Keystone microbial taxa organize micropollutant-related modules shaping the microbial community structure in estuarine sediments

Effect of intermittent water flow on biodegradation of organic micropollutants in the hyporheic zone

Water scarcity in the Mediterranean area has increased the number of intermittent rivers. Recently, hyporheic zones (HZ) of intermittent rivers have gained attention since a substantial part of the stream's natural purification capacity is located within these zones. Thus, understanding the flow dynamics in HZs is crucial for gaining insights into the degradation of organic micropollutants. A lab-scale study using column experiments was conducted in an attempt to elucidate the environmental processes accounting for the biodegradation capacity of the HZ under flow intermittency. A mixture of six compounds including pesticides (chloranthraniliprole, fluopyram and trifloxystrobin) and pharmaceuticals (venlafaxine, amisulpride and paroxetine) spiked at 1 μg/L level was used for degradation kinetic studies and at 1 mg/L for transformation products identification using suspect/non-target liquid chromatography high-resolution mass spectrometry approaches. The experiments lasted 60 days, divided into two 14-day phases: one before and one after a 5-week desiccation period. Bacterial community was charaterized by high-throughput DNA sequencing. The results suggested that intermittent flows stimulated the biodegradation of three compounds namely fluopyram, trifloxystrobin and venlafaxine, showing a large range of biodegradation profiles in batch water/sediment testing system according to OECD 308 tests. Biodegradation rate enhancement was ascribed to the occurrence of additional transformation routes after the desiccation period of river sediment, with the formation of new transformation products reported for the first time in the present work. 16S rDNA sequencing revealed that the desiccation period favored the growth of nitrifying and denitrifying bacteria which could partially explain the emergence of the new transformation pathways and most specifically those leading to N-oxide derivatives. Identification of transformation products also revealed that reductive transformation routes were relevant for this study, being dehydrogenation, dehalogenation, ether bond cleavage and sulfone reduction into sulphide important reactions. These results suggest that the intermittent flow conditions can influence the HZ biodegradation capacity.

Flooding promotes the coalescence of microbial community in estuarine habitats

Microbial community coalescence describes the mixing of microbial communities and their integration with the surrounding environment, which is common in natural ecosystems and has potential impacts on ecological processes. However, few studies have focused on microbial community coalescence between different habitats in estuarine regions. In this study, we comprehensively investigated the environmental characteristics and bacterial community changes of different habitats (water body (Water), subtidal sediments (SS) and intertidal salt marsh sediments (SM)) in Luanhe estuary during flood and normal flow periods. The results showed that flood event significantly reduced the salinity of the estuarine habitats, changed the nutrient structure and intensified the eutrophication of estuarine water. By calculating the proportion of overlapping groups and applying the 'FEAST' algorithm, we revealed that flood event facilitated the migration of bacterial communities along alternative pathways across habitats, markedly enhanced the cross-habitat mobility of bacterial communities, which underscores the pivotal role of flood event in driving bacterial community coalescence. Flood-induced community coalescence not only increased the α-diversity of bacterial communities within habitats, but also increased the proportion of overlapped species between habitats, ultimately leading to homogenization between habitats. Canonical correlation analysis combined co-occurrence network analysis revealed that flood event attenuated the role of environmental filtration in microbial assembly, while increased the impact of dispersal processes and intensified interspecific competition among microorganisms, led to the change of keystone species and reduced the complexity and stability of bacterial communities. In conclusion, this study demonstrates the complex effects of flood events on estuarine microbial communities from the perspective of multi-habitat interactions in the estuary, and emphasizes the key role of river hydrodynamic conditions in facilitating the coalescence of estuarine microbial communities. We look forward to further attention and research on estuarine microbial coalescence, which will provide new insights into assessing the stability and resilience of estuarine ecosystems under flood challenges and the sustainable management of estuarine wetlands.

Community coalescence under variable hydrochemical conditions of the Chesapeake Bay shaped bacterial diversity and functional traits

Community coalescence related to bacterial mixing events regulates community characteristics and affects the health of estuary ecosystems. At present, bacterial coalescence and its driving factors are still unclear. The present study used a dataset from the Chesapeake Bay (2017) to address how bacterial community coalescence in response to variable hydrochemistry in estuarine ecosystems. We determined that variable hydrochemistry promoted the deterioration of water quality. Temperature, orthophosphate, dissolved oxygen, chlorophyll a, Secchi disk depth, and dissolved organic phosphorus were the key environmental factors driving community coalescence. Bacteria with high tolerance to environmental change were the primary taxa accumulated in community coalescence, and the significance of deterministic processes to communities was revealed. Community coalescence was significantly correlated with the pathways of metabolism and organismal systems, and promoted the co-occurrence of antibiotic resistance and virulence factor genes. Briefly, community coalescence under variable hydrochemical conditions shaped bacterial diversity and functional traits, to optimise strategies for energy acquisition and lay the foundation for alleviating environmental pressures. However, potential pathogenic bacteria in community coalescence may be harmful to human health and environmental safety. The present study provides a scientific reference for ecological management of estuaries.

Insight investigation into the response pattern of microbial assembly succession and volatile profiles during the brewing of sauce-flavor baijiu based on bioaugmentation

To improve the flavor profile and sensory quality of baijiu, the utilization of bioaugmented fermentation inoculated with functional microbiota normally serves as an effective method for directional regulation during the baijiu fermentation process. In this study, a systematic analysis of the succession patterns and volatile flavor compound profiles of microbial communities was carried out by high-throughput sequencing and solid-phase microextraction gas chromatography-mass spectrometry, respectively. The results demonstrated that the Saccharomyces cerevisiae YS222-related bioaugmentation clearly altered the microbial composition, particularly the assembly of bacteria, and promoted the quantity of the most volatile flavoring compounds, including alcohols, esters, and pyrazines. In addition, the correlation analysis showed that Saccharomyces and Lactobacillus in the augmented group were the main biomarkers associated with the dynamics of microbial community and greatly contributed to the brewing of sauce-flavor baijiu, which congruent with the outcomes of the enrichment analysis of integrated metabolic pathway. Thus, this work is beneficial for promoting the quality of baijiu and will serve as a useful reference for clarifying the possible mechanism of augmented fermentation on flavor development.

Removal of thallium by MnOx coated limestone sand filter through regeneration of KMnO4: Combination of physiochemical and biochemical actions

Treatment of industrial thallium(Tl)-containing wastewater is crucial for mitigating environmental risks and health threats associated with this toxic metal. The incorporation of Mn oxides (MnOx) into the filtration system is a promising solution for efficient Tl(I) removal. However, further research is needed to elucidate the underlying mechanism behind MnOx-enhanced filtration and the rules of its stable operation. In this study, limestone, a cost-effective material, was selected as the filter media. Raw water with Mn(II), Tl(I), and other pollutants was prepared after a thorough investigation of actual industrial wastewater conditions. KMnO4 was added to induce the formation of MnO2 on limestone surfaces, while long-term operation led to enrichment of manganese oxidizing microorganisms (MnOM). Results revealed a dual mechanism. Firstly, most Mn(II) were oxidized by KMnO4 to form MnO2 attaching to limestone sands, and both Tl(I) and residual Mn(II) were adsorbed onto the newly formed MnO2. Subsequently, enzymes secreted by MnOM facilitated oxidation of remaining Mn(II), resulting in the generation of biogenic manganese oxides (BioMnOx) with numerous vacancies during long-term operation. The generated BioMnOx not only adsorbed Mn(II) and Tl(I) but also promoted their oxidation process. This approach offers an effective and sustainable method for removing both Mn(II) and Tl(I) from industrial wastewater, thereby addressing the challenges posed by thallium-contaminated effluents.

Distribution heterogeneity of sediment bacterial community in the river-lake system impacted by nonferrous metal mines: Diversity, composition and co-occurrence patterns

Metal(loid) pollution caused by mining activities can affect microbial communities. However, knowledge of the diversity, composition, and co-occurrence patterns of bacterial communities in aquatic systems impacted by nonferrous metal mines. Here, the metal(loid) contents and bacterial communities in sediments from the Zijiang River (tributary to mainstream) to Dongting Lake were investigated by geochemical and molecular biology methods. The results indicated that the river sediments had lower pH and higher ecological risk of metal(loid)s than the lake sediment. The diversity and composition of bacterial communities in river sediments significantly (p < 0.05) differed from those in lake sediments, showing distributional heterogeneity. The biomarkers of tributary, mainstream, and lake sediments were mainly members of Deltaproteobacteria, Firmicutes, and Nitrospirae, respectively, reflecting species sorting in different habitats. Multivariate statistical analysis demonstrated that total and bioavailable Sb, As, and Zn were positively correlated with bacterial community richness. pH, TOC, TN, and Zn were crucial factors in shaping the distribution difference of bacterial communities. Environment-bacteria network analysis indicated that pH, SO42-, and total and bioavailable As and Sb greatly influenced the bacterial composition at the genus level. Bacteria-bacteria network analysis manifested that the co-occurrence network in mainstream sediments with a higher risk of metal(loid) pollution exhibited higher modularity and connectivity, which might be the survival mechanism for bacterial communities adapted to metal(loid) pollution. This study can provide a theoretical basis for understanding the ecological status of aquatic systems.

Vertical variation in prokaryotic community composition and co-occurrence patterns in sediments of the Three Gorges Reservoir, China

Archaea and bacteria are distributed throughout the sediment; however, our understanding of their biodiversity patterns, community composition, and interactions is primarily limited to the surface horizons (0-20 cm). In this research, sediment samples were collected from three vertical sediment profiles (depths of 0-295 cm) in the Three Gorges Reservoir (TGR), one of the largest reservoirs in the world. Through 16S rRNA sequencing, it was shown that sediment microbial diversity did not significantly vary across the sediment. Nevertheless, a decline in the similarity of archaeal and bacterial communities over distance along sediment vertical profiles was noted. Nonmetric multidimensional scaling (NMDS) analysis revealed that archaeal and bacterial communities could be clearly separated into two groups, located in the upper sediments (0-135 cm) and deep sediments (155-295 cm). Meanwhile, at the fine-scale of the vertical section, noteworthy variations were observed in the relative abundance of prominent archaea (e.g., Euryarchaeota) and bacteria (e.g., Proteobacteria). The linear discriminant analysis effect size (LEfSe) demonstrated that twenty-four bacterial and twenty-six archaeal biomarker microbes exist in the upper and deep sediment layers. Each layer exhibited distinctive microbial divisions, suggesting that microbes with diverse biological functions are capable of thriving and propagating along the sediment profile. Co-occurrence network analysis further indicated that the microbial network in the upper sediments was more complex than that in the deep sediments. Additionally, the newly discovered anaerobic methanotrophic archaeon Candidatus Methanoperedens was identified as the most abundant keystone archaeal taxon in both sediment layers, highlighting the significance of methane oxidation in material cycling within the TGR ecosystem. In summary, our study examined the biodiversity and coexistence patterns of benthic microbial communities throughout the vertical sediment profile, providing detailed insights into the vertical geography of archaeal and bacterial communities in typical deep-water reservoir ecosystems.

Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges

Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.