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Burges A, Alkorta I, Epelde L, Garbisu C. From phytoremediation of soil contaminants to phytomanagement of ecosystem services in metal contaminated sites. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2018; 20:384-397. [PMID: 28862473 DOI: 10.1080/15226514.2017.1365340] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Since the emergence of phytoremediation, much research has focused on its development for (i) the removal of metals from soil and/or (ii) the reduction of metal bioavailability, mobility, and ecotoxicity in soil. Here, we review the lights and shades of the two main strategies (i.e., phytoextraction and phytostabilization) currently used for the phytoremediation of metal contaminated soils, irrespective of the level of such contamination. Both strategies face limitations to become successful at commercial scale and, then, often generate skepticism regarding their usefulness. Recent innovative approaches and paradigms are gradually establishing these phytoremediation strategies as suitable options for the management of metal contaminated soils. The combination of these phytotechnologies with a sustainable and profitable site use (a strategy called phytomanagement) grants value to the many benefits that can be obtained during the phytoremediation of metal contaminated sites, such as, for instance, the restoration of important ecosystem services, e.g. nutrient cycling, carbon storage, water flow regulation, erosion control, water purification, fertility maintenance, etc.
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Review |
7 |
114 |
2
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Urra J, Alkorta I, Mijangos I, Epelde L, Garbisu C. Application of sewage sludge to agricultural soil increases the abundance of antibiotic resistance genes without altering the composition of prokaryotic communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 647:1410-1420. [PMID: 30180347 DOI: 10.1016/j.scitotenv.2018.08.092] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/20/2018] [Accepted: 08/02/2018] [Indexed: 05/21/2023]
Abstract
The application of sewage sludge as soil amendment is a common agricultural practice. However, wastewater treatment plants, sewage sludge and sewage sludge-amended soils have been reported as hotspots for the appearance and dissemination of antibiotic resistance, driven, among other factors, by selection pressure exerted by co-exposure to antibiotics and heavy metals. To address this threat to environmental and human health, soil samples from a long-term (24 years) field experiment, carried out to study the impact of thermally dried and anaerobically digested sewage sludge (at different doses and frequencies of application) on agricultural soil quality, were investigated for the presence of genes encoding antibiotic resistance (ARGs) and mobile genetic elements (MGEs). Sewage sludge-induced changes in specific soil physicochemical and microbial properties, as indicators of soil quality, were also investigated. The application of sewage sludge increased the total concentration of copper and zinc in amended soils, but without affecting the bioavailability of these metals, possibly due to the high values of soil pH and organic matter content. Soil microbal quality, as reflected by the value of the Soil Quality Index, was higher in sewage sludge-amended soils. Similarly, the application of sewage sludge increased soil microbial activity and biomass, as well as the abundance of ARGs and MGE genes, posing a risk of dissemination of antibiotic resistance. In contrast, the composition of soil prokaryotic communities was not significantly altered by the application of sewage sludge. We found correlation between soil Cu and Zn concentrations and the abundance of ARGs and MGE genes. It was concluded that sewage sludge-derived amendments must be properly treated and managed if they are to be applied to agricultural soil.
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6 |
89 |
3
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Burges A, Epelde L, Garbisu C. Impact of repeated single-metal and multi-metal pollution events on soil quality. CHEMOSPHERE 2015; 120:8-15. [PMID: 25462295 DOI: 10.1016/j.chemosphere.2014.05.037] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/12/2014] [Accepted: 05/13/2014] [Indexed: 05/25/2023]
Abstract
Most frequently, soil metal pollution results from the occurrence of repeated single-metal and, above all, multi-metal pollution events, with concomitant adverse consequences for soil quality. Therefore, in this study, we evaluated the impact of repeated single-metal and multi-metal (Cd, Pb, Cu, Zn) pollution events on soil quality, as reflected by the values of a variety of soil microbial parameters with potential as bioindicators of soil functioning. Specifically, parameters of microbial activity (potentially mineralizable nitrogen, β-glucosidase and acid phosphatase activity) and biomass (fungal and bacterial gene abundance by RT-qPCR) were determined, in the artificially metal-polluted soil samples, at regular intervals over a period of 26 weeks. Similarly, we studied the evolution over time of CaCl2-extractable metal fractions, in order to estimate metal bioavailability in soil. Different metals showed different values of bioavailability and relative bioavailability ([metal]bio/[metal]tot) in soil throughout the experiment, under both repeated single-metal and multi-metal pollution events. Both repeated Zn-pollution and multi-metal pollution events led to a significant reduction in the values of acid phosphatase activity, and bacterial and fungal gene abundance, reflecting the negative impact of these repeated events on soil microbial activity and biomass, and, hence, soil quality.
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10 |
88 |
4
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Epelde L, Lanzén A, Blanco F, Urich T, Garbisu C. Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine. FEMS Microbiol Ecol 2014; 91:1-11. [PMID: 25764532 DOI: 10.1093/femsec/fiu007] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Toxicity of metals released from mine tailings may cause severe damage to ecosystems. A diversity of microorganisms, however, have successfully adapted to such sites. In this study, our objective was to advance the understanding of the indigenous microbial communities of mining-impacted soils. To this end, a metatranscriptomic approach was used to study a heavily metal-contaminated site along a metal concentration gradient (up to 3220 000 and 97 000 mg kg(-1) of Cd, Pb and Zn, respectively) resulting from previous mining. Metal concentration, soil pH and amount of clay were the most important factors determining the structure of soil microbial communities. Interestingly, evenness of the microbial communities, but not its richness, increased with contamination level. Taxa with high metabolic plasticity like Ktedonobacteria and Chloroflexi were found with higher relative abundance in more contaminated samples. However, several taxa belonging to the phyla Actinobacteria and Acidobacteria followed opposite trends in relation to metal pollution. Besides, functional transcripts related to transposition or transfer of genetic material and membrane transport, potentially involved in metal resistance mechanisms, had a higher expression in more contaminated samples. Our results provide an insight into microbial communities in long-term metal-contaminated environments and how they contrast to nearby sites with lower contamination.
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Research Support, Non-U.S. Gov't |
11 |
87 |
5
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Epelde L, Hernández-Allica J, Becerril JM, Blanco F, Garbisu C. Effects of chelates on plants and soil microbial community: comparison of EDTA and EDDS for lead phytoextraction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2008; 401:21-28. [PMID: 18499230 DOI: 10.1016/j.scitotenv.2008.03.024] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 03/18/2008] [Accepted: 03/19/2008] [Indexed: 05/26/2023]
Abstract
Most studies on chelate-induced phytoextraction have focused on EDTA-mediated Pb phytoextraction. But EDTA and the formed EDTA-Pb complexes have low biodegradability and high solubility in soil, resulting in an elevated risk of adverse environmental effects. EDDS is an easily biodegradable chelating agent that has recently been proposed as an environmentally sound alternative to EDTA. Consequently, a greenhouse experiment, using a completely randomized factorial design with four replications, was carried out to compare the potential of EDTA and EDDS for chelate-induced Pb phytoextraction with Cynara cardunculus, as well as to investigate the toxicity of these two chelates to both cardoon plants and soil microorganisms. The effects of chelate addition on soil microbial communities were studied through the determination of a variety of biological indicators of soil quality such as soil enzyme activities, basal and substrate-induced respiration, potentially mineralizable nitrogen, and community level physiological profiles. EDTA was much more efficient than EDDS for the enhancement of root Pb uptake and root-to-shoot Pb translocation. In a soil polluted with 5000 mg Pb kg(-1), as a result of the addition of 1 g EDTA kg(-1) soil, a value of 1332 mg Pb kg(-1) DW shoot was obtained. EDDS application resulted in a shoot Pb accumulation of only 310 mg kg(-1)DW. Plants treated with EDDS showed lower values of biomass than those treated with EDTA. EDDS proved to be rapidly degraded, and less toxic to the soil microbial community in control non-polluted soils. Pb-polluted EDDS-treated soils showed significantly higher values of basal and substrate-induced respiration than those treated with EDTA. Although EDDS had a lower capacity to enhance Pb phytoextraction than EDTA, it has the advantage of rapid biodegradation.
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Comparative Study |
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Epelde L, Becerril JM, Kowalchuk GA, Deng Y, Zhou J, Garbisu C. Impact of metal pollution and Thlaspi caerulescens growth on soil microbial communities. Appl Environ Microbiol 2010; 76:7843-53. [PMID: 20935131 PMCID: PMC2988604 DOI: 10.1128/aem.01045-10] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 09/26/2010] [Indexed: 11/20/2022] Open
Abstract
Soil microorganisms drive critical functions in plant-soil systems. As such, various microbial properties have been proposed as indicators of soil functioning, making them potentially useful in evaluating the recovery of polluted soils via phytoremediation strategies. To evaluate microbial responses to metal phytoextraction using hyperaccumulators, a microcosm experiment was carried out to study the impacts of Zn and/or Cd pollution and Thlaspi caerulescens growth on key soil microbial properties: basal respiration; substrate-induced respiration (SIR); bacterial community structure as assessed by PCR-denaturing gradient gel electrophoresis (DGGE); community sizes of total bacteria, ammonia-oxidizing bacteria, and chitin-degrading bacteria as assessed by quantitative PCR (Q-PCR); and functional gene distributions as determined by functional gene arrays (GeoChip). T. caerulescens proved to be suitable for Zn and Cd phytoextraction: shoots accumulated up to 8,211 and 1,763 mg kg(-1) (dry weight [DW]) of Zn and Cd, respectively. In general, Zn pollution led to decreased levels of basal respiration and ammonia-oxidizing bacteria, while T. caerulescens growth increased the values of substrate-induced respiration (SIR) and total bacteria. In soils polluted with 1,000 mg Zn kg(-1) and 250 mg Cd kg(-1) (DW), soil bacterial community profiles and the distribution of microbial functional genes were most affected by the presence of metals. Metal-polluted and planted soils had the highest percentage of unique genes detected via the GeoChip (35%). It was possible to track microbial responses to planting with T. caerulescens and to gain insight into the effects of metal pollution on soilborne microbial communities.
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research-article |
15 |
73 |
7
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Pardo T, Clemente R, Epelde L, Garbisu C, Bernal MP. Evaluation of the phytostabilisation efficiency in a trace elements contaminated soil using soil health indicators. JOURNAL OF HAZARDOUS MATERIALS 2014; 268:68-76. [PMID: 24468528 DOI: 10.1016/j.jhazmat.2014.01.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/18/2013] [Accepted: 01/03/2014] [Indexed: 06/03/2023]
Abstract
The efficiency of a remediation strategy was evaluated in a mine soil highly contaminated with trace elements (TEs) by microbiological, ecotoxicological and physicochemical parameters of the soil and soil solution (extracted in situ), as a novel and integrative methodology for assessing recovery of soil health. A 2.5-year field phytostabilisation experiment was carried out using olive mill-waste compost, pig slurry and hydrated lime as amendments, and a native halophytic shrub (Atriplex halimus L.). Comparing with non-treated soil, the addition of the amendments increased soil pH and reduced TEs availability, favoured the development of a sustainable vegetation cover (especially the organic materials), stimulated soil microorganisms (increasing microbial biomass, activity and functional diversity, and reducing stress) and reduced direct and indirect soil toxicity (i.e., its potential associated risks). Therefore, under semi-arid conditions, the use of compost and pig slurry with A. halimus is an effective phytostabilisation strategy to improve soil health of nutrient-poor soils with high TEs concentrations, by improving the habitat function of the soil ecosystem, the reactivation of the biogeochemical cycles of essential nutrients, and the reduction of TEs dissemination and their environmental impact.
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11 |
64 |
8
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Garbisu C, Garaiyurrebaso O, Epelde L, Grohmann E, Alkorta I. Plasmid-Mediated Bioaugmentation for the Bioremediation of Contaminated Soils. Front Microbiol 2017; 8:1966. [PMID: 29062312 PMCID: PMC5640721 DOI: 10.3389/fmicb.2017.01966] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 09/25/2017] [Indexed: 11/29/2022] Open
Abstract
Bioaugmentation, or the inoculation of microorganisms (e.g., bacteria harboring the required catabolic genes) into soil to enhance the rate of contaminant degradation, has great potential for the bioremediation of soils contaminated with organic compounds. Regrettably, cell bioaugmentation frequently turns into an unsuccessful initiative, owing to the rapid decrease of bacterial viability and abundance after inoculation, as well as the limited dispersal of the inoculated bacteria in the soil matrix. Genes that encode the degradation of organic compounds are often located on plasmids and, consequently, they can be spread by horizontal gene transfer into well-established, ecologically competitive, indigenous bacterial populations. Plasmid-mediated bioaugmentation aims to stimulate the spread of contaminant degradation genes among indigenous soil bacteria by the introduction of plasmids, located in donor cells, harboring such genes. But the acquisition of plasmids by recipient cells can affect the host’s fitness, a crucial aspect for the success of plasmid-mediated bioaugmentation. Besides, environmental factors (e.g., soil moisture, temperature, organic matter content) can play important roles for the transfer efficiency of catabolic plasmids, the expression of horizontally acquired genes and, finally, the contaminant degradation activity. For plasmid-mediated bioaugmentation to be reproducible, much more research is needed for a better selection of donor bacterial strains and accompanying plasmids, together with an in-depth understanding of indigenous soil bacterial populations and the environmental conditions that affect plasmid acquisition and the expression and functioning of the catabolic genes of interest.
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Review |
8 |
61 |
9
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Epelde L, Becerril JM, Mijangos I, Garbisu C. Evaluation of the efficiency of a phytostabilization process with biological indicators of soil health. JOURNAL OF ENVIRONMENTAL QUALITY 2009; 38:2041-2049. [PMID: 19704147 DOI: 10.2134/jeq2009.0006] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A phytostabilization process that combined the addition of a synthetic (Calcinit + urea + PK14% + calcium carbonate) or organic (cow slurry) amendment with Lolium perenne L. growth was used to remediate a mine soil moderately contaminated with Zn, Pb, and Cd. The reduced toxicity caused by both amendments allowed the establishment of a healthy L. perenne vegetation cover that had a positive influence on soil properties, increasing the biomass, activity, and functional diversity of the soil microbial community. The beneficial effects of phytostabilization on soil properties were more accentuated in organically amended than in synthetically amended soils. Root-to-shoot translocation factors were smaller in amended versus control plants, indicating a reduction in the risk of metals entering the food chain through phytostabilization. The sensitivity, rapid response, and integrative character of biological indicators of soil health make them valuable tools for assessing the efficiency of metal phytostabilization processes.
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Evaluation Study |
16 |
60 |
10
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Lanzén A, Epelde L, Blanco F, Martín I, Artetxe U, Garbisu C. Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient. Sci Rep 2016; 6:28257. [PMID: 27321429 PMCID: PMC4913321 DOI: 10.1038/srep28257] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/01/2016] [Indexed: 11/09/2022] Open
Abstract
Mountain elevation gradients are invaluable sites for understanding the effects of climate change on ecosystem function, community structure and distribution. However, relatively little is known about the impact on soil microbial communities, in spite of their importance for the functioning of the soil ecosystem. Previous studies of microbial diversity along elevational gradients were often limited by confounding variables such as vegetation, pH, and nutrients. Here, we utilised a transect in the Pyrenees established to minimise variation in such parameters, to examine prokaryotic, fungal, protist and metazoan communities throughout three consecutive years. We aimed to determine the influences of climate and environmental parameters on soil microbial community structure; as well as on the relationships between those microbial communities. Further, functional diversity of heterotrophic bacteria was determined using Biolog. Prokaryotic and fungal community structure, but not alpha-diversity, correlated significantly with elevation. However, carbon-to-nitrogen ratio and pH appeared to affect prokaryotic and protist communities more strongly. Both community structure and physicochemical parameters varied considerably between years, illustrating the value of long-term monitoring of the dynamic processes controlling the soil ecosystem. Our study also illustrates both the challenges and strengths of using microbial communities as indicators of potential impacts of climate change.
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Research Support, Non-U.S. Gov't |
9 |
54 |
11
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Burges A, Epelde L, Blanco F, Becerril JM, Garbisu C. Ecosystem services and plant physiological status during endophyte-assisted phytoremediation of metal contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 584-585:329-338. [PMID: 28040210 DOI: 10.1016/j.scitotenv.2016.12.146] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/21/2016] [Accepted: 12/21/2016] [Indexed: 05/06/2023]
Abstract
Mining sites shelter a characteristic biodiversity with large potential for the phytoremediation of metal contaminated soils. Endophytic plant growth-promoting bacteria were isolated from two metal-(hyper)accumulator plant species growing in a metal contaminated mine soil. After characterizing their plant growth-promoting traits, consortia of putative endophytes were used to carry out an endophyte-assisted phytoextraction experiment using Noccaea caerulescens and Rumex acetosa (singly and in combination) under controlled conditions. We evaluated the influence of endophyte-inoculated plants on soil physicochemical and microbial properties, as well as plant physiological parameters and metal concentrations. Data interpretation through the grouping of soil properties within a set of ecosystem services was also carried out. When grown together, we observed a 41 and 16% increase in the growth of N. caerulescens and R. acetosa plants, respectively, as well as higher values of Zn phytoextraction and soil microbial biomass and functional diversity. Inoculation of the consortia of putative endophytes did not lead to higher values of plant metal uptake, but it improved the plants' physiological status, by increasing the content of chlorophylls and carotenoids by up to 28 and 36%, respectively, indicating a reduction in the stress level of plants. Endophyte-inoculation also stimulated soil microbial communities: higher values of acid phosphatase activity (related to the phosphate solubilising traits of the endophytes), bacterial and fungal abundance, and structural diversity. The positive effects of plant growth and endophyte inoculation on soil properties were reflected in an enhancement of some ecosystem services (biodiversity, nutrient cycling, water flow regulation, water purification and contamination control).
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8 |
45 |
12
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Burges A, Epelde L, Benito G, Artetxe U, Becerril JM, Garbisu C. Enhancement of ecosystem services during endophyte-assisted aided phytostabilization of metal contaminated mine soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 562:480-492. [PMID: 0 DOI: 10.1016/j.scitotenv.2016.04.080] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/11/2016] [Accepted: 04/11/2016] [Indexed: 05/28/2023]
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9 |
38 |
13
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Alkorta I, Epelde L, Garbisu C. Environmental parameters altered by climate change affect the activity of soil microorganisms involved in bioremediation. FEMS Microbiol Lett 2018; 364:4159367. [PMID: 28961781 DOI: 10.1093/femsle/fnx200] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/14/2017] [Indexed: 11/14/2022] Open
Abstract
Bioremediation, based on the use of microorganisms to break down pollutants, can be very effective at reducing soil pollution. But the climate change we are now experiencing is bound to have an impact on bioremediation performance, since the activity and degrading abilities of soil microorganisms are dependent on a series of environmental parameters that are themselves being altered by climate change, such as soil temperature, moisture, amount of root exudates, etc. Many climate-induced effects on soil microorganisms occur indirectly through changes in plant growth and physiology derived from increased atmospheric CO2 concentrations and temperatures, the alteration of precipitation patterns, etc., with a concomitant effect on rhizoremediation performance (i.e. the plant-assisted microbial degradation of pollutants in the rhizosphere). But these effects are extremely complex and mediated by processes such as acclimation and adaptation. Besides, soil microorganisms form complex networks of interactions with a myriad of organisms from many taxonomic groups that will also be affected by climate change, further complicating data interpretation.
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Review |
7 |
32 |
14
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Gómez-Sagasti MT, Epelde L, Anza M, Urra J, Alkorta I, Garbisu C. The impact of nanoscale zero-valent iron particles on soil microbial communities is soil dependent. JOURNAL OF HAZARDOUS MATERIALS 2019; 364:591-599. [PMID: 30390579 DOI: 10.1016/j.jhazmat.2018.10.034] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/24/2018] [Accepted: 10/11/2018] [Indexed: 06/08/2023]
Abstract
The application of nanoscale zero-valent iron particles (nZVI) for the remediation of contaminated sites is very promising. However, information concerning the ecotoxicity of nZVI on soil microbial communities and, hence, soil quality, is still scarce. We carried out a three-month experiment to evaluate the impact of the application of different concentrations of nZVI (from 1 to 20 mg g DW soil-1) on soil microbial properties in a clay-loam versus a sandy-loam soil. Data on microbial biomass (total bacteria and fungi by qPCR, microbial biomass carbon), activity (β-glucosidase, arylsulphatase and urease activities), and functional (Biolog Ecoplates™) and structural (ARISA, 16S rRNA amplicon sequencing) diversity evidenced that the sandy-loam soil was more vulnerable to the presence of nZVI than the clay-loam soil. In the sandy-loam soil, arylsulphatase activity and bacterial abundance, richness and diversity were susceptible to the presence of nZVI. The high content of clay and organic matter present in the clay-loam soil may explain the observed negligible effects of nZVI on soil microbial properties. It was concluded that the impact of nZVI on soil microbial communities and, hence, soil quality, is soil dependent.
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6 |
29 |
15
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Lanzén A, Epelde L, Garbisu C, Anza M, Martín-Sánchez I, Blanco F, Mijangos I. The Community Structures of Prokaryotes and Fungi in Mountain Pasture Soils are Highly Correlated and Primarily Influenced by pH. Front Microbiol 2015; 6:1321. [PMID: 26640462 PMCID: PMC4661322 DOI: 10.3389/fmicb.2015.01321] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/10/2015] [Indexed: 12/04/2022] Open
Abstract
Traditionally, conservation and management of mountain pastures has been managed solely on the basis of visible biota. However, microorganisms play a vital role for the functioning of the soil ecosystem and, hence, pasture sustainability. Here, we studied the links between soil microbial (belowground) community structure (using amplicon sequencing of prokaryotes and fungi), other soil physicochemical and biological properties and, finally, a variety of pasture management practices. To this aim, during two consecutive years, we studied 104 environmental sites characterized by contrasting elevation, habitats, bedrock, and pasture management; located in or near Gorbeia Natural Park (Basque Country/Spain). Soil pH was found to be one of the most important factors in structuring soil microbial diversity. Interestingly, we observed a striking correlation between prokaryotic, fungal and macrofauna diversity, likely caused by interactions between these life forms. Further studies are needed to better understand such interactions and target the influence of different management practices on the soil microbial community, in face of the significant heterogeneity present. However, clearing of bushes altered microbial community structure, and in sites with calcareous bedrock also the use of herbicide vs. mechanical clearing of ferns.
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Journal Article |
10 |
25 |
16
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Epelde L, Becerril JM, Alkorta I, Garbisu C. Adaptive long-term monitoring of soil health in metal phytostabilization: ecological attributes and ecosystem services based on soil microbial parameters. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2014; 16:971-981. [PMID: 24933897 DOI: 10.1080/15226514.2013.810578] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Phytostabilization is a promising option for the remediation of metal contaminated soils which requires the implementation of long-term monitoring programs. We here propose to incorporate the paradigm of "adaptive monitoring", which enables monitoring programs to evolve iteratively as new information emerges and research questions change, to metal phytostabilization. Posing good questions that cover the chemical, toxicological and ecological concerns associated to metal contaminated soils is critical for an efficient long-term phytostabilization monitoring program. Regarding the ecological concerns, soil microbial parameters are most valuable indicators of the effectiveness of metal phytostabilization processes in terms of recovery of soil health. We suggest to group soil microbial parameters in higher-level categories such as "ecological attributes" (vigor, organization, stability) or "ecosystem services" in order to facilitate interpretation and, most importantly, to provide long-term phytostabilization monitoring programs with the required stability through time against changes in techniques, methods, interests, etc. that will inevitably occur during the monitoring program. Finally, a Phytostabilization Monitoring Card, based on both ecological attributes and ecosystem services, for soil microbial properties is provided.
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24 |
17
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Alkorta I, Epelde L, Mijangos I, Amezaga I, Garbisu C. Bioluminescent bacterial biosensors for the assessment of metal toxicity and bioavailability in soils. REVIEWS ON ENVIRONMENTAL HEALTH 2006; 21:139-52. [PMID: 16898676 DOI: 10.1515/reveh.2006.21.2.139] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A major factor governing the toxicity of heavy metals in soils is their bioavailability. Traditionally, sequential extraction procedures using different extractants followed by chemical analysis have been used for determining the biologically available fraction of metals in soils. Yet, the transfer of results obtained on non-biological systems to biological ones is certainly questionable. Therefore, bioluminescence-based bacterial biosensors have been developed using genetically engineered microorganisms, constructed by fusing transcriptionally active components of metal resistance mechanisms to lux genes from naturally bioluminescent bacteria like Vibrio fischeri for the assessment of metal toxicity and bioavailability in polluted soils. As compared to chemical methods, bacterial biosensors present certain advantages, such as selectivity, sensitivity, simplicity, and low cost. Despite certain inherent limitations, bacterial bioluminescent systems have proven their usefulness in soils under laboratory and field conditions. Finally, green fluorescent protein-based bacterial biosensors are also applicable for determining with high sensitivity the bioavailability of heavy metals in soil samples.
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Review |
19 |
19 |
18
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Epelde L, Jauregi L, Urra J, Ibarretxe L, Romo J, Goikoetxea I, Garbisu C. Characterization of Composted Organic Amendments for Agricultural Use. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00044] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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7 |
19 |
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Garaiyurrebaso O, Garbisu C, Blanco F, Lanzén A, Martín I, Epelde L, Becerril JM, Jechalke S, Smalla K, Grohmann E, Alkorta I. Long-term effects of aided phytostabilisation on microbial communities of metal-contaminated mine soil. FEMS Microbiol Ecol 2016; 93:fiw252. [DOI: 10.1093/femsec/fiw252] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/21/2016] [Accepted: 12/22/2016] [Indexed: 11/14/2022] Open
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Burges A, Fievet V, Oustriere N, Epelde L, Garbisu C, Becerril JM, Mench M. Long-term phytomanagement with compost and a sunflower - Tobacco rotation influences the structural microbial diversity of a Cu-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 700:134529. [PMID: 31693956 DOI: 10.1016/j.scitotenv.2019.134529] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
At a former wood preservation site contaminated with Cu, various phytomanagement options have been assessed in the last decade through physicochemical, ecotoxicological and biological assays. In a field trial at this site, phytomanagement with a crop rotation based on tobacco and sunflower, combined with the incorporation of compost and dolomitic limestone, has proved to be efficient in Cu-associated risk mitigation, ecological soil functions recovery and net gain of economic and social benefits. To demonstrate the long-term effectiveness and sustainability of phytomanagement, we assessed here the influence of this remediation option on the diversity, composition and structure of microbial communities over time, through a metabarcoding approach. After 9 years of phytomanagement, no overall effect was identified on microbial diversity; the soil amendments, notably the repeated compost application, led to shifts in soil microbial populations. This phytomanagement option induced changes in the composition of soil microbial communities, promoting the growth of microbial groups belonging to Alphaproteobacteria, many being involved in N cycling. Populations of Nitrososphaeria, which are crucial in nitrification, as well as taxa from phyla Planctomycetacia, Chloroflexi and Gemmatimonadetes, which are tolerant to metal contamination and adapted to oligotrophic soil conditions, decreased in amended phytomanaged plots. Our study provides an insight into population dynamics within soil microbial communities under long-term phytomanagement, in line with the assessment of soil ecological functions and their recovery.
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Jauregi L, Epelde L, Alkorta I, Garbisu C. Antibiotic Resistance in Agricultural Soil and Crops Associated to the Application of Cow Manure-Derived Amendments From Conventional and Organic Livestock Farms. Front Vet Sci 2021; 8:633858. [PMID: 33708812 PMCID: PMC7940349 DOI: 10.3389/fvets.2021.633858] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/03/2021] [Indexed: 11/28/2022] Open
Abstract
The application of organic amendments to agricultural soil can enhance crop yield, while improving the physicochemical and biological properties of the recipient soils. However, the use of manure-derived amendments as fertilizers entails environmental risks, such as the contamination of soil and crops with antibiotic residues, antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). In order to delve into these risks, we applied dairy cow manure-derived amendments (slurry, fresh manure, aged manure), obtained from a conventional and an organic farm, to soil. Subsequently, lettuce and wheat plants were grown in the amended soils. After harvest, the abundance of 95 ARGs and MGE-genes from the amended soils and plants were determined by high-throughput qPCR. The structure of soil prokaryotic communities was determined by 16S rRNA amplicon sequencing and qPCR. The absolute abundance of ARGs and MGE-genes differed between treatments (amended vs. unamended), origins of amendment (conventional vs. organic), and types of amendment (slurry vs. fresh manure vs. aged manure). Regarding ARG-absolute abundances in the amendments themselves, higher values were usually found in slurry vs. fresh or aged manure. These abundances were generally higher in soil than in plant samples, and higher in wheat grain than in lettuce plants. Lettuce plants fertilized with conventional amendments showed higher absolute abundances of tetracycline resistance genes, compared to those amended with organic amendments. No single treatment could be identified as the best or worst treatment regarding the risk of antibiotic resistance in soil and plant samples. Within the same treatment, the resistome risk differed between the amendment, the amended soil and, finally, the crop. In other words, according to our data, the resistome risk in manure-amended crops cannot be directly inferred from the analysis of the amendments themselves. We concluded that, depending on the specific question under study, the analysis of the resistome risk should specifically focus on the amendment, the amended soil or the crop.
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Epelde L, Becerril JM, Barrutia O, González-Oreja JA, Garbisu C. Interactions between plant and rhizosphere microbial communities in a metalliferous soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2010; 158:1576-1583. [PMID: 20036453 DOI: 10.1016/j.envpol.2009.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 12/02/2009] [Accepted: 12/07/2009] [Indexed: 05/28/2023]
Abstract
In the present work, the relationships between plant consortia, consisting of 1-4 metallicolous pseudometallophytes with different metal-tolerance strategies (Thlaspi caerulescens: hyperaccumulator; Jasione montana: accumulator; Rumex acetosa: indicator; Festuca rubra: excluder), and their rhizosphere microbial communities were studied in a mine soil polluted with high levels of Cd, Pb and Zn. Physiological response and phytoremediation potential of the studied pseudometallophytes were also investigated. The studied metallicolous populations are tolerant to metal pollution and offer potential for the development of phytoextraction and phytostabilization technologies. T. caerulescens appears very tolerant to metal stress and most suitable for metal phytoextraction; the other three species enhance soil functionality. Soil microbial properties had a stronger effect on plant biomass rather than the other way around (35.2% versus 14.9%). An ecological understanding of how contaminants, ecosystem functions and biological communities interact in the long-term is needed for proper management of these fragile metalliferous ecosystems.
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Epelde L, Lanzén A, Mijangos I, Sarrionandia E, Anza M, Garbisu C. Short-term effects of non-grazing on plants, soil biota and aboveground-belowground links in Atlantic mountain grasslands. Sci Rep 2017; 7:15097. [PMID: 29118337 PMCID: PMC5678074 DOI: 10.1038/s41598-017-15345-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/24/2017] [Indexed: 11/16/2022] Open
Abstract
Mountain grasslands in the Iberian Peninsula are the result of extensive grazing. However, a progressive abandonment of grazing activity is currently observed in the study region. The objective of this work was to evaluate the short-term (2 years) effects of non-grazing on the diversity and composition of plants, soil microorganisms (prokaryotes, fungi, arbuscular mycorrhiza), mesofauna, macrofauna and aboveground-belowground links, through the study of 16 grazed vs. non-grazed areas in Atlantic grasslands located in the Basque Country (Spain). Sites were divided between 4 habitat types with different elevation, pasture productivity, vegetation type and parent material. Herbivores appeared to influence plant community composition, contributing to increase aboveground diversity, while having unequal effects on belowground communities depending on the organisms analysed. This may be explained by the different habitat and trophic level of each soil organism, which may be more or less affected by the predominating negative effects of grazing, such as soil compaction, and only partially compensated by other positive effects. Finally, habitat type appeared to be the strongest influence on both above- and belowground communities, also influencing the effect of the absence of grazing.
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Mijangos I, Albizu I, Epelde L, Amezaga I, Mendarte S, Garbisu C. Effects of liming on soil properties and plant performance of temperate mountainous grasslands. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2010; 91:2066-2074. [PMID: 20538406 DOI: 10.1016/j.jenvman.2010.05.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 04/10/2010] [Accepted: 05/14/2010] [Indexed: 05/29/2023]
Abstract
The application of lime or liming materials to acid-soil grasslands might help mitigate soil acidity, a major constraint to forage productivity in many temperate mountainous grasslands. Nowadays, in these mountainous grasslands, it is essential to promote agricultural practices to increase forage yield and nutritive value while preserving biodiversity and agroecosystem functioning. Two different field experiments were conducted in the Gorbeia Natural Park, northern Spain: (i) one in a calcareous mountainous grassland (Arraba) and (ii) the other in a siliceous mountainous grassland (Kurtzegan) to study the effects of a single application of two liming products, i.e. 2429 kg lime (164.3% CaCO(3)) ha(-1) and 4734 kg calcareous sand (84.3% CaCO(3)) ha(-1), applied one month before the beginning of the sheep grazing season (May-October), on soil chemical (pH, organic C, total N, C/N ratio, %Al saturation, Olsen P, exchangeable K(+) and Ca(2+)) and biological parameters (dehydrogenase, beta-glucosidase, urease, acid phosphatase and arylsulphatase activity) as well as on botanical diversity (graminoids, forbs, shrubs) and forage yield and nutritive value (crude protein, modified acid detergent fibre, digestibility). Untreated control plots were also included in the experiment. Soil sampling was carried out at the end of the sheep grazing season (6 months after liming treatment), while botanical composition was determined one year after treatments application. Although no increase in soil pH was observed in Arraba, liming significantly increased dehydrogenase activity (an indicator of soil microbial activity) by 30.4 and 86.7% at Arraba and Kurtzegan site, respectively. Liming treatments significantly improved forage yield and nutritive value in Arraba but not in Kurtzegan. Furthermore, no differences in soil biological quality, evaluated using the "treated-soil quality index" as proposed in this work, were observed between treated and untreated soils, and between the two different lime treatments (lime, calcareous sand). It was concluded that, in acid-soil temperate mountainous grasslands, moderate liming treatments have no negative short-term effects either on soil quality or botanical composition, while resulting in improvements in forage yield and nutritive value under some conditions.
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Barrutia O, Epelde L, García-Plazaola JI, Garbisu C, Becerril JM. Phytoextraction potential of two Rumex acetosa L. accessions collected from metalliferous and non-metalliferous sites: effect of fertilization. CHEMOSPHERE 2009; 74:259-64. [PMID: 18951609 DOI: 10.1016/j.chemosphere.2008.09.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Revised: 09/09/2008] [Accepted: 09/11/2008] [Indexed: 05/15/2023]
Abstract
Metal tolerance and phytoextraction potential of two common sorrel (Rumex acetosa L.) accessions, collected from a Pb/Zn contaminated site (CS, Lanestosa) and an uncontaminated site (UCS, Larrauri), were studied in fertilized and non-fertilized pots prepared by combining soil samples from both sites in different proportions (i.e., 0%, 33%, 66% and 100% of Lanestosa contaminated soil). The original metalliferous mine soil contained 20480, 4950 and 14 mg kg(-1) of Zn, Pb and Cd, respectively. The microcosm experiment was carried out for two months under greenhouse controlled conditions. It was found that fertilization increased mean plant biomass of both accessions as well as their tolerance. However, only the CS accession survived all treatments even though its biomass decreased proportionally according to the percentage of contaminated mine soil present in the pots. This metallicolous accession would be useful for the revegetation and phytostabilization of mine soils. Due to its high concentration and bioavailability in the contaminated soil, the highest values of metal phytoextracted corresponded to Zn. The CS accession was capable of efficiently phytoextracting metal from the 100% mine soil, indeed reaching very promising phytoextraction rates in the fertilized pots (6.8 mg plant(-1) month(-1)), similar to the ones obtained with hyperaccumulator plants. It was concluded that fertilization is certainly worth being considered for phytoextraction and revegetation with native plants from metalliferous soils.
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