Xylanimonas oleitrophica sp. nov., a novel petroleum hydrocarbon degrading bacterium isolated from an Indian oil reservoir.

A novel Gram-stain-positive, aerobic, non-spore-forming, and rod-shaped bacterium designated as PW21was isolated from produced water sampled from an oil reservoir in Limbodara, Gujarat, India. Growth occurred at 30-45 °C (optimum 37 °C), at pH 6.5-9.5 (optimum pH 8.5) and in the presence of 0.5-5.0% (w/v) NaCl [optimum, 3% (w/v)]. Phylogenetic analysis based on the 16S rRNA gene sequences showed that PW21T belonged to the class Actinobacteria, order Actinomycetales, family Promicromonosporaceae, and genus Xylanimonas, with the highest sequence similarity to Isoptericola cucumis AP38 (97.95% with 98.8% completeness), followed by Xylanimonas pachnodae NBRC 107,786T (97.82%) and Xylanimonas allomyrinae 2JSPR-7T(97.75%) with 100% completeness for the mentioned strains of Xylanimonas. The genome size of PW21T was 3.4 Mbp with a G+C content of 73.0 mol% (draft genome sequence). The average nucleotide identity (ANI) value of the draft genomes between PW21T and related species were found in between 76.99 and 78.93%. Major cellular fatty acids (> 10% of total fatty acids) of PW21Twere iso-C15:0, anteiso-C15:0, and C16:0. Phylogenetic, physiological, and biochemical characterisation identified strain PW21T (= KCTC 49,338T = JCM 33,795T = MCC 3936T) as a novel species of the genus Xylanimonas, and hence, name Xylanimonas oleitrophica sp. nov. PW21T is proposed.

A novel, enantioselective, thermostable recombinant hydantoinase to aid the synthesis of industrially valuable non-proteinogenic amino acids.

Overexpression of a novel hydantoinase (hyuH) from P. aeruginosa (MCM B-887) in E. coli yielded optically pure carbamoyl amino acids. The use of optically pure carbamoyl amino acids as substrates facilitates the synthesis of non-proteinogenic amino acids. The enzyme hyuH shared a maximum of 92 % homology with proven hydantoinase protein sequences from the GenBank database, highlighting its novelty. Expression of hydantoinase gene was improved by >150 % by overexpressing it as a fusion protein in specialized E. coli CODON + host cells, providing adequate machinery for effective translation of the GC-rich gene. The presence of distinct residues in the substrate binding and active site of MCM B-887 hydantoinase enzyme explained its unique and broad substrate profile desirable for industrial applications. The purified enzyme, with a specific activity of 53U/mg of protein, was optimally active at 42 °C and pH 9.0 with a requirement of 2 mM Mn2+ ions. Supplementation of 500 mM of Na-glutamate enhanced the thermostability of the enzyme by more than 200 %.

Illustration of the microbial community selected by optimized process and nutritional parameters resulting in enhanced biomethanation of rice straw without thermo-chemical pretreatment.

Effects of different process and nutritional parameters on microbial community structure and function were investigated to enhance the biomethanation of rice straw without any thermochemical pre-treatment. The study was performed in a mesophilic anaerobic digester with cattle dung slurry as inoculum. The highest methane yield of 274 ml g-1 volatile solids was obtained from particulate rice straw (1 mm size, 7.5% solids loading rate) at 37 °C, pH-7, when supplemented with urea (carbon: nitrogen ratio, 25:1) and zinc as trace element (100 µM) at 21 days hydraulic retention time. The optimization of conditions selected Clostridium, Bacteroides, and Ruminococcus as dominant hydrolytic bacteria and Methanosarcina as the methanogen. Analysis of metagenome and metatranscriptome revealed wide array of bacterial lignocellulolytic enzymes that efficiently hydrolyzed the rice straw. The methane yield was >80% of the theoretical yield, making this green process a sustainable choice for efficient extraction of energy from rice straw.

Meta-omics based analyses of microbiome involved in biomethanation of rice straw in a thermophilic anaerobic bioreactor under optimized conditions.

Biomethanation of rice straw was performed at 55 °C without thermochemical pretreatment using cattle dung supplemented with Methanothermobacter thermautotrophicus strains. Methane yield of 323 ml g-1 VS obtained under optimized conditions such as particle size (1 mm), carbon to nitrogen ratio (15:1), substrate to inoculum ratio (1:1), organic loading rate (7.5% w/v) and hydraulic retention time (20 days), was one of the highest ever reported from rice straw. Metagenome analysis revealed several putative novel taxa among resident microbes. The genomes of Clostridium, Hungateiclostridium, Alkaliphilus, Anaerocolumna, Olsenella, Paenibacillus, Pseudoclostridium, Tepidanaerobacter and Turicibacter were recovered as metagenome assisted genomes. Clostridium spp. and M. thermautotrophicus were the dominant hydrolytic and methanogenic microbes, respectively. Syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis was found to be the major pathway for methane production. Efficient thermophilic biomethanation of rice straw without thermochemical pretreatment using cattle dung supplemented with M. thermautotrophicus is reported for the first time.

Process parameter optimization for hydantoinase-mediated synthesis of optically pure carbamoyl amino acids of industrial value using Pseudomonas aeruginosa resting cells.

Hydantoinase-mediated enzymatic synthesis of optically pure carbamoyl amino acids was investigated as an environmentally friendly, energy-efficient alternative to the otherwise energy-intensive, polluting chemical synthesis. Hydantoinase-producing bacterial strain was identified as Pseudomonas aeruginosa by 16S rRNA gene sequencing and biochemical profiling using the BIOLOG Microbial Identification System. Hydantoinase activity was assessed using hydantoin analogs and 5-monosubstituted hydantoins as substrates in a colorimetric assay. The hydantoinase gene was PCR amplified using gene-specific primers and sequenced on an automated gene analyzer. Hydantoinase gene sequence of P. aeruginosa MCM B-887 revealed maximum homology of only 87 % with proven hydantoinase gene sequences in GenBank. MCM B-887 resting cells converted >99 % of substrate into N-carbamoyl amino acids under optimized condition at 42 °C, pH 8.0, and 100 mM substrate concentration in <120 min. Hydantoin hydrolyzing activity was D-selective and included broad substrate profile of 5-methyl hydantoin, 5-phenyl hydantoin, 5-hydroxyphenyl hydantoin, o-chlorophenyl hydantoin, as well as hydantoin analogs such as allantoin, dihydrouracil, etc. MCM B-887 resting cells may thus be suitable for bio-transformations leading to the synthesis of optically pure, unnatural carbamoyl amino acids of industrial importance.

Diversity and physiology of culturable bacteria associated with a coastal Antarctic ice core.

Microbiological studies of polar ice at different depths may provide important comparisons, as they preserve records of microbial cells and past climate. In this study, we examined bacterial abundance, diversity and glaciochemical composition from three depths of an ice core from coastal Dronning Maud Land, East Antarctica. Higher bacterial abundance corresponded with high in situ sea-salt Na(+) and dust concentration, suggesting that bacteria might have been transported and deposited into ice along with dust particles and marine aerosols. Fourteen bacterial isolates belonging to the genera Methylobacterium, Brevundimonas, Paenibacillus, Bacillus and Micrococcus were retrieved. Frequent isolation of similar bacterial genera from different cold environments suggests that they possess features that enable survival and metabolism for extended periods of time at sub-zero temperatures. The highest number and diversity of recoverable bacteria was obtained from 49 m depth corresponding to 1926 AD and consisted of bacteria from 4 different genera whereas at 11 m (1989 AD) and 33 m (1953 AD) samples only species belonging to the genera Bacillus was recovered. Among the Bacillus species, Bacillus aryabhattai which has been reported only from the upper stratosphere, was isolated and is the first record from the Earth's surface. Methylobacterium was the most dominant genera at 49 m depth and its prevalence is attributable to a combination of high in situ methanesulfonate concentration, specialized metabolism and environmental hardiness of Methylobacterium. Some of the isolated bacteria were found to respire and grow using methanesulfonate, suggesting that they may utilize this substrate to sustain growth in ice. In addition, NO(3)(-) (2.93-3.69 µM), NH(4)(+) (1.45-3.90 µM) and PO(4)(3-) (0.01-0.75 µM) present in the ice could be potential sources fueling bacterial metabolism in this environment. It could be deduced from the study that variation in bacterial abundance and diversity was probably associated with the prevailing in situ conditions in ice.

Characterization of plant-growth-promoting traits of Acinetobacter species isolated from rhizosphere of Pennisetum glaucum.

A total of 31 Acinetobacter isolates were obtained from the rhizosphere of Pennisetum glaucum and evaluated for their plant-growth-promoting traits. Two isolates, namely Acinetobacter sp. PUCM1007 and A. baumannii PUCM1029, produced indole acetic acid (10-13 microgram/ml). A total of 26 and 27 isolates solubilized phosphates and zinc oxide, respectively. Among the mineral-solubilizing strains, A. calcoaceticus PUCM1006 solubilized phosphate most efficiently (84 mg/ml), whereas zinc oxide was solubilized by A. calcoaceticus PUCM1025 at the highest solubilization efficiency of 918%. All the Acinetobacter isolates, except PUCM1010, produced siderophores. The highest siderophore production (85.0 siderophore units) was exhibited by A. calcoaceticus PUCM1016. Strains PUCM1001 and PUCM1019 (both A. calcoaceticus) and PUCM1022 (Acinetobacter sp.) produced both hydroxamate- and catechol-type siderophores, whereas all the other strains only produced catechol-type siderophores. In vitro inhibition of Fusarium oxysporum under iron-limited conditions was demonstrated by the siderophore-producing Acinetobacter strains, where PUCM1018 was the most potent inhibitor of the fungal phytopathogen. Acinetobacter sp. PUCM1022 significantly enhanced the shoot height, root length, and root dry weights of pearl millet seedlings in pot experiments when compared with controls, underscoring the plant-growth-promoting potential of these isolates.