Skip to main content

Bioinocula and CROPping systems: an integrated biotechnological approach for improving crop yield, biodiversity and REsilience of Mediterranean agro-ecosystems (ReCrop; 2021-2024)

The Mediterranean economy is highly dependent on agriculture.
However, agricultural sustainability and productivity in this region are under serious threat due to climate change and depletion of water resources. This is worsened by poor management practices, such as the overuse of chemical fertilizers and pesticides, overgrazing, and monoculture farming. ReCROP aims to redesign Mediterranean agrosystems with improved resilience capacity and higher productivity, focusing on the development of sustainable agricultural production systems through the combined use of biotechnological tools and environmentally friendly agronomic practices. This will allow farming systems to face climate change trough the improvement of below and aboveground biodiversity, fertility, and water conservation. RECROP uses the novel approach of plant-microorganism management that relies on the increase of soils functions and health by using bioinocula, amendments, cropping systems, and climate-ready crops, to increase crop yields while providing ecological services, e.g., increasing carbon sequestration, organic matter, nutrient cycling and water conservation.

Read More


Agriculture is currently confronting an increasing human population and limitations of soil use due to, among other reasons, pollution levels above food safety threshold values. Some agricultural practices increase the heavy metal content (HM) of agricultural soil, representing an important threat for the European agricultural development. The use of microorganisms as plant growth promoters has been increasingly studied for a number of years, but it has only recently been proposed to improve plant metal tolerance. Regrettably, plant-microorganism-pollutant interactions are still poorly understood and the molecular underlying mechanisms are mostly unknown. The abovementioned challenges for agricultural production require the study of these mechanisms to better promote a more efficient and sustainable agriculture. This project will venture into new unchartered territory by focusing on the molecular interactions between a probiotic actinobacterium (Micromonospora cremea) and its host, Pisum sativum (garden pea), in the presence of HMs. We will evaluate the capacity of M. cremea CR30 to improve plant tolerance to HM polluted soils, in addition to unraveling the molecular dialogue during the first and late steps of their interaction. Early step interactions are crucial in plant promotion and protection against external stresses, like pollution by HM. Here, we propose the use of new -omic technologies to study these molecular interactions between plants and microorganisms under metal stress, providing a new pathway for an improved soil management. This project addresses a crucial objective in food security, the development of sustainable agricultural practices to control potentially adverse HM effects on plant health.

Avanzando en la aplicación de estrategias innovadoras de fitogestión en zonas contaminadas del espacio Sudoe (Phy2SUDOE; 2020-2023)

La fitogestión es una fitotecnología, surgida a partir de la fitorremediación, basada en el uso de plantas (árboles, arbustos, herbáceas) para controlar el riesgo asociado a la presencia de contaminantes en emplazamientos degradados, a la vez que: (i) se generan productos (e.g., madera, resina, aceites esenciales, bioenergía, ecocatalizadores) a partir de la biomasa cosechada; y (ii) se potencia el suministro de servicios ecosistémicos (e.g., secuestro de C, control de erosión, creación de hábitats).

Phy2SUDOE pretende valorizar emplazamientos contaminados con metales-metaloides y/o compuestos orgánicos en la región SUDOE mediante el empleo de estrategias de fitogestión encaminadas a la generación de productos y servicios ecosistémicos en dichos emplazamientos, a la vez que se minimiza el impacto ambiental que los contaminantes pudieran
ocasionar. Asimismo, este proyecto aspira a implantar estrategias de conservación de la biodiversidad endémica propia de algunos emplazamientos contaminados (e.g., flora metalícola, bacterias promotoras del crecimiento vegetal, etc.) por su valor intrínseco y utilitario (e.g., aplicaciones biotecnológicas).

Read More

Emergency and spread of antibiotic resistance (KONTRAE; 2020-2022)

In the KONTRAE project (funded by ELKARTEK, Basque Government), we will study in depth the links between human health, livestock, food and environment, in relation to antibiotic resistance.

According to the World Health Organization (WHO), antibiotic resistance is currently one of the greatest threats to human health, the economic sustainability of health systems, food security and overall socio-economic development. In the Autonomous Community of the Basque Country (CAPV), as in the rest of the world, this problem is increasing in a worrying way, as reflected in the growing detection in our hospitals of infections caused by multi-resistant or pan-resistant bacteria, with the resulting increase in deaths, health costs and productivity losses for companies.

To be able to successfully face this health and economic challenge, it is essential to approach it from a One Health perspective (“healthy people, healthy animals, safe and healthy food, healthy environment”), since the emergence and dissemination of many of the resistances to antibiotics occur in the environment and, through different routes of exposure, reach people.

Links between pesticide residues and antibiotic resistance dissemination in organically-managed agroecosystems (PRADA; 2020-2024)

The main objective of this PRADA project (PID2019-110058GB-C22, financed by the ministry of Science and Innovation) is to unravel the links between the presence of pesticide residues (copper-fungicide, glyphosate-herbicide) and animal manure-derived organic amendments (cow manure) on the emergence (resistome) and dissemination (mobilome) of antibiotic resistance (AR) in conventional and ecological agriculture systems, as well as to better understand the potential contribution of relevant edaphoclimatic factors (soil pH, temperature, moisture) on such AR.

Read More

URBAN KLIMA 2050 (2019-2025)

LIFE IP URBAN KLIMA 2050 is the largest climate action project in Basque Country for the next years and will demonstrate the effective and well-coordinated implementation of the KLIMA 2050 climate strategy in our territory. The project considers the urban settlements as the core for CC adaptation. One of the objectives is citizens’ empowerment for long-term engagement in environmentally responsible behaviours and healthier lifestyles. In this respect, our role in the project will be to take part in the design of a methodology for the creation of a platform for citizen science. This platform will include measurements from our Soil Health Cards, a tool that allows to evaluate the health of soil ecosystems in general and agroecosystems in particular, thus being able to monitor the evolution of the case studies of the project and choose those management alternatives that prove to be more sustainable from the point of view of the mitigation and adaptation to CC.

You will find more information about the project here


Design of a soil monitoring network for the Basque Country

It is increasingly recognized that soils provide multiple benefits to people, the environment and the economy, and that healthy soils are fundamental for achieving them. Soil functions include providing food, fibre and fuel, decomposing organic matter and recycling nutrients, distributing rainwater, etc. However, the soil resource and the functions it provides are constantly threatened by a wide range of risks at different scales, from local issues such as inadequate management, local pollution and erosion, to global issues such as air pollution and, of course, climate change. Furthermore, it is reasonable to assume that these risks will continue or intensify in the coming decades.

The state of soils needs to be monitored to see how they are changing and to understand the pressures on them. Soil monitoring networks can be described as: “A purpose-built set of sites to document changes in soil characteristics through periodic assessment of a broad set of soil parameters”. The use of custom-built soil monitoring networks is the most effective way to reliably assess temporary changes in soil status at the territorial level. Soil quality monitoring networks have been in operation in many European countries for years; the LURSARE project, funded by IHOBE, aims to fill this gap in the Basque Autonomous Community. In this sense, it is initially proposed to address a design phase of a soil quality monitoring programme, selecting the sampling points, depth(s), sampling frequency, soil properties to be determined, methodologies, etc.

Read More

Effect of biostimulant formulations on soil microbial parameters

We have started a collaboration with the company Ceres-Biotics, which works on the development of biostimulant formulations for agriculture.
Neiker’s work in collaboration with Ceres-Biotics will be to test the effect of different inoculations on soil health, through the measurement of a variety of parameters related to the activity, biomass and diversity of soil microbial communities. General parameters will be measured, but also specific parameters related to the potentiality of the strains under study.


We are about to start a new experiment on rhizoremediation of contaminated soil. Brassica juncea plants will be grown, under controlled Phytotron conditions, in soil simultaneously contaminated with metals and organic compounds.  Different amendments (chicken manure, horse manure, etc.) will be used to both facilitate plant growth and stimulate the rate of contaminant degradation by rhizosphere microbial communities (i.e., bioremediation through biostimulation). In addition, bacterial strains isolated from the contaminated soil will be initially selected according to their (i) contaminant degradation potential and (ii) plant growth-promoting traits. A consortium of these strains will then be used for bioaugmentation purposes. Finally, apart from the reduction in the concentrations of the target contaminants, we will study the recovery of soil health, using a variety of physicochemical and microbial indicators of soil functioning, as a result of the application of the abovementioned rhizoremediation strategies.

Project about the rational use of antibiotics in livestock

Several groups of Neiker are working on the research project URAGAN, which aims a rational use of antibiotics in livestock. In the case of the Soil Microbial Ecology Group, we are concerned about the potential dissemination of antibiotic resistance genes and mobile genetic elements as a result of the application of animal manure in agricultural soil. In the short term, we plan to establish a pot experiment where we will apply several manures and grow different crops. We will use high-throughput qPCR to simultaneously analyze a great variety of antibiotic resistance genes both in soil and plants. To this purpose, this week we have collected manure and slurry in two dairy farms under organic and intensive management.