Journal: Heliyon

Article Title: Diversity and functional assessment of indigenous culturable bacteria inhabiting fine-flavor cacao rhizosphere: Uncovering antagonistic potential against Moniliophthora roreri

doi: 10.1016/j.heliyon.2024.e28453

Figure Lengend Snippet: Native culturable bacterial isolates and functional characterization.

Article Snippet: For example, only the strain IA201 was located in a single clade with Sphingobium scionense WP01 and S. yanoikuyae GIFU 9882 at 100% of bootstrap, CB304 was found with Lysobacter cavernae YIM C01544 and L. tabacisoli C8 1 at 99% of bootstrap, CA205 grouped with Paenarthrobacter ilicis DSMZ 20138 at 98% of bootstrap, CA101 grouped with Isoptericola nanjingensis H17 at 100% of bootstrap, CA105 was found grouped with several Cellulosimicrobium strains at 84% of bootstrap and CA305 was found closely related to Sporosarcina thermotolerans CCUG 53480 at 85% of bootstrap.

Techniques: Functional Assay

Journal: BMC Genomics

Article Title: Comparative genomics of the plant-growth promoting bacterium Sphingobium sp . strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata

doi: 10.1186/s12864-022-08738-8

Figure Lengend Snippet: Plant-growth promotion assays using Arabidopsis and switchgrass inoculated with Sphingobium sp. strain AEW4 or uninoculated controls. Changes in root biomass were measured as increase in length for Arabidopsis seedlings ( A ), and final root weight ( B ) and length ( C ) in switchgrass. Graphed data represent mean ± SD of five biological replicates

Article Snippet: Sphingobium sp. strain AEW4 and Sphingobium xenophagum DSM 6383 (DSMZ) were grown on Schatz media with all carbon sources until they reached an OD 600 of 0.4 and were then transferred to Schatz media with only fructose as the sole carbon source.

Techniques:

Journal: BMC Genomics

Article Title: Comparative genomics of the plant-growth promoting bacterium Sphingobium sp . strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata

doi: 10.1186/s12864-022-08738-8

Figure Lengend Snippet: Phylogenetic tree of Sphingobium sp. strain AEW4 and closely related Sphingobium species. Sphingomonas ginsensoli was used as an outgroup. The maximum-likelihood tree was constructed using the MEGAX software with an alignment of 1494 nucleotides and bootstrapping ( n = 1000)

Article Snippet: Sphingobium sp. strain AEW4 and Sphingobium xenophagum DSM 6383 (DSMZ) were grown on Schatz media with all carbon sources until they reached an OD 600 of 0.4 and were then transferred to Schatz media with only fructose as the sole carbon source.

Techniques: Construct, Software

Journal: BMC Genomics

Article Title: Comparative genomics of the plant-growth promoting bacterium Sphingobium sp . strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata

doi: 10.1186/s12864-022-08738-8

Figure Lengend Snippet: Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) of Sphingobium species. Heat maps show the variation in A) Average Nucleotide Identity (ANI) and B) Average Amino Acid Identity (AAI) for Sphingobium sp . strain AEW4 and 17 different species in the genus Sphingobium . The values scale shows percent similarity based on nucleotides, with red representing a low identity and green representing a high identity

Article Snippet: Sphingobium sp. strain AEW4 and Sphingobium xenophagum DSM 6383 (DSMZ) were grown on Schatz media with all carbon sources until they reached an OD 600 of 0.4 and were then transferred to Schatz media with only fructose as the sole carbon source.

Techniques:

Journal: BMC Genomics

Article Title: Comparative genomics of the plant-growth promoting bacterium Sphingobium sp . strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata

doi: 10.1186/s12864-022-08738-8

Figure Lengend Snippet: Genome-wide comparison of orthologous clusters between strain AEW4 and its two closest relatives. Proportions of shared and unique clusters in comparisons with Sphingobium xenophagum and Sphingobium hydrophobicum are shown in the Venn diagram , based on OrthoVenn analysis. Strain AEW4 contains 80 unique clusters when compared to these two species, with 208 proteins which are classified in the pie chart based on their functional role

Article Snippet: Sphingobium sp. strain AEW4 and Sphingobium xenophagum DSM 6383 (DSMZ) were grown on Schatz media with all carbon sources until they reached an OD 600 of 0.4 and were then transferred to Schatz media with only fructose as the sole carbon source.

Techniques: Genome Wide, Comparison, Functional Assay

Journal: BMC Genomics

Article Title: Comparative genomics of the plant-growth promoting bacterium Sphingobium sp . strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata

doi: 10.1186/s12864-022-08738-8

Figure Lengend Snippet: Comparison of key functional gene categories in Sphingobium sp. strain AEW4 with the other members of the genus Sphingobium. Numbers of genes are shown for monosaccharide metabolism ( A ), osmotic stress ( B ), and fermentation ( C ) for Sphingobium sp. strain AEW4, its two closest relatives, S. xenophagum and S. hydrophobicum, and other genomes within the genus, including an average ± SD for these nine members

Article Snippet: Sphingobium sp. strain AEW4 and Sphingobium xenophagum DSM 6383 (DSMZ) were grown on Schatz media with all carbon sources until they reached an OD 600 of 0.4 and were then transferred to Schatz media with only fructose as the sole carbon source.

Techniques: Comparison, Functional Assay

Journal: BMC Genomics

Article Title: Comparative genomics of the plant-growth promoting bacterium Sphingobium sp . strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata

doi: 10.1186/s12864-022-08738-8

Figure Lengend Snippet: Organization of the fructose operon present in Sphingobium sp. strain AEW4. Unique genes identified in the genome of strain AEW4 are shown and compared to closest gene matches in operons of Novosphingobium mathurense and Novosphingobium pentaromativorans US6-1

Article Snippet: Sphingobium sp. strain AEW4 and Sphingobium xenophagum DSM 6383 (DSMZ) were grown on Schatz media with all carbon sources until they reached an OD 600 of 0.4 and were then transferred to Schatz media with only fructose as the sole carbon source.

Techniques:

Journal: BMC Genomics

Article Title: Comparative genomics of the plant-growth promoting bacterium Sphingobium sp . strain AEW4 isolated from the rhizosphere of the beachgrass Ammophila breviligulata

doi: 10.1186/s12864-022-08738-8

Figure Lengend Snippet: Fructose growth dynamics of Sphingobium species. Growth of Sphingobium sp. AEW4 and Sphingobium xenophagum on fructose as the sole carbon source. Growth dynamics data represent the mean ± SD between three biological replicates

Article Snippet: Sphingobium sp. strain AEW4 and Sphingobium xenophagum DSM 6383 (DSMZ) were grown on Schatz media with all carbon sources until they reached an OD 600 of 0.4 and were then transferred to Schatz media with only fructose as the sole carbon source.

Techniques: