Long-term tracking of the microbiology of uranium-amended water-saturated bentonite microcosms: A mechanistic characterization of U speciation.

Deep geological repositories (DGRs) stand out as one of the optimal options for managing high-level radioactive waste (HLW) such as uranium (U) in the near future. Here, we provide novel insights into microbial behavior in the DGR bentonite barrier, addressing potential worst-case scenarios such as waste leakage (e.g., U) and groundwater infiltration of electron rich donors in the bentonite. After a three-year anaerobic incubation, Illumina sequencing results revealed a bacterial diversity dominated by anaerobic and spore-forming microorganisms mainly from the phylum Firmicutes. Highly U tolerant and viable bacterial isolates from the genera Peribacillus, Bacillus, and some SRB such as Desulfovibrio and Desulfosporosinus, were enriched from U-amended bentonite. The results obtained by XPS and XRD showed that U was present as U(VI) and as U(IV) species. Regarding U(VI), we have identified biogenic U(VI) phosphates, U(UO2)·(PO4)2, located in the inner part of the bacterial cell membranes in addition to U(VI)-adsorbed to clays such as montmorillonite. Biogenic U(IV) species as uraninite may be produced as result of bacterial enzymatic U(VI) reduction. These findings suggest that under electron donor-rich water-saturation conditions, bentonite microbial community can control U speciation, immobilizing it, and thus enhancing future DGR safety if container rupture and waste leakage occurs.

Biodegradable plastics in Mediterranean coastal environments feature contrasting microbial succession.

Plastic pollution of the ocean is a top environmental concern. Biodegradable plastics present a potential "solution" in combating the accumulation of plastic pollution, and their production is currently increasing. While these polymers will contribute to the future plastic marine debris budget, very little is known still about the behavior of biodegradable plastics in different natural environments. In this study, we molecularly profiled entire microbial communities on laboratory confirmed biodegradable polybutylene sebacate-co-terephthalate (PBSeT) and polyhydroxybutyrate (PHB) films, and non-biodegradable conventional low-density polyethylene (LDPE) films that were incubated in situ in three different coastal environments in the Mediterranean Sea. Samples from a pelagic, benthic, and eulittoral habitat were taken at five timepoints during an incubation period of 22 months. We assessed the presence of potential biodegrading bacterial and fungal taxa and contrasted them against previously published in situ disintegration data of these polymers. Scanning electron microscopy imaging complemented our molecular data. Putative plastic degraders occurred in all environments, but there was no obvious "core" of shared plastic-specific microbes. While communities varied between polymers, the habitat predominantly selected for the underlying communities. Observed disintegration patterns did not necessarily match community patterns of putative plastic degraders.

A pilot study suggests the correspondence between SAR202 bacteria and dissolved organic matter in the late stage of a year-long microcosm incubation.

SAR202 bacteria are abundant in the marine environment and they have been suggested to contribute to the utilization of recalcitrant organic matter (RDOM) within the ocean's biogeochemical cycle. However, this functional role has only been postulated by metagenomic studies. During a one-year microcosm incubation of an open ocean microbial community with lysed Synechococcus and its released DOM, SAR202 became relatively more abundant in the later stage (after day 30) of the incubation. Network analysis illustrated a high degree of negative associations between SAR202 and a unique group of molecular formulae (MFs) in phase 2 (day 30 to 364) of the incubation, which is empirical evidence that SAR202 bacteria are major consumers of the more oxygenated, unsaturated, and higher-molecular-weight MFs. Further investigation of the SAR202-associated MFs suggested that they were potentially secondary products arising from initial heterotrophic activities following the amendment of labile Synechococcus-derived DOM. This pilot study provided a preliminary observation on the correspondence between SAR202 bacteria and more resistant DOM, further supporting the hypothesis that SAR202 bacteria play important roles in the degradation of RDOM and thus the ocean's biogeochemical cycle.

Metabolic Dysfunction-Associated Steatotic Liver Disease in a Dish: Human Precision-Cut Liver Slices as a Platform for Drug Screening and Interventions.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing healthcare problem with limited therapeutic options. Progress in this field depends on the availability of reliable preclinical models. Human precision-cut liver slices (PCLSs) have been employed to replicate the initiation of MASLD, but a comprehensive investigation into MASLD progression is still missing. This study aimed to extend the current incubation time of human PCLSs to examine different stages in MASLD. Healthy human PCLSs were cultured for up to 96 h in a medium enriched with high sugar, high insulin, and high fatty acids to induce MASLD. PCLSs displayed hepatic steatosis, characterized by accumulated intracellular fat. The development of hepatic steatosis appeared to involve a time-dependent impact on lipid metabolism, with an initial increase in fatty acid uptake and storage, and a subsequent down-regulation of lipid oxidation and secretion. PCLSs also demonstrated liver inflammation, including increased pro-inflammatory gene expression and cytokine production. Additionally, liver fibrosis was also observed through the elevated production of pro-collagen 1a1 and tissue inhibitor of metalloproteinase-1 (TIMP1). RNA sequencing showed that the tumor necrosis factor alpha (TNFα) signaling pathway and transforming growth factor beta (TGFß) signaling pathway were consistently activated, potentially contributing to the development of inflammation and fibrosis. In conclusion, the prolonged incubation of human PCLSs can establish a robust ex vivo model for MASLD, facilitating the identification and evaluation of potential therapeutic interventions.

Survival of surface bacteriophages and their hosts in in situ deep-sea environments.

IMPORTANCE: The survival of the sinking prokaryotes and viruses in the deep-sea environment is crucial for deep-sea ecosystems and biogeochemical cycles. Through an in situ deep-sea long-term incubation device, our results showed that viral particles and infectivity had still not decayed completely after in situ incubation for 1 year. This suggests that, via infection and lysis, surface viruses with long-term infectious activity in situ deep-sea environments may influence deep-sea microbial populations in terms of activity, function, diversity, and community structure and ultimately affect deep-sea biogeochemical cycles, highlighting the need for additional research in this area.

Functional changes in long-term incubated rat precision-cut lung slices.

BACKGROUND: Respiratory diseases represent a global health burden. Because research on therapeutic strategies of airway diseases is essential, the technique of precision-cut lung slices (PCLS) has been developed and widely studied. PCLS are an alternative ex vivo model and have the potential to replace and reduce in vivo animal models. So far, the majority of studies was conducted with short-term cultivated PCLS (≤ 72 h). As there is large interest in research of chronic diseases and chronic toxicity, feasibility of cultivating human PCLS long-term over 2 weeks and recently over 4 weeks was investigated by another research group with successful results. Our aim was to establish a model of long-term cultivated rat PCLS over a period of 29 days. METHODS: Rat PCLS were cultured for 29 days and analysed regarding viability, histopathology, reactivity and gene expression at different time points during cultivation. RESULTS: Cultivation of rat PCLS over a 29-day time period was successful with sustained viability. Furthermore, the ability of bronchoconstriction was maintained between 13 and 25 days, depending on the mediator. However, reduced relaxation, altered sensitivity and increased respiratory tone were observed. Regarding transcription, alteration in gene expression pattern of the investigated target genes was ascertained during long-term cultivation with mixed results. Furthermore, the preparation of PCLS seems to influence messenger ribonucleic acid (mRNA) expression of most target genes. Moreover, the addition of fetal bovine serum (FBS) to the culture medium did not improve viability of PCLS. In contrast to medium without FBS, FBS seems to affect measurements and resulted in marked cellular changes of metaplastic and/or regenerative origin. CONCLUSIONS: Overall, a model of long-term cultivated rat PCLS which stays viable for 29 days and reactive for at least 13 days could be established. Before long-term cultivated PCLS can be used for in-depth study of chronic diseases and chronic toxicity, further investigations have to be made.

Biosolids increase phosphate adsorption of semi-arid Mediterranean soils.

The impact of biosolid compost on the adsorption of orthophosphate (IP) to Mediterranean-type soils was studied. Eight soils were amended with a stable biosolid compost (ADSC) at 9:1 and 97:3 ratios (w/w). Four soils were amended with the dissolved organic matter (DOM) fraction of the ADSC at the amount added at the 9:1 mixture (810 mg C kg-1). Soils and their 9:1 soil‒ADSC mixtures were incubated for seven years. The maximum ADSC IP-adsorption capacity (SMAX, Langmuir model) at native pH (≈7.5) was 850 mg P kg-1. Mixing the ADSC with the soils increased their SMAX values by ca. 150 and 190 mg P kg-1 in the 9:1 and 97:3 mixtures, which exceeded additivity by 50% and 575%. The addition of DOM similarly increased the SMAX of three out of the four soils. Following the incubation, the soils' organic-C decreased by 34% and the ADSC-derived OC decreased by 60%. Still, the corresponding soil's and mixtures' average levels of labile IP either increased (by 60%) or remained steady (at Ì´30% of total-P). Incubation increased the SMAX of three soils and five soil‒ADSC mixtures and decreased their binding affinity (k), trends which were also reflected in the quantity/intensity parameters. This study showed that amending semi-arid Mediterranean soils with stable biosolids, and their long-term oxidative co-stabilization is conducive to increase their IP binding capacity and bioavailability. Finally, the often similar effects of the compost and its DOM on IP adsorption merits further research regarding the role of cation (Ca+2) bridging in IP‒DOM‒solid phase interactions.

Inhibitory effect of microplastics on soil extracellular enzymatic activities by changing soil properties and direct adsorption: An investigation at the aggregate-fraction level.

Microplastics (MPs), as a new type of environmental pollutant, pose a serious threat to soil ecosystems. The activities of soil extracellular enzymes produced by microorganisms are the potential sensitive indicators of soil quality. However, little is known about the response mechanism of enzyme activities toward MPs on a long-term scale. Moreover, information on differences in enzyme activities across different soil aggregates is lacking. In this study, 150 days of incubation experiments and soil aggregate fractionation were combined to investigate the influence of MPs on extracellular enzyme activities in soil. 28% concentration of polyethylene with size 100 µm was adopted in the treatments added with MPs. The results show that MPs inhibited enzyme activities through changing soil nutritional substrates and physicochemical properties or through adsorption. Moreover, MPs competed with soil microorganisms for physicochemical niches to reduce microbial activity and eventually, extracellular enzyme activity. Enzyme activities in different aggregate-size fractions responded differently to the MPs exposure. The catalase in the coarse particulate fraction and phenol oxidase and ß-glucosidase in the micro-aggregate fraction exerted the greatest response. With comparison, urease, manganese peroxidase, and laccase activities showed the greatest responses in the non-aggregated silt and clay fraction. These observations are believed to stem from differences in the key factors determining the enzyme activities in different aggregate-size fractions. The inhibitory pathway of microplastics on activities of extracellular enzymes in soil varies significantly across different aggregate fractions.

Decrease in bioavailability of soil heavy metals caused by the presence of microplastics varies across aggregate levels.

Microplastics can alter the physicochemical and biogeochemical processes in soil, but whether these alterations have further the effects on the transformation of soil heavy metal speciation, and if so, whether these effects vary across soil aggregate levels remain unknown. Herein, long-term soil culture experiments and soil fractionation are combined to investigate the effects of microplastics on chemical speciation of Cu, Cr, and Ni with different particle-size soil aggregates. Results show that microplastics in soil decrease the exchangeable, carbonate-bound, and Fe-Mn oxide-bound fractions of metals but increase their organic-bound fractions via direct adsorption and indirect effects on the soil microenvironment conditions. The findings suggest that microplastics can promote the transformation of heavy metal speciation from bioavailable to organic bound. Such promotion exerts notable differences across soil aggregate levels. The transformation of soil heavy metal speciation is greater in larger aggregates than in smaller aggregates in the early incubation period with microplastics but shows the opposite trend in the later incubation period. Therefore, this process is more sensitive to long-term microplastic pollution in smaller aggregates than in larger aggregates, most likely owing to the lag in the influence of microplastics on metal speciation transformation in the smaller aggregates.

Gas production from dredged sediment.

The anaerobic degradation of sediment organic matter leads to considerable gas production in constructions made from sediments and in landfills where contaminated sediments are disposed of, inducing problems with the mechanical stability of constructions or necessitating extraction and treatment of gas. However, little is known about the magnitude of gas generation from dredged sediment, hence validated input parameters for gas production modelling are missing. On the occasion of drillings performed for the installation of inclinometers on a mono-landfill for contaminated dredged sediment, eleven waste layers of known were sampled. Samples were analysed for gas generation in a long-term laboratory incubation experiment carried out for 757 days. It was found that the residual gas potential of the deposited dredged material ranged between 2 and 12 m3 MgDW-1, relating to 3-11% of the organic matter being degraded. Correlation analyses with material properties suggest a strong role of nitrogen, either directly or as indicative parameter, with the gas potential increasing with total nitrogen content and the share of degradable carbon decreasing with increasing TOC/TN ratio. The by far greatest share of organic matter was bound in the heavy density fraction >1.4 g cm-3, suggesting that the readily available light organic matter pool had already been depleted during pre-treatment of the dredged sediment in dewatering fields and the subsequent years of landfilling. Consequently, the correlation of the remaining gas potential with heavy fraction nitrogen was even stronger than for bulk nitrogen. The gas potential as revealed from the long-term test correlated well with short-term values, but outreached the commonly applied potential measured for 21 days by the factor of four. The data improve the state of knowledge on gas production from the large mineral waste stream of dredged material and serve to improve gas production modelling for these types of wastes. The strong correlation of gas potential to TN suggests that TN may serve as a proxy to estimate total gas potential.

Comparison of Different Cell Culture Media in the Model of the Isolated and Superfused Bovine Retina: Investigating the Limits of More Physiological Perfusion Solutions.

PURPOSE: The isolated superfused retina is a standardized tool in ophthalmological research. However, stable electroretinogram (ERG) responses can only be obtained for around eight hours; therefore, limiting its use. The aim of this study was to evaluate the short-term potential of different cell culture media and to promote long-term testing based on the results obtained. MATERIALS AND METHODS: For the experimental procedure bovine retinae were prepared and perfused with the standard Sickel solution and an ERG was performed. After recording stable a- or b-waves, different media (Dulbecco's Modified Eagle's Medium (DMEM), MACS, and Neurobasal) were superfused for 45 minutes. ERG recovery was monitored overall for 75 minutes. Analysis of the mRNA expression of Thy-1, GFAP, Bax/Bcl-2-ratio, Rhodopsin, and Opsin via qRT-PCR was performed directly after ERG recording on the same retina. RESULTS: None of the tested media had a negative effect on a-wave amplitudes, although b-wave amplitudes decreased (DMEM) or increased (MACS and Neurobasal) compared to the standard solution (Sickel) after 45 minutes of exposure. However, after 75 minutes of wash-out, no difference to the standard solution alone could be observed. Exposure to different media either had no effect or decreased the Opsin and Rhodopsin mRNA levels. Thy-1 expression was strongly diminished in DMEM and MACS (by 2-3-fold), whereas incubation in Neurobasal medium led to a slight increase compared to incubation with the standard solution. Furthermore, the Bax/Bcl-2 ratio indicated an anti-apoptotic effect (Bax/Bcl-2 = 0.16; p < 0.05) for Neurobasal. CONCLUSION: Neurobasal medium displayed the best electrophysiological properties in the short-term and may be applicable for stable long-term escalation testing.