LAPSE:2023.1263
Published Article
LAPSE:2023.1263
Diversity and Metabolic Potential of a PAH-Degrading Bacterial Consortium in Technogenically Contaminated Haplic Chernozem, Southern Russia
February 21, 2023
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are chemically recalcitrant carcinogenic and mutagenic compounds with primarily anthropogenic origin. The investigation of the effects of emissions from energy enterprises on soil microbiomes is of a high priority for modern soil science. In this study, metagenomic profiling of technogenic contaminated soils was carried out based on bioinformatic analysis of shotgun metagenome data with PAH-degrading genes identification. The use of prokaryotic consortia has been often used as one of the bio-remediation approaches to degrade PAHs with different molecular weight. Since the process of PAH degradation predominantly includes non-culturable or yet-to-be cultured species, metagenomic approaches are highly recommended for studying the composition and metabolic abilities of microbial communities. In this study, whole metagenome shotgun sequencing of DNA from two soils with varying PAH levels was performed. In the control site, the total content of 12 priority PAHs was 262 µg kg−1. The background soil levels in the polluted site for PAHs with 3 or more rings exceeded this, at 800 µg kg−1. The abundance of genes and taxa associated with PAH degradation in these two sites were estimated. Despite differences in PAH concentrations up to 1200 µg kg−1, individual and operon-organized PAH degradation genes were almost equally abundant and diverse in pristine and highly contaminated areas. The most numerous taxa in both spots were actinobacteria from Terrabacteria group. In addition to well-known PAH degraders such as Gordonia and Rhodococcus, genes corresponding to the PAH degradation were found in Azoarcus, Burkholderia and Variovorax. The data shows non-specificity and multifunctionality of metabolic pathways encoded in the genes of PAH-degrading microorganisms.
Polycyclic aromatic hydrocarbons (PAHs) are chemically recalcitrant carcinogenic and mutagenic compounds with primarily anthropogenic origin. The investigation of the effects of emissions from energy enterprises on soil microbiomes is of a high priority for modern soil science. In this study, metagenomic profiling of technogenic contaminated soils was carried out based on bioinformatic analysis of shotgun metagenome data with PAH-degrading genes identification. The use of prokaryotic consortia has been often used as one of the bio-remediation approaches to degrade PAHs with different molecular weight. Since the process of PAH degradation predominantly includes non-culturable or yet-to-be cultured species, metagenomic approaches are highly recommended for studying the composition and metabolic abilities of microbial communities. In this study, whole metagenome shotgun sequencing of DNA from two soils with varying PAH levels was performed. In the control site, the total content of 12 priority PAHs was 262 µg kg−1. The background soil levels in the polluted site for PAHs with 3 or more rings exceeded this, at 800 µg kg−1. The abundance of genes and taxa associated with PAH degradation in these two sites were estimated. Despite differences in PAH concentrations up to 1200 µg kg−1, individual and operon-organized PAH degradation genes were almost equally abundant and diverse in pristine and highly contaminated areas. The most numerous taxa in both spots were actinobacteria from Terrabacteria group. In addition to well-known PAH degraders such as Gordonia and Rhodococcus, genes corresponding to the PAH degradation were found in Azoarcus, Burkholderia and Variovorax. The data shows non-specificity and multifunctionality of metabolic pathways encoded in the genes of PAH-degrading microorganisms.
Record ID
Keywords
anthropogenic impact, long-term contamination, metagenomics, microbial communities, PAH-degrading bacteria, PAHs
Subject
Suggested Citation
Delegan Y, Sushkova S, Minkina T, Filonov A, Kocharovskaya Y, Demin K, Gorovtsov A, Rajput VD, Zamulina I, Grigoryeva T, Dudnikova T, Barbashev A, Maksimov A. Diversity and Metabolic Potential of a PAH-Degrading Bacterial Consortium in Technogenically Contaminated Haplic Chernozem, Southern Russia. (2023). LAPSE:2023.1263
Author Affiliations
Delegan Y: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia; G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Scienc
Sushkova S: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia [ORCID]
Minkina T: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia [ORCID]
Filonov A: G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 5 prosp. Nauki, Pushchino, 142290 Moscow, Russia [ORCID]
Kocharovskaya Y: G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 5 prosp. Nauki, Pushchino, 142290 Moscow, Russia; The Federal State Budget Educational Instit
Demin K: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia [ORCID]
Gorovtsov A: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia
Rajput VD: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia [ORCID]
Zamulina I: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia [ORCID]
Grigoryeva T: Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
Dudnikova T: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia
Barbashev A: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia [ORCID]
Maksimov A: National Medical Research Centre for Oncology, 344037 Rostov-on-Don, Russia
Sushkova S: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia [ORCID]
Minkina T: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia [ORCID]
Filonov A: G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 5 prosp. Nauki, Pushchino, 142290 Moscow, Russia [ORCID]
Kocharovskaya Y: G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 5 prosp. Nauki, Pushchino, 142290 Moscow, Russia; The Federal State Budget Educational Instit
Demin K: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia [ORCID]
Gorovtsov A: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia
Rajput VD: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia [ORCID]
Zamulina I: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia [ORCID]
Grigoryeva T: Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
Dudnikova T: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia
Barbashev A: Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia [ORCID]
Maksimov A: National Medical Research Centre for Oncology, 344037 Rostov-on-Don, Russia
Journal Name
Processes
Volume
10
Issue
12
First Page
2555
Year
2022
Publication Date
2022-12-01
ISSN
2227-9717
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Original Submission
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PII: pr10122555, Publication Type: Journal Article
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LAPSE:2023.1263
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https://doi.org/10.3390/pr10122555
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