Kineococcus gypseus sp. nov., isolated from saline sediment

Li, Qinyuan; Li, Gui-Ding; Chen, Xiu; Xu, Fang‐Ji; Li, Yong; Xu, Li-Hua; Jiang, Yi; Jiang, Cheng‐Lin

doi:10.1099/ijsem.0.000478

Cited by 12 publications

(7 citation statements)

References 41 publications

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“…In contrast with this, the genera Kocuria, Kineococcus, and Mycolicibacterium were isolated from five out of the six media used. In the case of Kineococcus spp., there are previous reports on their isolation from a wide diversity of media and their ability to grow on them too, including diluted TSA 0.1× (Liu et al, 2009), the rich starch-casein agar medium (Duangmal et al, 2008;Li et al, 2015), or pure TSA (Xu et al, 2017), which also happens for Mycolicibacterium species, as reported by Nouioui et al (2019). Moreover, Kaewkla and Franco (2013) reported a similar strategy of isolating novel culturable strains from trees by extending incubation times and using diluted media, which resulted in the isolation of a wide diversity of genera and new species, including several Nocardioides, Kribbella, and Amycolatopsis isolates, which have grown preferably in intermediate to low concentrations in the case of the samples from the Tabernas Desert.…”

Section: Simple Culture-based Strategies Rescue Significant Fractionsmentioning

confidence: 99%

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

et al. 2021

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One of the most diverse ecological niches for microbial bioprospecting is soil, including that of drylands. Drylands are one of the most abundant biomes on Earth, but extreme cases, such as deserts, are considered very rare in Europe. The so-called Tabernas Desert is one of the few examples of a desert area in continental Europe, and although some microbial studies have been performed on this region, a comprehensive strategy to maximize the isolation of environmental bacteria has not been conducted to date. We report here a culturomics approach to study the bacterial diversity of this dryland by using a simple strategy consisting of combining different media, using serial dilutions of the nutrients, and using extended incubation times. With this strategy, we were able to set a large (254 strains) collection of bacteria, the majority of which (93%) were identified through 16S ribosomal RNA (rRNA) gene amplification and sequencing. A significant fraction of the collection consisted of Actinobacteria and Proteobacteria, as well as Firmicutes strains. Among the 254 isolates, 37 different genera were represented, and a high number of possible new taxa were identified (31%), of which, three new Kineococcus species. Moreover, 5 out of the 13 genera represented by one isolate were also possible new species. Specifically, the sequences of 80 isolates held a percentage of identity below the 98.7% threshold considered for potentially new species. These strains belonged to 20 genera. Our results reveal a clear link between medium dilution and isolation of new species, highlight the unexploited bacterial biodiversity of the Tabernas Desert, and evidence the potential of simple strategies to yield surprisingly large numbers of diverse, previously unreported, bacterial strains and species.

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Section: Simple Culture-based Strategies Rescue Significant Fractionsmentioning

confidence: 99%

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

et al. 2021

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“…Values are percentages of total fatty acids. The FAME profiles of the species other than B12 T strain were taken from Phillips et al (2002), Li et al (2015), and Xu et al (2017).…”

Section: Phylogenetics Of Strain B12 Tmentioning

confidence: 99%

Description of Chloramphenicol Resistant Kineococcus rubinsiae sp. nov. Isolated From a Spacecraft Assembly Facility

et al. 2020

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A Gram-positive, coccoid, motile, aerobic bacterium, designated strain B12 T was isolated from a Jet Propulsion Laboratory spacecraft assembly cleanroom, Pasadena, CA, United States. Strain B12 T was resistant to chloramphenicol (100 µg/mL), and is a relatively slow grower (3-5 days optimal). Strain B12 T was found to grow optimally at 28 to 32 • C, pH 7 to 8, and 0.5% NaCl. Fatty acid methyl ester analysis showed that the major fatty acid of the strain B12 T was anteiso C 15:0 (66.3%), which is also produced by other Kineococcus species. However, arachidonic acid (C 20:4 ω6,9,12,16c) was present in strain B12 T and Kineococcus glutinatus YIM 75677 T but absent in all other Kineococcus species. 16S rRNA analysis revealed that strain B12 T was 97.9% similar to Kineococcus radiotolerans and falls within the Kineococcus clade. Low 16S rRNA gene sequence similarities (<94%) with other genera in the family Kineosporiaceae, including Angustibacter (93%), Kineosporia (94% to 95%), Pseudokineococcus (93%), Quadrisphaera (93%), and Thalassiella (94%) demonstrated that the strain B12 T does not belong to these genera. Phylogenetic analysis of the gyrB gene show that all known Kineococcus species exhibited <86% sequence similarity with B12 T. Multi-locus sequence and whole genome sequence analyses confirmed that B12 T clades with other Kineococcus species. Average nucleotide identity of strain B12 T were 75-78% with other Kineococcus species, while values ranged from 72-75% with species from other genera within family Kineosporiaceae. Average amino-acid identities were 66-72% with other Kineococcus species, while they ranged from 50-58% with species from other genera. The dDDH comparison of strain B12 T genome with members of genera Kineococcus showed 20-22% similarity, again demonstrating that B12 T is distantly related to other members of the genus. Furthermore, analysis of whole proteome deduced from WGS places strain B12 T in order Kineosporiales, confirming that strain B12 T is a novel member of family Kineosporiaceae. Based on these analyses and other genome characteristics, strain B12 T is assigned to a novel species within the genus Kineococcus, and the name Kineococcus rubinsiae sp. nov., is proposed. The type strain is B12 T (=FJII-L1-CM-PAB2 T ; NRRL B-65556 T , DSM 110506 T).

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“…The genus Kineococcus, belonging to the family Kineosporiaceae [ 1 ], was first proposed by Yokota et al in 1993 [ 2 ]. At the time of writing, the genus Kineococcus is comprised of 11 species with valid published names ( ) which were isolated from soil [ 2 , 3 , 4 , 5 ], saline environments [ 6 , 7 , 8 ], plants [ 9 , 10 ] and radioactive work areas [ 11 ]. This genus includes species with the ability to grow in a wide range of temperatures [ 5 ] and high salt concentrations [ 8 , 9 ].…”

Section: Introductionmentioning

confidence: 99%

Kineococcus vitellinus sp. nov., Kineococcus indalonis sp. nov. and Kineococcus siccus sp. nov., Isolated Nearby the Tabernas Desert (Almería, Spain)

et al. 2020

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Three novel Gram-positive, aerobic, chemoheterotrophic, motile, non-endospore-forming, orange-pigmented bacteria designated strains T13T, T90T and R8T were isolated from the Tabernas Desert biocrust (Almería, Spain). Cells of the three strains were coccus-shaped and occurred singly, in pairs or clusters. The three strains were oxidase-negative and catalase-positive, and showed a mesophilic, neutrophilic and non-halophilic metabolism. Based on the 16S rRNA gene sequences, the closest neighbours of strains T13T, T90T and R8T were Kineococcus aurantiacus IFO 15268T, Kineococcus gypseus YIM 121300T and Kineococcus radiotolerans SRS 30216T (98.5%, 97.1% and 97.9% gene sequence similarity, respectively). The genomes were sequenced, and have been deposited in the GenBank/EMBL/DDBJ databases under the accession numbers JAAALL000000000, JAAALM000000000 and JAAALN000000000, respectively, for strains T13T, T90T and R8T. The average nucleotide identity (ANIb) and digital DNA-DNA hybridization (dDDH) values confirmed their adscription to three new species within the genus Kineococcus. The genomic G + C content of strains T13T, T90T and R8T ranged from 75.1% to 76.3%. The predominant fatty acid of all three strains was anteiso-C15:0. According to a polyphasic study, strains T13T, T90T and R8T are representatives of three new species in the genus Kineococcus, for which names Kineococcus vitellinus sp. nov. (type strain T13T = CECT 9936T = DSM 110024T), Kineococcus indalonis sp. nov. (type strain T90T = CECT 9938T = DSM 110026T) and Kineococcus siccus sp. nov. (type strain R8T = CECT 9937T = DSM 110025T) are proposed.

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Kineococcus gypseus sp. nov., isolated from saline sediment

Cited by 12 publications

References 41 publications

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

Description of Chloramphenicol Resistant Kineococcus rubinsiae sp. nov. Isolated From a Spacecraft Assembly Facility

Kineococcus vitellinus sp. nov., Kineococcus indalonis sp. nov. and Kineococcus siccus sp. nov., Isolated Nearby the Tabernas Desert (Almería, Spain)

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