Paraflavitalea soli gen. nov., sp. nov., isolated from greenhouse soil

Polysaccharide utilization loci encoded DUF1735 likely functions as membrane-bound spacer for carbohydrate active enzymes

Proteins featuring the Domain of Unknown Function 1735 are frequently found in Polysaccharide Utilization Loci, yet their role remains unknown. The domain and vicinity analyzer programs we developed mine the Kyoto Encyclopedia of Genes and Genomes and UniProt to enhance the functional prediction of DUF1735. Our datasets confirmed the exclusive presence of DUF1735 in Bacteroidota genomes, with Bacteroidetes thetaiotaomicron harboring 46 copies. Notably, 97.8% of DUF1735 are encoded in PULs, and 89% are N-termini of multimodular proteins featuring C-termini like Laminin_G_3, F5/8-typeC, and GH18 domains. Predominantly possessing a predicted lipoprotein signal peptide and sharing an immunoglobulin-like β-sandwich fold with the BACON domain and the N-termini of SusE/F, DUF1735 likely functions as N-terminal, membrane-bound spacer for diverse C-termini involved in PUL-mediated carbohydrate utilization.

Paraflavitalea pollutisoli sp. nov., Pollutibacter soli gen. nov. sp. nov., Polluticoccus soli gen. nov. sp. nov., and Terrimonas pollutisoli sp. nov., four new members of the family Chitinophagaceae from polluted soil

A taxonomic investigation was conducted on four bacterial strains isolated from soil contaminated with polycyclic aromatic hydrocarbons and heavy metals. Phylogenetic analysis revealed that these strains belonged to the family Chitinophagaceae. Examination of the 16S rRNA genes indicated that their sequence identities were below 97.6 % compared to any known and validly nominated bacterial species. The genomes of the four strains ranged from 4.12 to 8.76 Mb, with overall G + C molar contents varying from 41.28 % to 50.39 %. Predominant cellular fatty acids included iso-C15:0, iso-C15:1 G, and iso-C17:0 3-OH. The average nucleotide identity ranged from 66.90 % to 74.63 %, and digital DNA-DNA hybridization was 12.5-12.8 %. Based on the genomic and phenotypic features of the new strains, four novel species and two new genera were proposed within the family Chitinophagaceae. The ecological distributions were investigated by data-mining of NCBI databases, and results showed that additional strains or species of the newly proposed taxa were widely distributed in various environments, including polluted soil and waters. Functional analysis demonstrated that strains H1-2-19XT, JS81T, and JY13-12T exhibited resistance to arsenite (III) and chromate (VI). The proposed names for the four novel species are Paraflavitalea pollutisoli (type strain H1-2-19XT = JCM 36460T = CGMCC 1.61321T), Terrimonas pollutisoli (type strain H1YJ31T = JCM 36215T = CGMCC 1.61343T), Pollutibacter soli (type strain JS81T = JCM 36462T = CGMCC 1.61338T), and Polluticoccus soli (type strain JY13-12T = JCM 36463T = CGMCC 1.61341T).

Longitalea arenae gen. nov., sp. nov. and Longitalea luteola sp. nov., two new members of the family Chitinophagaceae isolated from desert soil

Two strains designated as SYSU D01084^T and SYSU D00799^T, were isolated from a sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells of both strains were Gram-stain-negative, strictly aerobic, long-rod-shaped, oxidase- and catalase-negative, motile or non-motile. Colonies were circular, translucent, convex, smooth and light-yellow in color on R2A agar. The two isolates were found to grow at 4-50 ºC, at pH 6.0-8.0 and with 0-1.0% (w/v) NaCl. Analysis of their 16S rRNA gene sequences indicated that they belonged to the family Chitinophagaceae, and closely related to the genera Paraflavitalea, Niastella, Pseudoflavitalea and Flavitalea. The two novel strains shared 98.1% 16S rRNA sequence similarity and represent different species on the basis of low average nucleotide identity (ANI, 83.8%) and digital DNA-DNA hybridization (dDDH, 51.4%) values. The genomic DNA G + C contents of strains SYSU D01084^T and SYSU D00799^T were 46.0 and 45.6%, respectively. Phylogenetic trees showed that the two isolates were clustered in an individual lineage and not grouped consistently into any specific genus. The polar lipids contained of phosphatidylethanolamine, four unidentified aminolipids, two unidentified aminoglycolipids, and three or four unidentified lipids. The predominant respiratory quinone was MK-7 and the major fatty acids (> 10%) were identified as iso-C_15:0, iso-C_17:0 3-OH, and iso-C_15:1 G. Based on the combined phenotypic, genomic and phylogenetic analyses, the two strains represent two novel species of a new genus in the family Chitinophagaceae, for which the name Longitalea gen. nov. is proposed, comprising the type species Longitalea arenae sp. nov. (type strain SYSU D01084^T = CGMCC 1.18641^T = MCCC 1K05006^T = KCTC 82283^T) and Longitalea luteola sp. nov. (type strain SYSU D00799^T = MCCC 1K04987^T = KCTC 82282^T = NBRC 114888^T).

Paraflavitalea devenefica sp. nov., isolated from urban soil

A Gram-stain-negative, rod-shaped, mesophilic, milky white-pigmented, aerobic, non-spore-forming and non-flagellated bacterium, designated strain X16^T, was isolated from urban soil of Zibo, Shandong, China. According to 16S rRNA gene sequence analysis, the isolate showed highest similarities with Paraflavitalea soli 5GH32-13^T (97.6 %), Pseudoflavitalea soli KIS20-3^T (96.2 %), Pseudobacter ginsenosidimutans Gsoil 221^T (96.0 %) and Pseudoflavitalea rhizosphaerae T16R-265^T (95.8 %). The neighbour-joining tree based on 16S rRNA gene sequences showed that strain X16^T formed a subcluster with Paraflavitalea soli 5GH32-13^T, and the subcluster was closely related to Pseudoflavitalea soli KIS20-3^T, Pseudobacter ginsenosidimutans Gsoil 221^T and Pseudoflavitalea rhizosphaerae T16R-265^T. Strain X16^T also formed a subcluster with Paraflavitalea soli 5GH32-13^T in phylogenetic tree based on genomic sequences. The polar lipids are phosphatidylethanolamine, two unknown aminolipids, two unknown aminophospholipids, two unknown lipids and two unknown phospholipids. The major quinone of strain X16^T is menaquinone-7 and the main fatty acids (>10 % of total fatty acids) of strain X16^T are iso-C_15 : 0, iso-C_17 : 0 3-OH and iso-C_15 : 1 G. The genome length of strain X16^T is 8.7 Mb with a DNA G+C content of 47.4 %. ANI values among strain X16^T and strain Paraflavitalea soli 5GH32-13^T, Pseudobacter ginsenosidimutans Gsoil 221^T, and Pseudoflavitalea rhizosphaerae T16R-265^T are 78.1, 70.7, 70.6 %, respectively. On the basis of the results of the polyphasic characterization presented in this study, it is concluded that strain X16^T represents a novel species. Besides, strain X16^T can detoxify high toxicity selenite [Se(IV)] to low toxicity elemental selenium [Se(0)], for which the name Paraflavitale devenefica sp. nov. is proposed. The type strain is X16^T (=KACC 21698^T=GDMCC1.1757^T).