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The ISME Journal Jun 2024Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and...
Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Two planktonic, nitrification-inhibited enrichment cultures were established under continuous organic carbon and nitrate feeding, and cyclic oxygen availability. Over a third of the influent organic substrate was respired with nitrate as electron acceptor at high oxygen concentrations (> 6.5 mg/L). N2O accounted for up to one quarter of the nitrate reduced under oxic conditions. The enriched microorganisms maintained a constitutive abundance of denitrifying enzymes due to the oxic/anoxic frequencies exceeding their protein turnover - a common scenario in natural and engineered ecosystems. The aerobic denitrification rates are ascribed primarily to the residual activity of anaerobically synthesized enzymes. From an ecological perspective, the selection of organisms capable of sustaining significant denitrifying activity during aeration shows their competitive advantage over other heterotrophs under varying oxygen availabilities. Ultimately, we propose that the contribution of heterotrophic denitrification to aerobic nitrogen turnover and N2O emissions is currently underestimated in dynamic environments.
PubMed: 38913498
DOI: 10.1093/ismejo/wrae116 -
Scientific Reports Jun 2024The study presents a series of examples of magnetic nanoparticle systems designed for the diagnosis of viral diseases. In this interdisciplinary work, we describe one of...
The study presents a series of examples of magnetic nanoparticle systems designed for the diagnosis of viral diseases. In this interdisciplinary work, we describe one of the most comprehensive synthetic approaches for the preparation and functionalization of smart nanoparticle systems for rapid and effective RT-PCR diagnostics and isolation of viral RNA. Twelve different organic ligands and inorganic porous silica were used for surface functionalization of the FeO magnetic core to increase the number of active centres for efficient RNA binding from human swab samples. Different nanoparticle systems with common beads were characterized by HRTEM, SEM, FT-IR, XRD, XPS and magnetic measurements. We demonstrate the application of the fundamental models modified to fit the experimental zero-field cooling magnetization data. We discuss the influence of the nanoparticle shell parameters (morphology, thickness, ligands) on the overall magnetic performance of the systems. The prepared nanoparticles were tested for the isolation of viral RNA from tissue samples infected with hepatitis E virus-HEV and from biofluid samples of SARS-CoV-2 positive patients. The efficiency of RNA isolation was quantified by RT-qPCR method.
Topics: Silicon Dioxide; Humans; Magnetite Nanoparticles; RNA, Viral; SARS-CoV-2; COVID-19; Surface Properties; Pathology, Molecular; Virus Diseases
PubMed: 38910140
DOI: 10.1038/s41598-024-64839-2 -
The Science of the Total Environment Jun 2024Coastal areas are an important source of methane (CH). However, the exact origins of CH in the surface waters of coastal regions, which in turn drive sea-air emissions,...
Coastal areas are an important source of methane (CH). However, the exact origins of CH in the surface waters of coastal regions, which in turn drive sea-air emissions, remain uncertain. To gain a comprehensive understanding of the current and future climate change feedbacks, it is crucial to identify these CH sources and processes that regulate its formation and oxidation. This study investigated coastal CH dynamics by comparing water column data from six stations located in the brackish Tvärminne Archipelago, Baltic Sea. The sediment biogeochemistry and microbiology were further investigated at two stations (i.e., nearshore and offshore). These stations differed in terms of stratification, bottom water redox conditions, and organic matter loading. At the nearshore station, CH diffusion from the sediment into the water column was negligible, because nearly all CH was oxidized within the upper sediment column before reaching the sediment surface. On the other hand, at the offshore station, there was significant benthic diffusion of CH, albeit the majority underwent oxidation before reaching the sediment-water interface, due to shoaling of the sulfate methane transition zone (SMTZ). The potential contribution of CH production in the water column was evaluated and was found to be negligible. After examining the isotopic signatures of δC-CH across the sediment and water column, it became apparent that the surface water δC-CH values observed in areas with thermal stratification could not be explained by diffusion, advective fluxes, nor production in the water column. In fact, these values bore a remarkable resemblance to those detected below the SMTZ. This supports the hypothesis that the source of CH in surface waters is more likely to originate from ebullition than diffusion in stratified brackish coastal systems.
PubMed: 38909808
DOI: 10.1016/j.scitotenv.2024.174183 -
Nature Communications Jun 2024The importance of molecular docking in drug discovery lies in the precise recognition between potential drug compounds and their target receptors, which is generally...
The importance of molecular docking in drug discovery lies in the precise recognition between potential drug compounds and their target receptors, which is generally based on the computational method. However, it will become quite interesting if the rigid cavity structure of supramolecular macrocycles can precisely recognize a series of guests with specific fragments by mimicking molecular docking through co-crystallization experiments. Herein, we report a phenylphosphine oxide-bridged aromatic supramolecular macrocycle, F[3]A1-[P(O)Ph], which precisely recognizes benzonitrile derivatives through non-covalent interactions to form key-lock complexes by co-crystallization method. A total of 15 various benzonitrile derivatives as guest molecules are specifically bound by F[3]A1-[P(O)Ph] in co-crystal structures, respectively. Notably, among them, crisaborole (anti-dermatitis) and alectinib (anti-cancer) with the benzonitrile fragment, which are two commercial drug molecules approved by the U.S. Food and Drug Administration (FDA), could also form a key-lock complex with F[3]A1-[P(O)Ph] in the crystal state, respectively.
PubMed: 38909020
DOI: 10.1038/s41467-024-49540-2 -
Journal of Dairy Science Jun 2024Infant formulas (IFs), the sole adequate substitute to human milk, undergo several thermal treatments during production that can damage milk proteins and promote the...
Infant formulas (IFs), the sole adequate substitute to human milk, undergo several thermal treatments during production that can damage milk proteins and promote the formation of Maillard reaction products, modifying nutritional and sensory properties. The aim of this study was to determine the impact of a minimally processing route based on membrane filtration associated with different levels of heat treatment, on the odor, taste, texture and color attributes of IFs, then to compare with those of commercial milks. Three experimental IFs (produced with membrane filtration associated with low - T, medium - T, or high thermal treatments - T) were evaluated. Triangular tests conducted with a panel of 50 adults highlighted clear disparities between all the IFs. The same panel applied the Check-All-That-Apply method to evaluate the IFs: the range of variability between T and T was similar to that between the 2 commercial IFs, and the sensory characteristics of the experimental IFs were not far from the commercial brands for flavor and texture attributes. Analysis performed on the citation frequencies for each descriptor differentiated T/T from T, but all the experimental IFs were described with positive sensory characteristics, unlike one commercial IF. Volatile organic compounds (VOCs) content of IFs with low and high thermal treatments were analyzed. Forty VOCs were identified by gas chromatography-mass spectrometry. T contained a higher quantity of VOCs than T, except for benzaldehyde (Maillard reaction product), and aldehydes (oxidation-related products) were the most represented compounds. In conclusion, the processing was associated with sensory differences among IFs, but no marked difference in flavors was found according to CATA and physicochemical analysis. Additionally, no unpleasant sensory descriptors were noted. This shows that the minimally processed route leads to IFs that could fit well within the market from a sensory point of view.
PubMed: 38908693
DOI: 10.3168/jds.2024-24937 -
Ecotoxicology and Environmental Safety Jun 2024Humans are extensively exposed to organophosphate flame retardants (OPFRs), an emerging group of organic contaminants with potential nephrotoxicity. Nevertheless, the...
Humans are extensively exposed to organophosphate flame retardants (OPFRs), an emerging group of organic contaminants with potential nephrotoxicity. Nevertheless, the estimated daily intake (EDI) and prognostic impacts of OPFRs have not been assessed in individuals with chronic kidney disease (CKD). In this 2-year longitudinal study of 169 patients with CKD, we calculated the EDIs of five OPFR triesters from urinary biomonitoring data of their degradation products and analyzed the effects of OPFR exposure on adverse renal outcomes and renal function deterioration. Our analysis demonstrated universal OPFR exposure in the CKD population, with a median EDI of 360.45 ng/kg body weight/day (interquartile range, 198.35-775.94). Additionally, our study revealed that high tris(2-chloroethyl) phosphate (TCEP) exposure independently correlated with composite adverse events and composite renal events (hazard ratio [95 % confidence interval; CI]: 4.616 [1.060-20.096], p = 0.042; 3.053 [1.075-8.674], p = 0.036) and served as an independent predictor for renal function deterioration throughout the study period, with a decline in estimated glomerular filtration rate of 4.127 mL/min/1.73 m (95 % CI, -8.127--0.126; p = 0.043) per log ng/kg body weight/day of EDI. Furthermore, the EDI and EDI were positively associated with elevations in urinary 8-hydroxy-2'-deoxyguanosine and kidney injury molecule-1 during the study period, indicating the roles of oxidative damage and renal tubular injury in the nephrotoxicity of OPFR exposure. To conclude, our findings highlight the widespread OPFR exposure and its possible nephrotoxicity in the CKD population.
PubMed: 38908056
DOI: 10.1016/j.ecoenv.2024.116625 -
Scientific Reports Jun 2024Intensification of staple crops through conventional agricultural practices with chemical synthetic inputs has yielded positive outcomes in food security but with...
Intensification of staple crops through conventional agricultural practices with chemical synthetic inputs has yielded positive outcomes in food security but with negative environmental impacts. Ecological intensification using cropping systems such as maize edible-legume intercropping (MLI) systems has the potential to enhance soil health, agrobiodiversity and significantly influence crop productivity. However, mechanisms underlying enhancement of biological soil health have not been well studied. This study investigated the shifts in rhizospheric soil and maize-root microbiomes and associated soil physico-chemical parameters in MLI systems of smallholder farms in comparison to maize-monoculture cropping systems (MMC). Maize-root and rhizospheric soil samples were collected from twenty-five farms each conditioned by MLI and MMC systems in eastern Kenya. Soil characteristics were assessed using Black oxidation and Walkley methods. High-throughput amplicon sequencing was employed to analyze fungal and bacterial communities, predicting their functional roles and diversity. The different MLI systems significantly impacted soil and maize-root microbial communities, resulting in distinct microbe sets. Specific fungal and bacterial genera and species were mainly influenced and enriched in the MLI systems (e.g., Bionectria solani, Sarocladium zeae, Fusarium algeriense, and Acremonium persicinum for fungi, and Bradyrhizobium elkanii, Enterobacter roggenkampii, Pantoea dispersa and Mitsuaria chitosanitabida for bacteria), which contribute to nutrient solubilization, decomposition, carbon utilization, plant protection, bio-insecticides/fertilizer production, and nitrogen fixation. Conversely, the MMC systems enriched phytopathogenic microbial species like Sphingomonas leidyi and Alternaria argroxiphii. Each MLI system exhibited a unique composition of fungal and bacterial communities that shape belowground biodiversity, notably affecting soil attributes, plant well-being, disease control, and agroecological services. Indeed, soil physico-chemical properties, including pH, nitrogen, organic carbon, phosphorus, and potassium were enriched in MLI compared to MMC cropping systems. Thus, diversification of agroecosystems with MLI systems enhances soil properties and shifts rhizosphere and maize-root microbiome in favor of ecologically important microbial communities.
Topics: Zea mays; Soil Microbiology; Soil; Agriculture; Rhizosphere; Microbiota; Crops, Agricultural; Ecosystem; Plant Roots; Biodiversity; Bacteria; Fungi; Kenya; Crop Production
PubMed: 38906908
DOI: 10.1038/s41598-024-64138-w -
PloS One 2024Bandon Bay is a very fertile bay for coastal aquaculture, especially for blood cockles (Anadara granosa). Its structural pattern supports the flow of nutrients which...
Bandon Bay is a very fertile bay for coastal aquaculture, especially for blood cockles (Anadara granosa). Its structural pattern supports the flow of nutrients which directly sent from many rivers resulted the high production capacity of blood cockle at the top level in the country. Besides organic compounds present in sediment, inorganic substances are essential for growth, survival and shell development of blood cockles. A comparative study of minerals and oxide compounds which accumulated in the sediments at eight stations around the cockle culture area was conducted. These stations are located along the estuaries at Tha Thong, Tha Chang, Phum Riang, and Tapi. The proportion of oxide compounds were determinedusing X-Ray Fluorescence (XRF) technique and minerals were analyzed by Atomic Absorption Spectroscopy (AAS). Results showed that sediment characteristics, oxide composition and the amount of minerals among the stations are different from each other. The sediments of the eastern and the western coasts were characterized as crumble clay and muddy sand, respectively. Twelve types of oxide compounds, namely SiO2, Al2O3, Fe2O3, K2O, Cl, MgO, Na2O, SO3, CaO, TiO2, MnO, P2O5 were found in various quantities, with SiO2, Al2O3, and Fe2O3 were the fundamental minerals ranging from 85.64-90.82%. Tha Thong estuary in the east coast showed highly significant quantities (P<0.05) of potassium, calcium and manganese compared to the other estuaries.
Topics: Geologic Sediments; Thailand; Minerals; Oxides; Bays; Animals; Cardiidae; Aquaculture; Spectrometry, X-Ray Emission; Spectrophotometry, Atomic
PubMed: 38905193
DOI: 10.1371/journal.pone.0305061 -
MSystems Jun 2024Mixotrophy is an important trophic strategy for bacterial survival in the ocean. However, the global relevance and identity of the major mixotrophic taxa remain largely...
Mixotrophy is an important trophic strategy for bacterial survival in the ocean. However, the global relevance and identity of the major mixotrophic taxa remain largely elusive. Here, we combined phylogenetic, metagenomic, and metatranscriptomic analyses to characterize ubiquitous based on our deep-sea incubations and the global data. The phylogenomic tree of is divided into three large clades, among which members of clades A and B are almost all from terrestrial environments, while those of clade C are widely distributed in various marine habitats in addition to some terrestrial origins. All clades harbor genes putatively involved in chitin degradation, sulfide oxidation, hydrogen oxidation, thiosulfate oxidation, denitrification, dissimilatory nitrate reduction to ammonium, microaerophilic respiration, and metal (iron/manganese) reduction. Additionally, in clade C, more unique pathways were retrieved, including thiosulfate disproportionation, ethanol fermentation, methane oxidation, fatty acid oxidation, cobalamin synthesis, and dissimilatory reductions of sulfate, perchlorate, and arsenate. Within this clade, two mixotrophic Candidatus genera represented by UBA6211 and CAIJNA01 harbor genes putatively involved in the reverse tricarboxylic acid pathway for carbon fixation. Moreover, the metatranscriptomic data in deep-sea incubations indicated that the latter genus is a mixotroph that conducts carbon fixation by coupling sulfur oxidation and denitrification and metabolizing organic matter. Furthermore, global metatranscriptomic data confirmed the ubiquitous distribution and global relevance of in the expression of those corresponding genes across all oceanic regions and depths. Overall, these results highlight the contribution of previously unrecognized to carbon, nitrogen, and sulfur cycling in global oceans.IMPORTANCEMarine microorganisms exert a profound influence on global carbon cycling and ecological relationships. Mixotrophy, characterized by the simultaneous utilization of both autotrophic and heterotrophic nutrition, has a significant impact on the global carbon cycling. This report characterizes a group of uncultivated bacteria that thrived on the "hot time" of bulky particulate organic matter and exhibited mixotrophic strategy during the organic mineralization. Compared with clades A and B, more unique metabolic pathways were retrieved in clade C, including the reverse tricarboxylic acid pathway for carbon fixation, thiosulfate disproportionation, methane oxidation, and fatty acid oxidation. Global metatranscriptomic data from the Tara Oceans expeditions confirmed the ubiquitous distribution and extensive transcriptional activity of with the expression of genes putatively involved in carbon fixation, methane oxidation, multiple sulfur compound oxidation, and denitrification across all oceanic regions and depths.
PubMed: 38904399
DOI: 10.1128/msystems.00513-24 -
PeerJ 2024Dissolved oxygen is fundamental for chemical and biochemical processes occurring in natural waters and critical for the life of aquatic organisms. Many organisms are...
Dissolved oxygen is fundamental for chemical and biochemical processes occurring in natural waters and critical for the life of aquatic organisms. Many organisms are responsible for altering organic matter and oxygen transfers across ecosystem or habitat boundaries and, thus, engineering the oxygen balance of the system. Due to such features as small size, simple structure, vegetative reproduction and rapid growth, as well as frequent mass occurrence in the form of thick mats, they make them very effective in oxygenating water. The research was undertaken to assess the impact of various species of duckweed ( and ) on dissolved oxygen content and detritus production in water and the role of ecological factors (light, atmospheric pressure, conductivity, and temperature) in this process. For this purpose, experiments were carried out with combinations of and . On this basis, the content of oxygen dissolved in water was determined depending on the growth of duckweed. Linear regression models were developed to assess the dynamics of changes in oxygen content and, consequently, organic matter produced by the The research showed that the presence of causes an increase in dissolved oxygen content in water. It was also shown that an increase in atmospheric pressure had a positive effect on the ability of duckweed to produce oxygen, regardless of its type. The negative correlation between conductivity and water oxygenation, obtained in conditions of limited light access, allows us to assume that higher water conductivity limits oxygen production by all combinations of duckweeds when the light supply is low. Based on the developed models, it was shown that the highest increase in organic matter would be observed in the case of mixed duckweed and the lowest in the presence of the species, regardless of light conditions. Moreover, it was shown that pleustophytes have different heat capacities, and has the highest ability to accumulate heat in water for the tested duckweed combinations. The provided knowledge may help determine the good habitat conditions of duckweed, indicating its role in purifying water reservoirs as an effect of producing organic matter and shaping oxygen conditions with the participation of various species.
Topics: Araceae; Oxygen; Ecosystem; Temperature; Water; Atmospheric Pressure; Light
PubMed: 38903884
DOI: 10.7717/peerj.17322