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WORKSHOP PRESENTERS
Integrating metagenomics and metabolic modeling for the rational design of microbial consortia in pollutant degradation
Advances in high-resolution metagenomic sequencing are reshaping microbial deployment strategies by enabling the direct recovery of microbial genomes from complex environmental samples. This approach provides detailed insights into the functional potential of key species involved in pollutant degradation, including their detoxification pathways, nutrient requirements, and cooperative behaviors. In this study, microbial communities exposed to prelevant pollutants were analyzed to identify core members and mechanisms supporting community resilience and degradation efficiency. Protocol improvements enhanced genome recovery from single-end reads, allowing robust functional characterization. The results revealed synergistic interactions and metabolic complementarities that can be leveraged to design tailored consortia for effective bioremediation. This work illustrates how metagenomics-driven strategies support the rational deployment of microbial communities in contaminated environments.
“Development of coated seeds with biological agents for a sustainable agriculture”
Agriculture is responsible for more than 20% of greenhouse emissions, the consumption of 70% of water worldwide, and the soil, water and air pollution by the use of chemical fertilizers and pesticides. In this context, the general objective of the ecoSEED+ project is to design a biotechnological strategy to develop seeds coated with biological agents as fertilization and pest protection alternatives. Wheat and tomato seeds, two of the world’s most important cereal and horticultural crops, have been selected for the use of the coating technology with biological agents. In ecoSEED+, biotechnological alternatives based on the use of several species of microalgae, cyanobacteria and selected enzymes (phosphatases, amidohydrolases…) will be developed and tested at lab scale as new ecological fertilizers. ecoSEED+ coating materials will be based upon sustainability of their formulation; ecofriendly materials with the best retention of microbial biomass and enzyme activity, and presenting a high efficiency to apply on seeds, will be selected. The results of this project are expected to generate new knowledges about soil microbial enzymes, relation soil-microbiota-plant, and accelerate the transition towards a more sustainable and efficient agriculture. ecoSEED+ is funded by the MCIN/AEI/10.13039/501100011033 and FSE+ (PID2022-139246OB-I00 grant).
Electroactive microbial communities in bioremediation: The parts and the whole (and the little things in between)
Microbial electrochemical systems (MES) can be used to treat water and soil contaminated with compounds hazardous for human and animal life and the environment. In MES, electroactive microorganisms use the anode as a terminal acceptor for electrons released during the degradation of substrates (e.g. industrial effluents or wastewater). The combination of the metabolism of electroactive microorganisms with their extracellular electron transfer capacity enables the efficient removal of recalcitrant contaminants.
Electroactive microbial communities can be manipulated to direct their metabolic activities and electrical output toward more efficient processes. We will discuss results of recent work aimed at the detection and removal of pesticides, antibiotics, hydrocarbons, and heavy metals present in contaminated water and soil, and how metabolic modelling can be used to design more efficient synthetic microbial communities.
Bioelectrochemical Technologies: Applications, Challenges, and Opportunities for Bioremediation and Beyond
Bioelectrochemical systems (BES) are an emerging technology in the field of bioremediation, leveraging the ability of certain microorganisms to transfer electrons to and from solid electrodes. This presentation will introduce the fundamentals of BES and their evolution into a versatile technological platform, with a focus on their application in the remediation of polluted groundwater and soil. Case studies will be presented demonstrating the removal of heavy metals, hydrocarbons, and antibiotics through both abiotic and biological processes, including hybrid systems combining BES with phytoremediation. In addition, the talk will explore different reactor typologies, including innovative configurations that integrate wastewater treatment with energy recovery.
Biodegradation of antibiotic pollutants – A way to tackle the spreading of ARGs in One Health context?
Sulfonamides are the second most used antibiotics worldwide with a release of approximately 20,000 tons per year. Sulfamethoxazole (SMX) is often detected in environmental compartments. The spreading of antibiotic resistant bacteria and antibiotic resistant genes is of concern and shall be integrated in One Health approaches. The objective is to understand the role of sulfonamide degradation on the spreading of sulfonamide antibiotic resistance genes.
Validation of bioremediation strategies for field application: challenges and opportunities
Bioremediation offers a sustainable alternative and/or complementary approach to traditional technologies for treatment of contaminated soil and water systems using microbes and/or plants. Yet, challenges such as site heterogeneity, microbial survival, nutrient limitations, and regulatory constraints can hinder its successful implementation. The integration of Key Performance Indicators (KPIs) – such as contaminant reduction rates, microbial activity levels and plant fitness – is essential for evaluating technology readiness, designing, and optimizing field performance. Practical examples for EU bioremediation projects will be discussed.
Engineered Pseudomonas putida for the Degradation of Soil Pollutants
Pesticides and herbicides such as lindane and atrazine are persistent environmental contaminants found at various sites across Europe. Developing safe and effective bioremediation strategies for these compounds is critical for restoring affected ecosystems. In this talk, we explore the use of genetically engineered Pseudomonas putida, a non-pathogenic, model soil bacterium with a metabolic versatility, as a host for degrading these recalcitrant chemicals. Our work aims to demonstrate the potential of synthetic biology approaches to enable targeted, efficient detoxification of polluted soils and contribute to sustainable land reclamation.
Encapsulation strategies of beneficial microorganisms in agriculture based on biodegradable polymers
The use of Agrochemicals & phytosanitary products in agriculture can have unfavorable effects on plant production and ecosystems. For this reason, natural and biological products, such as microorganisms, are considered an alternative for nutrition and pest treatment. Due to their high sensitivity to certain environmental conditions, in this talk we will show the results obtained by encapsulating microorganisms and enzymes of different nature by conventional encapsulation methodologies such as spray drying, ionic gelation, as well as by their incorporation into polymeric matrices with existing extrusion processes. Such encapsulation is focused on the use of biopolymers as wall material where, once the effectiveness of the new treatments has been demonstrated, the potential scalability for the agricultural sector is studied.
From the petri dish to a polluted soil: unravelling the complexity of sunflower ‘cry-for-help’ root exudation triggered by petroleum hydrocarbons
Root exudation is a key driver for plant-microbe interactions in phyto-rhizoremediation strategies aimed to pollutant removal. Soil contamination may trigger a ‘cry-for-help’ response in plants consisting in a shift in root chemistry to recruit degrading microbial communities able to catabolize the pollutants and boost plant growth under stress. Systematic studies comparing exudation patterns of plants grown in laboratory versus field set-ups are lacking. In the NYMPHE project, sunflower ‘cry-for-help’ response to petroleum hydrocarbons (PHCs) pollution was investigated via untargeted metabolomics comparing i) a sterile in vitro hydroponic system where the plants were challenged with xylene and ii) a real contaminated soil setup in which plants were cultivated under outdoor conditions. The analyses performed indicate that the two experimental designs significantly impacted the detected exudation patterns. The metabolites identified in the soil setup showed a more complex profile than those in the hydroponic system, presumably mirroring the field conditions. A selection of these metabolites is under investigation for the influence on rhizocompetence traits of PHC-degrading strains. The knowledge on exudation profiles from controlled conditions with low metabolite background to complex soil systems will contribute to elucidate the ‘cry-for-help’ response to PHCs, with the final aim to boost bioremediation effectiveness.
Microbial response during bioremediation processes: advanced techniques currently applied in large-scale projects for monitor biotic remediation
Bioremediation appears as the most effective and sustainable treatment technology for both soil and groundwater contaminated with a wide variety of pollutants based on its cost, technical feasibility and eco-friendly features. In this context, microbial response monitoring represents a key factor to assess biotic remediation effectiveness and rapidly detect deviations over removal performance during the process. Depending on the specificity microbial metabolic pathway different techniques can be applied. On one hand, when pollutant degradation is conducted by microbial consortia, the quantification of global activity is the best way to assess biodegradation effectiveness. Global activity can be measured based on different target indicators as quantification of (i) dehydrogenase activity, an intracellular enzyme responsible for the biological oxidation of organic compounds in soil and (ii) adenosine triphosphate (ATP), a nucleotide that is present in all living cells, representing active biomass in a system.
On the other hand, when a microbial community or even a specific species are the main responsible of the metabolic pathway metagenomics as DNA metabarcoding or qPCR techniques can be applied.
Nature-based solutions (NBS), such as bioremediation and phytoremediation, offer promising avenues for soil restoration
Traditional NBS approaches focused solely on total pollutant removals have proven unpredictable and often fall short of legislative remediation goals. With a focus on hydrophobic organic pollutants and bioremediation, this overview presentation will explore the paradigm shift towards addressing bioavailability, surpassing mere total pollutant removals, to reach acceptable risk reductions. To achieve this, two questions must be addressed: (1) How to influence bioavailability processes related to the biodegradation of contaminants? And (2) How can this knowledge be used to sustainably reduce chemical risks in soil?
Application of Isotopic Methods to Explore Microbial Degradation and Fate of Organic Contaminants
The combined use of ¹⁴C and ¹³C isotopic techniques offers a robust framework for understanding the microbial degradation and environmental fate of organic pollutants. ¹⁴C-labeled compounds allow for precise quantification of mineralization (e.g., conversion to CO₂), incorporation into biomass, and formation of secondary metabolites, providing a complete mass balance of contaminant transformation. In parallel, ¹³C-based compound-specific isotope analysis (CSIA) enables the identification of biodegradation processes under environmentally relevant conditions, without the need for radiolabeling. By integrating both approaches, we can trace degradation pathways at both bulk and molecular levels, assess the activity of specific microbial populations, and improve the evaluation of bioremediation strategies for soils and sediments contaminated with petroleum hydrocarbons, pesticides, and other persistent organic pollutants.
Microbial Bioremediation in Ports: Addressing Hydrocarbon Pollution with Lyophilized Bacteria
Current state of regulation on soil bioremediation
A brief overview of regulatory requirements (on national and EU level) related to application of technologies. A “lessons
learned” report built on recently conducted interviews with site owners of contaminated sites across Europe;
Nature’s Cleanup Crew: Using Microbiomes for Real-World Bioaugmentation
Microbiomes can be considered nature’s discreet yet powerful cleanup crew, endowed with the remarkable ability to degrade pollutants and restore balance within contaminated environments. In environmental applications, microbial communities capable of breaking down chemicals in soil and groundwater hold significant promise as eco-friendly and cost-effective tools for site remediation.
This presentation will showcase a case study in which microbiome bioaugmentation has been applied. This example will show how the targeted introduction of specific microbial consortia achieved pollutant degradation and, possibly achieved restoration of ecological indices. Emphasis will be placed on the molecular techniques employed to monitor microbial activity over time, as well as the potential for translating these approaches into real-world interventions.
To ensure the long-term sustainability of any bioremediation strategy, it is imperative to deploy robust tools capable of tracking the activity and persistence—both physical and functional—of the augmented microbiomes. The effectiveness and ecological safety of such interventions hinge on our capacity to understand and evaluate the performance of these functional microbial communities in situ.
At the same time, this presentation will address the considerable gaps in our knowledge of the molecular mechanisms governing the degradation of certain legacy contaminants. A prominent example is hexachlorocyclohexane, a persistent organic pollutant whose widespread historical use has left a significant and lasting environmental burden across numerous industrial and agricultural sites in Europe.
Addressing the gap is crucial not only for improving the sustainability and predictability of bioremediation processes but also for supporting evidence-based environmental policies.
Advanced tools for integration and synergistic inTeRconnectIon of microBIOMEs in resilient food systems
The EU TRIBIOME project aims to promote a sustainable balance between food production and ecosystem conservation under climate change scenarios. Over the course of the 48-month project, human, soil, animal, and plant microbiomes will be studied with the goal of reducing the environmental impact of the food industry.
In a preliminary study, we investigated the soil and rhizosphere microbiomes of soft wheat (Triticum aestivum) and hard wheat (Triticum durum) grown under high drought stress and control conditions. Rhizosphere samples were collected from three countries—Italy, Spain, and South Africa—across regions differing in aridity. Sampling was conducted at two key developmental stages: the terminal spikelet phase and gleaning, in order to evaluate microbiome dynamics during plant development.
Microbial community composition was assessed using next-generation sequencing targeting the 16S rRNA gene and ITS region to characterise bacterial and fungal communities, respectively. Our analyses revealed significant shifts in microbiome structure under drought conditions, with the identification of specific microbial taxa potentially involved in supporting plant development and stress resilience.
These findings provide initial insights into the complex interactions between the soil microbiome and plant physiology under abiotic stress, and offer a basis for the development of microbiome-informed strategies to enhance crop performance in challenging environments.
Nature-based solutions for wastewater management
Nature-based Solutions (NBS) mimic natural processes to deliver multiple benefits and services to local communities. These solutions are multi-functional measures that provide sustainable approaches to wastewater management, urban drainage, and various types of treatment wetlands. Microorganisms play a vital role in these systems by breaking down pollutants and enhancing the natural purification processes.
SUMMER SCHOOL SPEAKERS
School lecture: “Evolving Bioinformatics: From Microbial Petri Dishes to GPU-Accelerated Clusters and Beyond”
Over the past two decades, microbial bioinformatics has evolved from basic sequence alignment on laboratory computers to sophisticated, GPU-accelerated pipelines operating on supercomputing clusters. This lecture will explore this evolution, highlighting key milestones such as the adoption of GPUs for metagenome assembly, the integration of deep learning and the development of cloud-native FAIR data infrastructures. A live demonstration will showcase real-time preprocessing and taxonomic classification of metagenomic datasets using GPU-accelerated software, demonstrating how computational innovations can provide rapid insights into microbial communities. Looking to the future, we will discuss nascent quantum-inspired approaches for small data sets and emerging hybrid classical–quantum architectures for mechanistic modelling. Bioinformaticians studying microorganisms must embrace HPC, AI, and quantum paradigms, moving beyond the wet lab to drive the next frontier of microbial research.
Constructing Networks in Microbiome Science: Advancing Our Understanding of Microbial Ecology and Behavior
We will explore a range of approaches and solutions for constructing microbiome networks, spanning from correlative to metabolic networks. The relationships between different network topologies and ecological behaviors will be examined, supported by concrete examples from recent publications across various microbiome research domains. Particular attention will be given to changes in marine microbiome network structures and their ecological implications within marine ecosystems. We will also investigate microbiome network dynamics at the plant–soil interface, emphasizing their connections to soil health and plant productivity. Finally, we will illustrate the importance of network alterations in the human gut microbiome, highlighting their association with lifestyle and dietary changes, aging, and evolutionary patterns. These last examples will underscore how network dynamics contribute to maintaining homeostasis within the human holobiont in response to environmental and physiological challenges.
From omics to models: Extracting functional information for bioremediation design 1/3
Omics data provide a strong foundation for understanding microbial communities in contaminated environments, but their value lies in enabling functional interpretation and predictive modelling. This session offers a hands-on perspective of how multi-omics approaches, mainly, how metagenomics, transcriptomics and proteomics can be integrated to support bioremediation design. It introduces different modelling strategies (descriptive, mechanistic, statistical) and highlights essential computational steps such as assembly, annotation, expression analysis, and pathway mapping and tools. Common pitfalls, including overreliance on taxonomy, poor annotation, and inadequate data integration, are briefly discussed. The session aims to outline best practices and conceptual strategies for using omics as a starting point for models that inform bioremediation decisions.
From omics to models: Extracting functional information for bioremediation design 2/3
Omics data provide a strong foundation for understanding microbial communities in contaminated environments, but their value lies in enabling functional interpretation and predictive modelling. This session offers a hands-on perspective of how multi-omics approaches, mainly, how metagenomics, transcriptomics and proteomics can be integrated to support bioremediation design. It introduces different modelling strategies (descriptive, mechanistic, statistical) and highlights essential computational steps such as assembly, annotation, expression analysis, and pathway mapping and tools. Common pitfalls, including overreliance on taxonomy, poor annotation, and inadequate data integration, are briefly discussed. The session aims to outline best practices and conceptual strategies for using omics as a starting point for models that inform bioremediation decisions.
From omics to models: Extracting functional information for bioremediation design 3/3
Omics data provide a strong foundation for understanding microbial communities in contaminated environments, but their value lies in enabling functional interpretation and predictive modelling. This session offers a hands-on perspective of how multi-omics approaches, mainly, how metagenomics, transcriptomics and proteomics can be integrated to support bioremediation design. It introduces different modelling strategies (descriptive, mechanistic, statistical) and highlights essential computational steps such as assembly, annotation, expression analysis, and pathway mapping and tools. Common pitfalls, including overreliance on taxonomy, poor annotation, and inadequate data integration, are briefly discussed. The session aims to outline best practices and conceptual strategies for using omics as a starting point for models that inform bioremediation decisions.
ORGANISATIONAL COMMITTEE
Interim Team Lead & Project Coordinator at IDENER.AI | PhD in Computational Chemistry
BIOSYSMO coordinator
Head of ICCRAM-EST (Environment, Sustainability and Toxicology) Group. University of Burgos
BIOREM coordinator
Head of Colloid Biology Group – Department of Environmental Sciences of the Jozef Stefan Insitute (JSI)
Senior Researcher. Colloid Biology Group – Department of Environmental Sciences of the Jozef Stefan Insitute (JSI)
Project Manager – Business Development at EXELISIS
Communication and dissemination manager of ICCRAM – University of Burgos
European R&D projects