scholarly journals Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 456 ◽  
Author(s):  
Daniel Garrido-Sanz ◽  
Miguel Redondo-Nieto ◽  
María Guirado ◽  
Oscar Pindado Jiménez ◽  
Rocío Millán ◽  
...  
Keyword(s):  
Aromatic Hydrocarbons ◽  
Bacterial Consortium ◽  
Polluted Soil ◽  
Total Petroleum Hydrocarbons ◽  
Ring Cleavage ◽  
Rrna Gene ◽  
Initial Oxidation ◽  
Microbiome Composition ◽  
Genes Encoding ◽  
Aliphatic And Aromatic Hydrocarbons

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

Efficient biodegradation of naphthalene by a newly characterized indigenous Achromobacter sp. FBHYA2 isolated from Tehran Oil Refinery Complex

2012 ◽  
Vol 66 (3) ◽  
pp. 594-602 ◽  
Author(s):  
Sima Farjadfard ◽  
Seyyed Mehdi Borghei ◽  
Amir Hessam Hassani ◽  
Bagher Yakhchali ◽  
Mehdi Ardjmand ◽  
...  
Keyword(s):  
Aromatic Hydrocarbons ◽  
Optimal Growth ◽  
Sole Source ◽  
Growth Conditions ◽  
American Petroleum Institute ◽  
Oil Refinery ◽  
Rrna Gene ◽  
Significant Difference ◽  
Aliphatic And Aromatic Hydrocarbons ◽  
Achromobacter Sp

A bacterial strain, FBHYA2, capable of degrading naphthalene, was isolated from the American Petroleum Institute (API) separator of the Tehran Oil Refinery Complex (TORC). Strain FBHYA2 was identified as Achromobacter sp. based on physiological and biochemical characteristics and also phylogenetic similarity of 16S rRNA gene sequence. The optimal growth conditions for strain FBHYA2 were pH 6.0, 30 °C and 1.0% NaCl. Strain FBHYA2 can utilize naphthalene as the sole source of carbon and energy and was able to degrade naphthalene aerobically very fast, 48 h for 96% removal at 500 mg/L concentration. The physiological response of Achromobacter sp., FBHYA2 to several hydrophobic chemicals (aliphatic and aromatic hydrocarbons) was also investigated. No biosurfactant was detected during bacterial growth on any aliphatic/aromatic hydrocarbons. The results of hydrophobicity measurements showed no significant difference between naphthalene- and LB-grown cells. The capability of the strain FBHYA2 to degrade naphthalene completely and rapidly without the need to secrete biosurfactant may make it an ideal candidate to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated sites.

scholarly journals Biodegradation of binary mixtures of octane with benzene, toluene, ethylbenzene or xylene (BTEX): insights on the potential of Burkholderia, Ralstonia, Pseudomonas, and Cupriavidus isolates

2021 ◽  
Author(s):  
Hernando P. Bacosa ◽  
Jhonamie Abiner Mabuhay-Omar ◽  
Rodulf Anthony T. Balisco ◽  
Dawin M. Omar ◽  
Chihiro Inoue
Keyword(s):  
Binary Mixtures ◽  
Aromatic Hydrocarbons ◽  
Bacterial Consortium ◽  
Final Concentration ◽  
Aliphatic Hydrocarbons ◽  
Alkane Hydroxylase ◽  
Benzene Toluene ◽  
Aliphatic And Aromatic Hydrocarbons ◽  
By Products ◽  
Btex Compounds

Abstract The contamination of the environment by crude oil and its by-products, which mainly composed of aliphatic and aromatic hydrocarbons, is a widespread problem. Biodegradation by bacteria is one of the processes responsible for the removal of these pollutants. This study was conducted to determine the abilities of Burkholderia sp. B5, Ralstonia sp. B1, Pseudomonas sp. T1, and Cupriavidus sp. X5 to degrade binary mixtures of octane (representing aliphatic hydrocarbons) with benzene, toluene, ethylbenzene, or xylene (BTEX as aromatic hydrocarbons) at a final concentration of 100 ppm under aerobic conditions. These strains were isolated from an enriched bacterial consortium (Yabase or Y consortium) that prefer to degrade aromatic hydrocarbon over aliphatic hydrocarbons. We found that B5 degraded all BTEX compounds more rapidly than octane. In contrast, B1, T1 and X5 utilized more of octane over BTX compounds. B5 also preferred to use benzene over octane with varying concentrations of up to 200 mg/l. B5 possesses alkane hydroxylase (alkB) and catechol 2,3-dioxygenase (C23D) genes, which are responsible for the degradation of alkanes and aromatic hydrocarbons, respectively. This study strongly supports our notion that Burkholderia played a key role in the preferential degradation of aromatic hydrocarbons over aliphatic hydrocarbons in the previously characterized Y consortium. The preferential degradation of more toxic aromatic hydrocarbons over aliphatics is crucial in risk-based bioremediation.

scholarly journals Molecular Characterization of Fusarium Solani Degrades a Mixture of Low and High Molecular Weight Polycyclic Aromatic Hydrocarbons

2017 ◽  
Vol 11 (1) ◽  
pp. 27-35 ◽  
Author(s):  
Abd El-Latif Hesham ◽  
Elsayed A. Mohamed ◽  
Asmaa M.M. Mawad ◽  
Ameer Elfarash ◽  
Bahaa S. Abd El-Fattah ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Polycyclic Aromatic Hydrocarbons ◽  
High Molecular Weight ◽  
Aromatic Hydrocarbons ◽  
Fusarium Solani ◽  
Polluted Soil ◽  
White Rot ◽  
White Rot Fungus ◽  
Rrna Gene ◽  
Polycyclic Aromatic

Objectives:This study evaluates the ability of a non-white rot fungus strain, HESHAM-1, to degrade a mixture of low (naphthalene and phenanthrene) and high (chrysene and benzo(a)pyrene) molecular weight polycyclic aromatic hydrocarbons (LMW and HMW PAHs).Methods:Strain HESHAM-1 was isolated from oil polluted soil by enrichment method using phenanthrene as the sole source of carbon and energy. The strain showed the ability to tolerate and degrade a mixture of both low and high molecular weight PAHs. In the presences of LMW-PAHs (naphthalene and phenanthrene) as co-substrate, chrysene and benzo(a)pyrene (HMW-PAHs) were, respectively degraded by the fungus strain HESHAM-1 which was confirmed by GC-MS analyses.Results:The degradation rate was found as 84.82% for naphthalene, 40.09% for phenanthrene, 57.84% for chrysene and 71.06% for benzo(a)pyrene at the end of 10 days. This is the first report describing the biodegradation of a mixture of four PAH compounds by non-white rot fungus strain HESHAM-1 isolated from Egyptian oil-polluted soil. The fungus strain HESHAM-1 was identified by morphological characteristics and molecular genetics technique based on PCR amplification and sequencing of the internal transcribed spacers (ITSs) of the rDNA region and intervening 5.8S rRNA gene. Blast result and phylogenetic analysis of gene sequencing suggested that strain HESHAM-1 was closely related toFusarium solaniwith 100% sequence identity.Conclusion:The present study clearly demonstrates that, strain HESHAM-1 could be used to remove the crude oil from the environment.

scholarly journals Markers of Genetic Variation in Blue Gourami (Trichogaster trichopterus) as a Model for Labyrinth Fish

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 228
Author(s):  
Gad Degani ◽  
Isana Veksler-Lublinsky ◽  
Ari Meerson
Keyword(s):  
Growth Hormone ◽  
Genetic Variation ◽  
Genetic Markers ◽  
Basic Research ◽  
Coi Gene ◽  
12S Rrna ◽  
Rrna Gene ◽  
Somatotropic Axis ◽  
Genes Encoding ◽  
Growth And Reproduction

Markers of genetic variation between species are important for both applied and basic research. Here, various genes of the blue gourami (Trichogaster trichopterus, suborder Anabantoidei, a model labyrinth fish), many of them involved in growth and reproduction, are reviewed as markers of genetic variation. The genes encoding the following hormones are described: kisspeptins 1 and 2, gonadotropin-releasing hormones 1, 2, and 3, growth hormone, somatolactin, prolactin, follicle- stimulating hormone and luteinizing hormone, as well as mitochondrial genes encoding cytochrome b and 12S rRNA. Genetic markers in blue gourami, representing the suborder Anabantoidei, differ from those in other bony fishes. The sequence of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene of blue gourami is often used to study the Anabantoidei suborder. Among the genes involved in controlling growth and reproduction, the most suitable genetic markers for distinguishing between species of the Anabantoidei have functions in the hypothalamic–pituitary–somatotropic axis: pituitary adenylate cyclase-activating polypeptide and growth hormone, and the 12S rRNA gene.

scholarly journals Identification and Genomic Characterization of Pathogenic Bacillus altitudinis from Common Pear Trees in Morocco

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1344
Author(s):  
Naima Lemjiber ◽  
Khalid Naamani ◽  
Annabelle Merieau ◽  
Abdelhi Dihazi ◽  
Nawal Zhar ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Genomic Islands ◽  
Rrna Gene ◽  
In Planta ◽  
Bacterial Strains ◽  
Bacillus Altitudinis ◽  
Genes Encoding ◽  
Bacillus Spp ◽  
Pear Trees ◽  
Rrna Gene Sequencing

Bacterial burn is one of the major diseases affecting pear trees worldwide, with serious impacts on producers and economy. In Morocco, several pear trees (Pyrus communis) have shown leaf burns since 2015. To characterize the causal agent of this disease, we isolated fourteen bacterial strains from different parts of symptomatic pear trees (leaves, shoots, fruits and flowers) that were tested in planta for their pathogenicity on Louise bonne and Williams cultivars. The results showed necrotic lesions with a significant severity range from 47.63 to 57.77% on leaves of the Louise bonne cultivar inoculated with isolate B10, while the other bacterial isolates did not induce any disease symptom. 16S rRNA gene sequencing did not allow robust taxonomic discrimination of the incriminated isolate. Thus, we conducted whole-genome sequencing (WGS) and phylogenetic analyzes based on gyrA, gyrB and cdaA gene sequences, indicating that this isolate belongs to the Bacillus altitudinis species. This taxonomic classification was further confirmed by the Average Nucleotide Identity (ANI) and the in silico DNA-DNA hybridization (isDDH) analyzes compared to sixty-five Bacillus spp. type strains. The genome was mined for genes encoding carbohydrate-active enzymes (CAZymes) known to play a role in the vegetal tissue degradation. 177 candidates with functions that may support the in planta phytopathogenicity results were identified. To the best of our knowledge, this is the first data reporting B. altitudinis as agent of leaf burn in P. communis in Morocco. Our dataset will improve our knowledge on spread and pathogenicity of B. altitudinis genotypes that appears as emergent phytopathogenic agent, unveiling virulence factors and their genomic location (i.e., within genomic islands or the accessory genome) to induce trees disease.

scholarly journals Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Marine Drugs ◽  
2020 ◽  
Vol 18 (6) ◽  
pp. 298
Author(s):  
Alison E. Murray ◽  
Nicole E. Avalon ◽  
Lucas Bishop ◽  
Karen W. Davenport ◽  
Erwan Delage ◽  
...  
Keyword(s):  
Marine Invertebrate ◽  
Bioactive Compound ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Specific Sequence ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
The Core ◽  
Synoicum Adareanum ◽  
Palmerolide A

Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.

scholarly journals Genetic Investigation of the Catabolic Pathway for Degradation of Abietane Diterpenoids by Pseudomonas abietaniphilaBKME-9

2000 ◽  
Vol 182 (13) ◽  
pp. 3784-3793 ◽  
Author(s):  
Vincent J. J. Martin ◽  
William W. Mohn
Keyword(s):  
Gene Cluster ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Ring Cleavage ◽  
Catabolic Pathway ◽  
Transcriptional Fusion ◽  
Abietane Diterpenoids ◽  
Genes Encoding ◽  
Dna Fragment ◽  
Reading Frames

ABSTRACT We have cloned and sequenced the dit gene cluster encoding enzymes of the catabolic pathway for abietane diterpenoid degradation by Pseudomonas abietaniphila BKME-9. Thedit gene cluster is located on a 16.7-kb DNA fragment containing 13 complete open reading frames (ORFs) and 1 partial ORF. The genes ditA1A2A3 encode the α and β subunits and the ferredoxin of the dioxygenase which hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8,13-abietadien acid. The dioxygenase mutant strain BKME-941 (ditA1::Tn5) did not grow on nonaromatic abietanes, and transformed palustric and abietic acids to 7-oxodehydroabietic acid in cell suspension assays. Thus, nonaromatic abietanes are aromatized prior to further degradation. Catechol 2,3-dioxygenase activity of xylEtranscriptional fusion strains showed induction of ditA1and ditA3 by abietic, dehydroabietic, and 7-oxodehydroabietic acids, which support the growth of strain BKME-9, as well as by isopimaric and 12,14-dichlorodehydroabietic acids, which are diterpenoids that do not support the growth of strain BKME-9. In addition to the aromatic-ring-hydroxylating dioxygenase genes, thedit cluster includes ditC, encoding an extradiol ring cleavage dioxygenase, and ditR, encoding an IclR-type transcriptional regulator. Although ditR is not strictly required for the growth of strain BKME-9 on abietanes, aditR::Kmr mutation in aditA3::xylE reporter strain demonstrated that it encodes an inducer-dependent transcriptional activator of ditA3. An ORF with sequence similarity to genes encoding permeases (ditE) is linked with genes involved in abietane degradation.

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