The contribution of seasonal variations and Zostera marina presence to the bacterial community assembly of seagrass bed sediments.

BACKGROUND: Microorganisms play pivotal roles in seagrass ecosystems by facilitating material and elemental cycling as well as energy flux. However, our understanding of how seasonal factors and seagrass presence influence the assembly of bacterial communities in seagrass bed sediments is limited. Employing high-throughput sequencing techniques, this study investigates and characterizes bacterial communities in the rhizosphere of eelgrass (Zostera marina) and the bulk sediments across different seasons. The research elucidates information on the significance of seasonal variations and seagrass presence in impacting the microbial communities associated with Zostera marina. RESULTS: The results indicate that seasonal variations have a more significant impact on the bacterial community in seagrass bed sediments than the presence of seagrass. We observed that the assembly of bacterial communities in bulk sediments primarily occurs through stochastic processes. However, the presence of seagrass leading to a transition from stochastic to deterministic processes in bacterial community assembly. This shift further impacts the complexity and stability of the bacterial co-occurrence network. Through LEfSe analysis, different candidate biomarkers were identified in the bacterial communities of rhizosphere sediments in different seasons, indicating that seagrass may possess adaptive capabilities to the environment during different stages of growth and development. CONCLUSIONS: Seasonal variations play a significant role in shaping these communities, while seagrass presence influences the assembly processes and stability of the bacterial community. These insights will provide valuable information for the ecological conservation of seagrass beds.

MIST-CF: Chemical Formula Inference from Tandem Mass Spectra.

Chemical formula annotation for tandem mass spectrometry (MS/MS) data is the first step toward structurally elucidating unknown metabolites. While great strides have been made toward solving this problem, the current state-of-the-art method depends on time-intensive, proprietary, and expert-parametrized fragmentation tree construction and scoring. In this work, we extend our previous spectrum Transformer methodology into an energy-based modeling framework, MIST-CF: Metabolite Inference with Spectrum Transformers for Chemical Formula prediction, for learning to rank chemical formula and adduct assignments given an unannotated MS/MS spectrum. Importantly, MIST-CF learns in a data-dependent fashion using a Formula Transformer neural network architecture and circumvents the need for fragmentation tree construction. We train and evaluate our model on a large open-access database, showing an absolute improvement of 10% top 1 accuracy over other neural network architectures. We further validate our approach on the CASMI2022 challenge data set, achieving nearly equivalent performance to the winning entry within the positive mode category without any manual curation or postprocessing of our results. These results demonstrate an exciting strategy to more powerfully leverage MS2 fragment peaks for predicting MS1 precursor chemical formulas with data-driven learning.

Combined transcriptomics and metabolomics analysis reveals salinity stress specific signaling and tolerance responses in the seagrass Zostera japonica.

KEY MESSAGE: Multiple regulatory pathways of Zostera japonica to salt stress were identified through growth, physiological, transcriptomic and metabolomic analyses. Seagrasses are marine higher submerged plants that evolved from terrestrial monocotyledons and have fully adapted to the high saline seawater environment during the long evolutionary process. As one of the seagrasses growing in the intertidal zone, Zostera japonica not only has the ability to quickly adapt to short-term salt stress but can also survive at salinities ranging from the lower salinity of the Yellow River estuary to the higher salinity of the bay, making it a good natural model for studying the mechanism underlying the adaptation of plants to salt stress. In this work, we screened the growth, physiological, metabolomic, and transcriptomic changes of Z. japonica after a 5-day exposure to different salinities. We found that high salinity treatment impeded the growth of Z. japonica, hindered its photosynthesis, and elicited oxidative damage, while Z. japonica increased antioxidant enzyme activity. At the transcriptomic level, hypersaline stress greatly reduced the expression levels of photosynthesis-related genes while increasing the expression of genes associated with flavonoid biosynthesis. Meanwhile, the expression of candidate genes involved in ion transport and cell wall remodeling was dramatically changed under hypersaline stress. Moreover, transcription factors signaling pathways such as mitogen-activated protein kinase (MAPK) were also significantly influenced by salt stress. At the metabolomic level, Z. japonica displayed an accumulation of osmolytes and TCA mediators under hypersaline stress. In conclusion, our results revealed a complex regulatory mechanism in Z. japonica under salt stress, and the findings will provide important guidance for improving salt resistance in crops.

Exploring the leaf regeneration cycles response of Zostera japonica to ocean acidification.

Ocean acidification is one of the major global environmental problems facing humankind today, and it has far-reaching impacts on marine organisms and the entire marine ecosystem. Zostera japonica, an important supporting species of intertidal seagrass beds, exhibits high photosynthetic productivity and plays an important role in the carbon cycle of nearshore waters. However, little is known about the characteristics, processes, and mechanisms of its response to ocean acidification. In this study, we conducted a 120-day acidification experiment in Z. japonica; here, plants underwent four leaf regeneration cycles to reveal the response mechanism of Z. japonica to ocean acidification (OA). We found that acidification significantly affected the seedling stage of Z. japonica, impacting leaf regeneration cycles by altering physiological and molecular responses. In one leaf regeneration cycle, the short-term exposure to CO2 affected the seagrass parameters, such as the regulation of inorganic carbon uptake modes and the regulation of photosynthesis between the dark and light reactions, with the potential to affect the carbon sinks of the marine organisms. The long-term effects on the regulation of antioxidant enzymes and antioxidant metabolites, caused an improvement in the marine life adaptation to OA. In a comparison of the different leaf regeneration cycles, the response pattern of Z. japonica showed an offset of the acidification during the short cycles and an adaption to the acidification during the long cycles. This study revealed the response mechanism of Z. japonica to OA at different time scales and could provide a theoretical basis for accurately assessing the impact of OA on seagrass and the entire seagrass bed ecosystem.

A comprehensive review of radioactive pollution treatment of uranium mill tailings.

Natural uranium is a crucial resource for clean nuclear energy, which has brought significant economic and social benefits to humanity. However, the development and utilization of uranium resources have also resulted in the accumulation of vast amounts of uranium mill tailings (UMTs), which pose a potential threat to human health and the ecological environment. This paper reviews the research progress on UMTs treatment technologies, including cover disposal, solidification disposal, backfilling disposal, and bioremediation methods. It is found that cover disposal is a versatile method for the long-term management of UMTs, the engineering performance and durability of the cover system can be improved by choosing suitable stabilizers for the cover layer. Solidification disposal can convert UMTs into solid waste for permanent disposal, but it produces a large amount of waste and requires high operating costs; it is necessary to explore the effectiveness and efficiency of solidification disposal for UMTs, while minimizing the bad environmental impact. Backfilling disposal realizes the resource utilization of solid waste, but the high radon exhalation rate caused by the UMTs backfilling also needs to be considered. Bioremediation methods have low investment costs and are less likely to cause secondary pollution, but the remediation efficiency is low, it can be combined with other treatment technologies to remedy the defects of a single remediation method. The article concludes with key issues and corresponding suggestions for the current UMTs treatment methods, which can provide theoretical guidance and reference for further development and application of radioactive pollution treatment of UMTs.

Response mechanisms of microalgal-bacterial granular sludge to zinc oxide nanoparticles.

Currently, zinc oxide nanoparticles (ZnO-NPs) with their widespread applications lead to their increasing dosages in wastewater, posing an urgent threat to wastewater treatment. Herein, the responses of the emerging microalgal-bacterial granular sludge (MBGS) to ZnO-NPs were investigated. The results showed that the performance of MBGS was significantly affected when the concentration of ZnO-NPs reached 10 mg/L, especially for the removal of ammonia and phosphorus. ZnO-NPs on the granular surface could affect microalgae photosynthesis by shading, while antioxidant enzymes could be generated against overproduced reactive oxygen species. Specifically, ZnO-NPs addition to MBGS systems altered the microbial community structure (e.g. Cyanobacteria) and function (e.g. biosynthesis) of prokaryotes rather than eukaryotes. Overall, the MBGS could exhibit multiple mechanisms to alleviate the ZnO-NPs toxicity. This study is expected to add knowledge on MBGS in the treatment of wastewater containing nanoparticles.