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Dyella agri sp. nov., isolated from reclaimed grassland soil
Chaudhary, Dhiraj Kumar,Kim, Jaisoo Microbiology Society 2017 International journal of systematic and evolutiona Vol.67 No.10
<P>A novel strain, DKC-1(T), was isolated from reclaimed grassland soil and was characterized taxonomically by a polyphasic approach. Strain DKC-1(T) was a Gram-staining-negative, light-yellow-coloured and rod shaped bacterium, motile with polar flagellum. It was able to grow at 20-37 degrees C, at pH 4.5-9.0 and with 0-3 % (w/v) NaCl concentration. Based on the 16S rRNA gene sequence analysis, strain DKC-1T formed a Glade within the members of the genus Dyella and showed highest sequence similarities to Dyella japonica XD53(T) (98.36 %), Rhodanobacter aciditrophus sjH1(T) (97.92 %), Rhodanobacter koreensis THG-DD7(T) (97.74 %), Dyella kyungheensis THG-B117(T) (97.65 %) and Rhodanobacter terrae GP18-1(T) (97.40 %). The only respiratory quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyl-N-methylethanolamine. The predominant fatty acids of strain DKC-1(T) were iso-C-16:0, iso-C-15:0, summed feature 9 (iso-C-17:1 omega 9c and/or C-16:0 10-methyl), iso-C-17:0, iso-C-11:0 3-OH and iso-C-11:0. The genomic DNA G+C content of this novel strain was 63.1 mol%. The DNA DNA relatedness between strain DKC-1(T) and its reference strains (a japonica XD53(T), R. aciditrophus sjH1(T), R. koreensis THG-DD7(T), a kyungheensis THG-B117(T) and R. terrae GP18-1(T)) was 52.3, 44.7, 38.7, 49.0 and 32.7 %, respectively, which falls below the threshold value of 70 % for the strain to be considered as novel. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain DKC-1(T) represents a novel species of the genus Dyella, for which the name Dyella agri sp. nov. is proposed. The type strain is DKC-1(T) (=KEMB 9005-57(T)=KACC 191 76(T)=JCM 31925(T)).</P>
Chaudhary Dhiraj Kumar,Kim Sang-Eon,Park Hye-Jin,Kim Kyoung-Ho 한국미생물·생명공학회 2024 Journal of microbiology and biotechnology Vol.34 No.6
The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in immune defense, nutrient absorption, and overall health. While the intestine's microbiome has been well-studied, there has been limited research investigating the stomach and hepatopancreas. The present study addresses this gap by profiling the bacterial community in these interconnected GI segments of Pacific whiteleg shrimp. To this end, shrimp samples were collected from a local aquaculture farm in South Korea, and 16S rRNA gene amplicon sequencing was performed. The results revealed significant variations in bacterial diversity and composition among GI segments. The stomach and hepatopancreas exhibited higher Proteobacteria abundance, while the intestine showed a more diverse microbiome, including Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia. Genera such as Oceaniovalibus, Streptococcus, Actibacter, Ilumatobacter, and Litorilinea dominated the intestine, while Salinarimonas, Sphingomonas, and Oceaniovalibus prevailed in the stomach and hepatopancreas. It is particularly notable that Salinarimonas, which is associated with nitrate reduction and pollutant degradation, was prominent in the hepatopancreas. Overall, this
Dhiraj Kumar Chaudhary,Rishikesh Bajagain,Seung-Woo Jeong,Jaisoo Kim 대한환경공학회 2020 Environmental Engineering Research Vol.25 No.3
A large residual fraction of aliphatic components of diesel prevails in soil, which has adverse effects on the environment. This study identified the most bio-recalcitrant aliphatic residual fraction of diesel through total petroleum-hydrocarbon fractional analysis. For this, the strain Acinetobacter sp. K-6 was isolated, identified, and characterized and investigated its ability to degrade diesel and n-alkanes (C18, C20, and C22). The removal efficiency was analysed after treatment with bacteria and nutrients in various soil microcosms. The fractional analysis of diesel degradation after treatment with the bacterial strains identified C18-C22 hydrocarbons as the most bio-recalcitrant aliphatic fraction of diesel oil. Acinetobacter sp. K-6 degraded 59.2% of diesel oil and 56.4% of C18-C22 hydrocarbons in the contaminated soil. The degradation efficiency was further improved using a combinatorial approach of biostimulation and bioaugmentation, which resulted in 76.7% and 73.7% higher degradation of diesel oil and C18-C22 hydrocarbons, respectively. The findings of this study suggest that the removal of mid-length, non-volatile hydrocarbons is affected by the population of bio-degraders and the nutrients used in the process of remediation. A combinatorial approach, including biostimulation and bioaugmentation, could be used to effectively remove large quantities of aliphatic hydrocarbons persisting for a longer period in the soil.