Articles | Volume 10, issue 2
https://doi.org/10.5194/soil-10-551-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/soil-10-551-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Original research article
| 
19 Aug 2024
Original research article |
| 19 Aug 2024
| 19 Aug 2024
Long-term legacy of phytoremediation on plant succession and soil microbial communities in petroleum-contaminated sub-Arctic soils
Mary-Cathrine Leewis
CORRESPONDING AUTHOR
Agriculture and Agri-Food Canada, Québec, G1V 2J3, Canada
Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, 99775, USA
Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, 99775, USA
Christopher Kasanke
Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, 99775, USA
Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, 99775, USA
Walla Walla Community College, Walla Walla, 99362, USA
Ondrej Uhlik
Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, 160 00, Czechia
Mary Beth Leigh
Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, 99775, USA
Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, 99775, USA
Related subject area
Soil pollution and remediation
Investigating the synergistic potential of Si and biochar to immobilize Ni in a Ni-contaminated calcareous soil after Zea mays L. cultivation
Estimations of soil metal accumulation or leaching potentials under climate change scenarios: the example of copper on a European scale
Model-based analysis of erosion-induced microplastic delivery from arable land to the stream network of a mesoscale catchment
Increase in bacterial community induced tolerance to Cr in response to soil properties and Cr level in the soil
Organic and inorganic nitrogen amendments reduce biodegradation of biodegradable plastic mulch films
Research and management challenges following soil and landscape decontamination at the onset of the reopening of the Difficult-to-Return Zone, Fukushima (Japan)
Impact of agricultural management on soil aggregates and associated organic carbon fractions: analysis of long-term experiments in Europe
Miniaturised visible and near-infrared spectrometers for assessing soil health indicators in mine site rehabilitation
The application of biochar and oyster shell reduced cadmium uptake by crops and modified soil fertility and enzyme activities in contaminated soil
Reusing Fe water treatment residual as a soil amendment to improve physical function and flood resilience
Are agricultural plastic covers a source of plastic debris in soil? A first screening study
Mapping soil slaking index and assessing the impact of management in a mixed agricultural landscape
Assessing soil salinity dynamics using time-lapse electromagnetic conductivity imaging
Effectiveness of landscape decontamination following the Fukushima nuclear accident: a review
Evaluating the carbon sequestration potential of volcanic soils in southern Iceland after birch afforestation
Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms
Development of a statistical tool for the estimation of riverbank erosion probability
Sediment loss and its cause in Puerto Rico watersheds
Carbon nanomaterials in clean and contaminated soils: environmental implications and applications
Hamid Reza Boostani, Ailsa G. Hardie, Mahdi Najafi-Ghiri, Ehsan Bijanzadeh, Dariush Khalili, and Esmaeil Farrokhnejad
SOIL, 10, 487–503, https://doi.org/10.5194/soil-10-487-2024, https://doi.org/10.5194/soil-10-487-2024, 2024
Short summary
Short summary
In this work, the combined SM500 + S2 treatment was the most effective with respect to reducing the Ni water-soluble and exchangeable fraction. Application of Si and biochars decreased the soil Ni diethylenetriaminepentaacetic acid and corn Ni shoot content. The study shows the synergistic potential of Si and sheep manure biochars for immobilizing soil Ni.
Laura Sereni, Julie-Maï Paris, Isabelle Lamy, and Bertrand Guenet
SOIL, 10, 367–380, https://doi.org/10.5194/soil-10-367-2024, https://doi.org/10.5194/soil-10-367-2024, 2024
Short summary
Short summary
We estimate the tendencies of copper (Cu) export in freshwater or accumulation in soils in Europe for the 21st century and highlight areas of importance for environmental monitoring. We develop a method combining computations of Cu partitioning coefficients between solid and solution phases with runoff data. The surfaces with potential for export or accumulation are roughly constant over the century, but the accumulation potential of Cu increases while leaching potential decreases for 2000–2095.
Raphael Rehm and Peter Fiener
SOIL, 10, 211–230, https://doi.org/10.5194/soil-10-211-2024, https://doi.org/10.5194/soil-10-211-2024, 2024
Short summary
Short summary
A carbon transport model was adjusted to study the importance of water and tillage erosion processes for particular microplastic (MP) transport across a mesoscale landscape. The MP mass delivered into the stream network represented a serious amount of MP input in the same range as potential MP inputs from wastewater treatment plants. In addition, most of the MP applied to arable soils remains in the topsoil (0–20 cm) for decades. The MP sink function of soil results in a long-term MP source.
Claudia Campillo-Cora, Daniel Arenas-Lago, Manuel Arias-Estévez, and David Fernández-Calviño
SOIL, 9, 561–571, https://doi.org/10.5194/soil-9-561-2023, https://doi.org/10.5194/soil-9-561-2023, 2023
Short summary
Short summary
Cr pollution is a global concern. The use of methodologies specifically related to Cr toxicity is appropriate, such as the pollution-induced community tolerance (PICT) methodology. The development of PICT was determined in 10 soils after Cr addition in the laboratory. The Cr-soluble fraction and dissolved organic carbon were the main variables determining the development of PICT (R2 = 95.6 %).
Sreejata Bandopadhyay, Marie English, Marife B. Anunciado, Mallari Starrett, Jialin Hu, José E. Liquet y González, Douglas G. Hayes, Sean M. Schaeffer, and Jennifer M. DeBruyn
SOIL, 9, 499–516, https://doi.org/10.5194/soil-9-499-2023, https://doi.org/10.5194/soil-9-499-2023, 2023
Short summary
Short summary
We added organic and inorganic nitrogen amendments to two soil types in a laboratory incubation study in order to understand how that would impact biodegradable plastic mulch (BDM) decomposition. We found that nitrogen amendments, particularly urea and inorganic nitrogen, suppressed BDM degradation in both soil types. However, we found limited impact of BDM addition on soil nitrification, suggesting that overall microbial processes were not compromised due to the addition of BDMs.
Olivier Evrard, Thomas Chalaux-Clergue, Pierre-Alexis Chaboche, Yoshifumi Wakiyama, and Yves Thiry
SOIL, 9, 479–497, https://doi.org/10.5194/soil-9-479-2023, https://doi.org/10.5194/soil-9-479-2023, 2023
Short summary
Short summary
Twelve years after the nuclear accident that occurred in Fukushima in March 2011, radioactive contamination remains a major concern in north-eastern Japan. The Japanese authorities completed an unprecedented decontamination programme. The central objective was to not expose local inhabitants to excessive radioactive doses. At the onset of the full reopening of the Difficult-to-Return Zone in 2023, the current review provides an update of a previous synthesis published in 2019.
Ioanna S. Panagea, Antonios Apostolakis, Antonio Berti, Jenny Bussell, Pavel Čermak, Jan Diels, Annemie Elsen, Helena Kusá, Ilaria Piccoli, Jean Poesen, Chris Stoate, Mia Tits, Zoltan Toth, and Guido Wyseure
SOIL, 8, 621–644, https://doi.org/10.5194/soil-8-621-2022, https://doi.org/10.5194/soil-8-621-2022, 2022
Short summary
Short summary
The potential to reverse the negative effects caused in topsoil by inversion tillage, using alternative agricultural practices, was evaluated. Reduced and no tillage, and additions of manure/compost, improved topsoil structure and OC content. Residue retention had a positive impact on structure. We concluded that the negative effects of inversion tillage can be mitigated by reducing tillage intensity or adding organic materials, optimally combined with non-inversion tillage.
Zefang Shen, Haylee D'Agui, Lewis Walden, Mingxi Zhang, Tsoek Man Yiu, Kingsley Dixon, Paul Nevill, Adam Cross, Mohana Matangulu, Yang Hu, and Raphael A. Viscarra Rossel
SOIL, 8, 467–486, https://doi.org/10.5194/soil-8-467-2022, https://doi.org/10.5194/soil-8-467-2022, 2022
Short summary
Short summary
We compared miniaturised visible and near-infrared spectrometers to a portable visible–near-infrared instrument, which is more expensive. Statistical and machine learning algorithms were used to model 29 key soil health indicators. Accuracy of the miniaturised spectrometers was comparable to the portable system. Soil spectroscopy with these tiny sensors is cost-effective and could diagnose soil health, help monitor soil rehabilitation, and deliver positive environmental and economic outcomes.
Bin Wu, Jia Li, Mingping Sheng, He Peng, Dinghua Peng, and Heng Xu
SOIL, 8, 409–419, https://doi.org/10.5194/soil-8-409-2022, https://doi.org/10.5194/soil-8-409-2022, 2022
Short summary
Short summary
Cadmium (Cd) contamination in soil has severely threatened human health. In this study, we investigated the possibility of applying oyster shell and biochar to reduce Cd uptake by crops and improve soil fertility and enzyme activities in field experiments under rice–oilseed rape rotation, which provided an economical and effective pathway to achieving an in situ remediation of the Cd-contaminated farmland.
Heather C. Kerr, Karen L. Johnson, and David G. Toll
SOIL, 8, 283–295, https://doi.org/10.5194/soil-8-283-2022, https://doi.org/10.5194/soil-8-283-2022, 2022
Short summary
Short summary
Adding an organo-mineral waste product from clean water treatment (WTR) is beneficial for a soil’s water retention, permeability, and strength properties. WTR added on its own significantly improves the shear strength and saturated hydraulic conductivity of soil. The co-application of WTR with compost provides the same benefits whilst also improving soil’s water retention properties, which is beneficial for environmental applications where the soil health is critical.
Zacharias Steinmetz, Paul Löffler, Silvia Eichhöfer, Jan David, Katherine Muñoz, and Gabriele E. Schaumann
SOIL, 8, 31–47, https://doi.org/10.5194/soil-8-31-2022, https://doi.org/10.5194/soil-8-31-2022, 2022
Short summary
Short summary
To scrutinize the contribution of agricultural plastic covers to plastic pollution, we quantified soil-associated plastic debris (≤ 2 mm) in and around agricultural fields covered with different plastics. PP fleeces and 50 µm thick PE films did not emit significant amounts of plastic debris into soil during their 4-month use. However, thinner and perforated PE foils (40 µm) were associated with elevated PE contents of up to 35 mg kg−1. Their long-term use may thus favor plastic accumulation.
Edward J. Jones, Patrick Filippi, Rémi Wittig, Mario Fajardo, Vanessa Pino, and Alex B. McBratney
SOIL, 7, 33–46, https://doi.org/10.5194/soil-7-33-2021, https://doi.org/10.5194/soil-7-33-2021, 2021
Short summary
Short summary
Soil physical health is integral to maintaining functional agro-ecosystems. A novel method of assessing soil physical condition using a smartphone app has been developed – SLAKES. In this study the SLAKES app was used to investigate aggregate stability in a mixed agricultural landscape. Cropping areas were found to have significantly poorer physical health than similar soils under pasture. Results were mapped across the landscape to identify problem areas and pinpoint remediation efforts.
Maria Catarina Paz, Mohammad Farzamian, Ana Marta Paz, Nádia Luísa Castanheira, Maria Conceição Gonçalves, and Fernando Monteiro Santos
SOIL, 6, 499–511, https://doi.org/10.5194/soil-6-499-2020, https://doi.org/10.5194/soil-6-499-2020, 2020
Short summary
Short summary
In this study electromagnetic induction (EMI) surveys and soil sampling were repeated over time to monitor soil salinity dynamics in an important agricultural area that faces risk of soil salinization. EMI data were converted to electromagnetic conductivity imaging through a mathematical inversion algorithm and converted to 2-D soil salinity maps until a depth of 1.35 m through a regional calibration. This is a non-invasive and cost-effective methodology that can be employed over large areas.
Olivier Evrard, J. Patrick Laceby, and Atsushi Nakao
SOIL, 5, 333–350, https://doi.org/10.5194/soil-5-333-2019, https://doi.org/10.5194/soil-5-333-2019, 2019
Short summary
Short summary
The Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident in March 2011 resulted in the contamination of Japanese landscapes with radioactive fallout. The objective of this review is to provide an overview of the decontamination strategies and their potential effectiveness in Japan. Overall, we believe it is important to synthesise the remediation lessons learnt following the FDNPP nuclear accident, which could be fundamental if radioactive fallout occurred somewhere on Earth in the future.
Matthias Hunziker, Olafur Arnalds, and Nikolaus J. Kuhn
SOIL, 5, 223–238, https://doi.org/10.5194/soil-5-223-2019, https://doi.org/10.5194/soil-5-223-2019, 2019
Short summary
Short summary
Afforestation on severely degraded volcanic soils/landscapes is an important process concerning ecological restoration in Iceland. These landscapes have a high potential to act as carbon sinks. We tested the soil (0–30 cm) of different stages of afforested (mountain birch) landscapes and analysed the quantity and quality of the soil organic carbon. There is an increase in the total SOC stock during the encroachment. The increase is mostly because of POM SOC. Such soils demand SOC quality tests.
Belinda C. Martin, Suman J. George, Charles A. Price, Esmaeil Shahsavari, Andrew S. Ball, Mark Tibbett, and Megan H. Ryan
SOIL, 2, 487–498, https://doi.org/10.5194/soil-2-487-2016, https://doi.org/10.5194/soil-2-487-2016, 2016
Short summary
Short summary
The aim of this paper was to determine the impact of citrate and malonate on microbial activity and community structure in uncontaminated and diesel-contaminated soil. The results suggest that these carboxylates can stimulate microbial activity and alter microbial community structure but appear to have a minimal effect on enhancing degradation of diesel. However, our results suggest that carboxylates may have an important role in shaping microbial communities even in contaminated soils.
E. A. Varouchakis, G. V. Giannakis, M. A. Lilli, E. Ioannidou, N. P. Nikolaidis, and G. P. Karatzas
SOIL, 2, 1–11, https://doi.org/10.5194/soil-2-1-2016, https://doi.org/10.5194/soil-2-1-2016, 2016
Short summary
Short summary
A statistical methodology is proposed to predict the probability of presence or absence of erosion in a river section considering locally spatial correlated independent variables.
The proposed tool is easy to use and accurate and can be applied to any region and river. It requires information from easy-to-determine geomorphological and/or hydrological variables to provide the vulnerable locations. This tool could be used to assist in managing erosion and flooding events.
Y. Yuan, Y. Jiang, E. V. Taguas, E. G. Mbonimpa, and W. Hu
SOIL, 1, 595–602, https://doi.org/10.5194/soil-1-595-2015, https://doi.org/10.5194/soil-1-595-2015, 2015
Short summary
Short summary
A major environmental concern in the Commonwealth of Puerto Rico is increased sediment load to water reservoirs, to estuaries, and finally to coral reef areas. Our research found that sediment loss was mainly caused by interactions of development, heavy rainfall events, and steep mountainous slopes. These results improve our understanding of sediment loss resulting from changes in land use/cover, and will allow stakeholders to make more informed decisions about future land use planning.
M. J. Riding, F. L. Martin, K. C. Jones, and K. T. Semple
SOIL, 1, 1–21, https://doi.org/10.5194/soil-1-1-2015, https://doi.org/10.5194/soil-1-1-2015, 2015
Short summary
Short summary
The behaviour of carbon nanomaterials (CNMs) in soils is highly complex and dynamic. As a result, assessments of the possible risks CNMs pose within soil should be conducted on a case-by-case basis. Further work to assess the long-term stability and toxicity of CNM-sorbed contaminants, as well as the toxicity of CNMs themselves, is required to determine if their sorptive abilities can be applied to remedy environmental issues such as land contamination.
Cited articles
Akaçin, İ., Ersoy, Ş., Doluca, O., and Güngörmüşler, M.: Comparing the significance of the utilization of next generation and third generation sequencing technologies in microbial metagenomics, Microbiol. Res., 264, 127154, https://doi.org/10.1016/j.micres.2022.127154, 2022.
Alaska Department of Environmental Conservation Spill Prevention and Response: Contaminated Sites Database, https://dec.alaska.gov/Applications/SPAR/PublicMVC/CSP/Search/, last access: 24 June 2024.
Allison, S. D. and Treseder, K. K.: Climate change feedbacks to microbial decomposition in boreal soils, Fungal Ecol., 4, 362–374, https://doi.org/10.1016/j.funeco.2011.01.003, 2011.
Allison, S. D., Gartner, T. B., Mack, M. C., McGuire, K., and Treseder, K.: Nitrogen alters carbon dynamics during early succession in boreal forest, Soil Biol. Biochem., 42, 1157–1164, https://doi.org/10.1016/j.soilbio.2010.03.026, 2010.
Bell, T. H., Yergeau, E., Martineau, C., Juck, D., Whyte, L. G., and Greer, C. W.: Identification of Nitrogen-Incorporating Bacteria in Petroleum-Contaminated Arctic Soils by Using [15N]DNA-Based Stable Isotope Probing and Pyrosequencing, Appl. Environ. Microb., 77, 4163–4171, https://doi.org/10.1128/AEM.00172-11, 2011.
Bell, T. H., Yergeau, E., Juck, D. F., Whyte, L. G., and Greer, C. W.: Alteration of microbial community structure affects diesel biodegradation in an Arctic soil, FEMS Microbiol. Ecol., 85, 51–61, https://doi.org/10.1111/1574-6941.12102, 2013.
Bell, T. H., El-Din Hassan, S., Lauron-Moreau, A., Al-Otaibi, F., Hijri, M., Yergeau, E., and St-Arnaud, M.: Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny, ISME J., 8, 331–343, https://doi.org/10.1038/ismej.2013.149, 2014.
Blanchet, G., Gavazov, K., Bragazza, L., and Sinaj, S.: Responses of soil properties and crop yields to different inorganic and organic amendments in a Swiss conventional farming system, Agr. Ecosyst. Environ., 230, 116–126, https://doi.org/10.1016/j.agee.2016.05.032, 2016.
Brown, S. P. and Jumpponen, A.: Contrasting primary successional trajectories of fungi and bacteria in retreating glacier soils, Mol. Ecol., 23, 481–497, https://doi.org/10.1111/mec.12487, 2014.
Chen, Z., Chen, W., Leblanc, S. G., and Henry, G. H. R.: Digital Photograph Analysis for Measuring Percent Plant Cover in the Arctic, ARCTIC, 63, 261–379, https://doi.org/10.14430/arctic1495, 2010.
Clark, C. M., Cleland, E. E., Collins, S. L., Fargione, J. E., Gough, L., Gross, K. L., Pennings, S. C., Suding, K. N., and Grace, J. B.: Environmental and plant community determinants of species loss following nitrogen enrichment, Ecol. Lett., 10, 596–607, https://doi.org/10.1111/j.1461-0248.2007.01053.x, 2007.
Cleland, E. E. and Harpole, W. S.: Nitrogen enrichment and plant communities, Ann. NY Acad. Sci., 1195, 46–61, https://doi.org/10.1111/j.1749-6632.2010.05458.x, 2010.
Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T., Garrity, G. M., and Tiedje, J. M.: The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis, Nucleic Acids Res., 37, 141–145, https://doi.org/10.1093/nar/gkn879, 2009.
Cole, J. R., Wang, Q., Fish, J. A., Chai, B., McGarrell, D. M., Sun, Y., Brown, C. T., Porras-Alfaro, A., Kuske, C. R., and Tiedje, J. M.: Ribosomal Database Project: data and tools for high throughput rRNA analysis, Nucleic Acids Res., 42, D633–D642, https://doi.org/10.1093/nar/gkt1244, 2014.
Pier, M. D., Zeeb, B. a, and Reimer, K. J.: Patterns of contamination among vascular plants exposed to local sources of polychlorinated biphenyls in the Canadian Arctic and Subarctic, Sci. Total Environ., 297, 215–227, 2002.
Elshamy, M. M., Heikal, Y. M., and Bonanomi, G.: Phytoremediation efficiency of Portulaca oleracea L. naturally growing in some industrial sites, Dakahlia District, Egypt, Chemosphere, 225, 678–687, https://doi.org/10.1016/j.chemosphere.2019.03.099, 2019.
Ferrera-Rodríguez, O., Greer, C. W., Juck, D., Consaul, L. L., Martínez-Romero, E., Whyte, L. G., and Martı, E.: Hydrocarbon-degrading potential of microbial communities from Arctic plants, J. Appl. Microbiol., 114, 71–83, https://doi.org/10.1111/jam.12020, 2012.
Fletcher, J. S. and Hegde, R. S.: Release of phenols by perennial plant roots and their potential importance in bioremediation, Chemosphere, 31, 3009–3016, https://doi.org/10.1016/0045-6535(95)00161-Z, 1995.
Geisseler, D. and Scow, K. M.: Long-term effects of mineral fertilizers on soil microorganisms – A review, Soil Biol. Biochem., 75, 54–63, https://doi.org/10.1016/j.soilbio.2014.03.023, 2014.
Gerhardt, K. E., Huang, X.-D., Glick, B. R., and Greenberg, B. M.: Phytoremediation and rhizoremediation of organic soil contaminants: Potential and challenges, Plant Sci., 176, 20–30, https://doi.org/10.1016/j.plantsci.2008.09.014, 2009.
Glick, B. R.: Using soil bacteria to facilitate phytoremediation, Biotechnol. Adv., 28, 367–374, https://doi.org/10.1016/j.biotechadv.2010.02.001, 2010.
Goordial, J., Davila, A., Lacelle, D., Pollard, W., Marinova, M. M., Greer, C. W., Di Ruggiero, J., McKay, C. P., and Whyte, L. G.: Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica, ISME J., 10, 1613–1624, https://doi.org/10.1038/ismej.2015.239, 2016.
Haines, J. R., Wrenn, B. A., Holder, E. L., Strohmeier, K. L., Herrington, R. T., and Venosa, A. D.: Measurement of hydrocarbon-degrading microbial populations by a 96-well plate most-probable-number procedure, J. Ind. Microbiol., 16, 36–41, https://doi.org/10.1007/BF01569919, 1996.
Kaiser, C., Frank, A., Wild, B., Koranda, M., and Richter, A.: Negligible contribution from roots to soil-borne phospholipid fatty acid fungal biomarkers 18 : 2ω6,9 and 18 : 1ω9, Soil Biol. Biochem., 42, 1650–1652, https://doi.org/10.1016/j.soilbio.2010.05.019, 2010.
Knelman, J. E., Legg, T. M., O'Neill, S. P., Washenberger, C. L., González, A., Cleveland, C. C., and Nemergut, D. R.: Bacterial community structure and function change in association with colonizer plants during early primary succession in a glacier forefield, Soil Biol. Biochem., 46, 172–180, https://doi.org/10.1016/j.soilbio.2011.12.001, 2012.
Kuiper, I., Lagendijk, E. L., Bloemberg, G. V., and Lugtenberg, B. J. J.: Rhizoremediation: A Beneficial Plant-Microbe Interaction, Mol. Plant-Microbe Interact., 17, 6–15, https://doi.org/10.1094/MPMI.2004.17.1.6, 2004.
Lauber, C. L., Hamady, M., Knight, R., and Fierer, N.: Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale, Appl. Environ. Microbiol., 75, 5111–5120, https://doi.org/10.1128/AEM.00335-09, 2009.
Leewis, M.-C.: mcleewis/FarmersLoop: FarmersLoop_SOILpub (FarmersLoop_SOILpub), Zenodo [code], https://doi.org/10.5281/zenodo.13288502, 2024.
Leewis, M.-C., Reynolds, C. M., and Leigh, M. B.: Long-term effects of nutrient addition and phytoremediation on diesel and crude oil contaminated soils in subarctic Alaska, Cold Reg. Sci. Technol., 96, 129–137, https://doi.org/10.1016/j.coldregions.2013.08.011, 2013.
Leewis, M.-C., Uhlik, O., Fraraccio, S., McFarlin, K., Kottara, A., Glover, C., Macek, T., and Leigh, M. B.: Differential Impacts of Willow and Mineral Fertilizer on Bacterial Communities and Biodegradation in Diesel Fuel Oil-Contaminated Soil, Front. Microbiol., 7, 837, https://doi.org/10.3389/fmicb.2016.00837, 2016a.
Leewis, M.-C., Uhlik, O., and Leigh, M. B.: Synergistic Processing of Biphenyl and Benzoate: Carbon Flow Through the Bacterial Community in Polychlorinated-Biphenyl-Contaminated Soil, Sci. Rep., 6, 22145, https://doi.org/10.1038/srep22145, 2016b.
Leewis, M.-C., Lawrence, C. R., Schulz, M. S., Tfaily, M. M., Ayala-Ortiz, C. O., Flores, G. E., Mackelprang, R., and McFarland, J. W.: The influence of soil development on the depth distribution and structure of soil microbial communities, Soil Biol. Biochem., 174, 108808, https://doi.org/10.1016/j.soilbio.2022.108808, 2022.
Leigh, M. B. M. B., Fletcher, J. S. J. S., Fu, X., and Schmitz, F. J. F. J.: Root turnover: an important source of microbial substrates in rhizosphere remediation of recalcitrant contaminants, Environ. Sci. Technol., 36, 1579–1583, https://doi.org/10.1021/es015702i, 2002.
Liang, Y., Zhao, H., Deng, Y., Zhou, J., Li, G., Sun, B., Hug, L. A., Flynn, T. M., Sun, B., Liang, Y., Zhao, H., Deng, Y., Zhou, J., Li, G., and Sun, B.: Long-term oil contamination alters the molecular ecological networks of soil microbial functional genes, Front. Microbiol., 7, 1–13, https://doi.org/10.3389/fmicb.2016.00060, 2016.
Liu, W., Hou, J., Wang, Q., Yang, H., Luo, Y., and Christie, P.: Collection and analysis of root exudates of Festuca arundinacea L. and their role in facilitating the phytoremediation of petroleum-contaminated soil, Plant Soil, 389, 109–119, https://doi.org/10.1007/s11104-014-2345-9, 2015.
Loehr, R. C. and Webster, M. T.: Performance of long-term, field-scale bioremediation processes, J. Hazard. Mater., 50, 105–128, https://doi.org/10.1016/0304-3894(96)01797-9, 1996.
Lopez-Echartea, E., Strejcek, M., Mukherjee, S., Uhlik, O., and Yrjälä, K.: Bacterial succession in oil-contaminated soil under phytoremediation with poplars, Chemosphere, 243, 125242, https://doi.org/10.1016/j.chemosphere.2019.125242, 2020.
Love, M. I., Huber, W., and Anders, S.: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 1–21, https://doi.org/10.1186/s13059-014-0550-8, 2014.
Luo, C., Tsementzi, D., Kyrpides, N., Read, T., and Konstantinidis, K. T.: Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample, PLoS One, 7, e30087, https://doi.org/10.1371/journal.pone.0030087, 2012.
Lupwayi, N. Z., Janzen, H. H., Bremer, E., Smith, E. G., Kanashiro, D. A., Eastman, A. H., and Petri, R. M.: The core soil bacterial genera and enzyme activities in incubated soils from century-old wheat rotations, Geoderma, 404, 115275, https://doi.org/10.1016/j.geoderma.2021.115275, 2021.
Macek, T., Uhlík, O., Ječná, K., Nováková, M., Lovecká, P., Rezek, J., Dudková, V., Štursa, P., Vrchotová, B., Pavlíková, D., Demnerová, K., and Macková, M.: Advances in phytoremediation and rhizoremediation, in: Advances in Applied Bioremediation, edited by: Singh, A., Kuhad, R., and Ward, O., Springer, Berlin, 257–277, 2009.
Man, J. C.: MPN tables, corrected, Eur. J. Appl. Microbiol., 17, 301–305, https://doi.org/10.1007/BF00508025, 1983.
McMurdie, P. J. and Holmes, S.: Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data, PLoS One, 8, e61217, https://doi.org/10.1371/journal.pone.0061217, 2013.
Mills, T., Arnold, B., Sivakumaran, S., Northcott, G., Vogeler, I., Robinson, B., Norling, C., and Leonil, D.: Phytoremediation and long-term site management of soil contaminated with pentachlorophenol (PCP) and heavy metals, J. Environ. Manage., 79, 232–241, https://doi.org/10.1016/j.jenvman.2005.07.005, 2006.
Mukherjee, S., Juottonen, H., Siivonen, P., Lloret Quesada, C., Tuomi, P., Pulkkinen, P., and Yrjälä, K.: Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site, ISME J., 8, 2131–2142, https://doi.org/10.1038/ismej.2014.151, 2014.
Musilova, L., Ridl, J., Polivkova, M., Macek, T., and Uhlik, O.: Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments, Int. J. Mol. Sci., 17, 1205, https://doi.org/10.3390/ijms17081205, 2016.
Ngosong, C., Gabriel, E., and Ruess, L.: Use of the Signature Fatty Acid 16 : 1ω5 as a Tool to Determine the Distribution of Arbuscular Mycorrhizal Fungi in Soil, J. Lipids, 2012, 1–8, https://doi.org/10.1155/2012/236807, 2012.
Oburger, E., Gruber, B., Wanek, W., Watzinger, A., Stanetty, C., Schindlegger, Y., Hann, S., Schenkeveld, W. D. C., Kraemer, S. M., and Puschenreiter, M.: Microbial decomposition of 13C-labeled phytosiderophores in the rhizosphere of wheat: Mineralization dynamics and key microbial groups involved, Soil Biol. Biochem., 98, 196–207, https://doi.org/10.1016/j.soilbio.2016.04.014, 2016.
Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P. R., O'Hara, R. B., Simpson, G. L., Solymos, P., Stevens, M. H. H., Szoecs, E., and Wagner, H.: vegan: Community Ecology Package, R package version 2.4-5, https://vegan.r-forge.r-project.org/ (last access: 9 August 2024), 2017.
Palmroth, M. R. T., Pichtel, J., and Puhakka, J. A.: Phytoremediation of subarctic soil contaminated with diesel fuel, Bioresource Technol., 84, 221–228, 2002.
Palmroth, M. R. T., Münster, U., Pichtel, J., and Puhakka, J. A.: Metabolic responses of microbiota to diesel fuel addition in vegetated soil, Biodegradation, 16, 91–101, 2005.
Papik, J., Strejcek, M., Musilova, L., Guritz, R., Leewis, M.-C., Leigh, M. B., and Uhlik, O.: Legacy Effects of Phytoremediation on Plant-Associated Prokaryotic Communities in Remediated Subarctic Soil Historically Contaminated with Petroleum Hydrocarbons, Microbiol. Spectr., 11, e04448-22, https://doi.org/10.1128/spectrum.04448-22, 2023.
Polivkova, M., Suman, J., Strejcek, M., Kracmarova, M., Hradilova, M., Filipova, A., Cajthaml, T., Macek, T., and Uhlik, O.: Diversity of root-associated microbial populations of Tamarix parviflora cultivated under various conditions, Appl. Soil Ecol., 125, 264–272, https://doi.org/10.1016/j.apsoil.2018.02.002, 2018.
R Core Team: R: A language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/ (last access: 5 July 2019), 2019.
Reeve, J. R., Schadt, C. W., Carpenter-Boggs, L., Kang, S., Zhou, J., and Reganold, J. P.: Effects of soil type and farm management on soil ecological functional genes and microbial activities, ISME J., 4, 1099–1107, https://doi.org/10.1038/ismej.2010.42, 2010.
Reynolds, C. M. and Koenen, B. A.: Rhizosphere-Enhanced Bioremediation, Mil. Eng., 586, 32–33, 1997.
Reynolds, C. M., Koenen, B. A., Perry, L. B., and Pidgeon, C. S.: Initial Field Results for Rhizosphere Treatment of Contaminated Soils in Cold Regions, in: International Association of Cold Regions Development Studies, Anchorage, Alaska, USA, 1997, 143–146, 1997a
Reynolds, C. M., Bhunia, P., and Koenen, B. A.: Soil Remediation Demonstration Project: Biodegradation of Heavy Fuel Oils, ACE CRREL Special Report 97-20, 1997b.
Reynolds, C. M., Perry, L. B., Pidgeon, C. S., Koenen, B. A., Pelton, D. K., and Foley, K. L.: Plant-Based Treatment of Organic-Contaminated Soils in Cold Climates, in: Proceeding of Assessment and Remediation of Contaminated Sites in Arctic and Cold Climates, Edmonton, Canada, 3–4 May 1999, 166–172, 1999.
Robichaud, K., Girard, C., Dagher, D., Stewart, K., Labrecque, M., Hijri, M., and Amyot, M.: Local fungi, willow and municipal compost effectively remediate petroleum-contaminated soil in the Canadian North, Chemosphere, 220, 47–55, https://doi.org/10.1016/j.chemosphere.2018.12.108, 2019.
Ruess, R. R. W., Van Cleve, K., Yarie, J., and Viereck, L. A.: Contributions of fine root production and turnover to the carbon and nitrogen cycling in taiga forests of the Alaskan interior, Can. J. Forest Res., 26, 1326–1336, https://doi.org/10.1139/x26-148, 1996.
Schloss, P. D., Gevers, D., and Westcott, S. L.: Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies, PLoS One, 6, e27310, https://doi.org/10.1371/journal.pone.0027310, 2011.
Schmid, M. W., van Moorsel, S. J., Hahl, T., De Luca, E., De Deyn, G. B., Wagg, C., Niklaus, P. A., and Schmid, B.: Effects of plant community history, soil legacy and plant diversity on soil microbial communities, J. Ecol., 109, 3007–3023, https://doi.org/10.1111/1365-2745.13714, 2021.
Siciliano, S. D. and Germida, J. J.: Mechanisms of phytoremediation: biochemical and ecological interactions between plants and bacteria, Environ. Rev., 6, 65–79, 1998.
Siciliano, S. D. D., Germida, J. J. J., Banks, K., and Greer, C. W.: Changes in Microbial Community Composition and Function during a Polyaromatic Hydrocarbon Phytoremediation Field Trial, Appl. Environ. Microb., 69, 483–489, https://doi.org/10.1128/AEM.69.1.483, 2003.
Singer, A. C., Smith, D., Jury, W. A., Hathuc, K., and Crowley, D. E.: IMPACT OF THE PLANT RHIZOSPHERE AND AUGMENTATION ON REMEDIATION OF POLYCHLORINATED BIPHENYL CONTAMINATED SOIL, Environ. Toxicol. Chem., 22, 1998–2004, https://doi.org/10.1897/02-471, 2003.
Singer, A. C., Thompson, I. P., and Bailey, M. J.: The tritrophic trinity: A source of pollutant-degrading enzymes and its implications for phytoremediation, Curr. Opin. Microbiol., 7, 239–244, https://doi.org/10.1016/j.mib.2004.04.007, 2004.
Slater, H., Gouin, T., and Leigh, M. B.: Assessing the potential for rhizoremediation of PCB contaminated soils in northern regions using native tree species, Chemosphere, 84, 199–206, https://doi.org/10.1016/j.chemosphere.2011.04.058, 2011.
Song, Y., Deng, S. P., Acosta-Martínez, V., and Katsalirou, E.: Characterization of redox-related soil microbial communities along a river floodplain continuum by fatty acid methyl ester (FAME) and 16S rRNA genes, Appl. Soil Ecol., 40, 499–509, https://doi.org/10.1016/j.apsoil.2008.07.005, 2008.
Stark, S., Julkunen-Tiitto, R., Holappa, E., Mikkola, K., and Nikula, A.: Concentrations of Foliar Quercetin in Natural Populations of White Birch (Betula pubescens) Increase with Latitude, J. Chem. Ecol., 34, 1382–1391, https://doi.org/10.1007/s10886-008-9554-8, 2008.
Stella, T., Covino, S., Burianová, E., Filipová, A., Křesinová, Z., Voříšková, J., Větrovský, T., Baldrian, P., and Cajthaml, T.: Chemical and microbiological characterization of an aged PCB-contaminated soil, Sci. Total Environ., 533, 177–186, https://doi.org/10.1016/j.scitotenv.2015.06.019, 2015.
Stow, J. P., Sova, J., and Reimer, K. J.: The relative influence of distant and local (DEW-line) PCB sources in the Canadian Arctic, Sci. Total Environ., 342, 107–118, https://doi.org/10.1016/j.scitotenv.2004.12.028, 2005.
Susarla, S., Medina, V. F., and McCutcheon, S. C.: Phytoremediation: An ecological solution to organic chemical contamination, Ecol. Eng., 18, 647–658, https://doi.org/10.1016/S0925-8574(02)00026-5, 2002.
Sutton, N. B., Maphosa, F., Morillo, J. A., Abu Al-Soud, W., Langenhoff, A. a M., Grotenhuis, T., Rijnaarts, H. H. M., Smidt, H., Al-Soud, W. A., Langenhoff, A. a M., Grotenhuis, T., Rijnaarts, H. H. M., Smidt, H., Abu, W., Langenhoff, A. a M., Grotenhuis, T., Huub, H., Rijnaarts, M., and Smidt, H.: Impact of long-term diesel contamination on soil microbial community structure, Appl. Environ. Microb., 79, 619–630, https://doi.org/10.1128/AEM.02747-12, 2013.
Talbot, J. M. and Treseder, K. K.: Interactions among lignin, cellulose, and nitrogen drive litter chemistry-decay relationships, Ecology, 93, 345–354, https://doi.org/10.1890/11-0843.1, 2012.
Uhlik, O., Wald, J., Strejcek, M., Musilova, L., Ridl, J., Hroudova, M., Vlcek, C., Cardenas, E., Mackova, M., and Macek, T.: Identification of Bacteria Utilizing Biphenyl, Benzoate, and Naphthalene in Long-Term Contaminated Soil, PLoS One, 7, e40653, https://doi.org/10.1371/journal.pone.0040653, 2012.
Van Aken, B., Correa, P. A., Schnoor, J. L., Van Aken, B., Correa, P. A., and Schnoor, J. L.: Phytoremediation of Polychlorinated Biphenyls: New Trends and Promises, Environ. Sci. Technol., 44, 2767–2776, https://doi.org/10.1021/es902514d, 2010.
Vanha-Majamaa, I., Salemaa, M., Tuominen, S., and Mikkola, K.: Digitized photographs in vegetation analysis – a comparison of cover estimates, Appl. Veg. Sci., 3, 89–94, https://doi.org/10.2307/1478922, 2000.
Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R.: Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microb., 73, 5261–5267, https://doi.org/10.1128/AEM.00062-07, 2007.
Wenzel, W. W.: Rhizosphere processes and management in plant-assisted bioremediation (phytoremediation) of soils, Plant Soil, 321, 385–408, https://doi.org/10.1007/s11104-008-9686-1, 2009.
White, P. M., Wolf, D. C., Thoma, G. J., and Reynolds, C. M.: Phytoremediation of Alkylated Polycyclic Aromatic Hydrocarbons in a Crude Oil-Contaminated Soil, Water, Air. Soil Pollut., 169, 207–220, https://doi.org/10.1007/s11270-006-2194-0, 2006.
Wu, Y., Ding, N., Wang, G., Xu, J., Wu, J., and Brookes, P. C.: Effects of different soil weights, storage times and extraction methods on soil phospholipid fatty acid analyses, Geoderma, 150, 171–178, https://doi.org/10.1016/j.geoderma.2009.02.003, 2009.
Yergeau, E., Bell, T., Champagne, J., Maynard, C., Tardif, S., Tremblay, J., and Greer, C.: Transplanting soil microbiomes leads to lasting effects on willow growth, but not on the rhizosphere microbiome, Front. Microbiol., 6, 1–14, https://doi.org/10.3389/fmicb.2015.01436, 2015.
Zubrova, A., Michalikova, K., Semerad, J., Strejcek, M., Cajthaml, T., Suman, J., and Uhlik, O.: Biphenyl 2,3-Dioxygenase in Pseudomonas alcaliphila JAB1 Is Both Induced by Phenolics and Monoterpenes and Involved in Their Transformation, Front. Microbiol., 12, 657311, https://doi.org/10.3389/fmicb.2021.657311, 2021.
Short summary
In 1995, an initial study determined that using plants and fertilizers increased degradation of petroleum in soil; the site was then abandoned. In 2010, we returned to find that initial choices of plant and fertilizer use continued to cause changes in the plant and soil microbiomes. We also found evidence for the restoration of native vegetation with certain treatments, which indicates that this could be an important tool for communities that experience soil contamination.
In 1995, an initial study determined that using plants and fertilizers increased degradation of...
