The Bacterial and Fungal Diversity of an Aged PAH- and Heavy Metal-Contaminated Soil is Affected by Plant Cover and Edaphic Parameters Amélia Bourceret, Aurélie Cebron, Emilie Tisserant, Pascal Poupin, Pascale Bauda, Thierry Beguiristain, Corinne Leyval To cite this version: Amélia Bourceret, Aurélie Cebron, Emilie Tisserant, Pascal Poupin, Pascale Bauda, et al.. The Bacterial and Fungal Diversity of an Aged PAH- and Heavy Metal-Contaminated Soil is Affected by Plant Cover and Edaphic Parameters. Microbial Ecology, Springer Verlag, 2016, 71 (3), pp.711-724. 10.1007/s00248-015-0682-8. hal-02341848 HAL Id: hal-02341848 https://hal.archives-ouvertes.fr/hal-02341848 Submitted on 13 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. 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Manuscript Click here to download Manuscript: publi parcelle_finalversionR2.doc Click here to view linked References 1 The bacterial and fungal diversity of an aged PAH- and heavy metal- 1 2 2 contaminated soil is affected by plant cover and edaphic parameters 3 4 3 5 1,2 1,2,† 3 4,5 6 4 BOURCERET Amélia , CÉBRON Aurélie , TISSERANT Emilie , POUPIN Pascal , 7 4,5 1,2 1,2 8 5 BAUDA Pascale , BEGUIRISTAIN Thierry , LEYVAL Corinne 9 10 6 11 7 1 CNRS, LIEC UMR7360, Faculté des Sciences et Technologies, BP70239, 54506 Vandoeuvre-lès-Nancy, 12 13 8 France. 14 9 2 Université de Lorraine, LIEC UMR7360, Faculté des Sciences et Technologies, BP 70239, 54506 Vandoeuvre- 15 16 10 lès-Nancy, France. 17 11 3 INRA, IAM UMR1136, Centre INRA de Nancy, 54280 Champenoux, France. 18 19 12 4 Université de Lorraine, LIEC UMR7360, Campus Bridoux - Rue du Général Delestraint, 57070 Metz Borny, 20 13 France. 21 22 14 5 CNRS, LIEC UMR7360, Campus Bridoux - Rue du Général Delestraint, 57070 Metz Borny, France. 23 15 24 25 16 † Corresponding author: [email protected]; Phone: (+33) 3 83 68 42 96 26 27 17 28 18 29 30 19 ABSTRACT 31 32 20 Industrial wasteland soils with aged PAH and heavy metal contaminations are environments 33 34 21 where pollutant toxicity has been maintained for decades. Although the communities may be 35 36 22 well adapted to the presence of stressors, knowledge about microbial diversity in such soils is 37 38 23 scarce. Soil microbial community dynamics can be driven by the presence of plants, but the 39 24 impact of plant development on selection or diversification of microorganisms in these soils 40 41 25 has not been established yet. To test these hypotheses, aged-contaminated soil samples from a 42 43 26 field trial were collected. Plots planted with alfalfa were compared to bare soil plots, and 44 45 27 bacterial and fungal diversity and abundance were assessed after 2 and 6 years. Using 46 47 28 pyrosequencing of 16S rRNA gene and ITS amplicons, we showed that the bacterial 48 49 29 community was dominated by Proteobacteria, Actinobacteria and Bacteroidetes and was 50 30 characterized by low Acidobacteria abundance, while the fungal community was mainly 51 52 31 represented by members of the Ascomycota. The short-term toxic impact of pollutants usually 53 54 32 reduces the microbial diversity, yet in our samples bacterial and fungal species richness and 55 56 33 diversity was high suggesting that the community structure and diversity adapted to the 57 58 34 contaminated soil over decades. The presence of plants induced higher bacterial and fungal 59 35 diversity than in bare soil. It also increased the relative abundance of bacterial members of the 60 61 62 63 64 65 36 Actinomycetales, Rhizobiales and Xanthomonadales orders and of most fungal orders. 1 2 37 Multivariate analysis showed correlations between microbial community structure and heavy 3 38 metal and PAH concentrations over time, but also with edaphic parameters (C/N, pH, 4 5 39 phosphorus and nitrogen concentrations). 6 7 40 8 9 41 Key words: bacteria, fungi, PAH, heavy metals, rhizosphere, 454-pyrosequencing 10 11 42 12 13 43 1. Introduction 14 15 16 44 The decline of coal-mining activities has left behind large areas of industrial wasteland soils 17 45 that display high levels of multi-contamination by polycyclic aromatic hydrocarbons (PAHs) 18 19 46 and heavy metals (HMs) [1]. During the 20th century, industrial facilities such as gas or 20 21 47 coking plants caused chronic pollution of soils. After an ageing period, both PAHs and HMs 22 23 48 persisted in the environment due to their low availability/mobility and low 24 25 49 degradability/reactivity. Thus the high concentrations of pollutants and their toxicity have 26 27 50 been exerting a selection pressure on microorganisms for decades. These particular 28 51 environmental conditions potentially enabled the microbial community to adapt, and favored 29 30 52 microorganisms able of using pollutant as carbon source or tolerate pollutant by detoxification 31 32 53 mechanisms [2]; [3]. This long-term process should lead to the development of a new 33 34 54 microbial community diversity after a few decades [4]; [5]. Yet, little is known about the 35 36 55 impact of ancient contamination on microbial diversity in such aged multi-polluted soils. 37 38 56 Most studies focus on the short-term modifications of microbial diversity following recent 39 57 contamination events, mainly in laboratory experiments (i.e. spiking of unpolluted soils) 40 41 58 [8];[9];[10]. Environmental conditions and edaphic parameters are components that shape the 42 43 59 soil microbial communities [11]. Similarly, chronic pollution could also be an important 44 45 60 parameter that can select soil microbial diversity. While the short-term impact of 46 47 61 contamination tends to decrease microbial abundance, richness and diversity, we 48 49 62 hypothesized that in an aged multi-contaminated soil the microbial community would adapt 50 63 over time toward a unique and rich diversity pattern [4]; [5]. 51 52 53 64 Some studies show that vegetation can help to restore contaminated environments. 54 55 65 Phytoremediation strategies have been developed based on plants’ contribution to the 56 57 66 stabilization, extraction and degradation of pollutants [12]. While shaping microbial diversity 58 59 67 by stimulating some microbial populations, plant root exudates could favor PAH degradation 60 61 62 63 64 65 68 through rhizodegradation processes [13];[14];[15] and modify HM speciation, mobility and 1 2 69 availability [12] in the rhizosphere. Among different plant species used in rhizoremediation 3 70 assays, alfalfa is described as tolerant to pollution and interesting for PAH remediation 4 5 71 [16];[17], similarly to other legumes such as red lentil [18]. A contribution of mycorrhizal 6 7 72 colonization of plant roots to PAH dissipation [19] and HM tolerance [20] has also been 8 9 73 shown. There is an effect of plants on soil microbial biomass and diversity because vegetal 10 11 74 litter or residues bring complex organic matter into soils [21] and also pose the question of 12 13 75 selection or diversification of microorganisms. As most studies focus on one particular 14 76 microbial function or population, little is known about the impact of plants and the effect of 15 16 77 the rhizosphere on bacterial and fungal richness and diversity in multi-contaminated soils. A 17 18 78 dramatic shift in the bacterial community structure in the rhizosphere of sunflower in a 19 20 79 creosote-contaminated soil was demonstrated in a pot experiment after 90 days in the 21 22 80 greenhouse during PAH-degradation [22]. Although fungal community dynamic is mainly 23 24 81 driven by plants [23], the diversity of this microbial community needs to be explored. Overall, 25 82 as the rhizosphere effect could modify soil parameters and fate of pollutants, there is still a 26 27 83 need to study the long-term impact of plants in comparison to bare soil, on shaping the 28 29 84 microbial communities during natural attenuation processes of aged multi-contaminated soils. 30 31 85 It is well established that environmental parameters impact microbial community composition 32 33 86 [11]. Although bacteria and fungi are in constant interaction in soils [24], these two 34 35 87 components of the microbial community have a different ecology (e.g. nutrient and carbon 36 88 source requirement, growth rate…) and respond differently to environmental conditions and 37 38 89 stressors. To study the system as a whole, bacterial and fungal diversity must be studied 39 40 90 together. To our knowledge, no study has yet evaluated how plants and edaphic parameters 41 42 91 drive both fungal and bacterial diversity of a multi-contaminated soil on the long term. 43 44 45 92 In this context, the aims of our study were to (1) describe the diversity of bacterial and fungal 46 47 93 communities in an aged multi-contaminated soil from a former coking plant site (Neuves- 48 94 Maisons, France), (2) determine the impact of plant development on microbial richness and 49 50 95 diversity, (3) characterize the temporal modifications of microbial diversity according to 51 52 96 evolution of edaphic parameters over 6 years. To address this issue, we collected soil samples 53 54 97 from a field trial where a long-term plant-assisted natural attenuation experiment was being 55 56 98 conducted [25].