Functional activity and functional gene diversity of a Cu-contaminated soil remediated by aided phytostabilization using compost, dolomitic limestone and a mixed tree stand
Abstract
Trace elements (TEs) availability, biochemical activity and functional gene diversity was studied in a Cu-contaminated soil, revegetated for six years with a mixed stand of willow, black poplar, and false indigo-bush, and amended or not with compost plus dolomitic limestone (OMDL). The OMDL amendment significantly reduced Cu and As availability and soil toxicity, and increased the biochemical activity and microbial functional diversity assessed with the GEOCHIP technique, as compared to the unamended soil (Unt). The OMDL soil showed significantly higher abundance of 25 functional genes involved in decomposition organic compounds, and 11, 3 and 11 functional genes involved in the N, P and S biogeochemical cycles. Functional gene abundance was positively correlated with nutrient contents but negatively correlated with Cu availability and soil toxicity. The abundance of microbial functional genes encoding for resistance to various TEs also increased, possibly due to the microbial proliferation and lower Cu exposure in the presence of high total soil Cu concentration. Genes encoding for antibiotic resistance due to the co-occurrence of TEs and antibiotic resistant genes on genetic mobile elements. Finally, overall, phytomanagement confirmed its potential to restore the biological fertility and diversity of a severely Cu-contaminated soil, but the increase of TEs andmore »
- Authors:
-
[2];
[4]
- Univ. of Chinese Academy of Sciences, Beijing (China). College of Resources and Environment; Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics and Dept. of Botany and Microbiology
- Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics and Dept. of Botany and Microbiology
- Univ. of Bordeaux, Pessac Cedex (France). BIOGECO, INRA
- Univ. of Florence (Italy). Dept. of Agrifood Production and Environmental Sciences
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1479455
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Environmental Pollution
- Additional Journal Information:
- Journal Volume: 242; Journal Issue: PA; Journal ID: ISSN 0269-7491
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES; Antibiotic resistance; Functional gene diversity; Metal resistance; Phytomanagement; Soil contamination; Soil functionality
Citation Formats
Xue, Kai, Zhou, Jizhong, Van Nostrand, Joy, Mench, Michel, Bes, Clemence, Giagnoni, Laura, and Renella, Giancarlo. Functional activity and functional gene diversity of a Cu-contaminated soil remediated by aided phytostabilization using compost, dolomitic limestone and a mixed tree stand. United States: N. p., 2018.
Web. doi:10.1016/j.envpol.2018.06.057.
Xue, Kai, Zhou, Jizhong, Van Nostrand, Joy, Mench, Michel, Bes, Clemence, Giagnoni, Laura, & Renella, Giancarlo. Functional activity and functional gene diversity of a Cu-contaminated soil remediated by aided phytostabilization using compost, dolomitic limestone and a mixed tree stand. United States. https://doi.org/10.1016/j.envpol.2018.06.057
Xue, Kai, Zhou, Jizhong, Van Nostrand, Joy, Mench, Michel, Bes, Clemence, Giagnoni, Laura, and Renella, Giancarlo. Thu .
"Functional activity and functional gene diversity of a Cu-contaminated soil remediated by aided phytostabilization using compost, dolomitic limestone and a mixed tree stand". United States. https://doi.org/10.1016/j.envpol.2018.06.057. https://www.osti.gov/servlets/purl/1479455.
@article{osti_1479455,
title = {Functional activity and functional gene diversity of a Cu-contaminated soil remediated by aided phytostabilization using compost, dolomitic limestone and a mixed tree stand},
author = {Xue, Kai and Zhou, Jizhong and Van Nostrand, Joy and Mench, Michel and Bes, Clemence and Giagnoni, Laura and Renella, Giancarlo},
abstractNote = {Trace elements (TEs) availability, biochemical activity and functional gene diversity was studied in a Cu-contaminated soil, revegetated for six years with a mixed stand of willow, black poplar, and false indigo-bush, and amended or not with compost plus dolomitic limestone (OMDL). The OMDL amendment significantly reduced Cu and As availability and soil toxicity, and increased the biochemical activity and microbial functional diversity assessed with the GEOCHIP technique, as compared to the unamended soil (Unt). The OMDL soil showed significantly higher abundance of 25 functional genes involved in decomposition organic compounds, and 11, 3 and 11 functional genes involved in the N, P and S biogeochemical cycles. Functional gene abundance was positively correlated with nutrient contents but negatively correlated with Cu availability and soil toxicity. The abundance of microbial functional genes encoding for resistance to various TEs also increased, possibly due to the microbial proliferation and lower Cu exposure in the presence of high total soil Cu concentration. Genes encoding for antibiotic resistance due to the co-occurrence of TEs and antibiotic resistant genes on genetic mobile elements. Finally, overall, phytomanagement confirmed its potential to restore the biological fertility and diversity of a severely Cu-contaminated soil, but the increase of TEs and antibiotic resistant gene abundances deserve attention in future studies.},
doi = {10.1016/j.envpol.2018.06.057},
journal = {Environmental Pollution},
number = PA,
volume = 242,
place = {United States},
year = {2018},
month = {11}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 9 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Molecular Mechanisms of Antibacterial Multidrug Resistance
journal, March 2007
- Alekshun, Michael N.; Levy, Stuart B.
- Cell, Vol. 128, Issue 6, p. 1037-1050
Call of the wild: antibiotic resistance genes in natural environments
journal, March 2010
- Allen, Heather K.; Donato, Justin; Wang, Helena Huimi
- Nature Reviews Microbiology, Vol. 8, Issue 4
Evolution and ecology of antibiotic resistance genes
journal, June 2007
- Aminov, Rustam I.; Mackie, Roderick I.
- FEMS Microbiology Letters, Vol. 271, Issue 2
Composition, biomass and activity of microflora, and leaf yields and foliar elemental concentrations of lettuce, after in situ stabilization of an arsenic-contaminated soil
journal, March 2009
- Ascher, J.; Ceccherini, M. T.; Landi, L.
- Applied Soil Ecology, Vol. 41, Issue 3
Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing “Stress-on-Stress” Responses
journal, June 2016
- Azarbad, Hamed; van Gestel, Cornelis; Niklińska, Maria
- International Journal of Molecular Sciences, Vol. 17, Issue 6
Co-selection of antibiotic and metal resistance
journal, April 2006
- Baker-Austin, Craig; Wright, Meredith S.; Stepanauskas, Ramunas
- Trends in Microbiology, Vol. 14, Issue 4
Antibiotic resistance genes in the environment: prioritizing risks
journal, April 2015
- Bengtsson-Palme, Johan; Larsson, D. G. Joakim
- Nature Reviews Microbiology, Vol. 13, Issue 6
Spatial variation of plant communities and shoot Cu concentrations of plant species at a timber treatment site
journal, October 2009
- Bes, Clémence M.; Mench, Michel; Aulen, Maurice
- Plant and Soil, Vol. 330, Issue 1-2
Gas Chromatographic Analysis of Soil Atmospheres
journal, September 1977
- Blackmer, A. M.; Bremner, J. M.
- Soil Science Society of America Journal, Vol. 41, Issue 5
Phosphodiesterase Activity of Soils
journal, March 1978
- Browman, M. G.; Tabatabai, M. A.
- Soil Science Society of America Journal, Vol. 42, Issue 2
Updated Functional Classification of -Lactamases
journal, December 2009
- Bush, K.; Jacoby, G. A.
- Antimicrobial Agents and Chemotherapy, Vol. 54, Issue 3
A comparison of methods for measuring ATP in soil
journal, January 1990
- Ciardi, C.; Nannipieri, P.
- Soil Biology and Biochemistry, Vol. 22, Issue 5
The metagenomics of soil
journal, June 2005
- Daniel, Rolf
- Nature Reviews Microbiology, Vol. 3, Issue 6
Influence of Soil Organic Matter on Copper Extraction from Contaminated Soil
journal, April 2007
- Di Palma, L.; Ferrantelli, P.; Merli, C.
- Soil and Sediment Contamination: An International Journal, Vol. 16, Issue 3
Impact of river overflowing on trace element contamination of volcanic soils in south Italy: Part II. Soil biological and biochemical properties in relation to trace element speciation
journal, November 2006
- D'Ascoli, R.; Rao, M. A.; Adamo, P.
- Environmental Pollution, Vol. 144, Issue 1
Impact of Metal Pollution and Thlaspi caerulescens Growth on Soil Microbial Communities
journal, December 2010
- Epelde, Lur; Becerril, José M.; Kowalchuk, George A.
- Applied and Environmental Microbiology, Vol. 76, Issue 23
Soil contamination near non-ferrous metal smelters: A review
journal, January 2016
- Ettler, Vojtěch
- Applied Geochemistry, Vol. 64
Bacterial diversity promotes community stability and functional resilience after perturbation
journal, March 2005
- Girvan, M. S.; Campbell, C. D.; Killham, K.
- Environmental Microbiology, Vol. 7, Issue 3
GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
journal, May 2007
- He, Zhili; Gentry, Terry J.; Schadt, Christopher W.
- The ISME Journal, Vol. 1, Issue 1
Ambient Copper Concentrations in Agricultural and Natural European Soils: an Overview
journal, January 2006
- Heijerick, Dagobert G.; Van Sprang, Patrick A.; Van Hyfte, Annick D.
- Environmental Toxicology and Chemistry, Vol. 25, Issue 3
Bacterial antimicrobial metal ion resistance
journal, May 2015
- Hobman, Jon L.; Crossman, Lisa C.
- Journal of Medical Microbiology, Vol. 64, Issue 5
A comparison of technologies for remediation of heavy metal contaminated soils
journal, November 2017
- Khalid, Sana; Shahid, Muhammad; Niazi, Nabeel Khan
- Journal of Geochemical Exploration, Vol. 182
Soil extracellular enzyme activities correspond with abiotic factors more than fungal community composition
journal, April 2013
- Kivlin, Stephanie N.; Treseder, Kathleen K.
- Biogeochemistry, Vol. 117, Issue 1
Contamination of vineyard soils with fungicides: A review of environmental and toxicological aspects
journal, January 2010
- Komárek, Michael; Čadková, Eva; Chrastný, Vladislav
- Environment International, Vol. 36, Issue 1
Microbial biomass, respiration and enzyme activities after in situ aided phytostabilization of a Pb- and Cu-contaminated soil
journal, January 2009
- Kumpiene, J.; Guerri, G.; Landi, L.
- Ecotoxicology and Environmental Safety, Vol. 72, Issue 1
Assessment of Methods for Determining Bioavailability of Trace Elements in Soils: A Review
journal, June 2017
- Kumpiene, Jurate; Giagnoni, Laura; Marschner, Bernd
- Pedosphere, Vol. 27, Issue 3
Short-term assays of soil proteolytic enzyme activities using proteins and dipeptide derivatives as substrates
journal, February 1972
- Ladd, J. N.; Butler, J. H. A.
- Soil Biology and Biochemistry, Vol. 4, Issue 1
Copper distribution and hydrolase activities in a contaminated soil amended with dolomitic limestone and compost
journal, October 2011
- Lagomarsino, A.; Mench, M.; Marabottini, R.
- Ecotoxicology and Environmental Safety, Vol. 74, Issue 7
Automated color correction method for Vibrio fischeri toxicity test. Comparison of standard and kinetic assays
journal, November 2001
- Lappalainen, Juha; Juvonen, Risto; Nurmi, Johanna
- Chemosphere, Vol. 45, Issue 4-5
Copper Dynamics and Impact on Microbial Communities in Soils of Variable Organic Status
journal, April 2008
- Lejon, David P. H.; Martins, Jean M. F.; Lévêque, Jean
- Environmental Science & Technology, Vol. 42, Issue 8
Assessment of Ecotoxicity of Topsoils from a Wood Treatment Site
journal, April 2009
- Mench, M.; Bes, C.
- Pedosphere, Vol. 19, Issue 2
Biochemical parameters and bacterial species richness in soils contaminated by sludge-borne metals and remediated with inorganic soil amendments
journal, November 2006
- Mench, Michel; Renella, Giancarlo; Gelsomino, Antonio
- Environmental Pollution, Vol. 144, Issue 1
Successes and limitations of phytotechnologies at field scale: outcomes, assessment and outlook from COST Action 859
journal, February 2010
- Mench, Michel; Lepp, Nick; Bert, Valérie
- Journal of Soils and Sediments, Vol. 10, Issue 6
Extent of copper tolerance and consequences for functional stability of the ammonia-oxidizing community in long-term copper-contaminated soils
journal, January 2010
- Mertens, Jelle; Wakelin, Steven A.; Broos, Kris
- Environmental Toxicology and Chemistry, Vol. 29, Issue 1
Use of 0·1 m pyrophosphate to extract urease from a podzol
journal, December 1974
- Nannipieri, P.; Ceccanti, B.; Cervelli, S.
- Soil Biology and Biochemistry, Vol. 6, Issue 6
Microbial heavy-metal resistance
journal, June 1999
- Nies, D. H.
- Applied Microbiology and Biotechnology, Vol. 51, Issue 6
A kinetic study of chelant-assisted remediation of contaminated dredged sediment
journal, October 2006
- Polettini, A.; Pomi, R.; Rolle, E.
- Journal of Hazardous Materials, Vol. 137, Issue 3
Interactions between metals and soil organic matter in various particle size fractions of soil contaminated with waste water
journal, March 2009
- Quenea, K.; Lamy, I.; Winterton, P.
- Geoderma, Vol. 149, Issue 3-4
Operationally defined extraction procedures for soil and sediment analysis I. Standardization
journal, May 1998
- Quevauviller, P.
- TrAC Trends in Analytical Chemistry, Vol. 17, Issue 5
Assessing phytotoxicity of trace element-contaminated soils phytomanaged with gentle remediation options at ten European field trials
journal, December 2017
- Quintela-Sabarís, Celestino; Marchand, Lilian; Kidd, Petra S.
- Science of The Total Environment, Vol. 599-600
Phytoremediation of metals: using plants to remove pollutants from the environment
journal, April 1997
- Raskin, Ilya; Smith, Robert D.; Salt, David E.
- Current Opinion in Biotechnology, Vol. 8, Issue 2
Availability and speciation of cadmium added to a calcareous soil under various managements: Availability and speciation of cadmium in soil
journal, December 2003
- Renella, G.; Adamo, P.; Bianco, M. R.
- European Journal of Soil Science, Vol. 55, Issue 1
Microbial activity and hydrolase activities during decomposition of root exudates released by an artificial root surface in Cd-contaminated soils
journal, April 2006
- Renella, Giancarlo; Egamberdiyeva, Dilfuza; Landi, Loretta
- Soil Biology and Biochemistry, Vol. 38, Issue 4
Long-term effects of aided phytostabilisation of trace elements on microbial biomass and activity, enzyme activities, and composition of microbial community in the Jales contaminated mine spoils
journal, April 2008
- Renella, Giancarlo; Landi, Loretta; Ascher, Judith
- Environmental Pollution, Vol. 152, Issue 3
Miscellaneous additives can enhance plant uptake and affect geochemical fractions of copper in a heavily polluted riparian grassland soil
journal, September 2015
- Rinklebe, Jörg; Shaheen, Sabry M.
- Ecotoxicology and Environmental Safety, Vol. 119
Short Rotation Coppice Culture of Willows and Poplars as Energy Crops on Metal Contaminated Agricultural Soils
journal, January 2011
- Ruttens, Ann; Boulet, Jana; Weyens, Nele
- International Journal of Phytoremediation, Vol. 13, Issue sup1
Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution
journal, November 1999
- Sandaa, Ruth-Anne; Torsvik, Vigdis; Enger, ÃIvind
- FEMS Microbiology Ecology, Vol. 30, Issue 3
Copper Inhibition of soil Organic Matter Decomposition in a Seventy-Year Field Exposure
journal, January 2006
- Sauvé, Sébastien
- Environmental Toxicology and Chemistry, Vol. 25, Issue 3
Greenhouse gas emissions from a Cu-contaminated soil remediated by in situ stabilization and phytomanaged by a mixed stand of poplar, willows, and false indigo-bush
journal, November 2017
- Šimek, M.; Elhottová, D.; Mench, M.
- International Journal of Phytoremediation, Vol. 19, Issue 11
Can landscape ecology untangle the complexity of antibiotic resistance?
journal, December 2006
- Singer, Randall S.; Ward, Michael P.; Maldonado, George
- Nature Reviews Microbiology, Vol. 4, Issue 12
Soil genomics
journal, August 2009
- Singh, Brajesh K.; Campbell, Colin D.; Sorenson, Soren J.
- Nature Reviews Microbiology, Vol. 7, Issue 10
Coselection for microbial resistance to metals and antibiotics in freshwater microcosms
journal, September 2006
- Stepanauskas, Ramunas; Glenn, Travis C.; Jagoe, Charles H.
- Environmental Microbiology, Vol. 8, Issue 9
Use of p-nitrophenyl phosphate for assay of soil phosphatase activity
journal, November 1969
- Tabatabai, M. A.; Bremner, J. M.
- Soil Biology and Biochemistry, Vol. 1, Issue 4
Arylsulfatase Activity of Soils
journal, March 1970
- Tabatabai, M. A.; Bremner, J. M.
- Soil Science Society of America Journal, Vol. 34, Issue 2
Microbial diversity and function in soil: from genes to ecosystems
journal, June 2002
- Torsvik, Vigdis; Øvreås, Lise
- Current Opinion in Microbiology, Vol. 5, Issue 3, p. 240-245
Heavy metals in agricultural soils of the European Union with implications for food safety
journal, March 2016
- Tóth, G.; Hermann, T.; Da Silva, M. R.
- Environment International, Vol. 88
Copper extraction effectiveness and soil dissolution issues of EDTA-flushing of artificially contaminated soils
journal, June 2007
- Tsang, Daniel C. W.; Zhang, Weihua; Lo, Irene M. C.
- Chemosphere, Vol. 68, Issue 2
Heavy-metal ecology of terrestrial plants, microorganisms and invertebrates: A review
journal, October 1989
- Tyler, G.; P�hlsson, A. - M. Balsberg; Bengtsson, G.
- Water, Air, and Soil Pollution, Vol. 47, Issue 3-4
Safe use of metal-contaminated agricultural land by cultivation of energy maize (Zea mays)
journal, July 2013
- Van Slycken, S.; Witters, N.; Meers, E.
- Environmental Pollution, Vol. 178
Bark decay by the white-rot fungus Lentinula edodes: Polysaccharide loss, lignin resistance and the unmasking of suberin
journal, January 2006
- Vane, Christopher H.; Drage, Trevor C.; Snape, Colin E.
- International Biodeterioration & Biodegradation, Vol. 57, Issue 1
A Critical Examination of a Rapid Method for Determining Organic Carbon in Soils—Effect of Variations in Digestion Conditions and of Inorganic soil Constituents
journal, January 1947
- Walkley, Allan
- Soil Science, Vol. 63, Issue 4
Phytoremediation, a sustainable remediation technology? II: Economic assessment of CO2 abatement through the use of phytoremediation crops for renewable energy production
journal, April 2012
- Witters, N.; Mendelsohn, R.; Van Passel, S.
- Biomass and Bioenergy, Vol. 39
Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands
journal, December 2012
- Xue, Kai; Wu, Liyou; Deng, Ye
- Applied and Environmental Microbiology, Vol. 79, Issue 4
Management with willow short rotation coppice increase the functional gene diversity and functional activity of a heavy metal polluted soil
journal, November 2015
- Xue, K.; van Nostrand, J. D.; Vangronsveld, J.
- Chemosphere, Vol. 138
DNA recovery from soils of diverse composition.
journal, January 1996
- Zhou, J.; Bruns, M. A.; Tiedje, J. M.
- Applied and environmental microbiology, Vol. 62, Issue 2
A protocol for the assay of arylesterase activity in soil
journal, March 2009
- Zornoza, Raul; Landi, Loretta; Nannipieri, Paolo
- Soil Biology and Biochemistry, Vol. 41, Issue 3
Arylesterase activity in trace element contaminated soils
journal, February 2011
- Renella, G.; Zornoza, R.; Landi, L.
- European Journal of Soil Science, Vol. 62, Issue 4
Works referencing / citing this record:
Effect of Liming with Various Water Regimes on Both Immobilization of Cadmium and Improvement of Bacterial Communities in Contaminated Paddy: A Field Experiment
journal, February 2019
- Shi, Lei; Guo, Zhaohui; Liang, Fang
- International Journal of Environmental Research and Public Health, Vol. 16, Issue 3
Identification of new microbial functional standards for soil quality assessment
journal, January 2020
- Thiele-Bruhn, Sören; Schloter, Michael; Wilke, Berndt-Michael
- SOIL, Vol. 6, Issue 1
Soils from an iron and steel scrap storage yard remediated with aided phytostabilization
journal, November 2018
- Radziemska, Maja; Koda, Eugeniusz; Vaverkovà, Magdalena D.
- Land Degradation & Development, Vol. 30, Issue 2