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The plastisphere microbiome in alpine soils alters the microbial genetic potential for plastic degradation and biogeochemical cycling


Rüthi, Joel; Rast, Basil M; Qi, Weihong; Perez-Mon, Carla; Pardi-Comensoli, Lucrezia; Brunner, Ivano; Frey, Beat (2023). The plastisphere microbiome in alpine soils alters the microbial genetic potential for plastic degradation and biogeochemical cycling. Journal of Hazardous Materials, 441:129941.

Abstract

Plastic is exceedingly abundant in soils, but little is known about its ecological consequences for soil microbiome functioning. Here we report the impacts of polyethylene and biodegradable Ecovio and BI-OPL plastic films buried in alpine soils for 5 months on the genetic potential of the soil microbiome using shotgun metagenomics. The microbiome was more affected by Ecovio and BI-OPL than by polyethylene. Fungi, α- and β-Proteobacteria dominated on the biodegradable films. Ecovio and BI-OPL showed signs of degradation after the incubation, whereas polyethylene did not. Genes involved in cellular processes and signaling (intracellular trafficking, secretion, vesicular transport), as well as metabolism (carbohydrate, lipid and secondary metabolism), were enriched in the plastisphere. Several α/β-hydrolase gene families (cutinase_like, polyesterase-lipase-cutinase, carboxylesterase), which encode enzymes essential to plastic degradation, and carbohydrate-active genes involved in lignin and murein degradation increased on Ecovio and BI-OPL films. Enriched nitrogen fixation and organic N degradation and synthesis genes and decreased nitrification genes on Ecovio altered the biogeochemical cycling, leading to higher ammonium concentrations and depletion of nitrite and nitrate in the soil. Our results indicate that plastics affect the alpine soil microbiome and its functions and suggest that the plastisphere has an untapped microbial potential for plastic biodegradation. + Graphical Abstract

Abstract

Plastic is exceedingly abundant in soils, but little is known about its ecological consequences for soil microbiome functioning. Here we report the impacts of polyethylene and biodegradable Ecovio and BI-OPL plastic films buried in alpine soils for 5 months on the genetic potential of the soil microbiome using shotgun metagenomics. The microbiome was more affected by Ecovio and BI-OPL than by polyethylene. Fungi, α- and β-Proteobacteria dominated on the biodegradable films. Ecovio and BI-OPL showed signs of degradation after the incubation, whereas polyethylene did not. Genes involved in cellular processes and signaling (intracellular trafficking, secretion, vesicular transport), as well as metabolism (carbohydrate, lipid and secondary metabolism), were enriched in the plastisphere. Several α/β-hydrolase gene families (cutinase_like, polyesterase-lipase-cutinase, carboxylesterase), which encode enzymes essential to plastic degradation, and carbohydrate-active genes involved in lignin and murein degradation increased on Ecovio and BI-OPL films. Enriched nitrogen fixation and organic N degradation and synthesis genes and decreased nitrification genes on Ecovio altered the biogeochemical cycling, leading to higher ammonium concentrations and depletion of nitrite and nitrate in the soil. Our results indicate that plastics affect the alpine soil microbiome and its functions and suggest that the plastisphere has an untapped microbial potential for plastic biodegradation. + Graphical Abstract

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Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Functional Genomics Center Zurich
04 Faculty of Medicine > University Hospital Zurich > Clinic for Thoracic Surgery
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Scopus Subject Areas:Physical Sciences > Environmental Engineering
Physical Sciences > Environmental Chemistry
Physical Sciences > Waste Management and Disposal
Physical Sciences > Pollution
Physical Sciences > Health, Toxicology and Mutagenesis
Uncontrolled Keywords:Health, Toxicology and Mutagenesis, Pollution, Waste Management and Disposal, Environmental Chemistry, Environmental Engineering
Language:English
Date:1 January 2023
Deposited On:23 Jan 2023 10:04
Last Modified:29 Mar 2024 02:38
Publisher:Elsevier
ISSN:0304-3894
OA Status:Hybrid
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1016/j.jhazmat.2022.129941
Project Information:
  • : FunderSwiss Federal Institute for Forest Snow and Landscape Research WSL
  • : Grant ID
  • : Project Title
  • Content: Published Version
  • Language: English
  • Licence: Creative Commons: Attribution 4.0 International (CC BY 4.0)