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Sphingobacterium prati sp. nov., isolated from agricultural soil and involved in lignocellulose deconstruction.

ABSTRACT: A bacterial strain, arapr2^T, was isolated from agricultural soil sampled in Reims, France. Based on its 16S rRNA gene sequence, the strain was affiliated to the family Sphingobacteriaceae and more specifically to the genus Sphingobacterium. The strain had 98.31 % 16S rRNA gene sequence similarity to its closest relative Sphingobacterium canadense CR11^T and 98.25 % to Sphingobacterium pakistanensis NCCP-246^T. Genome relatedness indexes revealed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between arapr2^T and its closest relative (S. canadense CR11^T) were 92.97 % and 52.00 %, respectively; for S. pakistanensis NCCP-246^T, the ANI and dDDH values were 82.46 and 27.6%, respectively. The genomic DNA of strain arapr2^T was 6.02 Mbp long, had a DNA G+C content of 40.4 mol% and had 5504 protein-coding genes. The results obtained in this study suggests that strain arapr2^T (CIP 111872^T=LMG 31848^T) represents a new species for which the name Sphingobacterium prati sp. nov. is proposed. Due to the fact that this strain has been isolated using wheat straw as carbon source, this novel bacterial strain represents a promising biotechnological tool for the fractionation of lignocellulosic biomass in the context of biorefinery development.

SUBMITTER: Besaury L

PROVIDER: S-EPMC8513620 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature

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Sphingobacterium prati sp. nov., isolated from agricultural soil and involved in lignocellulose deconstruction.

Besaury Ludovic L Floret Juliette J Rémond Caroline C

International journal of systematic and evolutionary microbiology 20210801 8

A bacterial strain, arapr2T, was isolated from agricultural soil sampled in Reims, France. Based on its 16S rRNA gene sequence, the strain was affiliated to the family Sphingobacteriaceae and more specifically to the genus Sphingobacterium. The strain had 98.31 % 16S rRNA gene sequence similarity to its closest relative Sphingobacterium canadense CR11T and 98.25 % to Sphingobacterium pakistanensis NCCP-246T. Genome relatedness indexes ...[more]

PMID: 34406922

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Project description:A total of 27 Listeria isolates that could not be classified to the species level were obtained from soil samples from different locations in the contiguous United States and an agricultural water sample from New York. Whole-genome sequence-based average nucleotide identity blast (ANIb) showed that the 27 isolates form five distinct clusters; for each cluster, all draft genomes showed ANI values of <95 % similarity to each other and any currently described Listeria species, indicating that each cluster represents a novel species. Of the five novel species, three cluster with the Listeria sensu stricto clade and two cluster with sensu lato. One of the novel sensu stricto species, designated L. cossartiae sp. nov., contains two subclusters with an average ANI similarity of 94.9%, which were designated as subspecies. The proposed three novel sensu stricto species (including two subspecies) are Listeria farberi sp. nov. (type strain FSL L7-0091T=CCUG 74668T=LMG 31917T; maximum ANI 91.9 % to L. innocua), Listeria immobilis sp. nov. (type strain FSL L7-1519T=CCUG 74666T=LMG 31920T; maximum ANI 87.4 % to L. ivanovii subsp. londoniensis) and Listeria cossartiae sp. nov. [subsp. cossartiae (type strain FSL L7-1447T=CCUG 74667T=LMG 31919T; maximum ANI 93.4 % to L. marthii) and subsp. cayugensis (type strain FSL L7-0993T=CCUG 74670T=LMG 31918T; maximum ANI 94.7 % to L. marthii). The two proposed novel sensu lato species are Listeria portnoyi sp. nov. (type strain FSL L7-1582T=CCUG 74671T=LMG 31921T; maximum ANI value of 88.9 % to L. cornellensis and 89.2 % to L. newyorkensis) and Listeria rustica sp. nov. (type strain FSL W9-0585T=CCUG 74665T=LMG 31922T; maximum ANI value of 88.7 % to L. cornellensis and 88.9 % to L. newyorkensis). L. immobilis is the first sensu stricto species isolated to date that is non-motile. All five of the novel species are non-haemolytic and negative for phosphatidylinositol-specific phospholipase C activity; the draft genomes lack the virulence genes found in Listeria pathogenicity island 1 (LIPI-1), and the internalin genes inlA and inlB, indicating that they are non-pathogenic.

Dataset Information

Sphingobacterium prati sp. nov., isolated from agricultural soil and involved in lignocellulose deconstruction.

Publications

<i>Sphingobacterium prati</i> sp. nov., isolated from agricultural soil and involved in lignocellulose deconstruction.

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