Taxonomic and Predictive Functional Profile of Hydrocarbonoclastic Bacterial Consortia Developed at Three Different Temperatures.

Microbial community exhibit shift in composition in response to temperature variation. We report crude oil-degrading activity and high-throughput 16S rRNA gene sequencing (metagenome) profiles of four bacterial consortia enriched at three different temperatures in crude oil-amended Bushnell-Hass Medium from an oily sludge sediment. The consortia were referred to as O (4 ± 2 â„ƒ in 3% w/v crude oil), A (25 ± 2 â„ƒ in 1% w/v crude oil), H (25 ± 2 â„ƒ in 3% w/v crude oil), and X (45 ± 2 â„ƒ in 3% w/v crude oil). The hydrocarbon-degrading activity was highest for consortium A and H and lowest for consortium O. The metagenome profile revealed the predominance of Proteobacteria (62.12-1.25%) in each consortium, followed by Bacteroidota (18.94-37.77%) in the consortium O, A, and H. Contrarily, consortium X comprised 7.38% Actinomycetota, which was essentially low (< 0.09%) in other consortia, and only 0.41% Bacteroidota. The PICRUSt-based functional analysis predicted major functions associated with the metabolism and 5060 common KEGG Orthology (KOs). A total of 296 KOs were predicted exclusively in consortium X. Additionally, 247 KOs were predicted from xenobiotic biodegradation pathways. This study found that temperature had a stronger influence on the composition and function of the bacterial community than crude oil concentration.

Dynamics and prevalence of specific hydrocarbonoclastic bacterial population with respect to nutrient treatment levels in crude oil sludge.

The bacterial community composition in soil sediments changes with respect to nutrient concentrations and environmental conditions. Reports on the correlation between bacterial populations and inorganic nutrient concentrations in oily sediments are limited. The present time series study reports the prevalence of specific hydrocarbon-degrading bacterial communities in nutrient-treated oily sludge microcosms. The hydrocarbon degradation was maximum at 625 µg nitrogen (N) and 62.5 µg phosphorus (P)/g sludge sediment. The 16S rRNA gene-based DGGE analyses revealed noticeable changes in bacterial community composition with time and levels of nutrient treatment. BLASTn analysis of the 16S rRNA gene clone sequence showed the abundance of γ-Proteobacteria (44%), α-Proteobacteria (16%), ß-Proteobacteria (10%), CFB (4%), and unidentified bacterial clones (26%). The catechol 1,2-dioxygenase (C12O) and catechol 2,3-dioxygenase (C23O) gene clones were affiliated to the genus Sphingomonas, highlighting the vital role of Sphingomonas in aromatic hydrocarbon degradation. The quantity of the 16S rRNA gene and the alkane hydroxylase (alkB) gene reached maximum levels in extended duration microcosms treated with 625 µg N and 62.5 µg P/g sludge sediment. In contrast, the C12O gene reached its highest abundance at a low N concentration.

Efficiency and kinetics of Assam crude oil degradation by Pseudomonas aeruginosa and Bacillus sp.

We report kinetics of Assam crude oil degradation by Pseudomonas aeruginosa AKS1 and Bacillus sp. AKS2, both isolated from Assam refinery sediments. The isolates exhibited appreciable degrees of hydrophobicity, emulsification index and biosurfactant production. Crude oil degradation efficiency of isolates was assessed in (1) liquid medium amended with 1% v/v crude oil and (2) microcosm sediments (125 mg crude oil/ 10 g sand). In liquid culture, biodegradation rate (k) and half-life (t1/2) values were found to be 0.038 day-1 and 18.09 days for P. aeruginosa AKS1, and 0.020 day-1 and 33.97 days in case of Bacillus sp. AKS2, respectively. In microcosm sediments, the estimated k and t 1/2 values were 0.014 day-1 and 50 days for P. aeruginosa AKS1, and 0.011 day-1 and 61.34 days in case of Bacillus sp. AKS2. The level of nutrient treatment in microcosm sand sediment was 125 µg N and 62.5 µg P/g sediment in case of P. aeruginosa AKS1 and 375 µg N and 37.5 µg P/g sediment in case of Bacillus sp. AKS2. In microcosms without inorganic nutrients, values of k and t1/2 were found to be 0.007 day-1 and 100 days for P. aeruginosa AKS1 and for Bacillus sp. AKS2, the respective values were 0.005 day-1 and 150.68 days. Our data provides important information for predictive hydrocarbon degradation in liquid medium and contaminated sediments.

Kinetics of hydrocarbon degradation by a newly isolated heavy metal tolerant bacterium Novosphingobium panipatense P5:ABC.

This study report kinetics of PAHs and crude oil degradation by a newly isolated multiple heavy metal tolerant Novosphingobium panipatense P5:ABC. The isolate showed hydrocarbon degrading enzyme activities namely alkane hydroxylase, catechol 1,2-dioxygenase and catechol 2,3-dioxygenase. The level of C23O activity was 9.63 times higher than C12O thus suggesting active involvement of meta-cleavage pathway. The data of biodegradation of hydrocarbons fitted well to the first order kinetic model. The degradation rate was highest for phenanthrene followed by crude oil, and fluoranthene. We have further reported the estimate of fundamental kinetic parameters, half-saturation constant (Ks) and maximum degradation rates (Vmax) for biodegradation of phenanthrene and fluoranthene. Overall characterization underscores the potential of Novosphingobium in bioremediation of crude oil polluted sites.

Hydrocarbon degradation potential and competitive persistence of hydrocarbonoclastic bacterium Acinetobacter pittii strain ABC.

Acinetobacter pittii strain ABC was isolated from oily sludge sediments and characterized with regard to utilization/degradation of hydrocarbons and competitive persistence in hydrocarbon-amended media. The isolate grew in both aliphatic- and aromatic hydrocarbon-amended Bushnell-Haas medium (BHM). When incubated in 1% (v/v) Assam crude oil-amended BHM for 5 and 10 days, this strain was able to degrade 88% and 99.8% of the n-hexane extractable crude oil components, respectively. The isolate showed appreciable emulsification index (E24 65.26 ± 1.2%), hydrophobicity (60.88 ± 3.5%) and produced lipopeptide biosurfactant (0.57 g L-1). The isolate was able to tolerate heavy metal salts at concentrations reported in crude oil-polluted sediments from Assam. A 16S rDNA DGGE-based screening showed the persistence of A. pittii strain ABC in hydrocarbon-amended microcosms co-inoculated with other hydrocarbonoclastic bacterial strains (Pseudomonas aeruginosa AKS1, Bacillus sp. AKS2, Arthrobacter sp. BC1, and Novosphingobium panipatense P5:ABC), each isolated from the same oily sludge sediment. These findings indicate A. pittii strain ABC as a potential agent for the bioremediation of crude oil-polluted environment.

Draft Genome Sequence of Novosphingobium panipatense Strain P5:ABC, Isolated from Hydrocarbon-Contaminated Soil from Noonmati Refinery, Assam, India.

Novosphingobium panipatense P5:ABC is a hydrocarbon-degrading bacterium isolated from petroleum-contaminated soil. Here, we present the 5.74-Mb draft genome sequence with 5,206 genes and an average G+C content of 64.7%. The genomic information will improve our understanding of the diversity of N. panipatense and the mechanisms of microbe-based hydrocarbon degradation.

Draft Genome Sequence of the Hydrocarbon-Degrading Bacterium Acinetobacter pittii Strain ABC Isolated from Noonmati Refinery, Assam, India.

We report here the 3.84-Mb draft genome sequence of hydrocarbon-degrading Acinetobacter pittii strain ABC isolated from oil-contaminated soil in Guwahati, India. The genome sequence contains 3,602 coding sequences and a G+C content of 38.83%. This is the first report of the genome sequence of an Acinetobacter pittii from an oil-contaminated environment.

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments.

Microbial remediation of oil polluted habitats remains one of the foremost methods for restoration of petroleum hydrocarbon contaminated environments. The development of effective bioremediation strategies however, require an extensive understanding of the resident microbiome of these habitats. Recent developments such as high-throughput sequencing has greatly facilitated the advancement of microbial ecological studies in oil polluted habitats. However, effective interpretation of biological characteristics from these large datasets remain a considerable challenge. In this study, we have implemented recently developed bioinformatic tools for analyzing 65 16S rRNA datasets from 12 diverse hydrocarbon polluted habitats to decipher metagenomic characteristics of the resident bacterial communities. Using metagenomes predicted from 16S rRNA gene sequences through PICRUSt, we have comprehensively described phylogenetic and functional compositions of these habitats and additionally inferred a multitude of metagenomic features including 255 taxa and 414 functional modules which can be used as biomarkers for effective distinction between the 12 oil polluted sites. Additionally, we show that significantly over-represented taxa often contribute to either or both, hydrocarbon degradation and additional important functions. Our findings reveal significant differences between hydrocarbon contaminated sites and establishes the importance of endemic factors in addition to petroleum hydrocarbons as driving factors for sculpting hydrocarbon contaminated bacteriomes.

Kinetics of nutrient enhanced crude oil degradation by Pseudomonas aeruginosa AKS1 and Bacillus sp. AKS2 isolated from Guwahati refinery, India.

Bacterial degradation of crude oil in response to nutrient treatments has been vastly studied. But there is a paucity of information on kinetic parameters of crude oil degradation. Here we report the nutrient stimulated kinetic parameters of crude oil degradation assessed in terms of CO2 production and oil removal by Pseudomonas aeruginosa AKS1 and Bacillus sp. AKS2. The hydrocarbon degradation rate of P. aeruginosa AKS1 in oil only amended sediment was 10.75 ± 0.65 µg CO2-C g(-1) sediment day(-1) which was similar to degradation rate in sediments with no oil. In presence of both inorganic N & P, the degradation rate increased to 47.22 ± 1.32 µg CO2-C g(-1) sediment day(-1). The half-saturation constant (Ks) and maximum degradation rate (Vmax) for P. aeruginosa AKS1 under increasing N and saturating P concentration were 13.57 ± 0.53 µg N g(-1) sediment and 39.36 ± 1.42 µg CO2-C g(-1) sediment day(-1) respectively. The corresponding values at increasing P and a constant N concentration were 1.60 ± 0.13 µg P g(-1) sediment and 43.90 ± 1.03 µg CO2-C g(-1) sediment day(-1) respectively. Similarly the degradation rate of Bacillus sp. AKS2 in sediments amended with both inorganic nutrients N & P was seven fold higher than the rates in oil only or nutrient only treated sediments. The Ks and Vmax estimates of Bacillus sp. AKS2 under increasing N and saturating P concentration were 9.96 ± 1.25 µg N g(-1) sediment and 59.96 ± 7.56 µg CO2-C g(-1) sediment day(-1) respectively. The corresponding values for P at saturating N concentration were 0.46 ± 0.24 µg P g(-1) sediment and 63.63 ± 3.54 µg CO2-C g(-1) sediment day(-1) respectively. The rates of CO2 production by both isolates were further stimulated when oil concentration was increased above 12.5 mg g(-1) sediment. However, oil degradation activity declined at oil concentration above 40 mg g(-1) sediment when treated with constant nutrient: oil ratio. Both isolates exhibited alkane hydroxylase activity but aromatic degrading catechol 1, 2-dioxygenase and catechol 2, 3-dioxygenase activities were shown by P. aeruginosa AKS1 only.

Draft Genome Sequence of Hydrocarbon-Degrading Enterobacter cloacae Strain S1:CND1, Isolated from Crude Oil-Contaminated Soil from the Noonmati Oil Refinery, Guwahati, Assam, India.

We report here the 4.57-Mb draft genome sequence of hydrocarbon-degrading Enterobacter cloacae strain S1:CND1 isolated from oil-contaminated soil in Guwahati, India. S1:CND1 contains 4,205 coding sequences and has a G+C content of 57.45%. This is the first report of the genome sequence of an E. cloacae adapted to an oil-contaminated environment.

Draft Genome Sequence of Hydrocarbon-Degrading Staphylococcus saprophyticus Strain CNV2, Isolated from Crude Oil-Contaminated Soil from the Noonmati Oil Refinery, Guwahati, Assam, India.

Here, we report the 2.6 Mb draft genome sequence of hydrocarbon-degrading Staphylococcus saprophyticus strain CNV2, isolated from oil-contaminated soil in Guwahati, India. CNV2 contains 2,545 coding sequences and has a G+C content of 33.2%. This is the first report of the genome sequence of an S. saprophyticus adapted to an oil-contaminated environment.