@article {8472, title = {Marinobacterium lacunae sp. nov. isolated from estuarine sediment [Next Gen Genomics Facility]}, journal = {Arch Microbiol}, volume = {205}, year = {2023}, month = {2023 Jul 22}, pages = {294}, abstract = {

A novel motile bacterium was isolated from a sediment sample collected in Kochi backwaters, Kerala, India. This bacterium is Gram negative, rod shaped, 1.0-1.5\ {\textmu}m wide, and 2.0-3.0\ {\textmu}m long. It was designated as strain AK27. Colonies were grown on marine agar displayed circular, off-white, shiny, moist, translucent, flat, margin entire, 1-2\ mm in diameter. The major fatty acids identified in this strain were C ω7c, C, and summed in feature 3. The composition of polar lipids in the strain AK27 included phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified amino lipid, two unidentified aminophospholipids, two unidentified phospholipids, and six unidentified lipids. The genomic DNA of strain AK27 exhibited a G+C content of 56.4\ mol\%. Based on the analysis of 16S rRNA gene sequence, strain AK27 showed sequence similarity to M. ramblicola D7 and M. zhoushanense WM3 as 98.99\% and 98.58\%, respectively. Compared to other type strains of the Marinobacterium genus, strain AK27 exhibited sequence similarities ranging from 91.7\% to 96.4\%. When compared to Marinobacterium zhoushanense WM3 and Marinobacterium ramblicola D7, strain AK27 exhibited average nucleotide identity values of 80.25\% and 79.97\%, and dDDH values of 22.9\% and 22.6\%, respectively. The genome size of the strain AK27 was 4.55\ Mb, with 4,229 coding sequences. Based on the observed phenotypic and chemotaxonomic features, and the results of phylogenetic and phylogenomic analysis, this study proposes the classification of strain AK27 as a novel species within the genus Marinobacterium. The proposed name for this novel species is Marinobacterium lacunae sp. nov.

}, keywords = {Agar, Alteromonadaceae, Cardiolipins, Phylogeny, RNA, Ribosomal, 16S}, issn = {1432-072X}, doi = {10.1007/s00203-023-03627-4}, author = {Tanuku, Srinivas Naga Radha and Pinnaka, Anil Kumar and Behera, Swarnaprava and Singh, Aditya and Pydi, Sudharani and Vasudeva, Gunjan and Vaidya, Bhumika and Sharma, Gunjan and Ganta, Sampath Kumar and Garbhapu, Naveen Sagar} } @article {8889, title = {Transcriptional transitions in Alphonso mango (Mangifera indica L.) during fruit development and ripening explain its distinct aroma and shelf life characteristics [Next Gen Genomics Facility]}, journal = {Sci Rep}, volume = {7}, year = {2017}, month = {2017 Aug 18}, pages = {8711}, abstract = {

Alphonso is known as the "King of mangos" due to its unique flavor, attractive color, low fiber pulp and long shelf life. We analyzed the transcriptome of Alphonso mango through Illumina sequencing from seven stages of fruit development and ripening as well as flower. Total transcriptome data from these stages ranged between 65 and 143 Mb. Importantly, 20,755 unique transcripts were annotated and 4,611 were assigned enzyme commission numbers, which encoded 142 biological pathways. These included ethylene and flavor related secondary metabolite biosynthesis pathways, as well as those involved in metabolism of starch, sucrose, amino acids and fatty acids. Differential regulation (p-value <= 0.05) of thousands of transcripts was evident in various stages of fruit development and ripening. Novel transcripts for biosynthesis of mono-terpenes, sesqui-terpenes, di-terpenes, lactones and furanones involved in flavor formation were identified. Large number of transcripts encoding cell wall modifying enzymes was found to be steady in their expression, while few were differentially regulated through these stages. Novel 79 transcripts of inhibitors of cell wall modifying enzymes were simultaneously detected throughout Alphonso fruit development and ripening, suggesting controlled activity of these enzymes involved in fruit softening.

}, keywords = {Cell Wall, Enzyme Inhibitors, Flowers, Fruit, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Gene Ontology, Genes, Plant, Glycoside Hydrolases, Mangifera, Odorants, Phylogeny, Reproducibility of Results, RNA, Messenger, Transcription, Genetic, Transcriptome}, issn = {2045-2322}, doi = {10.1038/s41598-017-08499-5}, author = {Deshpande, Ashish B and Anamika, Krishanpal and Jha, Vineet and Chidley, Hemangi G and Oak, Pranjali S and Kadoo, Narendra Y and Pujari, Keshav H and Giri, Ashok P and Gupta, Vidya S} } @article {458, title = {Proteomics and Metabolomics Analyses to Elucidate the Desulfurization Pathway of Chelatococcus sp.[Mass Spectrometry]}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016}, pages = {e0153547}, abstract = {

Desulfurization of dibenzothiophene (DBT) and alkylated DBT derivatives present in transport fuel through specific cleavage of carbon-sulfur (C-S) bonds by a newly isolated bacterium Chelatococcus sp. is reported for the first time. Gas chromatography-mass spectrometry (GC-MS) analysis of the products of DBT degradation by Chelatococcus sp. showed the transient formation of 2-hydroxybiphenyl (2-HBP) which was subsequently converted to 2-methoxybiphenyl (2-MBP) by methylation at the hydroxyl group of 2-HBP. The relative ratio of 2-HBP and 2-MBP formed after 96 h of bacterial growth was determined at 4:1 suggesting partial conversion of 2-HBP or rapid degradation of 2-MBP. Nevertheless, the enzyme involved in this conversion process remains to be identified. This production of 2-MBP rather than 2-HBP from DBT desulfurization has a significant metabolic advantage for enhancing the growth and sulfur utilization from DBT by Chelatococcus sp. and it also reduces the environmental pollution by 2-HBP. Furthermore, desulfurization of DBT derivatives such as 4-M-DBT and 4, 6-DM-DBT by Chelatococcus sp. resulted in formation of 2-hydroxy-3-methyl-biphenyl and 2-hydroxy -3, 3/- dimethyl-biphenyl, respectively as end product. The GC and X-ray fluorescence studies revealed that Chelatococcus sp. after 24 h of treatment at 37{\textdegree}C reduced the total sulfur content of diesel fuel by 12\% by per gram resting cells, without compromising the quality of fuel. The LC-MS/MS analysis of tryptic digested intracellular proteins of Chelatococcus sp. when grown in DBT demonstrated the biosynthesis of 4S pathway desulfurizing enzymes viz. monoxygenases (DszC, DszA), desulfinase (DszB), and an NADH-dependent flavin reductase (DszD). Besides, several other intracellular proteins of Chelatococcus sp. having diverse biological functions were also identified by LC-MS/MS analysis. Many of these enzymes are directly involved with desulfurization process whereas the other enzymes/proteins support growth of bacteria at an expense of DBT. These combined results suggest that Chelatococcus sp. prefers sulfur-specific extended 4S pathway for deep-desulphurization which may have an advantage for its intended future application as a promising biodesulfurizing agent.

}, keywords = {Air Pollutants, Bacterial Proteins, Beijerinckiaceae, Gas Chromatography-Mass Spectrometry, Gasoline, Metabolomics, Phylogeny, Proteomics, Signal Transduction, Sulfur}, issn = {1932-6203}, doi = {10.1371/journal.pone.0153547}, author = {Bordoloi, Naba K and Bhagowati, Pabitra and Chaudhuri, Mihir K and Mukherjee, Ashis K} } @article {8356, title = {Lunatimonas lonarensis gen. nov., sp. nov., a haloalkaline bacterium of the family Cyclobacteriaceae with nitrate reducing activity [Next Gen Genomics Facility]}, journal = {Syst Appl Microbiol}, volume = {37}, year = {2014}, month = {2014 Feb}, pages = {10-6}, abstract = {

Novel pinkish-orange pigmented, Gram-negative staining, half-moon shaped, non-motile, strictly aerobic strains designated AK24(T) and AK26 were isolated from water and sediment samples of Lonar Lake, Buldhana district, Maharahstra, India. Both strains were positive for oxidase, catalase and β-galactosidase activities. The predominant fatty acids were iso-C15:0 (41.5\%), anteiso-C15:0 (9.7\%), iso-C17:0 3OH (9.6\%), iso-C17:1 ω9c (10.2\%) and C16:1 ω7c/C16:1 ω6c/iso-C15:0 2OH (summed feature 3) (14.4\%). The strains contained MK-7 as the major respiratory quinone, and phosphatidylethanolamine and five unidentified lipids as the polar lipids. Blast analysis of the 16S rRNA gene sequence of strain AK24(T) showed that it was closely related to Aquiflexum balticum, with a pair-wise sequence similarity of 91.6\%, as well as to Fontibacter ferrireducens, Belliella baltica and Indibacter alkaliphilus (91.3, 91.2 and 91.2\% pair-wise sequence similarity, respectively), but it only had between 88.6 and 91.0\% pair-wise sequence similarity to the rest of the family members. The MALDI-TOF assay reported no significant similarities for AK24(T) and AK26, since they potentially represented a new species. A MALDI MSP dendrogram showed close similarity between the two strains, but they maintained a distance from their phylogenetic neighbors. The genome of AK24(T) showed the presence of heavy metal tolerance genes, including the genes providing resistance to arsenic, cadmium, cobalt and zinc. A cluster of heat shock resistance genes was also found in the genome. Two lantibiotic producing genes, LanR and LasB, were also found in the genome of AK24(T). Strains AK24(T) and AK26 were very closely related to each other with 99.5\% pair-wise sequence similarity. Phylogenetic analysis indicated that the strains were members of the family Cyclobacteriaceae and they clustered with the genus Mariniradius, as well as with the genera Aquiflexum, Cecembia, Fontibacter, Indibacter, and Shivajiella. DNA-DNA hybridization between strains AK24(T) and AK26 showed a relatedness of 82\% and their rep-PCR banding patterns were very similar. Based on data from the current polyphasic study, it is proposed that the isolates be placed in a new genus and species with the name Lunatimonas lonarensis gen. nov., sp. nov. The type strain of Lunatimonas lonarensis is AK24(T) (=JCM 18822(T)=MTCC 11627(T)).

}, keywords = {Bacterial Typing Techniques, Bacteroidetes, Cluster Analysis, DNA, Bacterial, DNA, Ribosomal, Fatty Acids, Fresh Water, Genome, Bacterial, Geologic Sediments, India, Molecular Sequence Data, Nitrates, Oxidation-Reduction, Phospholipids, Phylogeny, Quinones, RNA, Ribosomal, 16S, Sequence Analysis, DNA}, issn = {1618-0984}, doi = {10.1016/j.syapm.2013.10.003}, author = {Srinivas, T N R and Aditya, S and Bhumika, V and Kumar, P Anil} }