Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor

A novel bacterium, designated strain Msb3T, was recently isolated from leaves of the yam family plant Dioscorea bulbifera (Dioscoreaceae). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Paraburkholderia with Paraburkholderia xenovorans as nearest validly named neighbour taxon (99.3 % sequence similarity towards the P. xenovorans type strain). Earlier genome sequence analysis revealed a genome of 8.35 Mb in size with a G+C content of 62.5 mol%, which was distributed over two chromosomes and three plasmids. Here, we confirm that strain Msb3T represents a novel Paraburkholderia species. In silico DNA-DNA hybridization and average nucleotide identity (OrthoANIu) analyses towards P. xenovorans LB400T yielded 58.4 % dDDH and 94.5 % orthoANIu. Phenotypic and metabolic characterization revealed growth at 15 °C on tryptic soy agar, growth in the presence of 1 % NaCl and the lack of assimilation of phenylacetic acid as distinctive features. Together, these data demonstrate that strain Msb3T represents a novel species of the genus Paraburkholderia, for which we propose the name Paraburkholderia dioscoreae sp. nov. The type strain is Msb3T (=LMG 31881T, DSM 111632T, CECT 30342T).

Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil

RP11^T was isolated from forest soil following enrichment with 4-hydroxybenzoic acid. Cells of RP11^T are aerobic, non-sporulating, exhibit swimming motility, and are rods (0.8 µm by 1.4 µm) that often occur as diplobacillus or in short chains (3-4 cells). Optimal growth on minimal media containing 4-hydroxybenzoic acid (µ=0.216 hr^-1) occurred at 30 °C, pH 6.5 or 7.0 and 0% salinity. Comparative chemotaxonomic, genomic and phylogenetic analyses revealed the isolate was distinct from its closest relative type strains identified as Paraburkholderia aspalathi LMG 27731^T, Paraburkholderia fungorum LMG 16225^T and Paraburkholderia caffeinilytica CF1^T. Strain RP11^T is genetically distinct from P. aspalathi, its closest relative, in terms of 16S rRNA gene sequence similarity (98.7%), genomic average nucleotide identity (94%) and in silico DNA-DNA hybridization (56.7 %±2.8). The composition of fatty acids and substrate utilization pattern differentiated strain RP11^T from its closest relatives, including growth on phthalic acid. Strain RP11^T encoded the greatest number of aromatic degradation genes of all eleven closely related type strains and uniquely encoded a phthalic acid dioxygenase and paralog of the 3-hydroxybenzoate 4-monooxygenase. The only ubiquinone detected in strain RP11^T was Q-8, and the major cellular fatty acids were C_16 : 0, 3OH-C_16 : 0, C_17 : 0 cyclo, C_19 : 0 cyclo ω8c, and summed feature 8 (C_18 : 1 ω7c/ω6c). On the basis of this polyphasic approach, it was determined that strain RP11^T represents a novel species from the genus Paraburkholderia for which the name Paraburkholderia madseniana sp. nov. is proposed. The type strain is RP11^T (=DSM 110123^T=LMG 31517^T).

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 17 July 2019

Minutes of the closed meeting of the ICSP Subcommittee on the Taxonomy of Rhizobia and Agrobacteria held by videoconference on 17 July 2019, and list of recent species.

Dialysis as a new pre-treatment technique for online bacterial counting

Real-time bacteriological counting technology is capable of providing an online profile of bacterial removal during the wastewater treatment process, and can enhance the safety of recycled water for potable water reuse. However, autofluorescence emanating from dissolved organic compounds present in treated wastewater interferes with the analysis. In this study, a novel approach is adopted, viz., dialysis treatment for the removal of dissolved interfering substances from treated wastewater, and the efficiency of this treatment protocol is evaluated as a pre-treatment technique for real-time bacteriological counting. Dialysis using membranes having a molecular weight cut-off (MWCO) of 1000 kDa and 6-8 kDa were found to successfully reduce the intensity of autofluorescence emitted from the interfering substances; whereas the courser dialysis membrane having a MWCO of 1000 kDa was found to be more effective in removing the interfering substances. Here we demonstrate for the first time that continuous online dialysis treatment aids in the direct determination of the bacterial counts in ultrafiltration- and membrane bioreactor-treated wastewaters. The results of the study indicate that the dialysis pre-treatment technique is effective for continuously reducing the concentration of interfering substances in treated wastewater, and thus allows for direct online counting of bacteria.

Paraburkholderia flava sp. nov., isolated from cool temperate forest soil

A Gram-stain-negative, aerobic and short rod-shaped bacterial strain, designated LD6^T, was isolated from a forest soil sample in Suwon, Gyeonggi-do, Republic of Korea. Strain LD6^T grew at 10-37 °C (optimal temperature, 28 °C), and tolerated pH 8.0 and 2 % (w/v) NaCl. Strain LD6^T was related most closely to members of the genus Paraburkholderia, namely Paraburkholderia azotifigens NF2-5-3^T (98.2 % 16S rRNA gene sequence similarity), P. megapolitana A3^T (97.9 %), P. ginsengiterrae DCY85^T (97.9 %) and P. caribensis MWAP64^T (97.7 %). The strain grew well on R2A agar, tryptone soya agar, Mueller-Hinton agar and nutrient agar. The major polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and glycolipid. The major respiratory quinone was ubiquinone 8 (Q-8). The main fatty acids were C_17 : 0 cyclo, C_16 : 0, C_16 : 0 3-OH, C_19 : 0 cyclo ω8c and C_12 : 0. The DNA G+C content of the isolated strain based on the whole genome sequence was 63.4 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain LD6^T and its reference type strains ranged from 80.3 to 82.4%, and from 23.7 to 33.7%, respectively. Based on phenotypic, chemotypic and genotypic evidence, strain LD6^T could be differentiated phylogenetically and phenotypically from the recognized species of the genus Paraburkholderia. Therefore, strain LD6^T is considered to represent a novel species, for which the name Paraburkholderia flava sp. nov. is proposed. The type strain is LD6^T (=KACC 21387^T=JCM 33640^T).

Paraburkholderia lacunae sp. nov., isolated from soil near an artificial pond

A Gram-stain-negative, strictly aerobic bacterial strain, designated strain S27^T, was isolated from soil near an artificial pond in South Korea. Cells were non-motile short rods showing oxidase- and catalase-positive activities. Growth of strain S27^T was observed at 20-40°C (optimum, 30°C), pH 5.0-7.0 (optimum, pH 6.0), and 0-0.5% (w/v) NaCl (optimum, 0%). Ubiquinone-8 was detected as the sole respiratory quinone and the major fatty acids were C_16:0, cyclo-C_17:0, and cyclo-C_19:0ω8c. The G + C content of the genomic DNA was 62.4 mol%. Phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminophospholipid were detected as the major polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S27_T formed a clearly distinct phyletic lineage from closely related Paraburkholderia species within the genus Paraburkholderia. Strain S27^T was most closely related to Paraburkholderia rhynchosiae WSM3937^T, Paraburkholderia ginsengiterrae DCY85^T, Paraburkholderia fungorum NBRC 102489^T, and Paraburkholderia graminis C4D1M^T with 98.8%, 98.4%, 98.4%, and 97.7% 16S rRNA gene sequence similarities, respectively. The DNA-DNA relatedness level between strain S27^T and the type strain of P. rhynchosiae was 36.8 ± 2.6%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain S27^T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia lacunae sp. nov. is proposed. The type strain is S27^T (KACC 19714 ^T = JCM 32721^T).