Legacy Effects of Phytoremediation on Plant-Associated Prokaryotic Communities in Remediated Subarctic Soil Historically Contaminated with Petroleum Hydrocarbons

. 2023 Mar 28 ; 11 (2) : e0444822. [epub] 20230328

Status Publisher Jazyk angličtina Země Spojené státy americké Médium print-electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid36975310

Phytoremediation of petroleum hydrocarbons in subarctic regions relies on the successful establishment of plants that stimulate petroleum-degrading microorganisms, which can be challenging due to the extreme climate, limited nutrients, and difficulties in maintaining sites in remote locations. A long-term phytoremediation experiment was initiated in Alaska in 1995 with the introduction of grasses and/or fertilizer to petroleum hydrocarbon (PHC)-contaminated soils that were subsequently left unmanaged. In 2011, the PHC concentrations were below detection limits in all soils tested and the originally planted grasses had been replaced by volunteer plant species that had colonized the site. Here, we sought to understand how the original treatments influenced the structure of prokaryotic communities associated with plant species that colonized the soils and to assess the interactions between the rhizospheric and endophytic communities of the colonizing vegetation 20 years after the experiment was established. Metataxonomic analysis performed using 16S rRNA gene sequencing revealed that the original type of contaminated soil and phytoremediation strategy influenced the structure of both rhizospheric and endophytic communities of colonizing plants, even 20 years after the treatments were applied and following the disappearance of the originally planted grasses. Our findings demonstrate that the choice of initial phytoremediation strategy drove the succession of microorganisms associated with the colonizing vegetation. The outcome of this study provides new insight into the establishment of plant-associated microbial communities during secondary succession of subarctic areas previously contaminated by PHCs and indicates that the strategies for restoring these ecosystems influence the plant-associated microbiota in the long term. IMPORTANCE Subarctic ecosystems provide key services to local communities, yet they are threatened by pollution caused by spills and disposal of petroleum waste. Finding solutions for the remediation and restoration of subarctic soils is valuable for reasons related to human and ecosystem health, as well as environmental justice. This study provides novel insight into the long-term succession of soil and plant-associated microbiota in subarctic soils that had been historically contaminated with different sources of PHCs and subjected to distinct phytoremediation strategies. We provide evidence that even after the successful removal of PHCs and the occurrence of secondary succession, the fingerprint of the original source of contamination and the initial choice of remediation strategy can be detected as a microbial legacy in the rhizosphere, roots, and shoots of volunteer vegetation even 2 decades after the contamination had occurred. Such information needs to be borne in mind when designing and applying restoration approaches for PHC-contaminated soils in subarctic ecosystems.

Zobrazit více v PubMed

Schmidt CW. 2012. Offshore exploration to commence in the Arctic: can Shell’s oil-spill response plans keep up? Environ Health Perspect 120:A194–A199. PubMed PMC

Leigh MB, Matz A, Gamberg M. 2019. Contaminants in the northwest boreal region synthesis project—drivers of landscape change. In Sesser AL, Rockhill AP, Magness DR, Reid D, Delapp J, Burton PJ, Schroff E, Barber V, Markon C (ed), Drivers of landscape change in the northwest boreal region. University of Alaska Press, Fairbanks, AK.

Reynolds C, Koenen B, Perry L, Pidgeon C. 1997. Initial field results for rhizosphere treatment of contaminated soils in cold regions, p 143–146. In Zubeck H, Woolard C, White D, Vinson T (ed), Proceedings of the Fifth International Association of Cold Region Development. American Society of Civil Engineers, Anchorage, AK.

Yergeau E, Lawrence JR, Sanschagrin S, Waiser MJ, Korber DR, Greer CW. 2012. Next-generation sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities. Appl Environ Microbiol 78:7626–7637. doi:10.1128/AEM.02036-12. PubMed DOI PMC

Mohn WW, Stewart GR. 2000. Limiting factors for hydrocarbon biodegradation at low temperature in Arctic soils. Soil Biol Biochem 32:1161–1172. doi:10.1016/S0038-0717(00)00032-8. DOI

Truskewycz A, Gundry TD, Khudur LS, Kolobaric A, Taha M, Aburto-Medina A, Ball AS, Shahsavari E. 2019. Petroleum hydrocarbon contamination in terrestrial ecosystems—fate and microbial responses. Molecules 24:3400. doi:10.3390/molecules24183400. PubMed DOI PMC

Yang S, Wen X, Shi Y, Liebner S, Jin H, Perfumo A. 2016. Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments. Sci Rep 6:37473. doi:10.1038/srep37473. PubMed DOI PMC

Filler DM, Snape I, Barnes DL. 2008. Bioremediation of petroleum hydrocarbons in cold regions. Cambridge University Press, Cambridge, UK.

Gkorezis P, Daghio M, Franzetti A, Van Hamme JD, Sillen W, Vangronsveld J. 2016. The interaction between plants and bacteria in the remediation of petroleum hydrocarbons: an environmental perspective. Front Microbiol 7:1836. doi:10.3389/fmicb.2016.01836. PubMed DOI PMC

Macek T, Macková M, Káš J. 2000. Exploitation of plants for the removal of organics in environmental remediation. Biotechnol Adv 18:23–34. doi:10.1016/S0734-9750(99)00034-8. PubMed DOI

Correa-García S, Pande P, Séguin A, St-Arnaud M, Yergeau E. 2018. Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation. Microb Biotechnol 11:819–832. doi:10.1111/1751-7915.13303. PubMed DOI PMC

Leewis M-C, Reynolds CM, Leigh MB. 2013. 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. doi:10.1016/j.coldregions.2013.08.011. PubMed DOI PMC

Palmroth MR, Pichtel J, Puhakka JA. 2002. Phytoremediation of subarctic soil contaminated with diesel fuel. Bioresour Technol 84:221–228. doi:10.1016/s0960-8524(02)00055-x. PubMed DOI

Lopez-Echartea E, Strejcek M, Mukherjee S, Uhlik O, Yrjälä K. 2020. Bacterial succession in oil-contaminated soil under phytoremediation with poplars. Chemosphere 243:125242. doi:10.1016/j.chemosphere.2019.125242. PubMed DOI

Leewis M-C, Uhlik O, Fraraccio S, McFarlin K, Kottara A, Glover C, Macek T, Leigh MB. 2016. Differential impacts of willow and mineral fertilizer on bacterial communities and biodegradation in diesel fuel oil-contaminated soil. Front Microbiol 7:837. doi:10.3389/fmicb.2016.00837. PubMed DOI PMC

Leewis M-C, Uhlik O, Leigh MB. 2016. Synergistic processing of biphenyl and benzoate: carbon flow through the bacterial community in polychlorinated-biphenyl-contaminated soil. Sci Rep 6:1–12. doi:10.1038/srep22145. PubMed DOI PMC

Walworth J, Pond A, Snape I, Rayner J, Ferguson S, Harvey P. 2007. Nitrogen requirements for maximizing petroleum bioremediation in a sub-Antarctic soil. Cold Reg Sci Technol 48:84–91. doi:10.1016/j.coldregions.2006.07.001. DOI

Brown DM, Bonte M, Gill R, Dawick J, Boogaard PJ. 2017. Heavy hydrocarbon fate and transport in the environment. Q J Eng Geol Hydrogeol 50:333–346. doi:10.1144/qjegh2016-142. DOI

Murygina V, Gaydamaka S, Gladchenko M, Zubaydullin A. 2016. Method of aerobic-anaerobic bioremediation of a raised bog in Western Siberia affected by old oil pollution. A pilot test. Int Biodeterior Biodegradation 114:150–156. doi:10.1016/j.ibiod.2016.06.009. DOI

Coulon F, Brassington KJ, Bazin R, Linnet P, Thomas K, Mitchell T, Lethbridge G, Smith J, Pollard SJ. 2012. Effect of fertilizer formulation and bioaugmentation on biodegradation and leaching of crude oils and refined products in soils. Environ Technol 33:1879–1893. doi:10.1080/09593330.2011.650221. PubMed DOI

Zhang PP, Le Zhang Y, Jia JC, Cui YX, Wang X, Zhang XC, Wang YQ. 2020. Revegetation pattern affecting accumulation of organic carbon and total nitrogen in reclaimed mine soils. PeerJ 8:e8563. doi:10.7717/peerj.8563. PubMed DOI PMC

Buta M, Blaga G, Paulette L, Păcurar I, Roșca S, Borsai O, Grecu F, Sînziana PE, Negrușier C. 2019. Soil reclamation of abandoned mine lands by revegetation in northwestern part of Transylvania: a 40-year retrospective study. Sustainability 11:3393. doi:10.3390/su11123393. DOI

Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. 2013. Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799. doi:10.1038/nrmicro3109. PubMed DOI

White JF, Kingsley KL, Zhang Q, Verma R, Obi N, Dvinskikh S, Elmore MT, Verma SK, Gond SK, Kowalski KP. 2019. Review: endophytic microbes and their potential applications in crop management. Pest Manag Sci 75:2558–2565. doi:10.1002/ps.5527. PubMed DOI PMC

Papik J, Folkmanova M, Polivkova M, Suman J, Uhlik O. 2020. The invisible life inside plants: deciphering the riddles of endophytic bacterial diversity. Biotechnol Adv 44:107614. doi:10.1016/j.biotechadv.2020.107614. PubMed DOI

Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A. 2015. The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 79:293–320. doi:10.1128/MMBR.00050-14. PubMed DOI PMC

Oliveira V, Gomes NC, Almeida A, Silva AM, Simões MM, Smalla K, Cunha Â. 2014. Hydrocarbon contamination and plant species determine the phylogenetic and functional diversity of endophytic degrading bacteria. Mol Ecol 23:1392–1404. doi:10.1111/mec.12559. PubMed DOI

Zhu X, Ni X, Liu J, Gao Y. 2014. Application of endophytic bacteria to reduce persistent organic pollutants contamination in plants. Clean Soil Air Water 42:306–310. doi:10.1002/clen.201200314. DOI

Acuña-Rodríguez IS, Newsham KK, Gundel PE, Torres-Díaz C, Molina-Montenegro MA. 2020. Functional roles of microbial symbionts in plant cold tolerance. Ecol Lett 23:1034–1048. doi:10.1111/ele.13502. PubMed DOI

Giauque H, Connor EW, Hawkes CV. 2019. Endophyte traits relevant to stress tolerance, resource use and habitat of origin predict effects on host plants. New Phytol 221:2239–2249. doi:10.1111/nph.15504. PubMed DOI

Reynolds C, Koenen B, Carnahan J, Walworth J, Bhunia P. 1997. Rhizosphere and nutrient effects on remediating subarctic soils, p 297–302. In Alleman BC, Leeson A (ed), In situ and on-site bioremediation: Papers from the Fourth International In Situ and On-Site Bioremediation Symposium, vol 4. New Orleans, April 28-May 1, 1997. Battelle Memorial Institute, New Orleans, LA.

Reynolds C, Koenen BA. 1997. Rhizosphere-enhanced bioremediation. Mil Eng 89:32–33.

Reynolds C, Wolf D, Gentry T, Perry L, Pidgeon C, Koenen B, Rogers H, Beyrouty C. 1999. Plant enhancement of indigenous soil micro-organisms: a low-cost treatment of contaminated soils. Polar Rec 35:33–40. doi:10.1017/S0032247400026310. DOI

Coleman-Derr D, Desgarennes D, Fonseca-Garcia C, Gross S, Clingenpeel S, Woyke T, North G, Visel A, Partida-Martinez LP, Tringe SG. 2016. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol 209:798–811. doi:10.1111/nph.13697. PubMed DOI PMC

Yang R, Liu P, Ye W. 2017. Illumina-based analysis of endophytic bacterial diversity of tree peony (Paeonia Sect. Moutan) roots and leaves. Braz J Microbiol 48:695–705. doi:10.1016/j.bjm.2017.02.009. PubMed DOI PMC

Polivkova M, Suman J, Strejcek M, Kracmarova M, Hradilova M, Filipova A, Cajthaml T, Macek T, Uhlik O. 2018. Diversity of root-associated microbial populations of Tamarix parviflora cultivated under various conditions. Appl Soil Ecol 125:264–272. doi:10.1016/j.apsoil.2018.02.002. DOI

Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, Del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL. 2012. Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90. doi:10.1038/nature11237. PubMed DOI PMC

Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, Podar M, Karpinets T, Uberbacher E, Tuskan GA, Vilgalys R, Doktycz MJ, Schadt CW. 2011. Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol 77:5934–5944. doi:10.1128/AEM.05255-11. PubMed DOI PMC

Müller H, Berg C, Landa BB, Auerbach A, Moissl-Eichinger C, Berg G. 2015. Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees. Front Microbiol 6:138. doi:10.3389/fmicb.2015.00138. PubMed DOI PMC

Albrectsen BR, Siddique AB, Decker VHG, Unterseher M, Robinson KM. 2018. Both plant genotype and herbivory shape aspen endophyte communities. Oecologia 187:535–545. doi:10.1007/s00442-018-4097-3. PubMed DOI PMC

Ridl J, Kolar M, Strejcek M, Strnad H, Stursa P, Paces J, Macek T, Uhlik O. 2016. Plants rather than mineral fertilization shape microbial community structure and functional potential in legacy contaminated soil. Front Microbiol 7:995. doi:10.3389/fmicb.2016.00995. PubMed DOI PMC

Hassani MA, Durán P, Hacquard S. 2018. Microbial interactions within the plant holobiont. Microbiome 6:58. doi:10.1186/s40168-018-0445-0. PubMed DOI PMC

Massoni J, Bortfeld-Miller M, Jardillier L, Salazar G, Sunagawa S, Vorholt JA. 2020. Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species. ISME J 14:245–258. doi:10.1038/s41396-019-0531-8. PubMed DOI PMC

Carrell AA, Carper DL, Frank AC. 2016. Subalpine conifers in different geographical locations host highly similar foliar bacterial endophyte communities. FEMS Microbiol Ecol 92:fiw124. doi:10.1093/femsec/fiw124. PubMed DOI

Sheng HM, Gao HS, Xue LG, Ding S, Song CL, Feng HY, An LZ. 2011. Analysis of the composition and characteristics of culturable endophytic bacteria within subnival plants of the Tianshan Mountains, northwestern China. Curr Microbiol 62:923–932. doi:10.1007/s00284-010-9800-5. PubMed DOI

Lynch JM, Whipps JM. 1990. Substrate flow in the rhizosphere. Plant Soil 129:1–10. doi:10.1007/BF00011685. DOI

Tian T, Reverdy A, She Q, Sun B, Chai Y. 2020. The role of rhizodeposits in shaping rhizomicrobiome. Environ Microbiol Rep 12:160–172. doi:10.1111/1758-2229.12816. PubMed DOI

Paterson E, Gebbing T, Abel C, Sim A, Telfer G. 2007. Rhizodeposition shapes rhizosphere microbial community structure in organic soil. New Phytol 173:600–610. doi:10.1111/j.1469-8137.2006.01931.x. PubMed DOI

Fraraccio S, Strejcek M, Dolinova I, Macek T, Uhlik O. 2017. Secondary compound hypothesis revisited: selected plant secondary metabolites promote bacterial degradation of cis-1,2-dichloroethylene (cDCE). Sci Rep 7:1–11. doi:10.1038/s41598-017-07760-1. PubMed DOI PMC

Dungait JA, Hopkins DW, Gregory AS, Whitmore AP. 2012. Soil organic matter turnover is governed by accessibility not recalcitrance. Glob Change Biol 18:1781–1796. doi:10.1111/j.1365-2486.2012.02665.x. DOI

De Long JR, Heinen R, Jongen R, Hannula SE, Huberty M, Kielak AM, Steinauer K, Bezemer TM. 2021. How plant–soil feedbacks influence the next generation of plants. Ecol Res 36:32–44. doi:10.1111/1440-1703.12165. DOI

Heinen R, Hannula SE, De Long JR, Huberty M, Jongen R, Kielak A, Steinauer K, Zhu F, Bezemer TM. 2020. Plant community composition steers grassland vegetation via soil legacy effects. Ecol Lett 23:973–982. doi:10.1111/ele.13497. PubMed DOI PMC

Hannula SE, Heinen R, Huberty M, Steinauer K, De Long JR, Jongen R, Bezemer TM. 2021. Persistence of plant-mediated microbial soil legacy effects in soil and inside roots. Nat Commun 12:1–13. doi:10.1038/s41467-021-25971-z. PubMed DOI PMC

Xu X, Liu W, Tian S, Wang W, Qi Q, Jiang P, Gao X, Li F, Li H, Yu H. 2018. Petroleum hydrocarbon-degrading bacteria for the remediation of oil pollution under aerobic conditions: a perspective analysis. Front Microbiol 9:2885. doi:10.3389/fmicb.2018.02885. PubMed DOI PMC

Bidja Abena MT, Chen G, Chen Z, Zheng X, Li S, Li T, Zhong W. 2020. Microbial diversity changes and enrichment of potential petroleum hydrocarbon degraders in crude oil-, diesel-, and gasoline-contaminated soil. 3 Biotech 10:42. doi:10.1007/s13205-019-2027-7. PubMed DOI PMC

Morales-Guzmán G, Ferrera-Cerrato R, Rivera-Cruz M, Torres-Bustillos LG, Arteaga-Garibay RI, Mendoza-López MR, Esquivel-Cote R, Alarcón A. 2017. Diesel degradation by emulsifying bacteria isolated from soils polluted with weathered petroleum hydrocarbons. Appl Soil Ecol 121:127–134. doi:10.1016/j.apsoil.2017.10.003. DOI

Sutton NB, Maphosa F, Morillo JA, Abu Al-Soud W, Langenhoff AA, Grotenhuis T, Rijnaarts HH, Smidt H. 2013. Impact of long-term diesel contamination on soil microbial community structure. Appl Environ Microbiol 79:619–630. doi:10.1128/AEM.02747-12. PubMed DOI PMC

Stauffert M, Cravo-Laureau C, Jézéquel R, Barantal S, Cuny P, Gilbert F, Cagnon C, Militon C, Amouroux D, Mahdaoui F, Bouyssiere B, Stora G, Merlin FX, Duran R. 2013. Impact of oil on bacterial community structure in bioturbated sediments. PLoS One 8:e65347. doi:10.1371/journal.pone.0065347. PubMed DOI PMC

Qin J, Xiong H, Ma H, Li Z. 2019. Effects of different fertilizers on residues of oxytetracycline and microbial activity in soil. Environ Sci Pollut Res Int 26:161–170. doi:10.1007/s11356-018-3603-9. PubMed DOI

Gabi-Mirela M, Sorin M, Elena D, Marian S. 2018. Greenhouse study on the influence of natural biostimulators and fertilizers on improving bean plants growth and microbial activity in oil-polluted soil. Eurobiotech J 2:209–214. doi:10.2478/ebtj-2018-0051. DOI

Nkereuwem M, Edem I, Fagbola O. 2010. Bioremediation of oil-polluted soils with organomineral fertilizer (OMF) and Mexican sunflower (Tithonia diversifolia). Niger J Agric Food Environ 6:13–20.

Chang Y-S, Chang Y-J, Lin C-T, Lee M-C, Wu C-W, Lai Y-H. 2013. Nitrogen fertilization promotes the phytoremediation of cadmium in Pentas lanceolata. Int Biodeterior 85:709–714. doi:10.1016/j.ibiod.2013.05.021. DOI

Ruberto L, Dias R, Lo Balbo A, Vazquez SC, Hernandez EA, Mac Cormack WP. 2009. Influence of nutrients addition and bioaugmentation on the hydrocarbon biodegradation of a chronically contaminated Antarctic soil. J Appl Microbiol 106:1101–1110. doi:10.1111/j.1365-2672.2008.04073.x. PubMed DOI

Test Methods for Evaluating Solid Waste, Physical/Chemical Methods, EPA publication SW-846, Third Edition, Final Updates I (1993), II (1995), IIA (1994), IIB (1995), III (1997), IIIA (1999), IIIB (2005), IV (2008), and V (2015).

Lopez-Echartea E, Strejcek M, Mateju V, Vosahlova S, Kyclt R, Demnerova K, Uhlik O. 2019. Bioremediation of chlorophenol-contaminated sawmill soil using pilot-scale bioreactors under consecutive anaerobic-aerobic conditions. Chemosphere 227:670–680. doi:10.1016/j.chemosphere.2019.04.036. PubMed DOI

Lundberg DS, Yourstone S, Mieczkowski P, Jones CD, Dangl JL. 2013. Practical innovations for high-throughput amplicon sequencing. Nat Methods 10:999–1002. doi:10.1038/nmeth.2634. PubMed DOI

Callahan B, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583. doi:10.1038/nmeth.3869. PubMed DOI PMC

Strejcek M, Smrhova T, Junkova P, Uhlik O. 2018. Whole-cell MALDI-TOF MS versus 16S rRNA gene analysis for identification and dereplication of recurrent bacterial isolates. Front Microbiol 9:1294. doi:10.3389/fmicb.2018.01294. PubMed DOI PMC

Callahan B. 2018. Silva taxonomic training data formatted for DADA2 (Silva version 132). Zenodo, CERN, Geneva, Switzerland.

McMurdie PJ, Holmes S. 2013. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8:e61217. doi:10.1371/journal.pone.0061217. PubMed DOI PMC

Oksanen J, Blanchet F, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin P, O’Hara R, Simpson G, Solymos P. 2019. vegan: community ecology package. R package version 2.5-5.

Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. doi:10.1186/s13059-014-0550-8. PubMed DOI PMC

Wickham H. 2016. ggplot2: elegant graphics for data analysis, 2nd ed. Springer Nature, New York, NY.

Andersen KS, Kirkegaard RH, Karst SM, Albertsen M. 2018. ampvis2: an R package to analyse and visualise 16S rRNA amplicon data. BioRxiv doi:10.1101/299537. DOI

Callahan B, Sankaran K, Fukuyama J, McMurdie P, Holmes S. 2016. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000Res 5:1492. doi:10.12688/f1000research.8986.2. PubMed DOI PMC

Anderson MJ. 2001. A new method for non-parametric multivariate analysis of variance. Austral Ecol 26:32–46. doi:10.1046/j.1442-9993.2001.01070.x. DOI

Aitchison J, Greenacre M. 2002. Biplots of compositional data. J R Stat Soc 51:375–392. doi:10.1111/1467-9876.00275. DOI

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...