{"type": "FeatureCollection", "features": [{"id": "10.1016/j.jtbi.2024.111737", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:16:45Z", "type": "Journal Article", "created": "2024-01-25", "title": "A mathematical model of biofilm growth and spread within plant xylem: Case study of Xylella fastidiosa in olive trees", "description": "Xylem-limited bacterial pathogens cause some of the most destructive plant diseases. Though imposed measures to control these pathogens are generally ineffective, even among susceptible taxa, some hosts can limit bacterial loads and symptom expression. Mechanisms by which this resistance is achieved are poorly understood. In particular, it is still unknown how differences in vascular structure may influence biofilm growth and spread within a host. To address this, we developed a novel theoretical framework to describe biofilm behaviour within xylem vessels, adopting a polymer-based modelling approach. We then parameterised the model to investigate the relevance of xylem vessel diameters on Xylella fastidiosa resistance among olive cultivars. The functionality of all vessels was severely reduced under infection, with hydraulic flow reductions of 2-3 orders of magnitude. However, results suggest wider vessels act as biofilm incubators; allowing biofilms to develop over a long time while still transporting them through the vasculature. By contrast, thinner vessels become blocked much earlier, limiting biofilm spread. Using experimental data on vessel diameter distributions, we were able to determine that a mechanism of resistance in the olive cultivar Leccino is a relatively low abundance of the widest vessels, limiting X. fastidiosa spread.", "keywords": ["Xylella fastidiosa", "0301 basic medicine", "0303 health sciences", "Xylem-limited bacterial pathogen", "Olive", "Models", " Theoretical", "Xylella", "630", "olive", "03 medical and health sciences", "Xylem", "Olea", "Biofilms", "multiphase model", "biofilm formation", "Biofilm formation", "Multiphase model", "xylem-limited bacterial pathogen", "Plant Diseases"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/516500/1/Walker%20et%20al.%2c%202024.pdf"}, {"href": "https://eprints.soton.ac.uk/490090/1/1-s2.0-S0022519324000183-main.pdf"}, {"href": "https://doi.org/10.1016/j.jtbi.2024.111737"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Theoretical%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jtbi.2024.111737", "name": "item", "description": "10.1016/j.jtbi.2024.111737", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jtbi.2024.111737"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-03-01T00:00:00Z"}}, {"id": "10.1007/s13762-013-0250-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:15:29Z", "type": "Journal Article", "created": "2013-03-25", "title": "A poly-\u03b5-caprolactone based biofilm carrier for nitrate removal from water", "description": "Nitrate removal from water has been accomplished by heterotrophic biofilms using organic carbon as a source of reducing power. To overcome the natural limitation in organic carbon in water, a poly-e-caprolactone based biofilm carrier that serves simultaneously as a biofilm carrier and as a source of organic carbon was developed and tested in the present work. The feasibility of the new biofilm carrier for nitrate removal from water was evaluated in a packed bed reactor. The combination of size and structure provided a carrier element having high surface area and void volume, 1,170\u00a0m2/m3 and 67\u00a0%, respectively. A maximum denitrification rate of 4.4\u00a0mg\u00a0N\u2013NO3                 \u2212/(L.h) (9.2\u00a0mg\u00a0N\u2013NO3                 \u2212/(m2.h)) was achieved in the packed bed reactor at 20\u00a0\u00b0C and pH 7.0. Main advantages of the biofilm carrier developed in the present work are its mechanical stability in water even after biofilm formation and controlled release of organic carbon by enzymatic reactions. The proposed biotechnology to remove nitrate from groundwater is robust and easy to operate.", "keywords": ["Science & Technology", "Biofilm", "0207 environmental engineering", "02 engineering and technology", "Biofilm reactor", "01 natural sciences", "6. Clean water", "Solid carbon source", "Biofilters", "Biodegradable polymer", "Denitrification", "Packed bed reactor", "Tratamento de \u00e1guas residuais", "0105 earth and related environmental sciences"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1007/s13762-013-0250-z"}, {"href": "https://doi.org/10.1007/s13762-013-0250-z"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Journal%20of%20Environmental%20Science%20and%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s13762-013-0250-z", "name": "item", "description": "10.1007/s13762-013-0250-z", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s13762-013-0250-z"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-03-26T00:00:00Z"}}, {"id": "10.1016/j.advwatres.2019.01.011", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:15:31Z", "type": "Journal Article", "created": "2019-01-30", "title": "Interaction between biofilm growth and NAPL remediation: A pore-scale study", "description": "Abstract   In this paper, we introduce a pore-scale model to study the interaction between biofilm growth and non-aqueous-phase-liquid (NAPL) dissolution. Liquid flow and dissolved NAPL transport are coupled with a biofilm growth model to correctly describe the complex dynamics of the processes including fluid flow, NAPL dissolution/biodegradation and biofilm growth. Fluid flow is simulated using an immersed boundary-lattice Boltzmann (IB-LB) model; while solute transport is solved by a cut-cell finite volume method (FVM). A uniform dissolution approach is also adopted to capture the temporal evolution of trapped blobs. Spatio-temporal distributions of the biomass are investigated using a cellular automaton algorithm combined with the immersed boundary method (IBM). Simulations focused on NAPL dissolution in both abiotic and biotic conditions are conducted to assess the capability of the model. In abiotic conditions, we analyze the effects of the hydrodynamic regimes and the spatial distribution of NAPL blobs on the dissolution rate under different assumptions (i.e., blob size and Peclet number). In biotic conditions, a series of impact factors are also investigated (i.e., spatial distribution, reaction kinetics and NAPL-induced toxicity). Finally, the current model is used to evaluate the pore scale relevance of a local equilibrium assumption between fluid phase and biofilm phase in the vicinity of the NAPL source.", "keywords": ["570", "biofilm growth", "cellular automata", "0208 environmental biotechnology", "0207 environmental engineering", "02 engineering and technology", "530", "[SPI.MECA.MEFL]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Fluids mechanics [physics.class-ph]", "immersed boundary method", "porous media", "[SDE]Environmental Sciences", "NAPL biodegradation", "lattice Botzmann method", "[SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology"]}, "links": [{"href": "https://doi.org/10.1016/j.advwatres.2019.01.011"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Advances%20in%20Water%20Resources", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.advwatres.2019.01.011", "name": "item", "description": "10.1016/j.advwatres.2019.01.011", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.advwatres.2019.01.011"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-01T00:00:00Z"}}, {"id": "10.1016/j.bioelechem.2020.107621", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:15:54Z", "type": "Journal Article", "created": "2020-07-27", "title": "Tailored glycosylated anode surfaces: Addressing the exoelectrogen bacterial community via functional layers for microbial fuel cell applications", "description": "Grafting of aryldiazonium cations bearing a p-mannoside functionality over microbial fuel cell (MFC) anode materials was performed to investigate the ability of aryl-glycoside layers to regulate colonisation by biocatalytic biofilms. Covalent attachment was achieved via spontaneous reactions and via electrochemically-assisted grafting using potential step experiments. The effect of different functionalisation protocols on MFC performance is discussed in terms of changes in wettability, roughness and electrochemical response of modified electrodes. Water contact angle measurements (WCA) show that aryl-mannoside grafting yields a significant increase in hydrophilic character. Surface roughness determinations via atomic force microscopy (AFM) suggest a more disordered glycan adlayer when electrografting is used to facilitate chemisorption. MFCs were used as living sensors to successfully test the coated electrodes: the response of the MFCs in terms of start-up time was accelerated when compared to that of MFC equipped with non-modified electrodes, this suggests a faster development of a mature biofilm community resulting from aryldiazonium modifications, as confirmed by cyclic voltammetry of MFC anodes. These results therefore indicate that modification with glycans offers a bioinspired route to accelerating biofilm colonisation without any adverse effects on final MFC outputs.", "keywords": ["Microbial fuel cell", "Glycosylation", "Bacteria", "Bioelectric Energy Sources", "Surface Properties", "Microbiota", "02 engineering and technology", "Exoelectrogen biofilms", "540", "01 natural sciences", "7. Clean energy", "[SDV.BIO] Life Sciences [q-bio]/Biotechnology", "0104 chemical sciences", "Electricity", "[CHIM.OTHE] Chemical Sciences/Other", "Biofilms", "Aryl-mannoside layers", "Glycan adlayers", "0210 nano-technology", "Electrodes"]}, "links": [{"href": "https://doi.org/10.1016/j.bioelechem.2020.107621"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioelectrochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.bioelechem.2020.107621", "name": "item", "description": "10.1016/j.bioelechem.2020.107621", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.bioelechem.2020.107621"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-01T00:00:00Z"}}, {"id": "10.1016/j.chemosphere.2014.06.094", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:16:01Z", "type": "Journal Article", "created": "2014-08-13", "title": "Influence of tetracycline on the microbial community composition and activity of nitrifying biofilms", "description": "The present work aims to evaluate the bacterial composition and activity (carbon and nitrogen removal) of nitrifying biofilms exposed to 50 \u03bcg L(-1) of tetracycline. The tetracycline removal efficiency and the occurrence of tetracycline resistance (tet) genes were also studied. Two sequencing batch biofilm reactors (SBBRs) fed with synthetic wastewater were operated without (SBBR1) and with (SBBR2) the antibiotic. Both SBBRs showed similar organic matter biodegradation and nitrification activity. Tetracycline removal was about 28% and biodegradation was probably the principal removal mechanism of the antibiotic. Polymerase chain reaction-denaturing gradient gel electrophoresis analysis of the bacterial community showed shifts leading to not only the fading of some ribotypes, but also the emergence of new ones in the biofilm with tetracycline. The study of the tet genes showed that tet(S) was only detected in the biofilm with tetracycline, suggesting a relationship between its occurrence and the presence of the antibiotic.", "keywords": ["Science & Technology", "Polymers", "Microbiota", "Molecular Sequence Data", "Tetracycline Resistance", "0211 other engineering and technologies", "Resistance genes", "Sequence Analysis", " DNA", "02 engineering and technology", "Tetracycline", "Nitrification", "01 natural sciences", "6. Clean water", "Anti-Bacterial Agents", "Tetracycline removal", "Nitrifying biofilms", "Bacterial Proteins", "Antibiotics", "Biofilms", "11. Sustainability", "Bacterial community", "Adsorption", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.chemosphere.2014.06.094"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.chemosphere.2014.06.094", "name": "item", "description": "10.1016/j.chemosphere.2014.06.094", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.chemosphere.2014.06.094"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-12-01T00:00:00Z"}}, {"id": "10.1016/j.envres.2021.112649", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:16:15Z", "type": "Journal Article", "created": "2021-12-31", "title": "N-acyl-homoserine lactones in extracellular polymeric substances from sludge for enhanced chloramphenicol-degrading anode biofilm formation in microbial fuel cells", "description": "Exploring an efficient acclimation strategy to obtain robust bioanodes is of practical significance for antibiotic wastewater treatment by bioelectrochemical systems (BESs). This study investigated the effects of two acclimation conditions on chloramphenicol (CAP)-degrading anode biofilm formation in microbial fuel cells (MFCs). The one was continuously added the extracellular polymeric substances (EPS) extracted from anaerobic sludge and increasing concentrations of CAP after the first start-up phase, while the other was added the EPS-1 (N-acyl-homoserine lactones, namely AHLs were extracted from the EPS) at the same conditions. The results demonstrated that AHLs in the sludge EPS played a crucial role for enhanced CAP-degrading anode biofilm formation in MFCs. The AHL-regulation could not only maintain stable voltage outputs but also significantly accelerate CAP removal in the EPS MFC. The maximum voltage of 653.83\u00a0mV and CAP removal rate of 1.21\u00a0\u00b1\u00a00.05\u00a0mg/L\u00b7h were attained from the EPS MFC at 30\u00a0mg/L of CAP, which were 0.84 and 1.57 times higher than those from the EPS-1 MFC, respectively. These improvements were largely caused by the thick and 3D structured biofilm, strong and homogeneous cell viability throughout the biofilm, and high protein/polysaccharide ratio along with more conductive contents in the biofilm EPS. Additionally, AHLs facilitated the formation of a biofilm with rich biodiversity and balanced bacterial proportions, leading to more beneficial mutualism among different functional bacteria. More bi-functional bacteria (for electricity generation and antibiotic resistance/degradation) were specifically enriched by AHLs as well. These findings provide quorum sensing theoretical knowledge and practical instruction for rapid antibiotic-degrading electrode biofilm acclimation in BESs.", "keywords": ["Chloramphenicol", "Sewage", "Bioelectric Energy Sources", "Extracellular Polymeric Substance Matrix", "Biofilms", "Acyl-Butyrolactones", "Electrodes", "01 natural sciences", "6. Clean water", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Wu, Xiayuan, Zhang, Lina, Lv, Zuopeng, Xin, Fengxue, Dong, Weiliang, Liu, Guannan, Li, Yan, Jia, Honghua,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.envres.2021.112649"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.envres.2021.112649", "name": "item", "description": "10.1016/j.envres.2021.112649", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.envres.2021.112649"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-01T00:00:00Z"}}, {"id": "10.1016/j.foodres.2022.112202", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:16:20Z", "type": "Journal Article", "created": "2022-11-19", "title": "Evidence of virulence and antibiotic resistance genes from the microbiome mapping in minimally processed vegetables producing facilities", "description": "Daily consumption of fresh vegetables is highly recommended by international health organizations, because of their high content of nutrients. However, fresh vegetables might harbour several pathogenic microorganisms or contribute to spread antibiotic resistance, thus representing a hazard for consumers. In addition, little is known about the transmission routes of the residential microbiome from the food handling environment to vegetables. Therefore, we collected environmental and food samples from three manufactures producing fresh vegetables to estimate the relevance of the built environment microbiome on that of the finished products. Our results show that food contact surfaces sampled after routine cleaning and disinfection procedures host a highly diverse microbiome, including pathogens such as the enterotoxigenic Bacillus cereus sensu stricto. In addition, we provide evidence of the presence of a wide range of antibiotic resistance and virulence genes on food contact surfaces associated with multiple taxa, thus supporting the hypothesis that selection of resistant and pathogenic taxa might occur on sanitized surfaces. This study also highlights the potential of microbiome mapping routinely applied in food industries monitoring programs to ensure food safety.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Food industry", "Virulence", "3309 Tecnolog\u00eda de Los Alimentos", "Antimicrobials", "Biolog\u00eda", "Tecnolog\u00eda de los alimentos", "Biofilm", "Microbiota", "Drug Resistance", " Microbial", "Anti-Bacterial Agents", "03 medical and health sciences", "Bacillus cereus", "Vegetables", "Antimicrobials; Bacillus cereus; Biofilm; Food industry; Metagenomics", "Metagenomics", "2414 Microbiolog\u00eda"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/903001/1/1-s2.0-S0963996922012601-main.pdf"}, {"href": "https://doi.org/10.1016/j.foodres.2022.112202"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Food%20Research%20International", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.foodres.2022.112202", "name": "item", "description": "10.1016/j.foodres.2022.112202", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.foodres.2022.112202"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-12-01T00:00:00Z"}}, {"id": "10.1016/j.mex.2020.101021", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:16:46Z", "type": "Journal Article", "created": "2020-08-05", "title": "Simultaneous characterization of porous and non-porous electrodes in microbial electrochemical systems,", "description": "Adequate electrochemical characterization of electrode material/biofilms is crucial for a comprehensive understanding and comparative performance of bioelectrochemical systems (BES). However, their responses are greatly affected by the metabolic activity and growth of these living entities and/or the interference of electrode wiring that can act as an electroactive surface for growth or constitute a source of contamination by corrosion. This restricts the meaningful comparison of the performance of distinct electrode materials in BES. This work describes a methodology for simultaneous electrochemical control and measurement of the microbial response on different electrode materials under the same physicochemical and biological conditions. The method is based on the use of a single channel potentiostat and one counter and reference electrodes to simultaneously polarize several electrode materials in a sole bioelectrochemical cell. Furthermore, various strategies to minimize wiring corrosion are proposed. The proposed methodology, then, will enable a more rigorous characterization of microbial electrochemical responses for comparisons purposes.\u2022Experimental Set-up allows to polarize several working electrodes at the same time.\u2022Chronoamperometry can be performed simultaneously with a potentiostat.\u2022The physicochemical and biological conditions in each working electrode will be exactly the same.", "keywords": ["Science", "Q", "Porous and non-porous electrodes", "Electroactive biofilms", "02 engineering and technology", "QD Chemistry", "TP Chemical technology", "01 natural sciences", "0104 chemical sciences", "Bioelectrochemical systems", "Environmental Science", "Qu\u00edmica F\u00edsica", "Electrode materials", "0210 nano-technology"]}, "links": [{"href": "https://doi.org/10.1016/j.mex.2020.101021"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/MethodsX", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.mex.2020.101021", "name": "item", "description": "10.1016/j.mex.2020.101021", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.mex.2020.101021"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-01T00:00:00Z"}}, {"id": "10.1021/acs.est.1c03586", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:17:29Z", "type": "Journal Article", "created": "2021-11-02", "title": "Impact of Periodic Polarization on Groundwater Denitrification in Bioelectrochemical Systems.", "description": "Nitrate contamination is a common problem in groundwater around the world. Nitrate can be cathodically reduced in bioelectrochemical systems using autotrophic denitrifiers with low energy investment and without chemical addition. Successful denitrification was demonstrated in previous studies in both microbial fuel cells and microbial electrolysis cells (MECs) with continuous current flow, whereas the impact of intermittent current supply (e.g., in a fluidized-bed system) on denitrification and particularly the electron-storing capacity of the denitrifying electroactive biofilms (EABs) on the cathodes have not been studied in depth. In this study, two continuously fed MECs were operated in parallel under continuous and periodic polarization modes over 280 days, respectively. Under continuous polarization, the maximum denitrification rate reached 233 g NO3--N/m3/d with 98% nitrate removal (0.6 mg NO3--N/L in the effluent) with negligible intermediate production, while under a 30 s open-circuit/30 s polarization mode, 86% of nitrate was removed at a maximum rate of 205 g NO3--N/m3/d (4.5 mg NO3--N/L in the effluent) with higher N2O production (6.6-9.3 mg N/L in the effluent). Conversely, periodic polarization could be an interesting approach in other bioelectrochemical processes if the generation of chemical intermediates (partially reduced or oxidized) should be favored. Similar microbial communities dominated byGallionellaceaewere found in both MECs; however, swapping the polarization modes and the electrochemical analyses suggested that the periodically polarized EABs probably developed a higher ability for electron storage and transfer, which supported the direct electron transfer pathway in discontinuous operation or fluidized biocathodes.", "keywords": ["bioelectrochemical systems (BESs)", "periodic polarization", "Autotrophic Processes", "Technology and Engineering", "denitrification", "Nitrates", "AUTOTROPHIC DENITRIFICATION", "EABs", "Bioelectric Energy Sources", "NITRATE-CONTAMINATED GROUNDWATER", "02 engineering and technology", "6. Clean water", "REDUCTION", "REMOVAL", "13. Climate action", "Earth and Environmental Sciences", "BACTERIA", "ACETATE", "Denitrification", "MICROBIAL FUEL-CELLS", "ELECTRON-TRANSFER", "BIOFILM", "0210 nano-technology", "Groundwater", "STORAGE"]}, "links": [{"href": "https://pubs.acs.org/doi/pdf/10.1021/acs.est.1c03586"}, {"href": "https://doi.org/10.1021/acs.est.1c03586"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.est.1c03586", "name": "item", "description": "10.1021/acs.est.1c03586", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.est.1c03586"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-11-02T00:00:00Z"}}, {"id": "10.1038/s41396-020-00806-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:17:47Z", "type": "Journal Article", "created": "2020-10-19", "title": "Microbial competition reduces metabolic interaction distances to the low \u00b5m-range", "description": "Abstract                <p>Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional systems or without accounting for competition or other metabolite-removal, conditions which may not very often match natural ecosystems. We here analyze the impact of cell-to-cell distance on unidirectional cross-feeding in a three-dimensional aqueous system with competition for the exchanged metabolite. Effective interaction distances were computed with a reaction-diffusion model and experimentally verified by growing a synthetic consortium of 1\uffe2\uff80\uff89\uffc2\uffb5m-sized metabolite producer, receiver, and competitor cells in different spatial structures. We show that receivers cannot interact with producers located on average 15\uffe2\uff80\uff89\uffc2\uffb5m away from them, as product concentration gradients flatten close to producer cells. We developed an aggregation protocol and varied the receiver cells\uffe2\uff80\uff99 product affinity, to show that within producer\uffe2\uff80\uff93receiver aggregates even low-affinity receiver cells could interact with producers. These results show that competition or other metabolite-removal of a public good in a three-dimensional system reduces metabolic interaction distances to the low \uffc2\uffb5m-range, highlighting the importance of concentration gradients as physical constraint for cellular interactions.</p", "keywords": ["DYNAMICS", "0301 basic medicine", "BIOFILMS", "0303 health sciences", "Microbiota", "612", "GROWTH-RATE", "DIFFUSION", "EVOLUTION", "Article", "GLUCOSE", "Diffusion", "03 medical and health sciences", "SPATIAL STRUCTURE", "LACTOCOCCUS-LACTIS", "COOPERATION"]}, "links": [{"href": "https://www.nature.com/articles/s41396-020-00806-9.pdf"}, {"href": "https://doi.org/10.1038/s41396-020-00806-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41396-020-00806-9", "name": "item", "description": "10.1038/s41396-020-00806-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41396-020-00806-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-19T00:00:00Z"}}, {"id": "10.1039/c7ra12316g", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:17:56Z", "type": "Journal Article", "created": "2018-01-15", "title": "Composition and role of the attached and planktonic microbial communities in mesophilic and thermophilic xylose-fed microbial fuel cells", "description": "<p>A mesophilic (37 \u00b0C) and a thermophilic (55 \u00b0C) two-chamber microbial fuel cell (MFC) were studied and compared for their power production from xylose and the anode-attached, membrane-attached and planktonic microbial communities involved.</p>", "keywords": ["570", "waste-water", "116 Chemical sciences", "116", "bacterium", "01 natural sciences", "7. Clean energy", "biofilm", "3. Good health", "Chemistry", "sludge", "13. Climate action", "extracellular electron-transfer", "geobacter-sulfurreducens", "electricity-generation", "phylogenetic analyses", "enrichment culture", "performance", "0105 earth and related environmental sciences"]}, "links": [{"href": "http://pubs.rsc.org/en/content/articlepdf/2018/RA/C7RA12316G"}, {"href": "https://doi.org/10.1039/c7ra12316g"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/RSC%20Advances", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1039/c7ra12316g", "name": "item", "description": "10.1039/c7ra12316g", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1039/c7ra12316g"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-01-01T00:00:00Z"}}, {"id": "10.1093/ismejo/wrae012", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:18:26Z", "type": "Journal Article", "created": "2024-01-29", "title": "Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth", "description": "Abstract                <p>Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities established on plant roots. Here, a well-established four-species biofilm model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, and Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis roots to study the impact of multispecies biofilm on plant growth and the community spatial dynamics on the roots. SPMX co-culture notably promoted root development and plant biomass. Co-cultured SPMX increased root colonization and formed multispecies biofilms, structurally different from those formed by monocultures. By combining 16S rRNA gene amplicon sequencing and fluorescence in situ hybridization with confocal laser scanning microscopy, we found that the composition and spatial organization of the four-species biofilm significantly changed over time. Monoculture P. amylolyticus colonized plant roots poorly, but its population and root colonization were highly enhanced when residing in the four-species biofilm. Exclusion of P. amylolyticus from the community reduced overall biofilm production and root colonization of the three species, resulting in the loss of the plant growth-promoting effects. Combined with spatial analysis, this led to identification of P. amylolyticus as a keystone species. Our findings highlight that weak root colonizers may benefit from mutualistic interactions in complex communities and hereby become important keystone species impacting community spatial organization and function. This work expands the knowledge on spatial organization uncovering interspecific interactions in multispecies biofilm communities on plant roots, beneficial for harnessing microbial mutualism promoting plant growth.</p", "keywords": ["0301 basic medicine", "0303 health sciences", "mutualism", "multispecies biofilms", "plant growth", "15. Life on land", "interspecies interactions", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Biofilms", "Microbial Interactions", "Original Article", "Symbiosis", "In Situ Hybridization", " Fluorescence", "keystone species", "spatial organization"]}, "links": [{"href": "https://academic.oup.com/ismej/article-pdf/18/1/wrae012/56945954/wrae012.pdf"}, {"href": "https://doi.org/10.1093/ismejo/wrae012"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/ismejo/wrae012", "name": "item", "description": "10.1093/ismejo/wrae012", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/ismejo/wrae012"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-01T00:00:00Z"}}, {"id": "10.1099/mic.0.001477", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:18:32Z", "type": "Journal Article", "created": "2024-08-06", "title": "Mobility and growth in confined spaces are important mechanisms for the establishment of Bacillus subtilis in the rhizosphere", "description": "<p>The rhizosphere hosts complex and abundant microbiomes whose structure and composition are now well described by metagenomic studies. However, the dynamic mechanisms that enable micro-organisms to establish along a growing plant root are poorly characterized. Here, we studied how a motile bacterium utilizes the microhabitats created by soil pore space to establish in the proximity of plant roots. We have established a model system consisting of Bacillus subtilis and lettuce seedlings co-inoculated in transparent soil microcosms. We carried out live imaging experiments and developed image analysis pipelines to quantify the abundance of the bacterium as a function of time and position in the pore space. Results showed that the establishment of the bacterium in the rhizosphere follows a precise sequence of events where small islands of mobile bacteria were first seen forming near the root tip within the first 12\uffe2\uff80\uff9324\uffe2\uff80\uff89h of inoculation. Biofilm was then seen forming on the root epidermis at distances of about 700\uffe2\uff80\uff931000\uffe2\uff80\uff89\uffc2\uffb5m from the tip. Bacteria accumulated predominantly in confined pore spaces within 200\uffe2\uff80\uff89\uffc2\uffb5m from the root or the surface of a particle. Using probabilistic models, we could map the complete sequence of events and propose a conceptual model of bacterial establishment in the pore space. This study therefore advances our understanding of the respective role of growth and mobility in the efficient colonization of bacteria in the rhizosphere.</p", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Ecology and Microbiomes", "Seedlings", "Biofilms", "Rhizosphere", "Plant Roots", "Soil Microbiology", "Bacillus subtilis", "Lactuca"]}, "links": [{"href": "https://doi.org/10.1099/mic.0.001477"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1099/mic.0.001477", "name": "item", "description": "10.1099/mic.0.001477", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1099/mic.0.001477"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-08-06T00:00:00Z"}}, {"id": "10.1128/aem.00698-21", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:19:11Z", "type": "Journal Article", "created": "2021-06-23", "title": "Limitation of Microbial Processes at Saturation-Level Salinities in a Microbial Mat Covering a Coastal Salt Flat", "description": "<p>             Due to their abilities to survive intense radiation and low water availability, hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even on Earth, the limitations imposed on microbial processes by saturation-level salinity have rarely been studied             in situ             .           </p>", "keywords": ["aerobic respiration", "primary and secondary production", "0301 basic medicine", "Geologic Sediments", "hypersaline microbial mats", "microbial communities", "Sodium Chloride", "extremophiles/extremophily", "03 medical and health sciences", "CYANOBACTERIAL MATS", "REDUCING BACTERIA", "uncultured microbes", "BACTERIUM DESULFOVIBRIO-OXYCLINAE", "Environmental Microbiology", "14. Life underwater", "Photosynthesis", "Phylogeny", "DISSIMILATORY SULFATE REDUCTION", "106022 Mikrobiologie", "Bacteria", "Microbiota", "ANOXYGENIC PHOTOSYNTHESIS", "15. Life on land", "Archaea", "biofilm biology", "6. Clean water", "Oxygen", "sulfide microprofiles", "13. Climate action", "CHLOROFLEXUS-LIKE BACTERIA", "106022 Microbiology", "sulfate reduction rate", "GEN. NOV.", "sulfur cycling", "PHYSIOLOGICAL CHARACTERIZATION", "DUNALIELLA", "microbiology of unexplored habitats", "biofilm biology; element cycles and biogeochemical processes; extremophiles/extremophily; microbial communities; microbiology of unexplored habitats; primary and secondary production; uncultured microbes", "element cycles and biogeochemical processes", "key biogeochemical processes", "OXYGENIC PHOTOSYNTHESIS", "Sulfur"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.00698-21"}, {"href": "https://doi.org/10.1128/aem.00698-21"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.00698-21", "name": "item", "description": "10.1128/aem.00698-21", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.00698-21"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-11T00:00:00Z"}}, {"id": "10.1186/s12934-021-01520-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:19:22Z", "type": "Journal Article", "created": "2021-01-11", "title": "Multi-pathogen Infections and Alzheimer&rsquo;s Disease", "description": "<p>Alzheimer&amp;rsquo;s disease (AD) is a chronic neurodegenerative disease associated with the overproduction and accumulation of amyloid-&amp;beta; peptide and hyperphosphorylation of tau proteins in the brain. Despite extensive research on the amyloid-based mechanism of AD pathogenesis, the underlying cause of AD remains poorly understood. No disease-modifying therapies currently exist, and numerous clinical trials have failed to demonstrate any benefits. The recent discovery that the amyloid-&amp;beta; peptide has antimicrobial activities supports the possibility of an infectious aetiology of AD and suggests that amyloid-&amp;beta; plaque formation might be induced by infection. AD patients have a weakened blood-brain barrier and immune system and are thus at elevated risk of microbial infections. Such infections can cause chronic neuroinflammation, production of the antimicrobial amyloid-&amp;beta; peptide, and neurodegeneration. Various pathogens, including viruses, bacteria, fungi, and parasites have been associated with AD. Most research in this area has focused on individual pathogens, with herpesviruses and periodontal bacteria being most frequently implicated. The purpose of this review is to highlight the potential role of multi-pathogen infections in AD. Recognition of the potential coexistence of multiple pathogens and biofilms in AD's aetiology may stimulate the development of novel approaches to its diagnosis and treatment. Multiple diagnostic tests could be applied simultaneously to detect major pathogens, followed by anti-microbial treatment using antiviral, antibacterial, antifungal, and anti-biofilm agents.</p>", "keywords": ["0301 basic medicine", "Bacteria", "Review", "Antifungal", "Microbiology", "Antiviral Agents", "QR1-502", "3. Good health", "Antibacterial", "Anti-biofilm", "03 medical and health sciences", "0302 clinical medicine", "Anti-Infective Agents", "Alzheimer Disease", "Biofilms", "Animals", "Humans", "Antiviral", "Alzheimer\u2019s disease"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s12934-021-01520-7.pdf"}, {"href": "https://doi.org/10.1186/s12934-021-01520-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Cell%20Factories", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s12934-021-01520-7", "name": "item", "description": "10.1186/s12934-021-01520-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s12934-021-01520-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-11T00:00:00Z"}}, {"id": "10.13130/rd_unimi/qobyan", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:19:27Z", "type": "Dataset", "title": "SENSE_WP1_T1.5_Evaluate the effect of flavonoids in bacteria phenotypes_biofilm formation_v.01.ods", "description": "This dataset contains information about favonoid-mediated effect on biofilm formation by the PCB-degrading strain Paraburkholderia xenovorans LB400", "keywords": ["Agricultural Sciences", "PCBs", " flavonoids", " biofilm"], "contacts": [{"organization": "Rolli, Eleonora", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.13130/rd_unimi/qobyan"}, {"rel": "self", "type": "application/geo+json", "title": "10.13130/rd_unimi/qobyan", "name": "item", "description": "10.13130/rd_unimi/qobyan", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.13130/rd_unimi/qobyan"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-01T00:00:00Z"}}, {"id": "10.3389/fmats.2021.624631", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:20:47Z", "type": "Journal Article", "created": "2021-05-07", "title": "When Beneficial Biofilm on Materials Is Needed: Electrostatic Attachment of Living Bacterial Cells Induces Biofilm Formation", "description": "<p>Bacterial attachment is crucial in many biotechnological applications, but many important bacterial strains cannot form biofilms. Biofilms can damage materials, and current strategies to manage biofilms are focused on inhibition and removal of biofilm. Biofilm formation is inevitable when materials are exposed to microbes and instead of biofilm prevention, we propose management of microbial composition by formation of biofilms with beneficial microbes. Since bacteria need to overcome a high repulsive force to attach to the surface and later to grow and multiply on it, electrostatic modification of the surfaces of cells or the material by polyelectrolytes (PE) was used in our approach, enabling efficient attachment of viable bacterial cells. Since highly positively charged PEs are known to be bactericidal, they were acetylated to reduce their toxicity, while preserving their net positive charge and ensuring cell viability. In our study bacterial strains were selected according to their intrinsic capability of biofilm formation, their shape variety and cell wall structure. These strains were tested to compare how the artificially prepared vs. natural biofilms can be used to populate the surface with beneficial bacteria. Using an artificial biofilm constructed of the potentially probiotic isolate Bacillus sp. strain 25.2. M, reduced the attachment and induced complete inhibition of E. coli growth over the biofilm. This study also revealed that the modification of the surfaces of cells or material by polyelectrolytes allows the deposition of bacterial cells, biofilm formation and attachment of biofilm non-forming cells onto surfaces. In this way, artificial biofilms with extended stability can be constructed, leading to selective pressure on further colonization of environmental bacteria.</p", "keywords": ["0301 basic medicine", "2. Zero hunger", "Technology", "0303 health sciences", "T", "cell surface modification", "cell encapsulation", "7. Clean energy", "artificial biofilms", "polyelectrolytes", "polyelectrolytes (PEs)", "03 medical and health sciences", "13. Climate action", "biofilm management", "surface modification"]}, "links": [{"href": "https://doi.org/10.3389/fmats.2021.624631"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmats.2021.624631", "name": "item", "description": "10.3389/fmats.2021.624631", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmats.2021.624631"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-05-07T00:00:00Z"}}, {"id": "10.3390/fermentation9070625", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:20:59Z", "type": "Journal Article", "created": "2023-07-03", "title": "Advances in the Application of Quorum Sensing to Regulate Electrode Biofilms in Bioelectrochemical Systems", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Bioelectrochemical systems (BESs) are an emerging technology for wastewater treatment and resource recovery. These systems facilitate electron transfer between microorganisms and electrodes, enabling their application in various fields, such as electricity production, bioremediation, biosensors, and biocatalysis. However, electrode biofilms, which play a critical role in BESs, face several challenges (e.g., a long acclimation period, low attached biomass, high electron transfer resistance, and poor tolerance and stability) that limit the development of this technology. Quorum sensing (QS) is a communication method among microorganisms that can enhance the performance of BESs by regulating electrode biofilms. QS regulation can positively impact electrode biofilms by enhancing extracellular electron transfer (EET), biofilm formation, cellular activity, the secretion of extracellular polymeric substances (EPS), and the construction of microbial community. In this paper, the characteristics of anode electrogenic biofilms and cathode electrotrophic biofilms in BESs, EET mechanisms, and the main factors affecting biofilm formation were summarized. Additionally, QS regulation mechanisms for biofilm formation, strategies for enhancing and inhibiting QS, and the application of QS regulation for electrode biofilms in BESs were systematically reviewed and discussed. This paper provides valuable background information and insights for future research and development of BES platforms based on QS regulation of electrode biofilms.</p></article>", "keywords": ["0301 basic medicine", "TP500-660", "03 medical and health sciences", "Fermentation industries. Beverages. Alcohol", "quorum sensing", "bioenergy", "electrode biofilms", "01 natural sciences", "bioelectrochemical systems", "6. Clean water", "pollution treatment", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://www.mdpi.com/2311-5637/9/7/625/pdf"}, {"href": "https://doi.org/10.3390/fermentation9070625"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Fermentation", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/fermentation9070625", "name": "item", "description": "10.3390/fermentation9070625", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/fermentation9070625"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-06-30T00:00:00Z"}}, {"id": "10.3390/ijms26020673", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:21:00Z", "type": "Journal Article", "created": "2025-01-15", "title": "Biofilm Formation, Modulation, and Transcriptomic Regulation Under Stress Conditions in Halomicronema sp.", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>In nature, bacteria often form heterogeneous communities enclosed in a complex matrix known as biofilms. This extracellular matrix, produced by the microorganisms themselves, serves as the first barrier between the cells and the environment. It is composed mainly of water, extracellular polymeric substances (EPS), lipids, proteins, and DNA. Cyanobacteria form biofilms and have unique characteristics such as oxygenic photosynthesis, nitrogen fixation, excellent adaptability to various abiotic stress conditions, and the ability to secrete a variety of metabolites and hormones. This work focused on the characterization of the cyanobacterium Halomicronema sp. strain isolated from a brackish environment. This study included microscopic imaging, determination of phenolic content and antioxidant capacity, identification of chemicals interfering with biofilm formation, and transcriptomic analysis by RNA sequencing and real-time PCR. Gene expression analysis was centered on genes related to the production of EPS and biofilm-related transcription factors. This study led to the identification of wza1 and wzt as EPS biomarkers and luxR-05665, along with genes belonging to the TetR/AcrR and LysR families, as potential biomarkers useful for studying and monitoring biofilm formation under different environmental conditions. Moreover, this work revealed that Halomicronema sp. can grow even in the presence of strong abiotic stresses, such as high salt, and has good antioxidant properties.</p></article>", "keywords": ["570", "Extracellular Polymeric Substance Matrix", "Gene Expression Profiling", "Gene Expression Regulation", " Bacterial", "stress resilience", "Cyanobacteria", "cyanobacteria", "Article", "transcriptomics", "Bacterial Proteins", "Halomicronema sp", "Stress", " Physiological", "Biofilms", "biofilm formation", "EPS", "Transcriptome"], "contacts": [{"organization": "Marina Caldara, Henk Bolhuis, Marta Marmiroli, Nelson Marmiroli,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.3390/ijms26020673"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Journal%20of%20Molecular%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/ijms26020673", "name": "item", "description": "10.3390/ijms26020673", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/ijms26020673"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-01-15T00:00:00Z"}}, {"id": "10.3390/molecules26164755", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:21:04Z", "type": "Journal Article", "created": "2021-08-06", "title": "Controlling the Carbon-Bio Interface via Glycan Functional Adlayers for Applications in Microbial Fuel Cell Bioanodes", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Surface modification of electrodes with glycans was investigated as a strategy for modulating the development of electrocatalytic biofilms for microbial fuel cell applications. Covalent attachment of phenyl-mannoside and phenyl-lactoside adlayers on graphite rod electrodes was achieved via electrochemically assisted grafting of aryldiazonium cations from solution. To test the effects of the specific bio-functionalities, modified and unmodified graphite rods were used as anodes in two-chamber microbial fuel cell devices. Devices were set up with wastewater as inoculum and acetate as nutrient and their performance, in terms of output potential (open circuit and 1 k\u2126 load) and peak power output, was monitored over two months. The presence of glycans was found to lead to significant differences in startup times and peak power outputs. Lactosides were found to inhibit the development of biofilms when compared to bare graphite. Mannosides were found, instead, to promote exoelectrogenic biofilm adhesion and anode colonization, a finding that is supported by quartz crystal microbalance experiments in inoculum media. These differences were observed despite both adlayers possessing thickness in the nm range and similar hydrophilic character. This suggests that specific glycan-mediated bioaffinity interactions can be leveraged to direct the development of biotic electrocatalysts in bioelectrochemical systems and microbial fuel cell devices.</p></article>", "keywords": ["microbial fuel cells", "Bioelectric Energy Sources", "Surface Properties", "carbon", "Organic chemistry", "02 engineering and technology", "7. Clean energy", "Article", "Carbon", "6. Clean water", "aryldiazonium", "bioanodes", "QD241-441", "Polysaccharides", "Biofilms", "[CHIM] Chemical Sciences", "functionalization", "electrocatalysis", "Graphite", "0210 nano-technology", "Electrodes", "bioelectrochemical systems"]}, "links": [{"href": "http://www.mdpi.com/1420-3049/26/16/4755/pdf"}, {"href": "https://www.mdpi.com/1420-3049/26/16/4755/pdf"}, {"href": "https://doi.org/10.3390/molecules26164755"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecules", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/molecules26164755", "name": "item", "description": "10.3390/molecules26164755", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/molecules26164755"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-06T00:00:00Z"}}, {"id": "10.3390/w11010113", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:21:13Z", "type": "Journal Article", "created": "2019-01-11", "title": "Coupling Riverbank Filtration with Reverse Osmosis May Favor Short Distances between Wells and Riverbanks at RBF Sites on the River Danube in Hungary", "description": "<p>Bank filtration and other managed aquifer recharge techniques have extensive application in drinking water production throughout the world. Although the quality of surface water improves during these natural processes, residence time in the aquifer and length of the flow paths are critical factors. A wide range of data is available on the physical\uffe2\uff80\uff93chemical processes and hydraulic conditions, but there is limited knowledge about the top layer of the porous media. An investigation was conducted on the hydraulic behavior and on the change of microbiological indicator parameters in the filter cake. The purpose of the experiment was to: (1) investigate if the reverse osmosis is sustainable when fed with only slow filtered water, and (2) show that a short travel distance can provide extensive pathogen removal and beneficial conditions for the reverse osmosis. A slow sand filter was operated over a one-year long period while changes in head loss and microbiological parameters were being monitored. Head loss and membrane permeability were monitored between 3 November 2016 and 24 October 2018 and microbiological sampling was performed from 19 July 2017 to 6 November 2018. The filtered water was fed to a reverse osmosis (RO) filter as the water above the sand filter had been spiked with dissolved iron. Results show that even a thin biofilm cake of 1\uffe2\uff80\uff933 mm thickness can result in a significant (10\uffe2\uff80\uff93100%) reduction in microbiological activity in the infiltrate, while favorable short retention times and oxic conditions are maintained. Avoiding anoxic conditions, subsequent iron and manganese dissolution and precipitation is beneficial for membrane processes. Building on these results, it can be stated that when reverse osmosis is directly fed with slow filtered or bank filtered water, (1) a short distance from the surface water body is required to avoid dissolved iron and manganese from entering the groundwater and (2) proper pathogen rejection can be achieved even over short distances.</p>", "keywords": ["13. Climate action", "slow sand filtration", "11. Sustainability", "pressure loss", "clogging", "filter cake", "pathogen barrier", "01 natural sciences", "bank filtration", "biofilm", "6. Clean water", "0105 earth and related environmental sciences"]}, "links": [{"href": "http://www.mdpi.com/2073-4441/11/1/113/pdf"}, {"href": "https://doi.org/10.3390/w11010113"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/w11010113", "name": "item", "description": "10.3390/w11010113", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/w11010113"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-10T00:00:00Z"}}, {"id": "11381/3018373", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:25:02Z", "type": "Journal Article", "created": "2025-01-15", "title": "Biofilm Formation, Modulation, and Transcriptomic Regulation Under Stress Conditions in Halomicronema sp.", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>In nature, bacteria often form heterogeneous communities enclosed in a complex matrix known as biofilms. This extracellular matrix, produced by the microorganisms themselves, serves as the first barrier between the cells and the environment. It is composed mainly of water, extracellular polymeric substances (EPS), lipids, proteins, and DNA. Cyanobacteria form biofilms and have unique characteristics such as oxygenic photosynthesis, nitrogen fixation, excellent adaptability to various abiotic stress conditions, and the ability to secrete a variety of metabolites and hormones. This work focused on the characterization of the cyanobacterium Halomicronema sp. strain isolated from a brackish environment. This study included microscopic imaging, determination of phenolic content and antioxidant capacity, identification of chemicals interfering with biofilm formation, and transcriptomic analysis by RNA sequencing and real-time PCR. Gene expression analysis was centered on genes related to the production of EPS and biofilm-related transcription factors. This study led to the identification of wza1 and wzt as EPS biomarkers and luxR-05665, along with genes belonging to the TetR/AcrR and LysR families, as potential biomarkers useful for studying and monitoring biofilm formation under different environmental conditions. Moreover, this work revealed that Halomicronema sp. can grow even in the presence of strong abiotic stresses, such as high salt, and has good antioxidant properties.</p></article>", "keywords": ["570", "Extracellular Polymeric Substance Matrix", "Gene Expression Profiling", "Gene Expression Regulation", " Bacterial", "stress resilience", "Cyanobacteria", "cyanobacteria", "Article", "transcriptomics", "Bacterial Proteins", "Halomicronema sp", "Stress", " Physiological", "Biofilms", "biofilm formation", "EPS", "Transcriptome"]}, "links": [{"href": "https://doi.org/11381/3018373"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/International%20Journal%20of%20Molecular%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11381/3018373", "name": "item", "description": "11381/3018373", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11381/3018373"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-01-15T00:00:00Z"}}, {"id": "2914529931", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:26:01Z", "type": "Journal Article", "created": "2019-01-30", "title": "Interaction between biofilm growth and NAPL remediation: A pore-scale study", "description": "Abstract   In this paper, we introduce a pore-scale model to study the interaction between biofilm growth and non-aqueous-phase-liquid (NAPL) dissolution. Liquid flow and dissolved NAPL transport are coupled with a biofilm growth model to correctly describe the complex dynamics of the processes including fluid flow, NAPL dissolution/biodegradation and biofilm growth. Fluid flow is simulated using an immersed boundary-lattice Boltzmann (IB-LB) model; while solute transport is solved by a cut-cell finite volume method (FVM). A uniform dissolution approach is also adopted to capture the temporal evolution of trapped blobs. Spatio-temporal distributions of the biomass are investigated using a cellular automaton algorithm combined with the immersed boundary method (IBM). Simulations focused on NAPL dissolution in both abiotic and biotic conditions are conducted to assess the capability of the model. In abiotic conditions, we analyze the effects of the hydrodynamic regimes and the spatial distribution of NAPL blobs on the dissolution rate under different assumptions (i.e., blob size and Peclet number). In biotic conditions, a series of impact factors are also investigated (i.e., spatial distribution, reaction kinetics and NAPL-induced toxicity). Finally, the current model is used to evaluate the pore scale relevance of a local equilibrium assumption between fluid phase and biofilm phase in the vicinity of the NAPL source.", "keywords": ["570", "biofilm growth", "cellular automata", "0208 environmental biotechnology", "0207 environmental engineering", "02 engineering and technology", "530", "[SPI.MECA.MEFL]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Fluids mechanics [physics.class-ph]", "immersed boundary method", "porous media", "[SDE]Environmental Sciences", "NAPL biodegradation", "lattice Botzmann method", "[SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology"]}, "links": [{"href": "https://doi.org/2914529931"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Advances%20in%20Water%20Resources", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2914529931", "name": "item", "description": "2914529931", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2914529931"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-03-01T00:00:00Z"}}, {"id": "10.5281/zenodo.4139861", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:23:26Z", "type": "Dataset", "title": "Dataset associated to Tailored glycosylated anode surfaces: Addressing the exoelectrogen bacterial community via functional layers for microbial fuel cell applications", "description": "This file contains the dataset associated to the published research article 'Tailored glycosylated anode surfaces: Addressing the exoelectrogen bacterial community via functional layers for microbial fuel cell applications'. The dataset contains Atomic Force Microscopy, electrochemistry, Microbial Fuel Cells power output and water contact angle raw data from their relative instruments. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sk\u0142odowska-Curie grant agreement No. 799175 (HiBriCarbon). The results of this publication reflect only the authors' view and the Commission is not responsible for any use that may be made of the information it contains. This publication has also emanated from research conducted with the financial support of Science Foundation Ireland under Grant No. 13/CDA/2213. The authors also thank the France-Ireland PHC ULYSSES programme for support, project 36028UB. JAB acknowledges support from the Irish Research Council under Grant No. GOIPG/2014/399.", "keywords": ["microbial fuel cells", "exoelectrgenic biofilm", "13. Climate action", "Nanoscience & Materials", "BIOFILM FORMATION", "Fuel Cells", "7. Clean energy"], "contacts": [{"organization": "Iannaci, Alessandro, Myles, Adam, Flinois, Thomas, Behan A., James, Barri\u00e8re, Fr\u00e9d\u00e9ric, Scanlan M., Eoin, Colavita E., Paula,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.4139861"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.4139861", "name": "item", "description": "10.5281/zenodo.4139861", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.4139861"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-01T00:00:00Z"}}, {"id": "11370/eec3af77-a5dd-4442-aec9-c13f919655ba", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:25:01Z", "type": "Journal Article", "created": "2020-10-19", "title": "Microbial competition reduces metabolic interaction distances to the low \u00b5m-range", "description": "Abstract                   <p>Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional systems or without accounting for competition or other metabolite-removal, conditions which may not very often match natural ecosystems. We here analyze the impact of cell-to-cell distance on unidirectional cross-feeding in a three-dimensional aqueous system with competition for the exchanged metabolite. Effective interaction distances were computed with a reaction-diffusion model and experimentally verified by growing a synthetic consortium of 1\uffe2\uff80\uff89\uffc2\uffb5m-sized metabolite producer, receiver, and competitor cells in different spatial structures. We show that receivers cannot interact with producers located on average 15\uffe2\uff80\uff89\uffc2\uffb5m away from them, as product concentration gradients flatten close to producer cells. We developed an aggregation protocol and varied the receiver cells\uffe2\uff80\uff99 product affinity, to show that within producer\uffe2\uff80\uff93receiver aggregates even low-affinity receiver cells could interact with producers. These results show that competition or other metabolite-removal of a public good in a three-dimensional system reduces metabolic interaction distances to the low \uffc2\uffb5m-range, highlighting the importance of concentration gradients as physical constraint for cellular interactions.</p", "keywords": ["DYNAMICS", "0301 basic medicine", "BIOFILMS", "0303 health sciences", "Microbiota", "612", "GROWTH-RATE", "DIFFUSION", "EVOLUTION", "Article", "GLUCOSE", "Diffusion", "03 medical and health sciences", "SPATIAL STRUCTURE", "LACTOCOCCUS-LACTIS", "COOPERATION"]}, "links": [{"href": "https://www.nature.com/articles/s41396-020-00806-9.pdf"}, {"href": "https://doi.org/11370/eec3af77-a5dd-4442-aec9-c13f919655ba"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11370/eec3af77-a5dd-4442-aec9-c13f919655ba", "name": "item", "description": "11370/eec3af77-a5dd-4442-aec9-c13f919655ba", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11370/eec3af77-a5dd-4442-aec9-c13f919655ba"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-19T00:00:00Z"}}, {"id": "11392/2582471", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:25:02Z", "type": "Journal Article", "created": "2025-02-14", "title": "Different Denitrification Capacity in Phragmites australis and Typha latifolia Sediments: Does the Availability of Surface Area for Biofilm Colonization Matter?", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Denitrification is a permanent nitrogen removal pathway; thus, it is a desirable ecosystem function in water bodies receiving agricultural runoff. Knowledge of denitrification capacity in response to vegetation type and varying NO3\u2212 loads is essential for designing effectively constructed wetlands to control eutrophication. The aim of this study was to compare the nitrogen removal efficiency of two common wetland macrophytes, i.e., Phragmites australis and Typha latifolia in a NO3\u2212 enrichment experiment (50\u2212800 \u00b5M). Measurements of NO3\u2212 consumption, and N2 production were performed in vegetated and unvegetated mesocosms incubated in summer (26 \u00b0C) at biomass peak. Vegetated sediments demonstrated higher efficiency in converting NO3\u2212 to N2 via denitrification (&lt;600\u201318,000 \u00b5mol N m\u22122 h\u22121) than bare sediments (300\u20133300 \u00b5mol N m\u22122 h\u22121). However, the denitrification stimulation effect from NO3\u2212 pulsing differed significantly between plant types. It can be hypothesized that P. australis played a more beneficial role than T. latifolia due to its greater submerged surface area, which facilitated enhanced opportunities for contact between NO3\u2212 and denitrifying bacteria. This ultimately resulted in an increased treatment performance. Understanding the interactions between plants and environmental drivers regulating denitrification is critical information for optimal wetland species selection. With an increasing global focus on sustainable water quality management, this research provides valuable insights into optimizing nature-based solutions.</p></article>", "keywords": ["biofilms; constructed wetlands; denitrification; nature-based solutions; nitrate pollution; P. australis; T. latifolia"]}, "links": [{"href": "https://sfera.unife.it/bitstream/11392/2582471/1/water-17-00560-v2.pdf"}, {"href": "https://www.mdpi.com/2073-4441/17/4/560/pdf"}, {"href": "https://doi.org/11392/2582471"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Water", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "11392/2582471", "name": "item", "description": "11392/2582471", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/11392/2582471"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-02-14T00:00:00Z"}}, {"id": "20.500.11850/506000", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:25:29Z", "type": "Journal Article", "created": "2021-06-23", "title": "Limitation of Microbial Processes at Saturation-Level Salinities in a Microbial Mat Covering a Coastal Salt Flat", "description": "<p>             Due to their abilities to survive intense radiation and low water availability, hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even on Earth, the limitations imposed on microbial processes by saturation-level salinity have rarely been studied             in situ             .           </p", "keywords": ["aerobic respiration", "primary and secondary production", "0301 basic medicine", "Geologic Sediments", "hypersaline microbial mats", "microbial communities", "Sodium Chloride", "extremophiles/extremophily", "03 medical and health sciences", "CYANOBACTERIAL MATS", "REDUCING BACTERIA", "uncultured microbes", "BACTERIUM DESULFOVIBRIO-OXYCLINAE", "Environmental Microbiology", "14. Life underwater", "Photosynthesis", "Phylogeny", "DISSIMILATORY SULFATE REDUCTION", "106022 Mikrobiologie", "Bacteria", "Microbiota", "ANOXYGENIC PHOTOSYNTHESIS", "15. Life on land", "Archaea", "biofilm biology", "6. Clean water", "Oxygen", "sulfide microprofiles", "13. Climate action", "CHLOROFLEXUS-LIKE BACTERIA", "106022 Microbiology", "sulfate reduction rate", "GEN. NOV.", "sulfur cycling", "PHYSIOLOGICAL CHARACTERIZATION", "DUNALIELLA", "microbiology of unexplored habitats", "biofilm biology; element cycles and biogeochemical processes; extremophiles/extremophily; microbial communities; microbiology of unexplored habitats; primary and secondary production; uncultured microbes", "element cycles and biogeochemical processes", "key biogeochemical processes", "OXYGENIC PHOTOSYNTHESIS", "Sulfur"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.00698-21"}, {"href": "https://doi.org/20.500.11850/506000"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.11850/506000", "name": "item", "description": "20.500.11850/506000", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.11850/506000"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-11T00:00:00Z"}}, {"id": "20.500.14243/516500", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:25:34Z", "type": "Journal Article", "created": "2024-01-25", "title": "A mathematical model of biofilm growth and spread within plant xylem: Case study of Xylella fastidiosa in olive trees", "description": "Xylem-limited bacterial pathogens cause some of the most destructive plant diseases. Though imposed measures to control these pathogens are generally ineffective, even among susceptible taxa, some hosts can limit bacterial loads and symptom expression. Mechanisms by which this resistance is achieved are poorly understood. In particular, it is still unknown how differences in vascular structure may influence biofilm growth and spread within a host. To address this, we developed a novel theoretical framework to describe biofilm behaviour within xylem vessels, adopting a polymer-based modelling approach. We then parameterised the model to investigate the relevance of xylem vessel diameters on Xylella fastidiosa resistance among olive cultivars. The functionality of all vessels was severely reduced under infection, with hydraulic flow reductions of 2-3 orders of magnitude. However, results suggest wider vessels act as biofilm incubators; allowing biofilms to develop over a long time while still transporting them through the vasculature. By contrast, thinner vessels become blocked much earlier, limiting biofilm spread. Using experimental data on vessel diameter distributions, we were able to determine that a mechanism of resistance in the olive cultivar Leccino is a relatively low abundance of the widest vessels, limiting X. fastidiosa spread.", "keywords": ["Plant biology", "Xylella fastidiosa", "0301 basic medicine", "0303 health sciences", "Xylem-limited bacterial pathogen", "Olive", "Models", " Theoretical", "Xylella", "Microbiology", "630", "olive", "03 medical and health sciences", "Xylem", "Olea", "Biofilms", "multiphase model", "biofilm formation", "Multiphase model", "Biofilm formation", "xylem-limited bacterial pathogen", "Plant Diseases"]}, "links": [{"href": "https://iris.cnr.it/bitstream/20.500.14243/516500/1/Walker%20et%20al.%2c%202024.pdf"}, {"href": "https://eprints.soton.ac.uk/490090/1/1-s2.0-S0022519324000183-main.pdf"}, {"href": "https://doi.org/20.500.14243/516500"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Theoretical%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.14243/516500", "name": "item", "description": "20.500.14243/516500", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.14243/516500"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-03-01T00:00:00Z"}}, {"id": "2262/93879", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:25:44Z", "type": "Journal Article", "created": "2020-07-27", "title": "Tailored glycosylated anode surfaces: Addressing the exoelectrogen bacterial community via functional layers for microbial fuel cell applications", "description": "Grafting of aryldiazonium cations bearing a p-mannoside functionality over microbial fuel cell (MFC) anode materials was performed to investigate the ability of aryl-glycoside layers to regulate colonisation by biocatalytic biofilms. Covalent attachment was achieved via spontaneous reactions and via electrochemically-assisted grafting using potential step experiments. The effect of different functionalisation protocols on MFC performance is discussed in terms of changes in wettability, roughness and electrochemical response of modified electrodes. Water contact angle measurements (WCA) show that aryl-mannoside grafting yields a significant increase in hydrophilic character. Surface roughness determinations via atomic force microscopy (AFM) suggest a more disordered glycan adlayer when electrografting is used to facilitate chemisorption. MFCs were used as living sensors to successfully test the coated electrodes: the response of the MFCs in terms of start-up time was accelerated when compared to that of MFC equipped with non-modified electrodes, this suggests a faster development of a mature biofilm community resulting from aryldiazonium modifications, as confirmed by cyclic voltammetry of MFC anodes. These results therefore indicate that modification with glycans offers a bioinspired route to accelerating biofilm colonisation without any adverse effects on final MFC outputs.", "keywords": ["Microbial fuel cell", "Glycosylation", "Bacteria", "Bioelectric Energy Sources", "Surface Properties", "Microbiota", "02 engineering and technology", "Exoelectrogen biofilms", "540", "7. Clean energy", "01 natural sciences", "[SDV.BIO] Life Sciences [q-bio]/Biotechnology", "0104 chemical sciences", "Electricity", "[CHIM.OTHE] Chemical Sciences/Other", "Biofilms", "Aryl-mannoside layers", "Glycan adlayers", "0210 nano-technology", "Electrodes"]}, "links": [{"href": "https://doi.org/2262/93879"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioelectrochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2262/93879", "name": "item", "description": "2262/93879", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2262/93879"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-01T00:00:00Z"}}, {"id": "2262/93880", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:25:44Z", "type": "Dataset", "title": "Dataset associated to Tailored glycosylated anode surfaces: Addressing the exoelectrogen bacterial community via functional layers for microbial fuel cell applications", "description": "This file contains the dataset associated to the published research article 'Tailored glycosylated anode surfaces: Addressing the exoelectrogen bacterial community via functional layers for microbial fuel cell applications'. The dataset contains Atomic Force Microscopy, electrochemistry, Microbial Fuel Cells power output and water contact angle raw data from their relative instruments. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sk\u0142odowska-Curie grant agreement No. 799175 (HiBriCarbon). The results of this publication reflect only the authors' view and the Commission is not responsible for any use that may be made of the information it contains. This publication has also emanated from research conducted with the financial support of Science Foundation Ireland under Grant No. 13/CDA/2213. The authors also thank the France-Ireland PHC ULYSSES programme for support, project 36028UB. JAB acknowledges support from the Irish Research Council under Grant No. GOIPG/2014/399.", "keywords": ["microbial fuel cells", "exoelectrgenic biofilm", "13. Climate action", "Nanoscience & Materials", "BIOFILM FORMATION", "Fuel Cells", "7. Clean energy"], "contacts": [{"organization": "Iannaci, Alessandro, Myles, Adam, Flinois, Thomas, Behan A., James, Barri\u00e8re, Fr\u00e9d\u00e9ric, Scanlan M., Eoin, Colavita E., Paula,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/2262/93880"}, {"rel": "self", "type": "application/geo+json", "title": "2262/93880", "name": "item", "description": "2262/93880", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2262/93880"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-01T00:00:00Z"}}, {"id": "3093368279", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:26:16Z", "type": "Journal Article", "created": "2020-10-19", "title": "Microbial competition reduces metabolic interaction distances to the low \u00b5m-range", "description": "Abstract                <p>Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional systems or without accounting for competition or other metabolite-removal, conditions which may not very often match natural ecosystems. We here analyze the impact of cell-to-cell distance on unidirectional cross-feeding in a three-dimensional aqueous system with competition for the exchanged metabolite. Effective interaction distances were computed with a reaction-diffusion model and experimentally verified by growing a synthetic consortium of 1\uffe2\uff80\uff89\uffc2\uffb5m-sized metabolite producer, receiver, and competitor cells in different spatial structures. We show that receivers cannot interact with producers located on average 15\uffe2\uff80\uff89\uffc2\uffb5m away from them, as product concentration gradients flatten close to producer cells. We developed an aggregation protocol and varied the receiver cells\uffe2\uff80\uff99 product affinity, to show that within producer\uffe2\uff80\uff93receiver aggregates even low-affinity receiver cells could interact with producers. These results show that competition or other metabolite-removal of a public good in a three-dimensional system reduces metabolic interaction distances to the low \uffc2\uffb5m-range, highlighting the importance of concentration gradients as physical constraint for cellular interactions.</p", "keywords": ["DYNAMICS", "0301 basic medicine", "BIOFILMS", "0303 health sciences", "Microbiota", "612", "GROWTH-RATE", "DIFFUSION", "EVOLUTION", "Article", "GLUCOSE", "Diffusion", "03 medical and health sciences", "SPATIAL STRUCTURE", "LACTOCOCCUS-LACTIS", "COOPERATION"]}, "links": [{"href": "https://www.nature.com/articles/s41396-020-00806-9.pdf"}, {"href": "https://doi.org/3093368279"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3093368279", "name": "item", "description": "3093368279", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3093368279"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-19T00:00:00Z"}}, {"id": "3161587773", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:26:21Z", "type": "Journal Article", "created": "2021-05-07", "title": "When Beneficial Biofilm on Materials Is Needed: Electrostatic Attachment of Living Bacterial Cells Induces Biofilm Formation", "description": "<p>Bacterial attachment is crucial in many biotechnological applications, but many important bacterial strains cannot form biofilms. Biofilms can damage materials, and current strategies to manage biofilms are focused on inhibition and removal of biofilm. Biofilm formation is inevitable when materials are exposed to microbes and instead of biofilm prevention, we propose management of microbial composition by formation of biofilms with beneficial microbes. Since bacteria need to overcome a high repulsive force to attach to the surface and later to grow and multiply on it, electrostatic modification of the surfaces of cells or the material by polyelectrolytes (PE) was used in our approach, enabling efficient attachment of viable bacterial cells. Since highly positively charged PEs are known to be bactericidal, they were acetylated to reduce their toxicity, while preserving their net positive charge and ensuring cell viability. In our study bacterial strains were selected according to their intrinsic capability of biofilm formation, their shape variety and cell wall structure. These strains were tested to compare how the artificially prepared vs. natural biofilms can be used to populate the surface with beneficial bacteria. Using an artificial biofilm constructed of the potentially probiotic isolate Bacillus sp. strain 25.2. M, reduced the attachment and induced complete inhibition of E. coli growth over the biofilm. This study also revealed that the modification of the surfaces of cells or material by polyelectrolytes allows the deposition of bacterial cells, biofilm formation and attachment of biofilm non-forming cells onto surfaces. In this way, artificial biofilms with extended stability can be constructed, leading to selective pressure on further colonization of environmental bacteria.</p", "keywords": ["0301 basic medicine", "2. Zero hunger", "Technology", "0303 health sciences", "T", "cell surface modification", "cell encapsulation", "7. Clean energy", "artificial biofilms", "polyelectrolytes (PEs)", "03 medical and health sciences", "artificial biofilms", " polyelectrolytes (PEs)", " cell encapsulation", " cell surface modification", " biofilm management", "13. Climate action", "biofilm management"]}, "links": [{"href": "https://doi.org/3161587773"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3161587773", "name": "item", "description": "3161587773", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3161587773"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-05-07T00:00:00Z"}}, {"id": "3188229186", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:26:23Z", "type": "Journal Article", "created": "2021-08-06", "title": "Controlling the Carbon-Bio Interface via Glycan Functional Adlayers for Applications in Microbial Fuel Cell Bioanodes", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Surface modification of electrodes with glycans was investigated as a strategy for modulating the development of electrocatalytic biofilms for microbial fuel cell applications. Covalent attachment of phenyl-mannoside and phenyl-lactoside adlayers on graphite rod electrodes was achieved via electrochemically assisted grafting of aryldiazonium cations from solution. To test the effects of the specific bio-functionalities, modified and unmodified graphite rods were used as anodes in two-chamber microbial fuel cell devices. Devices were set up with wastewater as inoculum and acetate as nutrient and their performance, in terms of output potential (open circuit and 1 k\u2126 load) and peak power output, was monitored over two months. The presence of glycans was found to lead to significant differences in startup times and peak power outputs. Lactosides were found to inhibit the development of biofilms when compared to bare graphite. Mannosides were found, instead, to promote exoelectrogenic biofilm adhesion and anode colonization, a finding that is supported by quartz crystal microbalance experiments in inoculum media. These differences were observed despite both adlayers possessing thickness in the nm range and similar hydrophilic character. This suggests that specific glycan-mediated bioaffinity interactions can be leveraged to direct the development of biotic electrocatalysts in bioelectrochemical systems and microbial fuel cell devices.</p></article>", "keywords": ["microbial fuel cells", "Bioelectric Energy Sources", "Surface Properties", "carbon", "Organic chemistry", "02 engineering and technology", "7. Clean energy", "Article", "Carbon", "6. Clean water", "aryldiazonium", "bioanodes", "QD241-441", "Polysaccharides", "Biofilms", "[CHIM] Chemical Sciences", "functionalization", "electrocatalysis", "Graphite", "0210 nano-technology", "Electrodes", "bioelectrochemical systems"]}, "links": [{"href": "http://www.mdpi.com/1420-3049/26/16/4755/pdf"}, {"href": "https://www.mdpi.com/1420-3049/26/16/4755/pdf"}, {"href": "https://doi.org/3188229186"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecules", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3188229186", "name": "item", "description": "3188229186", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3188229186"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-06T00:00:00Z"}}, {"id": "34979128", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:26:31Z", "type": "Journal Article", "created": "2021-12-31", "title": "N-acyl-homoserine lactones in extracellular polymeric substances from sludge for enhanced chloramphenicol-degrading anode biofilm formation in microbial fuel cells", "description": "Exploring an efficient acclimation strategy to obtain robust bioanodes is of practical significance for antibiotic wastewater treatment by bioelectrochemical systems (BESs). This study investigated the effects of two acclimation conditions on chloramphenicol (CAP)-degrading anode biofilm formation in microbial fuel cells (MFCs). The one was continuously added the extracellular polymeric substances (EPS) extracted from anaerobic sludge and increasing concentrations of CAP after the first start-up phase, while the other was added the EPS-1 (N-acyl-homoserine lactones, namely AHLs were extracted from the EPS) at the same conditions. The results demonstrated that AHLs in the sludge EPS played a crucial role for enhanced CAP-degrading anode biofilm formation in MFCs. The AHL-regulation could not only maintain stable voltage outputs but also significantly accelerate CAP removal in the EPS MFC. The maximum voltage of 653.83\u00a0mV and CAP removal rate of 1.21\u00a0\u00b1\u00a00.05\u00a0mg/L\u00b7h were attained from the EPS MFC at 30\u00a0mg/L of CAP, which were 0.84 and 1.57 times higher than those from the EPS-1 MFC, respectively. These improvements were largely caused by the thick and 3D structured biofilm, strong and homogeneous cell viability throughout the biofilm, and high protein/polysaccharide ratio along with more conductive contents in the biofilm EPS. Additionally, AHLs facilitated the formation of a biofilm with rich biodiversity and balanced bacterial proportions, leading to more beneficial mutualism among different functional bacteria. More bi-functional bacteria (for electricity generation and antibiotic resistance/degradation) were specifically enriched by AHLs as well. These findings provide quorum sensing theoretical knowledge and practical instruction for rapid antibiotic-degrading electrode biofilm acclimation in BESs.", "keywords": ["Chloramphenicol", "Sewage", "Bioelectric Energy Sources", "Extracellular Polymeric Substance Matrix", "Biofilms", "Acyl-Butyrolactones", "Electrodes", "01 natural sciences", "6. Clean water", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Wu, Xiayuan, Zhang, Lina, Lv, Zuopeng, Xin, Fengxue, Dong, Weiliang, Liu, Guannan, Li, Yan, Jia, Honghua,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/34979128"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "34979128", "name": "item", "description": "34979128", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/34979128"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-01T00:00:00Z"}}, {"id": "39471942", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:26:37Z", "type": "Journal Article", "created": "2024-11-02", "title": "Uranium (VI) reduction by an iron-reducing Desulfitobacterium species as single cells and in artificial multispecies bio-aggregates", "description": "Microbial U(VI) reduction plays a major role in new bioremediation strategies for radionuclide-contaminated environments and can potentially affect the safe disposal of high-level radioactive waste in a deep geological repository. Desulfitobacterium sp. G1-2, isolated from a bentonite sample, was used to investigate its potential to reduce U(VI) in different background electrolytes: bicarbonate buffer, where a uranyl(VI)\u2011carbonate complex predominates, and synthetic Opalinus Clay pore water, where a uranyl(VI)-lactate complex occurs, as confirmed by time-resolved laser-induced fluorescence spectroscopic measurements. While Desulfitobacterium sp. G1-2 rapidly removed almost all U from the supernatants in bicarbonate buffer, only a low amount of U was removed in Opalinus Clay pore water. UV/Vis measurements suggest a speciation-dependent reduction by the microorganism. Scanning transmission electron microscopy coupled with energy-dispersive X-ray spectroscopy revealed the formation of two different U-containing nanoparticles inside the cells. In a subsequent step, artificial multispecies bio-aggregates were formed using derivatized polyelectrolytes with cells of Desulfitobacterium sp. G1-2 and Cobetia marina DSM 50416 to assess their potential for U(VI) reduction under aerobic and anaerobic conditions. These findings provide new perspectives on microbial U(VI) reduction and contribute to the development of a safety concept for high-level radioactive waste repositories, as well as to new bioremediation strategies.", "keywords": ["Biodegradation", " Environmental", "Iron", "Radioactive Waste", "Microbial uranium(VI) reduction", "Speciation-dependent reduction", "Uranium", "Artificial biofilms", "Desulfitobacterium", "Oxidation-Reduction", "Iron-reducing bacteria"]}, "links": [{"href": "https://doi.org/39471942"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "39471942", "name": "item", "description": "39471942", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/39471942"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-12-01T00:00:00Z"}}, {"id": "PMC10938371", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:28:06Z", "type": "Journal Article", "created": "2024-01-29", "title": "Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth", "description": "Abstract                <p>Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities established on plant roots. Here, a well-established four-species biofilm model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, and Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis roots to study the impact of multispecies biofilm on plant growth and the community spatial dynamics on the roots. SPMX co-culture notably promoted root development and plant biomass. Co-cultured SPMX increased root colonization and formed multispecies biofilms, structurally different from those formed by monocultures. By combining 16S rRNA gene amplicon sequencing and fluorescence in situ hybridization with confocal laser scanning microscopy, we found that the composition and spatial organization of the four-species biofilm significantly changed over time. Monoculture P. amylolyticus colonized plant roots poorly, but its population and root colonization were highly enhanced when residing in the four-species biofilm. Exclusion of P. amylolyticus from the community reduced overall biofilm production and root colonization of the three species, resulting in the loss of the plant growth-promoting effects. Combined with spatial analysis, this led to identification of P. amylolyticus as a keystone species. Our findings highlight that weak root colonizers may benefit from mutualistic interactions in complex communities and hereby become important keystone species impacting community spatial organization and function. This work expands the knowledge on spatial organization uncovering interspecific interactions in multispecies biofilm communities on plant roots, beneficial for harnessing microbial mutualism promoting plant growth.</p", "keywords": ["0301 basic medicine", "0303 health sciences", "mutualism", "multispecies biofilms", "plant growth", "15. Life on land", "interspecies interactions", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Biofilms", "Microbial Interactions", "Original Article", "Symbiosis", "In Situ Hybridization", " Fluorescence", "keystone species", "spatial organization"]}, "links": [{"href": "https://academic.oup.com/ismej/article-pdf/18/1/wrae012/56945954/wrae012.pdf"}, {"href": "https://doi.org/PMC10938371"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC10938371", "name": "item", "description": "PMC10938371", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC10938371"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-01T00:00:00Z"}}, {"id": "PMC11574552", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:28:08Z", "type": "Journal Article", "created": "2024-08-06", "title": "Mobility and growth in confined spaces are important mechanisms for the establishment of Bacillus subtilis in the rhizosphere", "description": "<p>The rhizosphere hosts complex and abundant microbiomes whose structure and composition are now well described by metagenomic studies. However, the dynamic mechanisms that enable micro-organisms to establish along a growing plant root are poorly characterized. Here, we studied how a motile bacterium utilizes the microhabitats created by soil pore space to establish in the proximity of plant roots. We have established a model system consisting of Bacillus subtilis and lettuce seedlings co-inoculated in transparent soil microcosms. We carried out live imaging experiments and developed image analysis pipelines to quantify the abundance of the bacterium as a function of time and position in the pore space. Results showed that the establishment of the bacterium in the rhizosphere follows a precise sequence of events where small islands of mobile bacteria were first seen forming near the root tip within the first 12\uffe2\uff80\uff9324\uffe2\uff80\uff89h of inoculation. Biofilm was then seen forming on the root epidermis at distances of about 700\uffe2\uff80\uff931000\uffe2\uff80\uff89\uffc2\uffb5m from the tip. Bacteria accumulated predominantly in confined pore spaces within 200\uffe2\uff80\uff89\uffc2\uffb5m from the root or the surface of a particle. Using probabilistic models, we could map the complete sequence of events and propose a conceptual model of bacterial establishment in the pore space. This study therefore advances our understanding of the respective role of growth and mobility in the efficient colonization of bacteria in the rhizosphere.</p", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Ecology and Microbiomes", "Seedlings", "Biofilms", "Rhizosphere", "Plant Roots", "Soil Microbiology", "Bacillus subtilis", "Lactuca"]}, "links": [{"href": "https://doi.org/PMC11574552"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC11574552", "name": "item", "description": "PMC11574552", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC11574552"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-08-06T00:00:00Z"}}, {"id": "PMC8400688", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:28:12Z", "type": "Journal Article", "created": "2021-08-06", "title": "Controlling the Carbon-Bio Interface via Glycan Functional Adlayers for Applications in Microbial Fuel Cell Bioanodes", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Surface modification of electrodes with glycans was investigated as a strategy for modulating the development of electrocatalytic biofilms for microbial fuel cell applications. Covalent attachment of phenyl-mannoside and phenyl-lactoside adlayers on graphite rod electrodes was achieved via electrochemically assisted grafting of aryldiazonium cations from solution. To test the effects of the specific bio-functionalities, modified and unmodified graphite rods were used as anodes in two-chamber microbial fuel cell devices. Devices were set up with wastewater as inoculum and acetate as nutrient and their performance, in terms of output potential (open circuit and 1 k\u2126 load) and peak power output, was monitored over two months. The presence of glycans was found to lead to significant differences in startup times and peak power outputs. Lactosides were found to inhibit the development of biofilms when compared to bare graphite. Mannosides were found, instead, to promote exoelectrogenic biofilm adhesion and anode colonization, a finding that is supported by quartz crystal microbalance experiments in inoculum media. These differences were observed despite both adlayers possessing thickness in the nm range and similar hydrophilic character. This suggests that specific glycan-mediated bioaffinity interactions can be leveraged to direct the development of biotic electrocatalysts in bioelectrochemical systems and microbial fuel cell devices.</p></article>", "keywords": ["microbial fuel cells", "Bioelectric Energy Sources", "Surface Properties", "carbon", "Organic chemistry", "02 engineering and technology", "7. Clean energy", "Article", "Carbon", "6. Clean water", "aryldiazonium", "bioanodes", "QD241-441", "Polysaccharides", "Biofilms", "[CHIM] Chemical Sciences", "functionalization", "electrocatalysis", "Graphite", "0210 nano-technology", "Electrodes", "bioelectrochemical systems"]}, "links": [{"href": "http://www.mdpi.com/1420-3049/26/16/4755/pdf"}, {"href": "https://www.mdpi.com/1420-3049/26/16/4755/pdf"}, {"href": "https://doi.org/PMC8400688"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Molecules", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC8400688", "name": "item", "description": "PMC8400688", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC8400688"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-08-06T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=BIOFILM&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=BIOFILM&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=BIOFILM&", "hreflang": "en-US"}, {"rel": "last", "type": "application/geo+json", "title": "items (last)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=BIOFILM&offset=38", "hreflang": "en-US"}], "numberMatched": 38, "numberReturned": 38, "distributedFeatures": [], "timeStamp": "2026-07-26T13:55:14.171131Z"}