BACKGROUND: Parasitic plants are affected by various abiotic stressors including water and drought stress, fluctuations or extremes of temperature, salinity, mineral deficiencies or toxic concentrations of heavy metals in soils. While the molecular mechanisms and the ecological roles of these parasitic angiosperms have been well-studied, their responses to abiotic stress remain poorly understood. This study explores the relationship between environmental metal stress and the seed endophytic bacterial community of the holoparasitic plant Orobanche lutea Baumg. (Orobanchaceae). RESULTS: Our findings reveal significant shifts in microbial community composition across different environmental conditions, developmental stages and time points. Orobanche lutea seeds selectively accumulate metals such as Zn and Pb. Significant differences in the O. lutea seed microbial community composition suggest a strong influence of both, environmental conditions and plant developmental stages. Certain bacterial genera, including Bacillus, Paenibacillus, Pantoea, Okibacterium, Staphylococcus and Micromonospora were consistently detected across all samples, suggesting a vertically transmitted core microbiome. Notably, seed endophytic bacterial communities in O. lutea, respond dynamically to metal stress. Several isolated strains (e.g. Bacillus, Paenibacillus, Curtobacterium and Mictobacterium) showed high tolerance to Zn and Pb salts. However, elevated Zn and Pb concentrations in seeds do not promote the enrichment of metal-tolerant endophytes. Furthermore, metal stress appeared to increase the frequency of plant growth-promoting (PGP) traits within the seed microbiome supporting the idea that endophytes contribute to the adaptation of holoparasitic plants to heavy metal stress. CONCLUSIONS: These results highlight the dynamic nature of seed-associated microbial communities under metal stress and underscore the critical role of seed endophytes in mediating the responses of holoparasitic plants to environmental challenges. The relationship between seed microbiome composition and metal exposure offers new insights of understanding stress resilience and developing microbial-based mitigation strategies.

Hydrocarbon-polluted sites are a global environmental concern. Although bioremediation is a cost-effective and sustainable remediation method, its efficiency is often impaired by various environmental and microbial factors. Further advancements in bioremediation require a deeper understanding of the relationship between the soil microbiome and the physicochemical parameters that limit biodegradation. Here, we investigated a 3-m-deep polycyclic aromatic hydrocarbon (PAH)-polluted soil core from a historically polluted site in The Netherlands. Soil samples were taken from six depths at 50 cm intervals, followed by a physicochemical characterisation, including measurements of PAH, electron acceptors, pH and electrical conductivity. These analyses were complemented by a detailed microbial community analysis. Our findings suggest that microbial communities are primarily shaped by a combination of the availability of electron acceptors and pollution levels. Additionally, groundwater level fluctuations appear to play an important role in the transport and replenishment of electron acceptors. In-depth community analysis further revealed a diversity of metabolic strategies employed by the different communities to cope with the oversupply of electrons. Collectively, these results demonstrate that microbial communities in PAH-polluted soils vary according to habitat-specific redox environments. Therefore, microbial community analysis can serve as an additional diagnostic tool to infer the specific physicochemical constraints that limit efficient biodegradation. Our findings provide a detailed, integrated interpretation of physicochemical and microbial field data, offering insight into the heterogeneous nature of in situ biodegradation. They further highlight the value of comprehensive and integrated microbial community and physicochemical analyses in identifying biodegradation-limiting factors in the field.

More than six decades of human activity in Antarctica resulted in chronic diesel contamination of soils surrounding research stations. Phytoremediation assisted by the native vascular plant Deschampsia antarctica is one of the few remediation strategies compatible with the Antarctic Treaty System guidelines. Securing suitable root-associated microbial resources is central to this approach. This work characterized the bacterial communities of the rhizosphere and root endosphere of D. antarctica growing in a chronically diesel-contaminated soil at Carlini Station and in three pristine sites on 25 de Mayo (King George) Island, South Shetland Islands, combining culture-independent 16S rRNA gene amplicon sequencing, PICRUSt2 functional prediction and culture-dependent bacterial strain isolation. The rhizospheric microbial community was consistently more diverse than those inhabiting the endosphere and was more strongly structured by site and associated soil physicochemical variables, with the contaminated site showing the most distinct composition, whereas the endosphere remained comparatively stable and host-selected. The community associated with the chronically contaminated site showed pronounced compositional differences and higher predicted abundances of hydrocarbon-degradation pathways in the rhizosphere. Polaromonas, Rhodococcus, Mycobacterium and Devosia were repeatedly associated with the community from the contaminated site across taxonomic, biomarker and predicted functional analyses. Members of the genera Polaromonas, Rhodococcus and Devosia were also recovered in culture. These taxa represent suitable candidates for the future development of microbe-assisted phytoremediation strategies in Antarctica.

Enhanced weathering (EW) is proposed as a key strategy for climate change mitigation and carbon dioxide removal technology. Dissolution of silicate minerals enhances the alkalinity of the pore water, resulting at a shift of the carbonate system towards carbonate and bicarbonate, leading to higher dissolved inorganic carbon when the water is equilibrated with the atmosphere. Here, we evaluated the effects of EW on a crop ecosystem under future climate change conditions within a macro-scale ecotron – an enclosed facility enabling complete quantification of carbon fluxes among the atmosphere, vegetation, soil, and leachates. We monitored all greenhouse gases in deep mesocosms representative of marginal soil conditions and, after liming and fertilization, applied 10 t ha−1 of basalt at the start of the experiment. EW treatment resulted in an almost three-fold enhancement of measured carbon flux into the soil, achieving rates up to 1.5 t ha−1 during the growing season. Moreover, the observed carbon sequestration surpassed the levels expected from weathering processes alone. This is notable because the near-neutral soil pH environment was not favourable to EW kinetics. Therefore, we conclude that EW facilitated significant carbon accrual in our simulated ecosystems via not only carbonate precipitation but also enhanced biogeochemical activities promoting additional carbon storage. Based on these findings, we speculate on the underlying pathways responsible for such outcomes.

To fully comprehend host-microorganism interactions, it is crucial to understand the composition and diversity of the microbiome, as well as the factors that shape these characteristics. We investigated microbiome variation using the freshwater planarian Schmidtea mediterranea, an invertebrate model in regeneration biology and (eco-)toxicology, by exposing the organisms to various controlled conditions. The microbiome composition exhibited high variability, with most of the bacteria belonging to the Betaproteobacteria. Among the diverse microbial communities, a few genera, such as Curvibacter, were consistently present, but exhibited significant alterations in response to changing conditions. The relative abundance of Curvibacter fluctuated during the regeneration process, initially increasing before returning to a composition similar to the beginning situation. After applying external stress, the relative abundance of Curvibacter and other genera decreased. Variation over time, between different origin laboratories and between individuals, showed that additional, yet to-be-identified, factors of variation are present. Taking all results together, our study provides a solid basis for future research focusing on bacterial functionality in planarians and other invertebrates.

Among emerging pollutants, residuals of phenoxy herbicides, including 2-chloro-4-methylphenoxy acid (MCPA), are frequently detected in non-targeted areas. MCPA can be removed from environmental matrices using biological remediation methods including endophyte-assisted phytoremediation. The interactions between selected plants excreting to the rhizosphere plant secondary metabolites (PSMs) and plant-associated bacteria (incl. endophytes) can speed up the removal of organics and increase the plants resistance to pollutants such as MCPA. The role of plant-associated bacteria in endophyte-assisted phytoremediation has been partially described, however neither MCPA-tolerant endophytic bacteria has been isolated nor characterized. So far, promising results were obtained by simultaneous cultivation of Cucurbita pepo (zucchini) and amendment of soil with structurally related PSM syringic acid (SA), which can substantially enhance removal of MCPA from soil. Hence, the main aim of this research was to study the effect of PSM (SA) on the presence of functional MCPA-tolerant endophytic bacteria using a culture-dependent and -independent approach. Comparison between the molecular and microbiological analysis revealed differences between applied methods. However, irrespectively of the genera identification methods, presence of phenolic compounds (MCPA or SA) favorized presence of potential MCPA-degraders. On the basis of MCPA tolerance tests of isolated bacteria, two Pseudomonas endophytic isolates from zucchini roots and three isolates from zucchini leaves i.e. Pseudomonas sp., Paenarthrobacter sp. and Acinetobacter sp. were selected for further screening of plant growth promoting properties (PGPP). MCPA-tolerant endophytic bacteria showed multiple PGPP. Therefore, these isolates can potentially contribute to an improved fitness of plants used for the purpose of enhancing phytoremediation of environments polluted with phenoxy herbicides.

In this study we evaluated over a 1-year period, the ability of Epipremnum aureum leaves to collect particulate matter (PM)-bound Pb from an indoor environment. Using Illumina MiSeq, we investigated the changes in the phylloplane microbiome connected with the accumulation of this pollutant. Plants were placed in a shooting room, where PM release from each shot was recorded, along with PM2.5 and PM10 sequestration and leaf element enrichment by ICP. Additionally, black carbon (BC) sequestration was determined, and SEM-EDX was performed on leaves after 12 months of exposure. Our results indicated that ambient air pollution shapes microbial leaf communities by affecting their diversity. At the order level, Pseudomonadales, along with Micrococcales, appeared (at a low relative abundance) after exposure to indoor PM-bound Pb air pollution. This study provides a unique comparison of Epipremnum aureum air filtration performance between a standard office environment and a firearm shooting range. The air filtration approach holds promise for reducing indoor air pollution, but more knowledge about the underlying mechanisms supporting genera capable of coping with airborne pollutants is still required.

Mutualistic interactions between plants and soil fungi, mycorrhizas, control carbon and nutrient fluxes in terrestrial ecosystems. Soil of ecosystems featuring a particular type of mycorrhiza exhibit specific properties across multiple dimensions of soil functioning. The knowledge about the impacts of mycorrhizal fungi on soil functioning accumulated so far, indicates that these impacts are of major importance, yet poorly conceptualized. We propose a concept of mycorrhizal fungal environments in soil. Within this concept, we discuss knowledge gaps related to the understanding and quantification of mycorrhizal fungal impacts. We introduce an experimental framework to address these gaps in a quantitative manner, and present the field experiment 'Mycotron', where we established vegetation series featuring three mycorrhizal types; ericoid (ERM), ecto- (ECM), and arbuscular mycorrhiza (AM), to quantitatively assess mycorrhizal fungal impacts on soil functioning. The experimental treatments entail manipulations in dominance levels of vegetation of three mycorrhizal types (AM, ECM, and ERM) in standardized soil conditions. This experiment constitutes a unique testbed to quantitatively evaluate the impacts of distinct mycorrhizal fungal environments on a large variety of ecosystem functions. Our approach aids the quantification of microbiota and plant-microbial interaction impacts on soil biochemical cycles.

Plastic pollution has emerged as a critical environmental challenge due to the widespread accumulation of petrochemical plastics in natural ecosystems. Conventional waste management strategies, including mechanical recycling and incineration, have demonstrated limited efficiency in addressing the persistence of plastics such as polyethylene, polypropylene, polyethylene terephthalate, and polyvinyl chloride. While incineration eliminates plastic material, it does not promote circularity and may generate toxic emissions. As a sustainable alternative, microbial biodegradation involves bacteria, fungi, and actinomycetes capable of degrading synthetic polymers through enzymatic processes. This review provides a comprehensive overview of microbial degradation of major plastics such as polyethylene, polypropylene, polyethylene terephthalate, and polyvinyl chloride, highlighting key strains, degradation rates, and enzymatic mechanisms. Importantly, biodegradation research also informs the development of in situ remediation technologies and supports new recycling strategies. Advances in protein engineering and synthetic biology are discussed for enhancing degradation efficiency. However, scaling biodegradation to environmental conditions remains challenging due to variable temperature, pH, microbial competition, and potentially toxic intermediates. Despite these limitations, microbial biodegradation represents a promising ecofriendly approach to address plastic waste and promote a biobased circular economy. Future work should integrate microbial processes into existing recycling infrastructure and design robust consortia guided by omics tools.

Meiofauna are frequently overlooked in biodiversity assessments, resulting in a lack of understanding regarding their current status, the potential impact of anthropogenic activities, and climate change. This study on the intertidal zone of the Small Beach of Ostend marks a new effort to characterize meiofaunal communities along the Belgian coast. Sampling was carried out on five separate occasions throughout the year, with abiotic data collected during each event. Collected specimens were sorted according to their taxonomic group, resulting in a retrieval of 1742 organisms. Among these, Platyhelminthes and Nematoda were most abundant. Through metabarcoding of the 18S ribosomal region, a biodiversity assessment was conducted, yielding a total of 106 Amplicon Sequence Variants (ASVs). After filtering out rare reads, 65 metazoan ASVs were retained: 18 representing Platyhelminthes, 16 Nematoda, 15 Copepoda, 12 Polychaeta, and 4 Acoela. Identification of the ASVs through blasting generated 23 unique species-level identifications. The highest species richness was observed among Proseriata and Nematoda, each comprising six different species. Additionally, four different species of Polychaeta and Copepoda, two species of Acoela, and one species of Rhabdocoela were identified. Compared to findings on similar beaches along the Belgian coast from about 40 years ago, the meiofaunal communities on this beach exhibit an overall low species richness. Finding fewer and other species might be linked to the potential impact of beach nourishments, human trampling, and climate change. However, confirming this hypothesis requires future research.

Metals are natural components of the lithosphere, whose amounts and bioavailability are increasing in many areas due to their continuous release from both natural sources and intensive human activities. Some metals are essential or beneficial for living organisms, while others are non-essential and potentially toxic. When present at higher concentrations, even essential and beneficial metal ions can become harmful to all forms of life. Bacteria, unicellular organisms that have been exposed to metals since the earliest stages of life on Earth, have evolved metabolic pathways involving essential metals as well as diverse strategies to cope with metal toxicity. In the domain Bacteria, two main strategies have been identified: (i) metal exclusion, which includes cell wall sequestration and immobilization of metals in extracellular exopolysaccharides, siderophores, and other soluble microbial products, as well as (ii) metal tolerance, involving intracellular sequestration of metals (e.g., by metallothioneins, or low molecular weight thiols) as well as enzymatic conversion of metals to less toxic forms and/or its active efflux. Microorganisms possessing such adaptive traits are considered valuable agents for potential application in medicine, environmental sciences, and bioengineering (e.g., bioremediation and/or biomining).

1. Microbiome studies in Platyhelminthes have predominantly focused on a limited number of taxa, overlooking the vast diversity of turbellarian hosts. Here, we aimed to expand our understanding of microbial associations in a selection of free-living representatives of Rhabdocoela, a group of turbellarian flatworms that is very species rich and ecologically diverse. 2. Using 16S rRNA sequencing, we characterised the microbiomes of three species of Rhabdocoela, representing the two most speciose lineages within this taxon: Dalytyphloplanida and Kalyptorhynchia. The specimens were captured in the wild and obtained from marine or freshwater habitats. 3. The microbiomes of Gyratrix hermaphroditus (Kalyptorhynchia) and Mesostoma ehrenbergii (Dalytyphloplanida) were both dominated by Proteobacteria, while Phaenocora evelinae (Dalytyphloplanida) was predominantly associated with Cyanobacteria, more specifically Oxyphytobacteria (chloroplasts). 4. Based on the observed genera, our analysis revealed distinct microbial patterns, possibly associated with the habitat and lifestyle of the studied species. We could not exclude the presence of a phylosymbiotic signal as a limited core microbiome was present for each rhabdocoel species, although no set of bacteria common to all three rhabdocoel species was found. 5. This explorative study contributes to the expanding knowledge of invertebrate microbiomes, providing new insights into the microbial associations of a selection of turbellarians. The descriptive results presented here open up several promising avenues for future research, including the search for functional roles of turbellarian bacterial symbionts and exploring potential correlations between microbiome compositions, turbellarian phylogeny and environmental variables.

Several members of the cucurbit family (Cucurbitaceae) have a great potential to take up highly hydrophobic compounds, such as persistent organic pollutants (POPs), from environmental matrices, and translocate them to the aboveground parts of the plants. Moreover, recent research showed that they can effectively enhance the removal of emerging organic pollutants (EOPs) from the environment. Several studies provided evidence that plant-associated microorganisms and root exudates (including plant secondary metabolites, PSMs) can enhance the effective removal of POPs and EOPs from environmental matrices (i.e. soil, sediments, water reservoirs) by cucurbits. Hence, the main aims of this chapter are: (i) to gather information about processes underlying an exceptional ability of cucurbits to accumulate hydrophobic compounds; (ii) to combine the most pronounced and recent data on the removal of POPs and EOPs using cucurbits; and (iii) to point out opportunities and challenges for the use of cucurbits as phytoremediators of polluted environments.

Extensive green roofs provide for many ecosystem services in urban environments. The efficacy of these services is influenced by the vegetation structure. Despite their key role in plant performance and productivity, but also their contribution to nitrogen fixation or carbon sequestration, green roof microbial communities have received little attention so far. No study included a spatiotemporal aspect to investigate the core microbiota residing in the substrates of extensive green roofs, although these key taxa are hypothesized to be amongst the most ecologically important taxa. Here, we identified the core microbiota residing in extensive green roof substrates and investigated whether microbial community composition is affected by the vegetation that is planted on extensive green roofs. Eleven green roofs from three different cities in Flanders (Belgium), planted either with a mixture of grasses, wildflowers and succulents (Sedum spp.; Sedum–herbs–grasses roofs) or solely species of Sedum (Sedum–moss roofs), were seasonally sampled to investigate prokaryotic and fungal communities via metabarcoding. Identifying the key microbial taxa revealed that most taxa are dominant phylotypes in soils worldwide. Many bacterial core taxa are capable of nitrogen fixation, and most fungal key taxa are stress-tolerant saprotrophs, endophytes, or both. Considering that soil microbes adapted to the local edaphic conditions have been found to improve plant fitness, further investigation of the core microbiome is warranted to determine the extent to which these stress-tolerant microbes are beneficial for the vegetational layer. Although Sedum–herbs–grasses roofs contained more plant species than Sedum–moss roofs, we observed no discriminant microbial communities between both roof types, likely due to sharing the same substrate textures and the vegetational layers that became more similar throughout time. Future studies are recommended to comprehensively characterize the vegetational layer and composition to examine the primary drivers of microbial community assembly processes.

Extensive green roofs provide for many ecosystem services in urban environments. The efficacy of these services is influenced by the substrate characteristics and vegetational composition. Despite their key role in plant performance and productivity, or their contribution to nitrogen fixation or carbon sequestration, green roof microbial communities have received little attention so far. Here, we investigated whether microbial communities in extensive green roof substrates contain a core community, as well as whether they are affected by green roof plant diversity. Eleven green roofs, planted either with a mixture of grasses, wildflowers and succulents (Sedum spp.), or solely species of Sedum, were seasonally sampled to investigate prokaryotic and fungal communities via metabarcoding. Although Sedum-herbs-grasses roofs contained more plant species, we observed no discriminant microbial communities between both roof types, likely due to sharing the same substrate textures and the vegetational layers that became more similar throughout time. Examining key microbial taxa revealed that most taxa are also dominant phylotypes in soils across different biomes. Many bacterial core taxa are capable of nitrogen fixation and most fungal key taxa are stress-tolerant saprotrophs, endophytes, or both. Microbial community composition further revealed high similarities with aerial samples taken in urban environments. Considering the extreme edaphic conditions that periodically arise in green roof substrates, further investigation is warranted to determine the extent to which the dynamic and intriguing microbial communities are influenced by the aeromicrobiome.

In both developed and developing countries, atmospheric pollution with particulate matter (PM) remains an important issue. Despite the health effects of poor air quality, studies on air pollution are often limited by the high costs of continuous monitoring and the need for extensive sampling. Furthermore, these particles are often enriched with potentially toxic trace elements and organic pollutants. This study evaluates both the composition of atmospheric dust accumulated during a certain timespan on Hedera helix and Senecio cineraria leaves and the potential for their use as bio-monitors. The test plants were positioned near automatic air quality monitoring stations at four different sites with respectively high, moderate and low traffic intensity. The gravimetric deposition of PM10 and PM2.5 on leaves was compared with data recorded by the monitoring stations and related to the weather conditions reported by Argentina’s National Meteorological Service. To determine the presence of trace elements enriching the PM deposited on leaves, two analytical techniques were applied: XRF (not destructive) and ICP (destructive). The results indicated that only in the unpaved street location (site 2) did PM10 and PM2.5 concentrations (90 µg m−3 and 9 µg m−3) in the air exceed more than five times WHO guidelines (15 µg m−3 and 5 µg m−3). However, several trace elements were found to be enriching PM deposited on leaves from all sites. Predominantly, increased concentrations of Cd, Cu, Ti, Mn, Zn and Fe were found, which were associated with construction, traffic and unpaved street sources. Furthermore, based on its capability to sequester above 2800 µg cm−2 of PM10, 2450 µg cm−2 of PM2.5 and trace elements, Senecio cineraria can be taken into consideration for adoption as a bio-monitor or even for PM mitigation.

Industrial development has enhanced the release into the environment of large quantities of chemical compounds with high toxicity and limited prospects of degradation. The pollution of soil and water with xenobiotic chemicals has become a major ecological issue; therefore, innovative treatment technologies need to be explored. Fungal bioremediation is a promising technology exploiting their metabolic potential to remove or lower the concentrations of xenobiotics. In particular, white rot fungi (WRF) are unique microorganisms that show high capacities to degrade a wide range of toxic xenobiotic compounds such as synthetic dyes, chlorophenols, polychlorinated biphenyls, organophosphate pesticides, explosives and polycyclic aromatic hydrocarbons (PAHs). In this review, we address the main classes of enzymes involved in the fungal degradation of organic pollutants, the main mechanisms used by fungi to degrade these chemicals and the suitability of fungal biomass or extracellular enzymes for bioremediation. We also exemplify the role of several fungi in degrading pollutants such as synthetic dyes, PAHs and emerging pollutants such as pharmaceuticals and perfluoroalkyl/polyfluoroalkyl substances (PFASs). Finally, we discuss the existing current limitations of using WRF for the bioremediation of polluted environments and future strategies to improve biodegradation processes.

Growing crops on marginal lands is a promising solution to alleviate the increasing pressure on agricultural land in Europe. Such crops will however be at the same time exposed to increased drought and pathogen prevalence, on already challenging soil conditions. Some sustainable practices, such as Silicon (Si) foliar fertilization, have been proposed to alleviate these two stress factors, but have not been tested under controlled, future climate conditions. We hypothesized that Si foliar fertilization would be beneficial for crops under future climate, and would have cascading beneficial effects on ecosystem processes, as many of them are directly dependent on plant health. We tested this hypothesis by exposing spring barley growing on marginal soil macrocosms (three with, three without Si treatment) to 2070 climate projections in an ecotron facility. Using the high-capacity monitoring of the ecotron, we estimated C, water, and N budgets of every macrocosm. Additionally, we measured crop yield, the biomass of each plant organ, and characterized bacterial communities using metabarcoding. Despite being exposed to water stress conditions, plants did not produce more biomass with the foliar Si fertilization, whatever the organ considered. Evapotranspiration (ET) was unaffected, as well as water quality and bacterial communities. However, in the 10-day period following two of the three Si applications, we measured a significant increase in C sequestration, when climate conditions where significantly drier, while ET remained the same. We interpreted these results as a less significant effect of Si treatment than expected as compared with literature, which could be explained by the high CO2 levels under future climate, that reduces need for stomata opening, and therefore sensitivity to drought. We conclude that making marginal soils climate proof using foliar Si treatments may not be a sufficient strategy, at least in this type of nutrient-poor, dry, sandy soil.