Metagenomic analysis of a keratin-degrading bacterial consortium
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PROVIDER: PRJEB38982 | ENA |
REPOSITORIES: ENA
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Project description:Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source. This consortium is able to grow on biphenyl, benzoate, and protocatechuate. Whole-community DNA extracted from the consortium was used to analyze biodiversity by Illumina sequencing of a 16S rRNA gene amplicon library and to determine the metagenome by whole-genome shotgun Illumina sequencing. Biodiversity analysis shows that the consortium consists of 24 operational taxonomic units (≥97% identity). The consortium is dominated by strains belonging to the genus Pseudomonas, but also contains betaproteobacteria and Rhodococcus strains. whole-genome shotgun (WGS) analysis resulted in contigs containing 78.3 Mbp of sequenced DNA, representing around 65% of the expected DNA in the consortium. Bioinformatic analysis of this metagenome has identified the genes encoding the enzymes implicated in three pathways for the conversion of biphenyl to benzoate and five pathways from benzoate to tricarboxylic acid (TCA) cycle intermediates, allowing us to model the whole biodegradation network. By genus assignment of coding sequences, we have also been able to determine that the three biphenyl to benzoate pathways are carried out by Rhodococcus strains. In turn, strains belonging to Pseudomonas and Bordetella are the main responsible of three of the benzoate to TCA pathways while the benzoate conversion into TCA cycle intermediates via benzoyl-CoA and the catechol meta-cleavage pathways are carried out by beta proteobacteria belonging to genera such as Achromobacter and Variovorax. We have isolated a Rhodococcus strain WAY2 from the consortium which contains the genes encoding the three biphenyl to benzoate pathways indicating that this strain is responsible for all the biphenyl to benzoate transformations. The presented results show that metagenomic analysis of consortia allows the identification of bacteria active in biodegradation processes and the assignment of specific reactions and pathways to specific bacterial groups.
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Project description: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.
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Project description:Terephthalate (TA) is one of the top 50 chemicals produced worldwide. Its production results in a TA-containing wastewater that is treated by anaerobic processes through a poorly understood methanogenic syntrophy. Using metagenomics, we characterized the methanogenic consortium inside a hyper-mesophilic (that is, between mesophilic and thermophilic), TA-degrading bioreactor. We identified genes belonging to dominant Pelotomaculum species presumably involved in TA degradation through decarboxylation, dearomatization, and modified ?-oxidation to H(2)/CO(2) and acetate. These intermediates are converted to CH(4)/CO(2) by three novel hyper-mesophilic methanogens. Additional secondary syntrophic interactions were predicted in Thermotogae, Syntrophus and candidate phyla OP5 and WWE1 populations. The OP5 encodes genes capable of anaerobic autotrophic butyrate production and Thermotogae, Syntrophus and WWE1 have the genetic potential to oxidize butyrate to CO(2)/H(2) and acetate. These observations suggest that the TA-degrading consortium consists of additional syntrophic interactions beyond the standard H(2)-producing syntroph-methanogen partnership that may serve to improve community stability.
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