Description of desferrioxamine-producing bacterium Chitinophaga agrisoli sp. nov., isolated from soil

Jin, Chun-Zhi; Jin, Long; Kang, Dong Hyo; Liu, Min-Jiao; Lee, Jong Min; Park, Dong-Jin; Kim, Chang‐Jin

doi:10.1007/s10482-021-01554-2

Cited by 4 publications

(2 citation statements)

References 38 publications

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“…Oxidase activity was tested using oxidase reagent from an API 20E kit (bioMérieux, Lyon, France) under the manufacturer’s instructions. The antibiotic susceptibility was determined on R2A utilising paper discs containing the following antibiotics (µg per disc): amikacin (30), ampicillin/sulbactam (20), chloramphenicol (30), erythromycin (30) gentamicin (30), kanamycin (30), lincomycin (15), rifampicin (30), spectinomycin (25), streptomycin (25), teicoplanin (30), tetracycline (30) and vancomycin (30) [ 21 , 22 ]. Other metabolic properties were analysed using API 50CH and API ZYM kits (bioMérieux, Lyon, France) according to the manufacturer’s instructions.…”

Section: Methodsmentioning

confidence: 99%

Genomic Insight into Shimazuella Soli Sp. Nov. Isolated from Soil and Its Putative Novel Class II Lasso Peptide

et al. 2022

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The strain designated as AN120528T was isolated from farmland soil in South Korea. This strain grows well on R2A medium at 28 °C. The cells are an off-white colour and have no hyphae. The phylogenetic analysis indicated that the strain is a member of the genus Shimazuella with a 98.11% similarity to Shimazuella alba KC615T and a 97.05% similarity to S. kribbensis KCTC 9933T, respectively. The strain AN120528T shares common chemotaxonomic features with the other two type strains in the genus. It has MK-9 (H4) and MK-10 (H4) as its predominant menaquinones. The major fatty acids are iso-C14:0, iso-C15:0, anteiso-C15:0 and iso-C16:0. Diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), lipids (L), and aminolipids (AL) were identified as the major cellular polar lipids. Analysis of the peptidoglycan showed the presence of meso-diaminopimelic acid. Whole-genome sequencing revealed that the genome of the strain is approximately 3.3 Mbp in size. The strain showed a 77.5% average nucleotide identity (ANI) with S. alba KC615T. The genomic DNA (gDNA) G + C content is 39.0%. Based on polyphasic taxonomy analysis, it is proposed that this strain, AN120528T, represents a novel species in the genus Shimazuella, designated as Shimazuella soli sp. nov. The type stain is AN120528T (=KCTC 39810T = DSM 103571T). Furthermore, shimazuellin I, a new 15-amino-acid peptide, was discovered in the AN120528T through genome mining; it has the features of a lasso peptide, containing eight amino acids (-G-Q-G-G-S-N-N-D-) that form a macrolactam ring and seven amino acids (-D-G-W-Y-H-S-K-) that form a tail.

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Section: Methodsmentioning

confidence: 99%

Genomic Insight into Shimazuella Soli Sp. Nov. Isolated from Soil and Its Putative Novel Class II Lasso Peptide

et al. 2022

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“…Burkholderiaare common soil inhabitants and some species can oxidize sulfur [7]. Chitinophagacan be found in soil and have the capability to hydrolyze chitin and some species contained deferoxamine producing genes [24].Mucilaginibacter are heterotrophic bacteria capable of degrading pectin, xylan, laminarin, and some other polysaccharides [36]. Geobacterspecies have been found in anaerobic conditions in soils and aquatic sediment [30] and can oxidize organic compounds and metals, including iron, radioactive metals, and petroleum compounds into carbon dioxide [10].…”

Section: Taxonomic Features Of Metagenomes Across Sediment Stratamentioning

confidence: 99%

Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment

et al. 2023

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The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.

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Encephalartos natalensis association with non-cyanobacterial species increased reliance on atmospheric nitrogen in acidic and nutrient-deficient savanna woodland ecosystem soils

Ndlovu,

Motsomane,

Suinyuy

et al. 2024

Transactions of the Royal Society of South Africa

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Description of desferrioxamine-producing bacterium Chitinophaga agrisoli sp. nov., isolated from soil

Cited by 4 publications

References 38 publications

Genomic Insight into Shimazuella Soli Sp. Nov. Isolated from Soil and Its Putative Novel Class II Lasso Peptide

Genomic Insight into Shimazuella Soli Sp. Nov. Isolated from Soil and Its Putative Novel Class II Lasso Peptide

Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment

Encephalartos natalensis association with non-cyanobacterial species increased reliance on atmospheric nitrogen in acidic and nutrient-deficient savanna woodland ecosystem soils

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