Diversity and PAH growth abilities of bacterial strains isolated from a contaminated soil in Slovakia

Analysis of bacterial communities of three cassava-based traditionally fermented Nigerian foods (abacha, fufu and garri)

Globally, cassava is an important food crop that contributes significantly to food security. In Nigeria, cassava can be traditionally processed into abacha (fermented strips), fufu (submerged-fermented porridge) and garri (solid-state fermented farinated granules) for human consumption. Despite the widespread consumption of these foods, there is a major knowledge gap in understanding their core bacterial diversity. This study, therefore, applied next-generation sequencing of 16S rRNA gene to delineate the bacterial diversity in abacha, fufu and garri. Amplicon sequence variants belonging to nine phyla were present in the three foods. Firmicutes dominated the bacterial community of abacha and fufu, whereas, Proteobacteria was the dominant phylum in garri. At genus level taxa, Lactococcus, Lysinibacillus and Pseudomonas dominated the bacterial community in abacha, fufu and garri, respectively. Other dominant phylotypes reported in the foods belonged to Bacillus, Clostridium sensu stricto (cluster 1), Cupriavidus, Enterobacter, Sphingomonas and Staphylococcus. To the best of our knowledge, Clostridium sensu stricto cluster 1 and Lysinibacillus in fufu, and Brevundimonas, Cupriavidus, Sphingomonas and Strenotrophomomas in garri are reported for the first time. Although some potential pathogenic genera were recorded, the foods contained potentially functional species that could be explored to improve artisanal food production, food security and safeguard consumer health.

Investigating the performance of an anaerobic baffled bioreactor for the biodegradation of alkaline-surfactant-polymer in oilfield water

The anaerobic baffled reactor (ABR) was used to treat alkaline-surfactant-polymer (ASP) flooding wastewater in the Daqing oilfield. With the ABR, hydraulic retention time (HRT)was reduced from 72  to 24 h, the bioreactor purification capability gradually improved. After the ABR running for 100 days, the removal rate of raw oil, suspended solid and surfactant reached 99.8%, 94.4% and 50%, respectively; alkali, polymer and viscosity were removed at a rate of about 16%, 7% and 20%, respectively. There were 39 kinds of organic materials detected by GCMS in the original water sample, while only 12 kinds of organics were left in the ABR outfall. The above results showed that the anaerobic, facultative anaerobic and aerobic compartment of ABR have strong capability of biodegrading petroleum pollution matter. Pyrosequencing analysis of the 16S rRNA indicated that Acinetobacter, Arcobacter, Pseudomonas and Paracoccus were the dominant bacteria genera present in the ABR reactor, among them Acinetobacter was the dominant species in the bacterial community.

In silico engineering of Pseudomonas metabolism reveals new biomarkers for increased biosurfactant production

BACKGROUND

Rhamnolipids, biosurfactants with a wide range of biomedical applications, are amphiphilic molecules produced on the surfaces of or excreted extracellularly by bacteria including Pseudomonas aeruginosa. However, Pseudomonas putida is a non-pathogenic model organism with greater metabolic versatility and potential for industrial applications.

METHODS

We investigate in silico the metabolic capabilities of P. putida for rhamnolipids biosynthesis using statistical, metabolic and synthetic engineering approaches after introducing key genes (RhlA and RhlB) from P. aeruginosa into a genome-scale model of P. putida. This pipeline combines machine learning methods with multi-omic modelling, and drives the engineered P. putida model toward an optimal production and export of rhamnolipids out of the membrane.

RESULTS

We identify a substantial increase in synthesis of rhamnolipids by the engineered model compared to the control model. We apply statistical and machine learning techniques on the metabolic reaction rates to identify distinct features on the structure of the variables and individual components driving the variation of growth and rhamnolipids production. We finally provide a computational framework for integrating multi-omics data and identifying latent pathways and genes for the production of rhamnolipids in P. putida.

CONCLUSIONS

We anticipate that our results will provide a versatile methodology for integrating multi-omics data for topological and functional analysis of P. putida toward maximization of biosurfactant production.

Regulations of essential amino acids and proteomics of bacterial endophytes Sphingomonas sp. Lk11 during cadmium uptake

Endophytic bacteria have been recently known for their potential to bioaccumulate metal from contaminated mediums. However, little is known about the physiological responses of phytohormone producing (gibberellins and auxins) endophytes during metal stressed environment. Endophytic bacteria Sphingomonas sp. LK11 was assessed for metals bioaccumulation and its physiological responses towards metal stress. The endophyte was grown in cadmium (Cd), zinc (Zn), aluminum (Al), manganese (Mn), and copper (Cu) contaminated mediums. The results revealed significantly higher endophytic growth potentials in Cd, Cu and Zn contaminations; however, the bio-accumulation rate of Cd was more prolific as compared to Zn and Cu. Interestingly, the SDS-PAGE profile showed increased expressions of proteins in Zn and Cu than in Cd. A similar attenuate response of amino acids was also observed for Cd than in case of Zn and Cu. Only asparagine, glutamate and proline showed significant impact in Cd while Cu and Zn had significantly higher responses of almost all amino acids. Detailed protein profile showed the activation of chaperone, antioxidative and detoxification proteins. Increased regulations of oxidoreductases, superoxide dismutase, thioredoxin, malate dehydrogenase, 2-oxoisovalerate dehydrogenase, 2-oxoisovalerate dehydrogenase, and dihydrolipoyl dehydrogenase were observed. The cellular defense-related protein responses were potent against Cd stress. The results conclude that Sphingomonas sp. LK11 reprogram its amino acids and proteomic expressions and maintain a steady growth during Cd stress. Using such phytohromones producing endophytic bacterium can be ideal approach to increase the phytoextraction potential of metal remediating plants. © 2014 Wiley Periodicals, Inc. Environ Toxicol 31: 887-896, 2016.

Biosurfactant production by Pseudomonas aeruginosa DSVP20 isolated from petroleum hydrocarbon-contaminated soil and its physicochemical characterization

Among 348 microbial strains isolated from petroleum hydrocarbon-contaminated soil, five were selected for their ability to produce biosurfactant based on battery of screening assay including hemolytic activity, surface tension reduction, drop collapse assay, emulsification activity, and cell surface hydrophobicity studies. Of these, bacterial isolate DSVP20 was identified as Pseudomonas aeruginosa (NCBI GenBank accession no. GQ865644) based on biochemical characterization and the 16S rDNA analysis, and it was found to be a potential candidate for biosurfactant production. Maximum biosurfactant production recorded by P. aeruginosa DSVP20 was 6.7 g/l after 72 h at 150 rpm and at a temperature of 30 °C. Chromatographic analysis and high-performance liquid chromatography-mass spectrometry (HPLC-MS) revealed that it was a glycolipid in nature which was further confirmed by nuclear magnetic resonance (NMR) spectroscopy. Bioremediation studies using purified biosurfactant showed that P. aeruginosa DSVP20 has the ability to degrade eicosane (97%), pristane (75%), and fluoranthene (47%) when studied at different time intervals for a total of 7 days. The results of this study showed that the P. aeruginosa DSVP20 and/or biosurfactant produced by this isolate have the potential role in bioremediation of petroleum hydrocarbon-contaminated soil.

Characterization of hydrocarbon-degrading and biosurfactant-producing Pseudomonas sp. P-1 strain as a potential tool for bioremediation of petroleum-contaminated soil

The Pseudomonas sp. P-1 strain, isolated from heavily petroleum hydrocarbon-contaminated soil, was investigated for its capability to degrade hydrocarbons and produce a biosurfactant. The strain degraded crude oil, fractions A5 and P3 of crude oil, and hexadecane (27, 39, 27 and 13% of hydrocarbons added to culture medium were degraded, respectively) but had no ability to degrade phenanthrene. Additionally, the presence of gene-encoding enzymes responsible for the degradation of alkanes and naphthalene in the genome of the P-1 strain was reported. Positive results of blood agar and methylene blue agar tests, as well as the presence of gene rhl, involved in the biosynthesis of rhamnolipid, confirmed the ability of P-1 for synthesis of glycolipid biosurfactant. 1H and 13C nuclear magnetic resonance, Fourier transform infrared spectrum and mass spectrum analyses indicated that the extracted biosurfactant was affiliated with rhamnolipid. The results of this study indicate that the P-1 and/or biosurfactant produced by this strain have the potential to be used in bioremediation of hydrocarbon-contaminated soils.