Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site.
16S rRNA
18S rRNA
Brownfields
Contamination
Heavy metals
ITS
Soil microbiome
eDNA
Journal
Microbial ecology
ISSN: 1432-184X
Titre abrégé: Microb Ecol
Pays: United States
ID NLM: 7500663
Informations de publication
Date de publication:
Apr 2023
Apr 2023
Historique:
received:
17
01
2022
accepted:
21
06
2022
medline:
5
5
2023
pubmed:
9
7
2022
entrez:
8
7
2022
Statut:
ppublish
Résumé
Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.
Identifiants
pubmed: 35802172
doi: 10.1007/s00248-022-02061-1
pii: 10.1007/s00248-022-02061-1
pmc: PMC10156844
doi:
Substances chimiques
Soil
0
Volatile Organic Compounds
0
Soil Pollutants
0
Metals, Heavy
0
Petroleum
0
Environmental Pollutants
0
Cobalt
3G0H8C9362
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
998-1012Subventions
Organisme : Office of the President, University of California
ID : CA-16-376437
Organisme : La Kretz and Stunt Ranch Reserve Grant
ID : 443952-SR-69085
Informations de copyright
© 2022. The Author(s).
Références
Microorganisms. 2020 Oct 27;8(11):
pubmed: 33121104
Environ Pollut. 2021 Apr 15;275:116639
pubmed: 33578318
J Hazard Mater. 2021 Aug 5;415:125727
pubmed: 34088197
Ecotoxicol Environ Saf. 2013 Feb;88:9-15
pubmed: 23218497
J Environ Biol. 2005 Jun;26(2 Suppl):301-13
pubmed: 16334259
Genome Biol. 2011 Jun 24;12(6):R60
pubmed: 21702898
J Hazard Mater. 2021 Mar 15;406:124296
pubmed: 33268205
Environ Microbiol. 2013 Oct;15(10):2829-40
pubmed: 23663419
Nat Rev Microbiol. 2011 Mar;9(3):177-92
pubmed: 21297669
Microbiol Res. 2009;164(3):352-63
pubmed: 17604613
Sci Total Environ. 2022 Jan 15;804:150162
pubmed: 34798730
J Hazard Mater. 2022 Apr 15;428:128246
pubmed: 35030484
BMC Biol. 2019 May 30;17(1):45
pubmed: 31146755
BMC Biol. 2014 Aug 22;12:69
pubmed: 25184604
Sci Total Environ. 2020 Dec 20;749:141555
pubmed: 32841857
Environ Sci Process Impacts. 2014 May;16(5):1015-21
pubmed: 24599331
Appl Microbiol Biotechnol. 1999 Jun;51(6):730-50
pubmed: 10422221
Mol Ecol. 2010 Mar;19 Suppl 1:21-31
pubmed: 20331767
Sci Total Environ. 2018 Dec 10;644:1591-1601
pubmed: 30743871
Environ Pollut. 2020 Jul;262:114328
pubmed: 32443216
Chemosphere. 2015 Nov;138:863-73
pubmed: 25576132
Microorganisms. 2021 Jan 12;9(1):
pubmed: 33445679
Nat Methods. 2016 Jul;13(7):581-3
pubmed: 27214047
Appl Environ Microbiol. 2009 Dec;75(23):7537-41
pubmed: 19801464
J Zhejiang Univ Sci B. 2007 Mar;8(3):192-207
pubmed: 17323432
Environ Pollut. 2008 Jan;151(1):67-78
pubmed: 17481789
BMC Microbiol. 2009 Jan 08;9:4
pubmed: 19128515
J Hazard Mater. 2007 Jul 19;146(1-2):270-7
pubmed: 17218056
J Ind Microbiol. 1995 Feb;14(2):164-8
pubmed: 7766209
Microb Ecol. 1996 May;31(3):249-68
pubmed: 8661531
Int J Phytoremediation. 2020;22(10):1048-1058
pubmed: 32062985
Int J Biol Macromol. 2021 Jul 1;182:1528-1536
pubmed: 34022308
Microbiome. 2018 Dec 17;6(1):226
pubmed: 30558668
Environ Microbiol. 2003 Dec;5(12):1242-56
pubmed: 14641571
Environ Int. 2008 Aug;34(6):821-38
pubmed: 18054081
Ecotoxicol Environ Saf. 2019 Jan 30;168:450-456
pubmed: 30415167
Microb Ecol. 2023 Jan;85(1):100-107
pubmed: 34997311
Microb Ecol. 2019 May;77(4):993-1013
pubmed: 30467715
Sci Total Environ. 2016 Jul 1;557-558:785-90
pubmed: 27046142
Science. 2014 May 16;344(6185):691-2
pubmed: 24833374
ISME J. 2021 Oct;15(10):2853-2864
pubmed: 33846564
Int J Mol Sci. 2016 Jun 14;17(6):
pubmed: 27314330
Bioresour Technol. 2006 May;97(8):1018-25
pubmed: 16324839
Environ Pollut. 2020 Oct 12;273:115667
pubmed: 33497944
Science. 2005 Apr 22;308(5721):554-7
pubmed: 15845853
Soil Use Manag. 2015 Oct;31(Suppl Suppl 1):1-15
pubmed: 27667890
PLoS One. 2009 Jul 27;4(7):e6372
pubmed: 19633714
Front Microbiol. 2020 Dec 21;11:582016
pubmed: 33408701
J Environ Sci (China). 2011;23(5):824-30
pubmed: 21790056
Biotechnol Rep (Amst). 2016 Dec 23;13:58-71
pubmed: 28352564
Biodegradation. 2011 Jul;22(4):687-98
pubmed: 21053056
Appl Environ Microbiol. 2020 Jan 7;86(2):
pubmed: 31704678
Microb Ecol. 2006 Feb;51(2):209-19
pubmed: 16463132
Nucleic Acids Res. 2016 Jan 4;44(D1):D67-72
pubmed: 26590407
Plasmid. 1992 Jan;27(1):17-28
pubmed: 1741458
Biotechnol Rep (Amst). 2020 Apr 09;26:e00452
pubmed: 32617263
Environ Sci Technol. 2021 Oct 19;55(20):14258-14268
pubmed: 34585579
Microb Biotechnol. 2017 Sep;10(5):1244-1249
pubmed: 28834380
Environ Pollut. 2017 Dec;231(Pt 1):589-600
pubmed: 28843898
Sci Total Environ. 2017 Dec 15;605-606:436-444
pubmed: 28672232
Nat Commun. 2018 Jul 16;9(1):2738
pubmed: 30013066
Chemosphere. 2022 Jan;286(Pt 3):131899
pubmed: 34426292
J Environ Manage. 2019 Aug 15;244:313-319
pubmed: 31129463
Fungal Biol. 2011 Dec;115(12):1197-209
pubmed: 22115439