In natural environments, microalgae are invariably associated with bacteria, yet the role of these microbial consortia in modulating microalgal physiological responses to chemical stress remains largely unexplored. This study investigates whether native bacterial communities enhance the tolerance of field-isolated microalgae to toxic compounds. Microalgae-bacteria consortia were isolated from the Mediterranean coastal Or Lagoon (South of France), chronically impacted by herbicides and trace metals. The chlorophyte Chlamydomonas sp. Or2023a and the diatom Entomoneis sp. Or2023b were isolated and axenised. Both axenic and xenic cultures were exposed to the herbicide diuron and the trace metal copper in 72-hr dose-response assessments, following the evaluation of the bacterial diversity of their native phycosphere. Both isolates displayed elevated intrinsic tolerance, particularly Entomoneis sp., whose effective concentration inhibiting 50% of growth (Half-maximal Effective Concentration-EC50) values (77 µg L-1 for diuron; 109 µg L-1for free ion copper) exceeded most published benchmarks for marine diatoms, a pattern consistent with possible prior selection or acclimation to chronic chemical exposure. Beyond this baseline, native bacteria further modulated sensitivity in a species- and compound-specific manner. In Chlamydomonas sp., bacteria mitigated diuron toxicity (EC50 from 6 to 11 µg L-1), though at the cost of reduced growth under non-stressed conditions, suggesting a growth-defence trade-off. In Entomoneis sp., bacteria alleviated copper toxicity (∼30% EC50 increase) and induced hormetic growth responses, consistent with copper bioavailability regulation by metal-tolerant Rhodobacteraceae dominating its phycosphere. These findings suggest that microalgal sensitivity to contaminants is jointly shaped by environmental history and native microbial consortia, underscoring the need to incorporate field-isolated algal-bacterial assemblages into ecotoxicological frameworks.

This study investigated the mesophilic anaerobic digestion (AD) of food waste at a semi-continuous pilot scale, assessing process stability, performance, and microbial dynamics under current and emerging treatment scenarios. With the EU requirement for separate bio-waste collection, food waste streams are expanding from those produced by medium/large-sized producers (FW-ML) to include household food waste (FW-HH), likely to contain biodegradable bags. Envisioning this, four feedstock configurations were evaluated: one representing current FW-ML treatment and three others simulating its treatment alongside FW-HH containing either cellulose-based bags, PBAT/starch-based bags, or thermo-alkaline pre-treated PBAT/starch-based bags. The scenario including untreated PBAT/starch-based bags exhibited the most pronounced acidification, with volatile organic acids reaching 4.1 ± 0.6 gHAc/L and total alkalinity decreasing to 8.3 ± 0.8 gCaCO3/L. System acidification was likely associated with the identified presence of terephthalic acid, a monomer released during PBAT biotransformation. Correspondingly, methane yield declined to 469 ± 10 NLCH4/kgVS, compared to 518 ± 9 NLCH4/kgVS for FW-ML alone. In contrast, thermo-alkaline pretreated bags enhanced buffering capacity and limited performance losses, achieving 504 ± 46 NLCH4/kgVS. Microbial analyses revealed stable overall diversity and a resilient methanogenic community dominated by Methanoculleus sp. Redundancy and discriminant analyses indicated both global and taxon‑specific shifts associated with the presence of untreated and pre-treated PBAT/starch-based bags, notably the enrichment of Defluviitoga under pre‑treated conditions. Conducted at pilot scale, this work offers practical insights into the operational challenges and mitigation strategies for treating FW‑HH when biodegradable plastics are present.

This study investigated the semicontinuous mesophilic anaerobic digestion of food waste, assessing process stability, performance, and microbial communities across emerging treatment scenarios. Following the EU mandate for separate bio-waste collection, food waste streams are expanding from medium/large-sized producers (FW-ML) to household food waste (FW-HH) likely to introduce biodegradable bags. Consequently, four scenarios were evaluated: one representing current FW-ML treatment and three simulating its treatment alongside FW-HH containing cellulose-based bags, PBAT/starch-based bags, or thermoalkaline pretreated PBAT/starch-based bags. The PBAT/starch-based bags led to a progressive acidification, with volatile organic acids reaching 4.1 ± 0.6 gHAc/L and total alkalinity decreasing to 8.3 ± 0.8 gCaCO3/L. Correspondingly, methane yield declined to 469 ± 10 NLCH4/kgVS, compared to 518 ± 9 NLCH4/kgVS for FW-ML alone. The qualitative detection of terephthalic acid, a monomer of PBAT, suggests that incomplete biodegradation may have contributed to acidic stress. Conversely, the thermoalkaline pretreatment (3 M KOH, 70 °C, 4 h) provided the dual benefit of plastic solubilization and alkalinity enhancement (11 ± 1 g CaCO₃/L), minimizing performance losses (504 ± 46 NL CH₄/kg VS). Microbial analyses revealed stable overall diversity and a resilient methanogenic community dominated by Methanoculleus sp. Redundancy and discriminant analyses indicated active community structure shifts associated with the presence of FW-HH and the PBAT/starch-based bags, despite their low concentration (2.2 ± 0.3% of the organic loading rate). This study outlines operational challenges and mitigation strategies for treating FW-HH alongside biodegradable plastics, establishing a baseline that invites future techno-economic and life cycle assessment studies.

Microbial mercury (Hg) methylation drives the formation of methylmercury (MeHg) hotspots in natural environments, but the cellular pathways that determine MeHg fate and isotopic signatures remain largely unresolved. In this study, we cultured the model sulfate-reducing bacterium Pseudodesulfovibrio hydrargyri BerOc1 anaerobically under fumarate respiration for 30 h and quantified Hg speciation and fraction- and species-specific Hg isotopic compositions. The results showed that intracellular MeHg was rapidly exported and dominated the extracellular pool by 30 h (> 80%). Exported MeHg bound to specific bioligands across size fractions, likely associated with its export mechanisms. Mass-dependent Hg isotope fractionation revealed temporal shifts in extracellular MeHg isotopic signatures (δ202HgMeHg= -1.10‰ to -0.82‰, 4-30 h), suggesting demethylation of bioligand-bound MeHg upon export. This isotopic observation refines previously reported suppressed mass-dependent fractionation signatures of MeHg in bulk bacterial cultures. Our results demonstrate that bacterially produced MeHg is rapidly exported from cells, potentially bound to specific biomolecules, and subsequently undergoes extracellular demethylation, thereby shaping aqueous MeHg isotopic signatures. These findings provide insight into the key factors that govern MeHg fate and accumulation during bacterial Hg methylation in aquatic ecosystems.

The integration of biodegradable plastics into source-separated biowaste collection, as permitted by the European Union (EU) regulations, has opened new valorization pathways through anaerobic digestion (AD), motivating research into their biodegradation behavior and associated microbial communities. This study characterized the microbial dynamics driving degradation of 19 compostable food packaging products (made of polylactic acid (PLA) or poly(3 hydroxybutyrate co 3 hydroxyvalerate) (PHBV), or from fossil-based sources such as polybutylene adipate co terephthalate (PBAT), polybutylene succinate (PBS), and blends) through Biochemical Methane Potential (BMP) assays and 16S rDNA amplicon sequencing. PHBV-based products exhibited higher biodegradability (> 80%), while PLA-based materials showed limited degradation (< 40-60%). Based on MiSEQ diversity analyses of the 16S rDNA, redundancy analysis (RDA) revealed a strong influence of biodegradable packaging composition on microbial community structure. Linear discriminant analysis Effect Size (LEfSe) identified polymer-specific microbial biomarkers: Acholeplasmataceae family, and Alkaliphilus genus, were associated with PHBV products; and Dysgonomonadaceae family, and Bacteroidia class associated with PLA. These findings highlighted specific microorganisms associated with different polymers origin, suggesting potential links between microbial composition and polymer-specific biodegradation under AD conditions.

Sulfides accumulation during anaerobic digestion negatively affects biogas quality, process stability, and infrastructure integrity, making efficient desulfurization strategies essential. This study investigated sulfur-oxidizing bacterial communities associated with anaerobic digesters and a Thiopaq® bioreactor at the Marrakech wastewater treatment plant. High-throughput 16S rRNA gene sequencing revealed a marked ecological contrast between the two systems. While the Thiopaq® bioreactor was largely dominated by a single Thioalkalibacteraceae lineage, anaerobic sludge environments harbored a phylogenetically diverse assemblage of sulfur-oxidizing bacteria spanning multiple proteobacterial families, including Thiobacillaceae, Rhodobacteraceae, Hyphomicrobiaceae, Paracoccaceae, Comamonadaceae, Rhodocyclaceae, Zoogloeaceae, Azonexaceae, and Burkholderiaceae. Phylogenetic reconstruction and culture-based isolation showed only partial overlap between sequencing-derived operational taxonomic units and cultivated strains, highlighting the complementarity of molecular and physiological approaches. Functional assays demonstrated that several indigenous isolates were capable of oxidizing sulfide produced by sulfate-reducing bacteria under both microaerophilic and nitrate-reducing conditions. Sulfide concentrations decreased from 14.87 mM to 0.03 mM, corresponding to a removal efficiency of 99.8

In search of a Cr(VI) removal bioprocess, within a circular economy perspective, we combined two autochthonous bacterial consortia obtained from industrial residues and an agricultural waste (rice husk of Oryza sativa). After characterizing the rice husk (rh) properties, the bacterial growth and biofilm formation, we studied the taxonomical profile of the bacterial consortia (C55, C33, and C21, the last is a combination 2:1 of the previous ones). By using SEM analysis, we confirmed the presence of a smooth layer of exopolysaccharides (EPS) over the rice husk surface. Total bacterial biodiversity, assessed through MiSeq analysis, showed that the addition of Cr(VI) stimulated the growth of two main populations (Cellulosimicrobium and Siminovitchia) while inhibiting Peptoniphilus, Cutibacterium and Rhodococcus. We also evaluated chromium depletion, in batch experiments, with particular emphasis on its sorption to the agroresidue and its biotransformation by the biomass. When exposed to 200 mg.l-1 Cr(VI), the system containing both rh and the bacterial consortium completely removed Cr(VI) from the effluent with half-times between 53 and 67 h. The combination of Cr(VI) biosorption by rh and its biotransformation to Cr(III) by bacterial consortia confirmed an effective synergy capable of removing 92% of Cr(VI). This work supports the potential of an innovative bioprocess based on bacterial biofilms grown on rh for the mitigation of Cr(VI) contamination.

Biotic methylation of inorganic mercury (iHg) in aquatic systems is largely driven by microorganisms such as sulfate-reducing bacteria (SRB). Using the SRB model strain Pseudodesulfovibrio hydrargyri BerOc1 we investigated biotic iHg methylation aiming to assess the rates of mono-methylmercury (CH3Hg) production and to characterize the carbon (C) isotopic signatures (δ13C) of the CH3Hg product. BiogenicCH3Hg exhibited δ13C values averaging −23.1 ± 2.0‰, representing a 13C-depletion of 14.4‰ compared to the pyruvate carbon source used for the growing of the strain and a 9‰ depletion relative to the microbial biomass. The maximum methylation yield observed in our samples was around 15

Two bacterial consortia (C55 and C33), obtained from an industrial residue contaminated with hexavalent chromium (Cr(VI)), were used to study the behavior of their mixture for depleting this ion in liquid media. In the absence of Cr(VI), C55 showed a greater growth rate than C33, while the latter exhibited biofilm formation. In the presence of this ion, C55 showed resistance up to 800 mg·L −1 and an ability to diminish up to 400 mg·L −1 of the Cr(VI) from the medium, while for C33, these concentrations were 400 and 200 mg·L −1 , respectively. Bacterial synergism between these consortia was evaluated using different compound ratios (C55:C33 ratios of 1:1, 1:2, and 2:1), growing at 50, 100, and 200 mg·L −1 Cr(VI). The best half‐lives of Cr(VI) decrease were 16, 31, and 98 h, respectively, for the 1:1 mixture. The ability of C33 and the mixed consortia to form biofilms was verified. MiSeq sequencing revealed 4 major populations for C55 (in a total of 14) and 3 for C33 (8), most of which were common. After an isolation process, 2 bacterial strains were obtained from C55 and 4 from C33. Three of these strains (QRePLB33E, similar to Oceanobacillus profundus ; QRePLB33G, to Shouchella clausii ; and QRePLB55C, to Cellulosimicrobium funkei ) showed resistance to Cr(VI) and the ability to remove 100% of it at least up to 300 mg·L −1 . Thus, synergism between different bacterial consortia obtained from the same site is possible and can improve, by complementing their capacities, both the growth rate and the ability to diminish the xenobiotic from the medium.

Endophytes inhabit plant tissues, offering various benefits to their hosts. Understanding their roles in sustainable agriculture is a key focus of research. Using 16S rRNA gene and fungal-specific ITS2 region amplicon sequencing, we investigated how 11 different potato cultivars and 3 different growing conditions influence the diversity of microbial endophytes in potato roots. We compared plants grown on two different soils in greenhouse conditions and plantlets grown in agar media (i.e., in vitro), representing the planting material without the effect of the soil microbiome. Our results revealed that growing conditions significantly influenced the alpha and beta diversity of endophytic bacteria. In plants grown in soils, the bacterial endophytic community was mainly represented by the Pseudomonadaceae family, whereas for in vitro plants, the Paenibacillaceae, a spore-forming bacteria family, was the main representative. The fungal community comprised many possible fungal pathogens, such as Colletotrichum, Fusarium, and Verticillium. For the endophytic fungi, both soil types and cultivars affected fungal diversity, and a stronger effect for cultivars was seen for fungi as compared with bacteria. Overall, our findings indicate that endophytic bacteria exhibit strong recruitment potential from soil communities, and the identity of cultivars has also influenced fungal dynamics in communities. These findings shed light on the intricate interactions among potato cultivars and soil microbiomes, which can affect the design of sustainable agricultural strategies.Copyright (c) 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Grapevine trunk diseases (GTDs), particularly Esca, represent a major challenge for viticulture worldwide, leading to substantial economic losses. With no effective control treatments available, developing new methods such as biocontrol is crucial for managing GTDs. Our aim was to select biocontrol bacteria effective against the white-rot fungal pathogen Fomitiporia mediterranea (Fmed) and to investigate their mechanisms of action. A stepwise screening of 58 bacterial strains was conducted in vitro to assess their ability to inhibit Fmed growth through volatile and diffusible metabolites production. The screening was also done on wood sawdust from seven different grapevine cultivars. Out of 58 tested strains, 49 inhibited Fmed growth by over 50% through their volatile organic compounds, only eight achieving this through their agar-diffusible metabolites. Pseudomonas lactis SV9, Pseudomonas paracarnis S45, and Paenibacillus polymyxa SV13 exhibited a strong efficacy in inhibiting Fmed on wood sawdust in a cultivar-dependent manner. We selected these strains for whole genome analysis and metabolomic profiling via LC-MS/MS for diffusible compounds and SPME GC-MS for volatile compounds. P. polymyxa SV13 inhibited Fmed primarily through diffusible metabolites, producing mainly fusaricidin-type compounds. Conversely, Pseudomonas strains acted mainly via their volatile metabolites, producing mainly the antifungal compound dimethyl disulfide. Genome analysis of the three bacterial strains revealed gene clusters responsible for regulating both direct and indirect mechanisms in biocontrol agents (BCAs). Our findings highlight the importance of comprehensive studies that combine in vitro experiments mimicking field conditions, with detailed investigations into modes of action to improve BCAs efficacy.

Mutualistic interactions between plants and microbiomes are vital for plant growth and resilience. However, traditional breeding has undermined these interactions. Here, we explore the Grime’s triangle from a microbiome perspective and discuss how traits from stress-tolerant species can aid in identifying cultivars with enhanced microbiome interactions.

Root traits significantly shape rhizosphere microbiomes, yet their interaction with microbes is often overlooked in plant breeding programs. Here, we propose that selecting modern cultivars based on microbiome interactive trait (MIT), such as root biomass, exudate patterns and the rhizosphere microbiome, can enhance agricultural sustainability by interacting effectively with soil microbiomes, which in turn, promotes plant growth and resistance to stress, thereby reducing reliance on synthetic crop protectants. Through a stepwise selection process (in silico and in vitro) that started with approximately 1000 potato genotypes, we chose 51 potato cultivars based on known phenotypical properties and distinct root exudate patterns. We conducted a greenhouse experiment to evaluate their capacity to interact with the soil microbiome and to assess their MIT scores. Our findings revealed that cultivars significantly influence plant growth, metabolite profiles, and rhizosphere fungal community composition. Moreover, we observed a positive correlation between microbial community diversity and root biomass. Additionally, leaf metabolites were correlated with rhizosphere bacterial composition, supporting the plant holobiont framework. Utilising z-scores, we aggregated all data related to plant growth, metabolomes, and microbiomes, creating a classification of 51 cultivars based on a gradient of MIT scores. By examining the distribution of low, intermediate, and high MIT, we identified a group of 11 potato cultivars suitable for further studies to assess their resilience and productivity under low-input production systems. This study provides an in-depth correlation between microbiome and several plant traits across 51 cultivars, offering tools to facilitate and expedite the incorporation of microbiome traits into breeding goals to support sustainable agriculture.

Sulfidic hot springs harbor unique microbial communities and are important in mercury (Hg) species transformations, although the fine scale drivers of these processes remain poorly understood. Here we studied Hg speciation in water, biofilms, and sediment across three sampling seasons in a French sulfidic hot spring with low Hg concentrations. Microbial Hg species methylation and demethylation potentials were evaluated using incubation experiments with species-specific Hg isotope tracers. Temporal variation in inorganic Hg (iHg) and methylmercury (MeHg) concentrations in water, biofilm, and sediment was observed. The incubation of microbial communities in biofilms and sediment under dark conditions exhibited low iHg methylation potentials, whereas a significant extent of biotic MeHg demethylation to oxidized iHg was found in relation to MeHg concentrations. Results from microbial diversity (16S rDNA) and the metabolic inhibition experiments suggest an important role of sulfur-linked bacterial metabolism dynamics. Specifically, sulfate-reducers and anoxygenic phototrophs were important factors in the regulation of MeHg concentrations in our study site. Overall, the observed dominance of microbial MeHg demethylation demonstrates a strong Hg detoxification capacity in sulfidic aquatic environments.

The interaction between plant cultivars and the soil microbiome is essential for agricultural productivity. We hypothesise that cultivars with a strong microbiome interactive trait (MIT) can reach high performance with reduced dependence on chemical inputs. To test this, we conducted a field experiment evaluating seven pre-selected potato cultivars with different MIT scores under biological and conventional agricultural management. Cultivars with higher MIT scores outperformed a commercial cultivar, D & eacute;sir & eacute;e. Below-ground biomass was positively associated with MIT scores, underscoring the relevance of this approach for future breeding strategies. Biological management enhanced inter-kingdom microbial interactions, thereby improving plant performance. In contrast, chemical management disrupted these interactions, severing the microbiome from its beneficial effects on plant growth. Piecewise structural equation models further confirmed the importance of integrating cultivar choice with sustainable practices. Overall, this study provides empirical evidence and lays the groundwork for further research to promote robust plant-microbiome interactions in sustainable agriculture.

The origin of the bioaccumulative neurotoxin methylmercury (MeHg) in the ocean remains elusive. The current paradigm suggests that microbial methylation of inorganic Hg within the oceanic water column produces monomethylmercury (MMHg) and potentially dimethylmercury (DMHg). Reaction rates and main drivers governing MeHg levels (sum of MMHg and DMHg) are poorly constrained. We conducted ambient Hg species measurements and enriched isotopic tracer experiments in waters of two contrasting marine environments, the oligotrophic Mediterranean Sea (MED) and the mesotrophic Atlantic Ocean (ATL). Maximum subsurface MeHg levels were ~2 times higher in the MED compared to the ATL, essentially driven by higher DMHg concentrations (0.45 ± 0.06 vs 0.16 ± 0.02 pM). Methylation was only detectable in unfiltered subsurface waters and presumably biotically driven. The highest methylation rate (MMHg to DMHg) was observed in subsurface MED waters while reduction and demethylation rates were highest in surface waters of both environments. Experimental reaction rates and the potential microbial activity (based on 16S rDNA) aligned with ambient Hg species distributions. Assuming high DMHg stability and applying our fast experimental DMHg formation rates, a newly developed 1D water column model (MED) successfully reproduced MeHg species distribution, suggesting DMHg plays a key role in the global marine Hg cycle.

Recent studies on anaerobic digestion (AD) off-gas valorization have explored ways to enhance biological methane production by enriching the digestate with carbon dioxide (CO2). This approach aims to increase AD profitability by biological conversion of CO2 to methane (CH4). However, existing research lacks consensus on the effectiveness of CO2 injection, with the underlying biological mechanisms remaining poorly understood.This study investigates the impact of CO2 injection on AD in a pilot-scale setup using standard on-farm feedstocks. Two pilot-scale reactors were operated in parallel: one serving as a control, and the other featuring CO2 injection through a bubble column with digestate recirculation. Results showed no demonstrable improvement in biomethane yields from CO2 enrichment. In fact, a high-rate CO2 injection had a detrimental effect on methane production.

Members of the phylum Synergistota are important but understudied components of microbial communities during anaerobic digestion. In this study, their diversity was assessed in full-scale anaerobic digester sludge samples from Marrakesh wastewater treatment plant (Morocco), using 16S rRNA gene community profiling, as well as targeted isolation, physiological characterization, and genome sequencing of novel Synergistaceae isolates. The 16S rRNA gene analysis identified 23 operational taxonomic units (OTUs) belonging to the family of Synergistaceae, representing 8.8 % of the total microbial community. 17 of these OTUs belonged to previously uncultured taxa. A dominant OTU19, presumably a new representative of the family of Synergistaceae was isolated in pure culture (strain DS-S4T) and subjected to both culture- and genome-based characterizations. Phylogenetic analysis revealed that strain DZ-S4T was related to Cloacibacillus porcorum CL-84T and Cloacibacillus evryensis 158T but with low sequence similarity of 89.94 % and 88.60 %, respectively. Based on genome relatedness, including Average Nucleotide Identity (ANI) and Amino Acid Identity (AAI), strain DZ-S4T is considered to represent a novel genus for which the name Caenicola gen.nov is proposed. Moreover, several phenotypic and eco-physiological properties differentiated the novel isolate from its related species, indicating that the strain represents a new species for which the name Caenicola nitritireducens sp. nov. is proposed, with strain DZ-S4T (=DSM 104940T = JCM 31897T) being the type strain. Additionally, this study investigates the ecological role of strain DZ-S4T, specifically the protein degradation, the bioconversion of carbohydrates, and the nitrite reduction during anaerobic digestion.

In recent studies, the bacterial and fungal communities associated with plant wood have received considerable attention. Due to microorganisms’ vertical migration from roots to leaves, these communities provide critical links between the rhizosphere and phyllosphere microbiome. Recent investigations have shown that anatomical and chemical wood characteristics shape the microbiota inhabiting living or dead wood tissues, leading to variation in the observed decomposition of these materials. Despite the fact that bacteria have limited ability to degrade polymeric lignocelluloses compared to fungi, those inhabiting wood tissues have demonstrated a significant role in these habitats. Bacteria and fungi coexist in wood and form differing relationships with each other, with consequences for community structures that, in turn, impact plant health. The aim of this review is to present an overview of current insights regarding bacterial profiles and functions in lignocellulosic plants and their interaction with fungal communities colonising the same habitat. A better understanding of plant–bacteria–fungi interactions will allow for better exploitation of these tripartite interactions and possibly improve plant health.