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Introduction

The SOIL MICROBIAL ECOLOGY GROUP at NEIKER-Tecnalia (www.soilmicrobialecology.com) is most interested in the impact of different sources of environmental stress (contamination, agricultural practices, climate change) on soil health. Our research is focused on the utilization of soil microbial properties (mainly, those related to the biomass, activity and structural/functional diversity of soil microbial communities) as biological indicators of (i) the impact of disturbances on soil health and (ii) the efficiency of remediation methods (bioremediation and phytoremediation of contaminated soils). Regarding agricultural practices, we work on the utilization of soil microbial properties as biomonitoring tools for the assessment of the improvement in soil health derived from the application of environmentally-friendly practices (e.g., no-tillage, organic fertilization). Finally, an important part of our research is nowadays focused on the risk of dissemination of emerging contaminants (e.g., antibiotics and antibiotic resistance genes) in agricultural soils and crops.

We determine a great variety of parameters as indicators of soil microbial (i) BIOMASS: biomass carbon, ATP, DNA, ergosterol, glomalin, substrate-induced respiration, total bacteria, total fungi, total archaea, gene abundance by qPCR/high-throughput qPCR/droplet digital PCR, etc.; (ii) ACTIVITY: basal respiration, potentially mineralizable N, nitrification potential rate, enzyme activities (ß-glucosidase, ß-glucosaminidase, cellulose, chitinase, xylosidase, urease, arginine deaminase, amidase, protease, L-leucine aminopeptidase, L-alanine aminopeptidase, arylsulfatase, acid and alkaline phosphatase, dehydrogenase, FDA-fluorescein diacetate hydrolysis, gyrase), etc.; and (iii) DIVERSITY: community-level genetic profiles with ARISA and DGGE, community-level physiological profiles with Biolog™ plates, functional microarrays, high-throughput sequencing (16S rRNA/18S rRNA/ITS metabarcoding and shotgun), etc. In addition, we quantify functional genes (biodegradation, nutrient cycling, antibiotic resistance, horizontal gene transfer) and ecosystem attributes (resistance, resilience, suppresiveness, etc.). Last but not least, we study the traits of plant growth-promoting rhizobacteria and bacterial endophytes (ACC deaminase activity, siderophore production, phosphate solubilisation, indolacetic production, etc.) and perform soil ecotoxicity tests (Microtox, MARA, LumiMARA, PICT, MIC values, etc.).

 

Relevant papers in the last years:

Authors: Epelde L, Lanzén A, Mijangos I, Sarrionandia E, Anza M, Garbisu C
Title: Short-term effects of non-grazing on plants, soil biota and aboveground-belowground links in Atlantic mountain grasslands
Journal:  Scientific reports
Vol: 7, 15097 Date: 2017

Authors: Alkorta I, Epelde L, Garbisu C
Title: Environmental parameters altered by climate change affect the activity of soil microorganisms involved in bioremediation
Journal:  FEMS Microbiology Letters
Vol: 364 Date: 2017

Authors: Garbisu C, Garaiyurrebaso O, Epelde L, Grohmann E, Alkorta I
Title: Plasmid-mediated bioaugmentation for the bioremediation of contaminated soils
Journal:  Frontiers in Microbiology
Vol: 8:1966 Date: 2017

Authors: Burges A, Epelde L, Blanco F, Becerril JM, Garbisu C
Title: Ecosystem services and plant physiological status during endophyte-assisted phytoremediation of metal contaminated soil
Journal:  Science of the Total Environment
Vol: 584-585 Pages: 329-338 Date: 2017

Authors: Garaiyurrebaso O, Garbisu C, Blanco F, Lanzén A, Martín I, Epelde L, Becerril JM, Jechalke S, Smalla K, Grohmann E, Alkorta I
Title: Long-term effects of aided phytostabilization on microbial communities of metal-contaminated mine soil
Journal: FEMS Microbiology Ecology
Vol: 93 Date: 2017

Authors: Anza M, Epelde L, Artetxe U, Becerril JM, Garbisu C
Title: Control of Cortaderia selloana with a glyphosate-based herbicide led to a short-term stimulation of soil fungal communities
Journal: Environmental Monitoring and Assessment
Vol: 188 Pages: 631 Date: 2016

Authors: Lanzén A, Epelde L, Martín I, Artetxe A, Garbisu C
Title: Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient
Journal: Scientific Reports
Open access. Date: 2016

Authors: Gómez-Sagasti MT, Epelde L, Alkorta I, Garbisu C
Title: Reflections on soil contamination research from biologist´s point of view
Journal: Applied Soil Ecology
Vol: 105 Pages: 207-210 Date: 2016

Authors: Burges A, Epelde L, Benito G, Artetxe U, Becerril JM, Garbisu C
Title: Enhancement of ecosystem services during endophyte-assisted aided phytostabilization of metal contaminated mine soil
Journal: Science of the Total Environment
Vol: 562 Pages: 480-492 Date: 2016

Authors: Epelde L, Muñiz O, Garbisu C
Title: Microbial properties for the derivation of critical risk limits in cadmium contaminated soil
Journal: Applied Soil Ecology
Vol: 99 Pages: 19-28 Date: 2016

Authors: Anza M, Epelde L, Martín-Sánchez I, Blanco F, Garbisu C
Title: Microbial indicators for assessing the adverse impact of technical-grade hexachlorocyclohexane on soil quality
Journal: Spanish Journal of Soil Science
Vol: 6 Pages: 1-14 Date: 2016

Authors: Mijangos Amezaga I, Muguerza Elustondo E, Garbisu Crespo C, Anza Hortalá M, Epelde Sierra L
Title: Health cards for the evaluation of agricultural sustainability
Journal: Spanish Journal of Soil Science
Vol: 6 Pages: 15-20 Date: 2016

Authors: Rodríguez E, Peche R, Garbisu C, Gorostiza I, Epelde L, Artetxe U, Irizar A, Soto E, Becerril JM, Etxebarria J
Title: Dynamic quality index for agricultural soils based on fuzzy logic
Journal: Ecological Indicators
Vol: 60 Pages: 678-692 Date: 2016

Authors: Lanzén A, Epelde L, Garbisu C, Anza M, Martín-Sánchez I, Blanco F, Mijangos I
Title: The community structures of prokaryotes and fungi in mountain pasture soils are highly correlated and primarily influenced by pH
Journal: Frontiers in Microbiology
Vol: 6 Pages: 1-15 Date: 2015

Authors: Gómez-Sagasti MT, Becerril JM, Epelde L, Alkorta I, Garbisu C
Title: Early gene expression in Pseudomonas fluorescens exposed to a polymetallic solution
Journal: Cell Biology and Toxicology
Vol: 31 Pages: 39-81 Date: 2015

Authors: Gutiérrez L, Garbisu C, Cipriána E, Becerril JM, Soto M, Etxebarria J, Madariaga JM, Antigüedad I, Epelde L
Title: Application of ecological risk assessment based on a novel TRIAD-tiered approach to contaminated soil surrounding a closed non-sealed landfill
Journal: Science of the Total Environment
Vol: 514 Pages: 49-59 Date: 2015

Authors: Epelde L, Lanzén A, Blanco F, Urich T, Garbisu C
Title: Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine
Journal: FEMS Microbiology Ecology
Vol: 91 Date: 2015

Authors: Burges A, Epelde L, Garbisu C
Title: Impact of repeated single-metal and multi-metal pollution events on soil quality
Journal: Chemosphere
Vol: 120 Pages: 8-15 Date: 2015

Authors: Gómez-Sagasti MT, Becerril JM, Martín I, Epelde L, Garbisu C
Title: cDNA microarray assessment of early gene expression profiles in Escherichia coli cells exposed to a mixture of heavy metals
Journal: Cell Biology and Toxicology
Vol: 30 Pages: 207-232 Date: 2014

Authors: Galende MA, Becerril JM, Gómez-Sagasti M, Barrutia O, Garbisu C, Hernández A
Title: Agro-industrial wastes as effective amendments for ecotoxicity reduction and soil health improvement in aided phytostabilization
Journal: Environmental Science and Pollution Research
Vol: 21 Pages: 10036-10044 Date: 2014

Authors: Mijangos I, Epelde L, Garbisu C, González-Oreja JA
Title: Modification of soil enzyme activities as a consequence of replacing meadows by pine plantations under temperate climate
Journal: Pedobiologia
Vol: 57 Pages: 61-66 Date: 2014

Authors: Galende MA, Becerril JM, Gómez-Sagasti M, Barrutia O, Epelde L, Garbisu C, Hernández A
Title: Chemical stabilization of metal contaminated mine soil: early soil-amendment interactions and their effects on biological and chemical parameters
Journal: Water, Air and Soil Pollution
Vol: 225 Pages: 1863- Date: 2014

Authors: Pardo T, Clemente R, Epelde L, Garbisu C, Bernal MP
Title: Evaluation of the phytostabilisation efficiency in a trace elements contaminated soil using soil health indicators
Journal: Journal of Hazardous Materials
Vol: 268 Pages: 68-76 Date: 2014

Authors: Epelde L, Burges A, Mijangos I, Garbisu C
Title: Microbial properties and attributes of ecological relevance for soil quality monitoring during a chemical stabilization field study
Journal: Applied Soil Ecology
Vol: 75 Pages: 1-12 Date: 2014

Authors: Epelde L, Becerril JM, Alkorta I, Garbisu C
Title: Adaptive long-term monitoring of soil health in metal phytostabilization: ecological attributes and ecosystem services based on soil microbial parameters
Journal: International Journal of Phytoremediation
Vol: 16 Pages: 971-981 Date: 2014

Authors: Muñoz-Leoz B, Garbisu C, Charcosset J-Y, Sánchez-Pérez JM, Antigüedad I, Ruiz-Romera E
Title: Non-target effects of three formulated pesticides on microbially-mediated processes in a clay-loam soil
Journal: Science of the Total Environment
Vol: 449 Pages: 345-354 Date: 2013

Authors: Núñez-Zofío M, Larregla S, Garbisu C, Guerrero MM, Lacasa CM, Lacasa A
Title: Application of sugar beet vinasse followed by solarization reduces the incidence of Meloidogyne incognita in pepper crops while improving soil quality
Journal: Phytoparasitica
Vol: 41 Pages: 181-191 Date: 2013

Authors: González-Oreja JA, Garbisu C, Mijangos I, Mendarte S, Albizu I
Title: Reducing costs in biodiversity monitoring: shortcuts for plant diversity in meadows as a case study
Journal: Ecological Indicators
Vol: 24 Pages: 96-104 Date: 2013

Authors: Epelde L, Martín-Sánchez I, González-Oreja JA, Anza M, Gómez-Sagasti MT, Garbisu C
Title: Impact of sources of environmental degradation on microbial community dynamics in non-polluted and metal-polluted soils
Journal: Science of the Total Environment
Vol: 433 Pages: 264-272 Date: 2012

Authors: Epelde L, Becerril JM, Blanco F, Kowalchuk GA, Garbisu C
Title: Links between pseudometallophytes and rhizosphere microbial communities in a metalliferous soil
Journal: Pedobiologia
Vol: 55 Pages: 219-225 Date: 2012

Authors: Nuñez-Zofío M, Larregla S, Garbisu C
Title: Repeated biodisinfection controls the incidence of Phytophthora root and crown rot of pepper while improving soil quality
Journal: Spanish Journal of Agricultural Research
Vol: 10 Pages: 794-805 Date: 2012

Authors: Gómez-Sagasti M, Alkorta I, Becerril JM, Epelde L, Anza M, Garbisu C
Title: Microbial monitoring of the recovery of soil quality during heavy metal phytoremediation
Journal: Water, Air & Soil Pollution
Vol: 223 Pages: 3249-3262 Date: 2012

Authors: Muñoz-Leoz B, Garbisu C, Antigüedad I, Ruiz-Romera E
Title: Fertilization can modify the non-target effects of pesticides on soil microbial communities
Journal: Soil Biology and Biochemistry
Vol: 48 Pages: 125-134 Date: 2012

Authors: Nuñez-Zofío M, Larregla S, Garbisu C
Title: Application of organic amendments followed by soil plastic mulching reduces the incidence of Phytophthora capsici in pepper crops under temperate climate
Journal: Crop Protection
Vol: 30 Pages: 1563-1572 Date: 2011

Authors: Garbisu C, Alkorta I, Epelde L
Title: Assessment of soil quality using microbial properties and attributes of ecological relevance
Journal: Applied Soil Ecology
Vol: 49 Pages: 1-4 Date: 2011

Authors: Barrutia O, Garbisu C, Epelde L, Sampedro MC, Goicolea MA, Becerril JM
Title: Plant tolerance to diesel minimizes its impact on soil microbial characteristics during rhizoremediation of diesel-contaminated soils
Journal: Science of the Total Environment
Vol: 409 Pages: 4087-4093 Date: 2011

Authors: Muñoz-Leoz B, Ruiz-Romera E, Antigüedad I, Garbisu C
Title: Tebuconazole application decreases soil microbial biomass and activity
Journal: Soil Biology and Biochemistry
Vol: 43 Pages: 2176-2183 Date: 2011

Authors: Muñoz-Leoz B, Antigüedad I, Garbisu C, Ruiz-Romera E
Title: Nitrogen transformations and greenhouse gas emissions from a riparian wetland soil: an undisturbed soil column study
Journal: Science of the Total Environment
Vol: 409 Pages: 763-770 Date: 2011

Authors: Barrutia O, Artetxe U, Hernández A, Olano JM, García-Plazaola JI, Garbisu C, Becerril JM
Title: Native plant community growing on an abandoned lead-zinc mining area in northern Spain: implications for phytoremediation and germplasm preservation
Journal: International Journal of Phytoremediation
Vol: 13 Pages: 256-270 Date: 2011

Authors: Epelde L, Becerril JM, Kowalchuk GA, Deng Y, Zhou J, Garbisu C
Title: Impact of metal pollution and Thlaspi caerulescens growth on soil microbial communities
Journal: Applied and Environmental Microbiology
Vol: 76 Pages: 7843-7853 Date: 2010

Authors: Mijangos I, Garbisu C
Title: Consequences of soil sampling depth during the assessment of the effects of tillage on soil quality: a common oversight
Journal: Soil and Tillage Research
Vol: 109 Pages:169-173 Date: 2010

Authors: Mijangos I, Albizu I, Epelde L, Amezaga I, Mendarte S, Garbisu C
Title: Effects of liming on soil properties and plant performance of temperate mountainous grasslands
Journal: Journal Environmental Management
Vol: 91 Pages: 2066-2074 Date: 2010

Authors: Mijangos I, Albizu I, Garbisu C
Title: Beneficial effects of organic fertilization and no-tillage on fine-textured soil properties under two different forage crop rotations
Journal: Soil Science
Vol: 175 Pages: 173-185 Date: 2010

Authors: Epelde L, Becerril JM, Barrutia O, González-Oreja JA, Garbisu C
Title: Interactions between plant and rhizosphere microbial communities in a metalliferous soil
Journal: Environmental Pollution
Vol: 158 Pages: 1576-1583 Date: 2010

Authors: González-Oreja JA, Garbisu C, Mendarte S, Ibarra A, Albizu I
Title: Assessing the performance of nonparametric estimators of species richness in meadows
Journal: Biodiversity and Conservation
Vol: 19 Pages: 1417-1436 Date: 2010

Authors: Barrutia O, Garbisu C, Hernández-Allica J, García-Plazaola JI, Becerril JM
Title: Differences in EDTA-assisted metal phytoextraction between metallicolous and non-metallicolous accessions of Rumex acetosa L.
Journal: Environmental Pollution
Vol: 158 Pages: 1710-1715 Date: 2010