoli Gsoil 191 ( NR_041369 [100]) Rhodanobacter 1,503 OTU-10 Rhodanobacter rhizosphaerae CR164 ( NR_156938 [100]) Open in a separate window Phylogenetic characterization for the major bacterial genera detected from the consortium.

Techniques: Bacteria, Produced

Journal: Journal of Antimicrobial Chemotherapy

Article Title: Antibacterial activity of the human host defence peptide LL-37 and selected synthetic cationic lipids against bacteria associated with oral and upper respiratory tract infections

doi: 10.1093/jac/dks434

Figure Lengend Snippet: Antibacterial activity of LL-37 peptide and different cationic lipids against pathogens associated with oral infections

Article Snippet: A concentration of cationic lipid even at one-tenth of MBC values could eradicate 19%–82% of bacteria added to a saliva/dental plaque mixture. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Bacterial strain Antibacterial agents (MBC/MIC mg/L) LL-37 CSA-13 CSA-90 CSA-92 D2S AMC MIC (mg/L) Staphylococcus aureus ATCC 29213 28/14 1.4/0.7 2.8/0.7 0.75/0.75 2.1/2.1 0.3 Streptococcus salivarius ATCC 13419 28/14 1.4/0.7 1.4/0.7 3 /1.5 2.1/1.1 0.037 Streptococcus sanguinis ATCC 10556 28/14 0.7/0.7 1.4/1.6 3/1.5 2.1/1.1 0.037 Streptococcus mutans ATCC 35668 28/28 1.4/0.7 1.4/0.7 1.5/0.75 1.1/1.1 0.037 Staphylococcus epidermidis * 56/56 0.7/0.35 1.4/0.7 3/3 2.1/2.1 ND Streptococcus pneumoniae * 14/14 0.7/0.35 1.4/0.7 1.5/1.5 1.1/0.55 0.015 Streptococcus pyogenes * 14/14 0.7/0.7 1.4/0.35 0.75/0.75 2.1/01.1 0.007 Haemophilus influenzae * 56/28 0.7/0.35 1.4/0.7 1.5/0.7 1.1/1.1 ND Enterococcus faecalis ATCC 29212 56/28 2.8/2.8 2.8/1.4 3/8 2.1/1.1 0.3 Moraxella catarrhalis ATCC 23246 28/28 1.4/1.4 1.4/0.7 1.5/0.35 2.1/1.1 0.075 Helicobacter pylori * 28/14 0.7/0.7 1.4/0.7 1.5/0.75 1.1/0.55 0.075 Peptostreptococcus anaerobius ATCC 27337 224/224 5.6/5.6 22.4/22.4 11.7/5.8 32.4/16.2 1.2 Porphyromonas gingivalis ATCC 33277 224/224 5.6/5.6 11.2/11.2 23.4/11.7 16.2/16.2 1.2 Fusobacterium nucleatum ATCC 25586 224/224 22.4/11.2 11.2/11.2 23.4/11.7 32.4/16.2 2.4 Lactobacillus casei ssp. casei ATCC 393 224/224 44.8/22.4 44.8/44.8 46.8/46.8 64.8/32.4 2.4 Tannerella forsythensis ATCC 43037 224/224 22.4/22.4 44.8/44.8 46.8/46.8 32.4/16.2 2.4 Staphylococcus aureus Xen 29 (pleural fluid isolate NCTC8532) 28/28 2.8/1.4 2.8/1.4 5.8/2.9 4.05/4.05 0.15 Pseudomonas aeruginosa Xen 5 (derived from P. aeruginosa strain ATCC 19660) 448/224 11.2/5.6 22.4/22.4 23.4/11.7 8.1/8.1 2.4 Neisseria meningitidis (B) 56/28 0.7/0.7 1.4/1.4 5.8/2.9 8.1/2.1 ND Neisseria meningitidis (C) 112/28 1.4/0.7 1.4/1.4 5.8/2.9 4.05/2.1 ND Open in a separate window Clinical strains are indicated with asterisks.

Techniques: Activity Assay, Derivative Assay

Journal:

Article Title: Isolation and Molecular Characterization of pMG160, a Mobilizable Cryptic Plasmid from Rhodobacter blasticus

doi: 10.1128/AEM.69.2.725-733.2003

Figure Lengend Snippet: Bacterial strains and plasmids used in this study

Article Snippet: On the other hand, no kanamycin-resistant transformants or transconjugants were recovered from R. rubrum ATCC 11170, R. gelatinosus ATCC 17011, Bradyrhizobium japonicum ATCC 10324, or phototrophic Bradyrhizobium strains USDA 4362 and USDA 4377.

Techniques: Plasmid Preparation, Clone Assay, Mutagenesis