Marinobacter halodurans sp. nov., a halophilic bacterium isolated from sediment of a salt flat.

A Gram-staining-negative, aerobic, cream-coloured, marine bacterium, with rod-shaped cells, designated strain YJ-S3-2T, was isolated from salt flat sediment of Yongyu-do, Republic of Korea. YJ-S3-2T grew at pH 5.0-9.0 (optimum pH 7.0), 4-45 °C (optimum 30 °C) and with 1-18 % (w/v) NaCl (optimum 6 %). The results of 16S rRNA gene sequence analysis indicated that YJ-S3-2T was closely related to Marinobacter segnicrescens SS011B1-4T (97.0 %) followed by, 'Marinobacter nanhaiticus' D15-8W (96.7 %), Marinobacter bryozoorum 50-11T (96.7 %), Marinobacter koreensis DSMZ 179240T T (96.5 %) and Marinobacter bohaiensis T17T (96.5 %). The average nucleotide identity (ANI) and the genome to genome distance calculator (GGDC) estimate values between YJ-S3-2T and related type strains were 73.7-79.8 and 19.9-22.5 %, and also 73.5 and 20.7 % with Marinobacter hydrocarbonoclasticus. YJ-S3-2T was characterized as having Q-9 as the predominant respiratory quinone and the principal fatty acids (>10 %) were C16 : 0 (22.3 %), summed feature 9 (C17 : 1iso ω9c/C16 : 0 10-methyl, 13.8 %) and 3 (C16 : 1ω7c/C16 : 1ω6c, 11.9 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids and two unidentified phospholipids. The DNA G+C content of YJ-S3-2T is 60.9 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, YJ-S3-2T should be classified as representing a novel species within the genus Marinobacter, for which name Marinobacter halodurans sp. nov. is proposed, with the type strain YJ-S3-2T (=KACC 19883T=KCTC 62937T=JCM 33109T).

A proposed stepwise screening framework for the selection of polycyclic aromatic hydrocarbon (PAH)-degrading white rot fungi.

This study suggests a simple three-step screening protocol for the selection of white rot fungi (WRF) capable of degrading polycyclic aromatic hydrocarbons (PAHs), which combines easily applicable bioassay techniques, and verifies that protocol by evaluating the PAH degradation activity, ligninolytic enzyme secretion, and relevant gene expressions of the selected PAH-degraders. Using 120 fungal strains, a sequence of bioassay techniques was applied: Bavendamm's reaction (Step 1), remazol brilliant blue R (RBBR) decolorization (Step 2); assays for tolerance to four mixed PAHs-phenanthrene, anthracene, fluoranthene, and pyrene (Step 3). This stepwise protocol selected 14 PAH-degrading WRF, including Microporus vernicipes, Peniophora incarnata, Perenniporia subacida, Phanerochaete sordida, Phlebia acerina, and Phlebia radiata. Of these, P. incarnata exhibited the highest PAH degradative activity, ranging from 40 to > 90%, which was related to the time-variable secretions of three extracellular ligninolytic enzymes: laccase, manganese-dependent peroxidase (MnP) and lignin peroxidase (LiP). Laccase and MnP production by P. incarnata tended to be greater in the early stages of PAH degradation, whereas its LiP production became intensified with decreasing laccase and MnP production. Pilc1 and pimp1 genes encoding laccase and MnP were expressed, indicating the occurrence of extracellular enzyme-driven biodegradation of PAH by the fungal strains.

Serinicoccus sediminis sp. nov., isolated from tidal flat sediment.

A novel Gram-strain-positive, non-spore-forming bacterial strain, designated GP-T3-3T, was isolated from sediment sampled at a tidal flat in Gopado, Republic of Korea. Cells were aerobic, catalase-negative, oxidase-positive, non-motile cocci that occurred singly, in pairs or in clusters. Strain GP-T3-3T grew at 4-45 °C (optimum, 28-37 °C), at pH 4.0-12.0 (pH 8.0-9.0) and in the presence of 0-15 % (w/v) NaCl (3-5 %). Colonies of strain GP-T3-3T were deep-yellow, circular, smooth and pulvinate. The results of the phylogenetic analyses based on 16S rRNA gene sequences indicated that strain GP-T3-3T was closely related to Serinicoccus profundi MCCC 1A05965T (99.1 %), Serinicoccus chungangensis CAU 9536T (99.0 %) and Serinicoccus marinus JC1078T (98.0 %). The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant respiratory quinone was MK-8(H4) and the major fatty acids were anteiso-C17 : 0, iso-C16 : 0, iso-C15 : 0 and anteiso-C15 : 0. The polar lipid profile consisted of diphosphadidylglycerol, phosphadidylglycerol, phosphatidylcholine, phosphatidylinositol and two unidentified phospholipids. The DNA G+C content was 72.9 mol%. DNA-DNA relatedness values between strain GP-T3-3T and type strains of the genus Serinicoccus ranged from 28.9 to 50.5 %. On the basis of the phenotypic differences and DNA-DNA relatedness data, the isolate represents a new species of the genus Serinicoccus, for which the name Serinicoccussediminis sp. nov. is proposed. The type strain is GP-T3-3T (=KCTC 49173T=JCM 32825T=KCCM 43309T=KACC 19850T).

Gemmobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat.

A novel cream-pigmented marine bacterium, designated strain YJ-T1-11T, was isolated from a tidal flat at Yeongjong-do, Republic of Korea. Cells were rod-shaped, non-motile, aerobic, Gram-reaction-negative, oxidase-positive and catalase-positive. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain YJ-T1-11T clustered with Gemmobacter fontiphilus JS43T (98.3 %) within the genus Gemmobacter and its closest neighbours were G.emmobacter aquatilis DSM 3857T (98.5 %), Gemmobacter aquaticus A1-9T (98.4 %), Gemmobacterlanyuensis Orc-4T (98.4 %), Gemmobacterfontiphilus JS43T (98.3 %), Gemmobactercaeni DCA-1T (98.2 %), Gemmobacternanjingensis Y12T (97.5 %) and Gemmobactertilapiae Ruye-53T (97.2 %). Average nucleotide identity values between the genome sequences of strain YJ-T1-11T and the related type strains ranged from 77.08 to 90.48 %. The predominant fatty acid of strain YJ-T1-11T was summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major isoprenoid quinone was Q-10 and the DNA G+C content was 65.6 mol%. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and three unidentified lipids. The DNA-DNA relatedness values between strain YJ-T1-11T and the type strains of the 12 phylogenetically related species of the genus Gemmobacter were 23.6-53.7 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain YJ-T1-11T is considered to represent a novel species of the genus Gemmobacter, for which the name Gemmobacter lutimaris sp. nov. is proposed. The type strain is YJ-T1-11T (=KCTC 62715T=JCM 32828T).

Importance of functional diversity in assessing the recovery of the microbial community after the Hebei Spirit oil spill in Korea.

Over 10 years after the Hebei Spirit oil spill (HSOS), the concentrations of pollutants, such as TPH and PAHs, in spilled crude oil have recovered to background levels, but in some areas, the environment has not fully recovered. In particular, PAHs were more resistant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem. This study aimed to evaluate the microbial recovery of coastal sediments from the HSOS by analyzing the structure and diversity of the microbial community and its functional contribution to PAHs degradation. High-throughput sequencing on the MiSeq platform was conducted using tidal flat sediments collected in 2014 and 2016 from the area contaminated by the HSOS. The microbial recovery was evaluated by various diversity factors, including microbial composition and structure and functional diversity based on PICRUSt analysis. The abundance of microbial taxa associated with TPH degradation was higher in 2014 than that in 2016, but the taxa associated with PAHs degradation were similar between years. These results are consistent with the dynamics of microbes associated with the fate of pollutants, and they also showed similar tendency in functional profiles. That is, even if the pollutants are completely degraded, the microbial community has not yet completely recovered from the HSOS. The evaluation of microbial ecosystems in contaminated environments should consider both the fate of pollutants and the dynamics of microbial species that make functional contributions to the degradation of pollutants.

Optimization of bioleaching conditions for metal removal from CCA-treated wood by using an unknown Polyporales sp. KUC8959.

The purpose of this study was to investigate the effect of extraction conditions (i.e., culture filtrate concentration, extraction temperature, and extraction time) on the removal of metals from chromated copper arsenate (CCA)-treated wood particles by using an unknown Polyporales sp. KUC8959. As the first research, a 20-run central composite design using response surface methodology was applied to optimize the system and construct the models, which predicted metal removal by bioleaching. The coefficients of determination of fitted models were 0.874-0.989, which indicated that the models can predict the metal removal yield accurately under various conditions. The Cu removal model suggested that the following conditions, culture filtrate concentration of 45.8%, extraction temperature of 34.2 °C, and extraction time of 20.6 h, were required for maximal removal of Cu (82.1%). The model predicted that extraction conditions of increased severity would result in complete removal of Cr and As from CCA-treated wood particles. In order to confirm actual metals removal efficiency, metals extraction was subsequently conducted under optimal bioleaching condition evaluated in this study. By applying the model, we demonstrated 83.9% Cu, 96.0% Cr, and 99.3% As removal from treated wood particles.

Decolorization and degradation of synthetic dyes by Irpex lacteus KUC8958.

This study was carried out to evaluate the dye decolorizing and detoxifying abilities of Irpex lacteus. The decolorization abilities of 14 strains of I. lacteus were investigated in agar-plates containing 3 synthetic dyes: Congo Red (CR), Orange II (OII), and Reactive Blue 4 (RB4). In an agar plate test, I. lacteus KUC8958 showed the highest dye decolorizing rate with all 3 dyes. Subsequently, we investigated the decolorizing and detoxifying abilities of I. lacteus KUC8958 on synthetic dyes in liquid media under both shaking and static conditions. I. lacteus KUC8958 showed high decolorization rates for CR and BR4 (more than 95%) under shaking conditions, but only moderate decolorization of OII (up to 53%). The dye decolorizing rates of I. lacteus KUC8958 were approximately 20% to 60% higher under shaking conditions than under static conditions. In a detoxification assay, the toxicities of CR and OII solutions increased, whereas the toxicity of RB4 decreased after decolorization by I. lacteus KUC8958. Subsequently, high-performance liquid chromatography analysis detected 2 compounds in CR and 1 compound in OII that were newly formed during the decolorizing process, and which might be involved in the increased toxicities. Further studies are required to identify these newly formed compounds.

Improving the efficiency of metal removal from CCA-treated wood using brown rot fungi.

The purpose of this study was to evaluate the bioremediation of CCA-treated wood wastes by brown rot fungi, as well as to improve the metal removal from treated wood by altering an existing bioremediation process. In Process I, CCA-treated wood sawdust was added and bioremediated after accumulating oxalic acid in a fermentation broth. In Process II, simplification of the bioremediation process and improvement of metal removal efficiency were attempted. Thus, the treated sawdust and fungal inocula were simultaneously placed in a fermentation broth. In addition, the efficiency of the fermentation broth containing oxalic acid was compared with that of commercial oxalic acid. The results obtained using Process I showed that the greatest reduction in arsenic and chromium (98% and 91%, respectively) was achieved by an unknown Polyporales species. On the other hand, the most efficient removal of copper (82%) was achieved by Daedalea dickinsii, which had the lowest oxalic acid production. Using Process II, the highest copper, chromium and arsenic removal rates (96%, 92% and 98%, respectively) were obtained by Fomitopsis palustris. Process II could be a very valuable method for metal removal from CCA-treated wood when F. palustris is used. Our results also suggest that oxalic acid produced from fungus can be used as an alternative to commercial oxalic acid.