Elsevier

Pedosphere

Volume 29, Issue 3, June 2019, Pages 283-297
Pedosphere

Soil Microbiomes—a Promising Strategy for Contaminated Soil Remediation: A Review

https://doi.org/10.1016/S1002-0160(18)60061-XGet rights and content

Abstract

Bioremediation is a process mediated by microorganisms and represents a sustainable and eco-friendly way to degrade and detoxify environmental contaminants. Soil microbiomes clearly become a key component of bioremediation as they are more stable and efficient than pure cultures, being recognized as one of the scientific frontiers of the soil environmental science and technology fields. Recently, many advancements have been made regarding the investigation of remediation mechanisms by soil microbiomes and the interactions inside them. This has greatly expanded our ability to characterize the remediating function of soil microbiomes and identify the factors that influence their efficiency for remediation. Here, we suggest that soil microbiomes are a promising strategy for soil remediation. Research is now needed to identify how we can manipulate and manage soil microbiomes to improve remediation efficiency and increase soil fertility at the same time. Therefore, this review aims to emphasize the importance of soil microbiomes in bioremediation and promote further development of this strategy into a widely accepted technique.

References (130)

  • A K Haritash et al.

    Biodegradation aspects of polycyclic aromatic hydrocarbons (PAHs): A review

    J Hazard Mater

    (2009)
  • B Hendrickx et al.

    Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation: Distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site

    J Microbiol Methods

    (2006)
  • C H Kang et al.

    Bioremediation of heavy metals by using bacterial mixtures

    Ecol Eng

    (2016)
  • J Kotaś et al.

    Chromium occurrence in the environment and methods of its speciation

    Environ Pollut

    (2000)
  • S Kuppusamy et al.

    Remediation approaches for polycyclic aromatic hydrocarbons (PAHs) contaminated soils: Technological constraints, emerging trends and future directions

    Chemosphere

    (2017)
  • Y Kuzyakov et al.

    Microbial hotspots and hot moments in soil: Concept & review

    Soil Biol Biochem

    (2015)
  • S Lamichhane et al.

    Polycyclic aromatic hydrocarbons (PAHs) removal by sorption: A review

    Chemosphere

    (2016)
  • R Lohmann et al.

    Global fate of POPs: Current and future research directions

    Environ Pollut

    (2007)
  • M Madhaiyan et al.

    Metal tolerating methylotrophic bacteria reduces nickel and cadmium toxicity and promotes plant growth of tomato (Lycopersicon esculentum L.)

    Chemosphere

    (2007)
  • T F C Mah et al.

    Mechanisms of biofilm resistance to antimicrobial agents

    Trends Microbiol

    (2001)
  • S Mineki et al.

    Degradation of polyaromatic hydrocarbons by fungi isolated from soil in Japan

    Polycyclic Aromat Compd

    (2015)
  • A Nzila

    Update on the cometabolism of organic pollutants by bacteria

    Environ Pollut

    (2013)
  • M Okai et al.

    Crystal structure of γ-hexachlorocyclohexane dehydrochlorinase LinA from Sphingobium japonicum UT26

    J Mol Biol

    (2010)
  • L Passatore et al.

    Phytoremediation and bioremediation of polychlorinated biphenyls (PCBs): State of knowledge and research perspectives

    J Hazard Mater

    (2014)
  • C A Peters et al.

    Urbanization is a major influence on microplastic ingestion by sunfish in the Brazos River Basin, Central Texas, USA

    Environ Pollut

    (2016)
  • G D Ren et al.

    Pyrene dissipation potential varies with soil type and associated bacterial community changes

    Soil Biol Biochem

    (2016)
  • A A Shah et al.

    Biological degradation of plastics: A comprehensive review

    Biotechnol Adv

    (2008)
  • A P Alivisatos et al.

    A unified initiative to harness earth's microbiomes

    Science

    (2015)
  • P K Arora et al.

    OxDBase: A database of oxygenases involved in biodegradation

    BMC Res Notes

    (2009)
  • P K Arora et al.

    Application of monooxygenases in dehalogenation, desulphurization, denitrification and hydroxylation of aromatic compounds

    J Bioremed Biodegrad

    (2010)
  • J Chakraborty et al.

    Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants

    Environ Sci Pollut Res

    (2016)
  • S Chandra et al.

    Application of bioremediation technology in the environment contaminated with petroleum hydrocarbon

    Ann Microbiol

    (2013)
  • G U Chibuike et al.

    Heavy metal polluted soils: Effect on plants and bioremediation methods

    Appl Environ Soil Sci

    (2014)
  • A Chowdhury et al.

    Impact of pesticides on soil microbiological parameters and possible bioremediation strategies

    Indian J Microbiol

    (2008)
  • K Z Coyte et al.

    The ecology of the microbiome: Networks, competition, and stability

    Science

    (2015)
  • V M D'Costa et al.

    Sampling the antibiotic resistome

    Science

    (2006)
  • K De Roy et al.

    Synthetic microbial ecosystems: An exciting tool to understand and apply microbial communities

    Environ Microbiol

    (2014)
  • J M DeBruyn et al.

    Horizontal transfer of PAH catabolism genes in Mycobacterium: Evidence from comparative genomics and isolated pyrene-degrading bacteria

    Environ Sci Technol

    (2012)
  • M Delgado-Baquerizo et al.

    Relative importance of soil properties and microbial community for soil functionality: Insights from a microbial swap experiment

    Funct Ecol

    (2016)
  • N Dubilier et al.

    Microbiology: Create a global microbiome effort

    Nature

    (2015)
  • S J Edwards et al.

    Applications of biofilms in bioremediation and biotransformation of persistent organic pollutants, pharmaceuticals/personal care products, and heavy metals

    Appl Microbiol Biotechnol

    (2013)
  • A E Escalante et al.

    Ecological perspectives on synthetic biology: Insights from microbial population biology

    Front Microbiol

    (2015)
  • N Fierer

    Embracing the unknown: Disentangling the complexities of the soil microbiome

    Nat Rev Microbiol

    (2017)
  • J K Fredrickson

    Ecological communities by design

    Science

    (2015)
  • M Gambino et al.

    Mini-review: Biofilm responses to oxidative stress

    Biofouling

    (2016)
  • M S Girvan et al.

    Bacterial diversity promotes community stability and functional resilience after perturbation

    Environ Microbiol

    (2005)
  • C Gounou et al.

    Influence of the iron-reducing bacteria on the release of heavy metals in anaerobic river sediment

    Water Air Soil Pollut

    (2010)
  • A Gupta et al.

    Microbes as potential tool for remediation of heavy metals: A review

    J Microb Biochem Technol

    (2016)
  • G Gupta et al.

    Biodegradation of polycyclic aromatic hydrocarbons by microbial consortium: A distinctive approach for decontamination of soil

    Soil Sediment ContamInt J

    (2016)
  • R Gurav et al.

    Degradation of n-alkanes and PAHs from the heavy crude oil using salt-tolerant bacterial consortia and analysis of their catabolic genes

    Environ Sci Pollut Res

    (2017)
  • Cited by (0)

    View full text