Pelagibacterium xiamenense sp. nov., isolated from intertidal sediment

A Gram-stain-negative, obligately aerobic bacterium, designated as HS1C4-1T, was isolated from a sediment sample from the tidal zone of the Haicang Coast, Xiamen, Fujian Province, PR China. The strain was yellowish-coloured, non-gliding, rod-shaped and motile, with a single polar flagellum. Cells of HS1C4-1T were oxidase- and catalase-positive. The strain could grow at 15–55 °C (optimum 37 °C), pH 6.0–10.0 (optimum, pH 7.0–9.0), in the presence of 0–12 % (optimum, 1 %) NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that HS1C4-1T represented a member of the genus Pelagibacterium , and shared the highest similarity to Pelagibacterium luteolum CGMCC 1.10267T (97.6 %). Digital DNA–DNA hybridization values and average nucleotide identity between HS1C4-1T and all the species of genus Pelagibacterium were 18.7–20.2 % and 77.3–78.4 %, respectively. The principal fatty acids (>10 %) were C19 : 0 cyclo ω8c (50.5 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 29.1%). Q-10 was the sole respiratory quinone. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and six unidentified lipids. The G+C content of the chromosomal DNA was 62.9 %. On the basis of phylogenetic, phenotypic, chemotaxonomic and genomic characteristics, HS1C4-1T represents a novel species within the genus Pelagibacterium , for which the name Pelagibacterium xiamenense sp. nov. is proposed. The type strain is HS1C4-1T (=MCCC 1A18759T=KCTC 92097T).

Structure and variation of root-associated bacterial communities of Cyperus rotundus L. in the contaminated soils around Pb/Zn mine sites

Soil contamination due to mining activities is a great concern in China. Although the effects of mining pollution resulting in changes of soil characteristics and the microbiome have been documented, studies on the responses of plant root-associated microbial assemblages remain scarce. In this work, we collected bulk soil, rhizosphere soil, and root endosphere samples of Cyperus rotundus L (Cyp) plants from two Pb/Zn mines, of which, one was abandoned (SL) and the other was active (GD), to investigate the bacterial community responses across different site contamination levels and Cyp plant compartments. For comparison, one unpolluted site (SD) was included. Results revealed that soils from the SL and GD sites were seriously contaminated by metal(loid)s, including Pb, Zn, As, and Sb. Bacterial richness and diversity depended on the sampling site and plant compartment. All sample types from the SL site had the lowest bacterial diversities and their bacterial communities also exhibited distinct patterns compared to GD and SD samples. As for the specific sampling site, bacterial communities from the root endosphere exhibited different patterns from those in bulk and rhizosphere soil. Compared to the GD and SD sites, the root endosphere and the rhizosphere soil from the SL site shared core microbes, including Halomonas, Pelagibacterium, and Chelativorans, suggesting that they play key roles in Cyp plant survival in such harsh environments.

Pelagibacterium limicola sp. nov., isolated from a soda alkali-saline soil

A Gram-staining negative, motile, non-spore-forming, rod-shaped bacterium, designated NAJP-14^T, was isolated from the alkali-saline soil in Heilongjiang, Northeast China. Phylogenetic analysis based on 16S rRNA gene sequencing illustrated that strain NAJP-14^T was a member of the genus Pelagibacterium, and shared 94.6-96.6% sequence identities to species from the genus Pelagibacterium. Strain NAJP-14^T grew at 20-45 °C (optimum, 30 °C), pH 7.0-10.0 (optimum, pH 8.0) and in the presence of up to 5% w/v NaCl. The menaquinone was determined to be Q (10). The major fatty acids were identified as C_18:1w6c (38.7%), C_16:0 (16.2%) and C_19:0 cyclo w8c (13.9%). The G + C content of the genomic DNA was 61.2%. Out of the 3442 predicted genes, 3391 were protein-coding genes and 51 were ncRNA. Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) of the strain NAJP-14^T and the type strains of related species in the same family ranged between 17.9 and 21.8% and between 61.4 and 78.7%, respectively. Based on these data, it is concluded that strain NAJP-14^T possesses sufficient characteristics to differentiate it from all recognized Pelagibacterium species, and should be considered as a novel species for which the name Pelagibacterium limicola sp. nov. is proposed. The type strain is NAJP-14^T (= CGMCC 1.16631^T, = JCM 33746^T).

Co-enhanced activated sludge system by static magnetic field and two halotolerant yeasts for azo dye treatment

The effect of static magnetic field (SMF) on azo dye Acid Red B (ARB) decolorization by the co-culture of activated sludge (AS) and two halotolerant yeasts Candida tropicalis A1 and Pichia occidentalis A2 was investigated. Microbial community structure of the co-cultures before and after treatment with SMFs of different intensity was analyzed through high-throughput sequencing and quantitative real-time polymerase chain reaction. The results showed that ARB decolorization efficiency by the defined co-culture was 1.25-fold to 1.51-fold elevated by 24.6-305.0 mT SMF. The best ARB decolorization and chemical oxygen demand (COD) removal performances by the co-culture were both achieved with 95.0 mT SMF. By contrast, biomass multiplication and sedimentation property of AS systems were not significantly influenced by SMF. Higher activities of intracellular key enzymes were determined (with 95.0 mT SMF) as responsible for better decolorization and COD removal performances. Bacteria belonging to Prolixibacter, Corynebacterium, Pelagibacterium, Demequina, and Sphingobacterium which might be responsible for azo dye decolorization and aromatic compounds biodegradation were significantly enriched only in presence of SMF. Fungal genera Candida and Pichia were also significantly enriched by 41.4-305.0 mT SMF, which might be responsible for higher treatment efficiency. PRACTITIONER POINTS: Dye degradation was enhanced by combination of static magnetic field and yeasts. Improvement of enzyme activity was responsible for better treatment performance. Putative azo-degrading-related bacteria and fungi were selectively enriched. High relative abundance of Candida and Pichia ensured high decolorization effects. Potentially effective improvement of bioprocesses for treating hypersaline wastewater.

Pelagibacterium sediminicola sp. nov., isolated from tidal flat sediment

A Gram-stain-negative, obligately aerobic, cream-coloured, non-gliding, motile with a single polar flagellum and rod-shaped bacterium, designated IMCC34151^T, was isolated from tidal flat sediment of the Yellow Sea, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC34151^T belonged to the genus Pelagibacterium of the family Hyphomicrobiaceae and shared 94.7-96.8 % sequence similarities to Pelagibacterium species. Whole-genome sequencing of strain IMCC34151^T revealed a genome size of 3.2 Mbp and a DNA G+C content of 62.6 mol%. The strain contained summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c), C_19 : 0cyclo ω8c and C_16 : 0 as the major fatty acids and ubiquinone-10 (Q-10) as the major respiratory quinone. The polar lipids detected in the strain were phosphatidylglycerol, diphosphatidylglycerol, two unidentified glycolipids and 12 unidentified lipids. On the basis of its phylogenetic and phenotypic characteristics, strain IMCC34151^T is considered to represent a novel species of the genus Pelagibacterium, for which the name Pelagibacteriumsediminicola sp. nov. (type strain IMCC34151^T =KACC 19595^T=NBRC 113420^T) is proposed.

Pelagibacterium lacus sp. nov., isolated from lake water

A Gram-stain-negative, strictly aerobic, oxidase- and catalase-positive, non-gliding, motile with a single polar flagellum, and short rod-shaped bacterial strain, designated XYN52^T, was isolated from a freshwater lake in the west of China. Phylogenetic analysis of the 16S rRNA gene determined that strain XYN52^T was a member of the genus Pelagibacterium within the family Hyphomicrobiaceae. Strain XYN52^T was able to grow at 4-37 °C (optimum, 30 °C), pH 6.0-9.0 (pH 7.5) and in the presence of up to 7.0 % w/v NaCl (0.5 %).The major quinone was ubiquinone 10. The major cellular fatty acids were C18 : 1ω6c/C18 : 1ω7c, C19 : 0ω8c cyclo and 11-methyl C18 : 1ω7c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and three kinds of glycolipids. The genomic DNA G+C content was 64.5 mol%. On the basis of these data, strain XYN52^T represents a novel species in the genus Pelagibacterium, for which the name Pelagibacterium lacus sp. nov. is proposed. The type strain is XYN52^T (=KCTC 62845^T=MCCC 1H00348^T).