Pedobacter ureilyticus sp. nov., isolated from tomato rhizosphere soil

Metabacillus rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants

A Gram-positive, endospore-forming, rod-shaped and aerobic bacterium, with swarming and swimming motility, designated strain DBTR6^T, was isolated from the rhizosphere soil of tomato plants. Strain DBTR6^T grew at 20-45 ℃ (optimum 30-37℃), pH 4-9 (optimum 7-8) and at salinities from 0 to 5% (optimum 1%). Phylogenetic analysis using 16S rRNA gene sequences showed this strain belonged to the genus Metabacillus and was most closely related to Metabacillus litoralis DSM 16303 ^T (98.3%) and Metabacillus sediminilitoris MCCC 1K03777^T (98.3%). The DNA G + C content of the genomic DNA was 36.4%. The digital DNA-DNA hybridization value between strain DBTR6^T and reference strains M. sediminilitoris MCCC 1K03777^T and "M. bambusae" BG109^T were less than 70% (26.7% and 26.0%), and the average nucleotide identity score were less than 95% (78.55% and 78.38%), and the Amino Acid Identity values calculated were less than 96% (79.99% and 80.18%), respectively, suggesting that strain DBTR6^T represented a novel species in the genus Metabacillus. Chemotaxonomic analysis showed that strain DBTR6^T contained MK-7 as the major respiratory quinone. The predominant fatty acids (> 10.0%) were iso-C_15:0, anteiso-C_15:0 and C_16:0. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), glycolipids (GL) and three unidentified lipids (L). Based on the differential physiological properties, biochemical characteristics and genotypic data, strain DBTR6^T represents a novel species of the genus Metabacillus, for which the name Metabacillus rhizolycopersici sp. nov. is proposed. The type strain is DBTR6^T (= ACCC 61900 ^T = JCM 35080 ^T).

Pedobacter riviphilus sp. nov., isolated from stream sediment

A Gram-stain-negative, aerobic, motile by gliding, rod-shaped and pink-coloured bacterium, designated strain SW-16^T, was isolated from the sediment of small stream in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SW-16^T formed a lineage within the genus Pedobacter of the family Sphingobacteriaceae. Phylogenetic analysis also showed that strain SW-16^T was most closely related to Pedobacter soli 15-51^T (98.0% 16S rRNA gene sequence similarity), Pedobacter humicola R135^T (97.5%), Pedobacter suwonensis 15-52^T (97.4%), Pedobacter sandarakinus DS-27^T (97.0%) and Pedobacter kyungheensis THG-T17^T (97.0%). Growth was observed at 10-37 °C (optimum at 30 °C), pH 6-8 (optimum at pH 7) and with 0-2.0 % NaCl (optimum at 0%). The major fatty acids of the bacterial strain were iso-C_15 : 0, iso-C_17 : 0 3-OH and summed feature 3 (iso-C_15 : 0 2-OH and/or C_16 : 1  ω7c). The predominant respiratory quinone was menaquinone-7 and the major polar lipids were phosphatidylethanolamine, two unidentified amino lipids, one unidentified phospholipid and three unidentified lipids. The genome size of strain SW-16^T was 5.8 Mbp and the G+C content was 38.5 mol%. Based on the results of phenotypic, genomic and phylogenetic analyses, strain SW-16^T represents a novel species of the genus Pedobacter, for which the name Pedobacter riviphilus sp. nov. is proposed. The type strain is SW-16^T (=KEMB 1602-396^T=KCTC 82079^T=JCM 34181^T).

Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer

Recovery of nutrients from source-separated urine can truncate our dependency on synthetic fertilizers, contributing to more sustainable food production. Urine-derived fertilizers have been successfully applied in soilless cultures. However, little is known about the adaptation of the plant to the nutrient environment. This study investigated the impact of urine-derived fertilizers on plant performance and the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Shoot biomass, chlorophyll, phenolic, antioxidant, and mineral content were associated with shifts in the root-associated bacterial community structures. K-struvite, a high-performing urine-derived fertilizer, supported root-associated bacterial communities that overlapped most strongly with control NPK fertilizer. Contrarily, lettuce performed poorly with electrodialysis (ED) concentrate and hydrolyzed urine and hosted distinct root-associated bacterial communities. Comparing the identified operational taxonomic units (OTU) across the fertilizer conditions revealed strong correlations between specific bacterial genera and the plant physiological characteristics, salinity, and NO₃⁻/NH₄⁺ ratio. The root-associated bacterial community networks of K-struvite and NPK control fertilized plants displayed fewer nodes and node edges, suggesting that good plant growth performance does not require highly complex ecological interactions in hydroponic growth conditions.

Pedobacter helvus sp. nov., isolated from farmland soil

A strictly aerobic, Gram-stain-negative, rod-shaped, yellow, non-spore-forming bacterial strain, designated P-25^T, was isolated from soil collected in Yantai, Shandong Province, PR China. The temperature, pH and NaCl concentration ranges for the growth of strain P-25^T were 10-37 °C (optimum, 28-30 °C), pH 6.0-9.0 (optimum, pH 7.5-8.0) and 0-4 % (w/v) (optimum, 1 % w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P-25^T was most closely related to Pedobacter xixiisoli S27^T (98.1 % 16S rRNA gene sequence similarity), followed by Pedobacter chitinilyticus CM134L-2^T (97.2 %) and Pedobacter ureilyticus THG-T11^T (97.1 %). The genomic DNA G+C content of strain P-25^T based on its draft genome sequence was 38.1 %. MK-7 was the major respiratory quinone, and iso-C_15 : 0, C_16 : 1ω7c and/or C_16 : 1ω6c (summed feature 3) and iso-C_17 : 0 3-OH were the major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, two unidentified lipids, five unidentified aminolipids and two unidentified glycolipids. Average nucleotide identity values for the draft genomes between strain P-25^T and strains S27^T, CM134L-2^T and THG-T11^T were 81.8, 77.6 and 81.2 %, respectively, and the digital DNA-DNA hybridization (dDDH) values were 30.0, 19.2 and 27.6 %, respectively. Based on their phylogenetic and phenotypic characteristics, chemotaxonomic data, and dDDH results, strain P-25^T is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter helvus sp. nov. is proposed; the type strain is strain P-25^T (KCTC 62821^T=CCTCC AB 2018185^T).

Pedobacter aquicola sp. nov., isolated from freshwater

A non-motile, pink-pigmented bacterial strain designated IMCC25679^T, was isolated from freshwater Lake Chungju of Korea. Phylogenetic trees based on 16S rRNA gene sequences showed that the strain IMCC25679^T formed a lineage within the genus Pedobacter. The strain IMCC25679^T was closely related to Pedobacter daechungensis Dae 13^T (96.4% sequence similarity), Pedobacter rivuli HME8457^T (95.3%) and Pedobacter lentus DS-40^T (94.3%). The major fatty acids of IMCC- 25679^T were iso-C_15:0, iso-C_16:0 and summed feature 3 (comprising C_16:1ω6c and/or C_16:1ω7c). The major respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine (PE), an unidentified sphingolipid (SL), an unidentified aminolipid (AL) and three unidentified polar lipids (PL). The DNA G + C content of IMCC25679^T was 32.2 mol%. Based on the evidence presented in this study, the strain IMCC25679^T represents a novel species within the genus Pedobacter, with the proposed name Pedobacter aquicola, sp. nov. The type strain is IMCC25679^T (= KACC 19486^T = NBRC113131^T).

Pedobacter panacis sp. nov., isolated from Panax ginseng soil

A novel strain, DCY108^T was isolated from soil of a Panax ginseng field, Yeoncheon province (38°04'N 126°57'E), Republic of Korea. Strain DCY108^T is Gram-negative, non-motile, non-flagellate, rod-shaped, and aerobic. The bacterium grows optimally at 25-30 °C, pH 6.5-7.0 and 1 % NaCl. Phylogenetically, strain DCY108^T is closely related to Pedobacter jejuensis JCM 18824^T, Pedobacter aquatilis JCM 13454^T, Pedobacter kyungheensis LMG 26577^T and the type strain of the genus Pedobacter heparinus DSM 2366^T. The DNA-DNA relatedness values between strain DCY108^T and its close phylogenetic neighbors were below 30.0 %. The DNA G+C content of strain DCY108^T was determined to be 45.1 mol%. The predominant quinone was menaquinone 7 (MK-7). The major polar lipids were identified as phosphatidylethanolamine and three unidentified aminolipids AL1, AL13 and AL17. Iso-C_15:00, iso-C_17:03OH and summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) were identified as the major fatty acids present in strain DCY108^T. The results of physiological and biochemical tests allowed strain DCY108^T to be differentiated phenotypically from other recognized species belonging to the genus Pedobacter. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Pedobacter panacis sp. nov is proposed with the type strain designated as DCY108^T (=CCTCCAB 2015196^T = KCTC 42748^T).

Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine

A Gram-stain-negative, light pink, non-motile, rod-shaped, aerobic bacterium, designated strain XNV015T, was isolated from soil of a vanadium mine. Phylogenetic analyses based on 16S rRNA gene sequences indicated that it belongs to the genus Pedobacter and was closely related to Pedobacter suwonensis DSM 18130T (96.93 % sequence similarity), Pedobacter alluvionis NWER-II11T (96.66 %), Pedobacter terrae DS-57T (96.54 %), Pedobacter kyungheensis KACC 16221T (96.54 %) and Pedobacter soli KACC 14939T (96.47 %). This strain clearly differed from the closely related species in terms of acid production from rhamnose and ethanol. Menaquinone-7 was the predominant respiratory quinone. The predominant fatty acids included iso-C15 : 0, C16 : 1ω5c, summed feature 3, iso-C17 : 0 3-OH and C17 : 0 2-OH. The major polar lipids were phosphatidylethanolamine, glycolipids, lipids and aminolipids. The genomic DNA G+C content was 43.8 mol%. The genotypic analysis, biochemical properties, and phenotypic and chemotaxonomic characteristics indicate that strain XNV015T represents a novel species of the genus Pedobacter, for which the name Pedobacter vanadiisoli sp. nov. is proposed. The type strain is XNV015T (=CCTCC AB 2015319T=KCTC 42866T).

Pedobacter lignilitoris sp. nov., isolated from wood falls

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterial strain, designated W-WS13T, was isolated from wood falls collected around Wando, an island in the South Sea of South Korea, and subjected to a polyphasic taxonomic study. Strain W-WS13T grew optimally at 30 °C, at pH 7.5 and in the presence of 0.5 % NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain W-WS13T belonged to the genus Pedobacter, clustering robustly with the type strain of Pedobacter arcticus, sharing 95.9 % sequence similarity. Strain W-WS13T exhibited 16S rRNA gene sequence similarity of 90.1–95.6 % to the type strains of the other species of the genus Pedobacter. Strain W-WS13T contained MK-7 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipid detected in strain W-WS13T was phosphatidylethanolamine. The DNA G+C content of strain W-WS13T was 36.9 mol%. Phylogenetic distinctiveness and differential phenotypic properties of strain W-WS13T revealed that the novel strain is separated from recognized species of the genus Pedobacter. On the basis of the data presented, strain W-WS13T is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter lignilitoris sp. nov. is proposed. The type strain is W-WS13T ( = KCTC 42500T = CECT 8725T).