Exploring the Diversity and Functional Profile of Microbial Communities of Brazilian Soils with High Salinity and Oil Contamination

Overview

Journal Heliyon

Specialty Social Sciences

Date 2024 Jul 31

PMID 39082007

Authors

Danielly C O Mariano

Graciela Maria Dias

Michele Rocha Castro

Diogo Antonio Tschoeke

Fernando J S de Oliveira

Eliana Flavia C Servulo

Bianca Cruz Neves

Affiliations

Soon will be listed here.

Abstract

Environmental pollution associated with the petroleum industry is a major problem worldwide. Microbial degradation is extremely important whether in the extractive process or in bioremediation of contaminants. Assessing the local microbiota and its potential for degradation is crucial for implementing effective bioremediation strategies. Herein, contaminated soil samples of onshore oil fields from a semiarid region in the Northeast of Brazil were investigated using metagenomics and metataxonomics. These soils exhibited hydrocarbon contamination and high salinity indices, while a control sample was collected from an uncontaminated area. The shotgun analysis revealed the predominance of Actinomycetota and Pseudomonadota, while 16S rRNA gene amplicon analysis of the samples showed Actinomycetota, Bacillota, and Pseudomonadota as the most abundant. The Archaea domain phylotypes were assigned to Thermoproteota and Methanobacteriota. Functional analysis and metabolic profile of the soil microbiomes exhibited a broader metabolic repertoire in the uncontaminated soil, while degradation pathways and surfactant biosynthesis presented higher values in the contaminated soils, where degradation pathways of xenobiotic and aromatic compounds were also present. Biosurfactant synthetic pathways were abundant, with predominance of lipopeptides. The present work uncovers several microbial drivers of oil degradation and mechanisms of adaptation to high salinity, which are pivotal traits for sustainable soil recovery strategies.

References

Tang S, Rao Y, Huang S, Xu Y, Zeng K, Liang X . Impact of environmental factors on the ammonia-oxidizing and denitrifying microbial community and functional genes along soil profiles from different ecologically degraded areas in the Siding mine. J Environ Manage. 2022; 326(Pt A):116641. DOI: 10.1016/j.jenvman.2022.116641. View

Gutierrez-Chavez C, Benaud N, Ferrari B . The ecological roles of microbial lipopeptides: Where are we going?. Comput Struct Biotechnol J. 2021; 19:1400-1413. PMC: 7960500. DOI: 10.1016/j.csbj.2021.02.017. View

Na H, Song Y, Yu Y, Chung J . Comparative Analysis of Primers Used for 16S rRNA Gene Sequencing in Oral Microbiome Studies. Methods Protoc. 2023; 6(4). PMC: 10460062. DOI: 10.3390/mps6040071. View

OBrien F, Almaraz M, Foster M, Hill A, Huber D, King E . Soil Salinity and pH Drive Soil Bacterial Community Composition and Diversity Along a Lateritic Slope in the Avon River Critical Zone Observatory, Western Australia. Front Microbiol. 2019; 10:1486. PMC: 6614384. DOI: 10.3389/fmicb.2019.01486. View

Cheng Q, Chang H, Yang X, Wang D, Wang W . Salinity and nutrient modulate soil bacterial communities in the coastal wetland of the Yellow River Delta, China. Environ Sci Pollut Res Int. 2020; 28(12):14621-14631. DOI: 10.1007/s11356-020-11626-x. View

Xie W, Zhang C, Zhou X, Wang P . Salinity-dominated change in community structure and ecological function of Archaea from the lower Pearl River to coastal South China Sea. Appl Microbiol Biotechnol. 2014; 98(18):7971-82. DOI: 10.1007/s00253-014-5838-9. View

Zhu H, Fu Y, Yu J, Jing W, Zhou M . Metagenomic insight on consortium degradation of soil weathered petroleum and its supplement based on gene abundance change. Enzyme Microb Technol. 2023; 169:110285. DOI: 10.1016/j.enzmictec.2023.110285. View

Kuczynski J, Lauber C, Walters W, Parfrey L, Clemente J, Gevers D . Experimental and analytical tools for studying the human microbiome. Nat Rev Genet. 2011; 13(1):47-58. PMC: 5119550. DOI: 10.1038/nrg3129. View

Salam L, Obayori S, Nwaokorie F, Suleiman A, Mustapha R . Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil. Environ Sci Pollut Res Int. 2017; 24(8):7139-7159. DOI: 10.1007/s11356-017-8364-3. View

10.

Oni F, Esmaeel Q, Onyeka J, Adeleke R, Jacquard C, Clement C . Lipopeptide-Mediated Biocontrol: Chemotaxonomy and Biological Activity. Molecules. 2022; 27(2). PMC: 8777863. DOI: 10.3390/molecules27020372. View

11.

Navarro-Noya Y, Valenzuela-Encinas C, Sandoval-Yuriar A, Jimenez-Bueno N, Marsch R, Dendooven L . Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil. Archaea. 2015; 2015:646820. PMC: 4444560. DOI: 10.1155/2015/646820. View

12.

Paul D . Osmotic stress adaptations in rhizobacteria. J Basic Microbiol. 2012; 53(2):101-10. DOI: 10.1002/jobm.201100288. View

13.

Li J, Wang L, Liu Y, Zhou L, Gang H, Liu J . Microbial Lipopeptide-Producing Strains and Their Metabolic Roles under Anaerobic Conditions. Microorganisms. 2021; 9(10). PMC: 8540375. DOI: 10.3390/microorganisms9102030. View

14.

Medic A, Ljesevic M, Inui H, Beskoski V, Kojic I, Stojanovic K . Efficient biodegradation of petroleum -alkanes and polycyclic aromatic hydrocarbons by polyextremophilic san ai with multidegradative capacity. RSC Adv. 2022; 10(24):14060-14070. PMC: 9051604. DOI: 10.1039/c9ra10371f. View

15.

Johnston J, Lim E, Roh H . Impact of upstream oil extraction and environmental public health: A review of the evidence. Sci Total Environ. 2018; 657:187-199. PMC: 6344296. DOI: 10.1016/j.scitotenv.2018.11.483. View

16.

Shan J, Zhao X, Sheng R, Xia Y, Ti C, Quan X . Dissimilatory Nitrate Reduction Processes in Typical Chinese Paddy Soils: Rates, Relative Contributions, and Influencing Factors. Environ Sci Technol. 2016; 50(18):9972-80. DOI: 10.1021/acs.est.6b01765. View

17.

Gao H, Wu M, Liu H, Xu Y, Liu Z . Effect of petroleum hydrocarbon pollution levels on the soil microecosystem and ecological function. Environ Pollut. 2021; 293:118511. DOI: 10.1016/j.envpol.2021.118511. View

18.

Behera S, Das S . Potential and prospects of Actinobacteria in the bioremediation of environmental pollutants: Cellular mechanisms and genetic regulations. Microbiol Res. 2023; 273:127399. DOI: 10.1016/j.micres.2023.127399. View

19.

Patel V, Sharma A, Lal R, Al-Dhabi N, Madamwar D . Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates. BMC Microbiol. 2016; 16:50. PMC: 4802719. DOI: 10.1186/s12866-016-0669-8. View

20.

Camacho-Montealegre C, Rodrigues E, Kumazawa Morais D, Totola M . Prokaryotic community diversity during bioremediation of crude oil contaminated oilfield soil: effects of hydrocarbon concentration and salinity. Braz J Microbiol. 2021; 52(2):787-800. PMC: 8105486. DOI: 10.1007/s42770-021-00476-5. View