Search Results (46)

Rice paddy fields are sustainable agricultural systems as soil microorganisms help maintain nitrogen fertility through generating ammonium. In these soils, dissimilatory nitrate reduction to ammonium (DNRA), nitrogen fixation, and denitrification are closely linked. DNRA and denitrification share the same initial steps and nitrogen gas, the end product of denitrification, can serve as a substrate for nitrogen fixation. However, the microorganisms responsible for these three reductive nitrogen transformations, particularly those focused on ammonium generation, have not been comprehensively characterized. In this study, we used stable isotope probing with ¹⁵NO₃⁻, ¹⁵N₂O, and ¹⁵N₂, combined with 16S rRNA high-throughput sequencing and metatranscriptomics, to identify ammonium-generating microbial consortia in paddy soils. Our results revealed that several bacterial families actively contribute to ammonium generation under different nitrogen substrate conditions. Specifically, Geobacteraceae (N₂O and +N₂), Bacillaceae (+NO₃⁻ and +N₂), Rhodocyclaceae (+N₂O and +N₂), Anaeromyxobacteraceae (+NO₃⁻ and +N₂O), and Clostridiaceae (+NO₃⁻ and +N₂) were involved. Many of these bacteria participate in key ecological processes typical of paddy environments, including iron or sulfate reduction and rice straw decomposition. This study revealed the ammonium-generating microbial consortia in paddy soil that contain several key bacterial drivers of multiple reductive nitrogen transformations and suggested their diverse functions in paddy soil metabolism. Full article

The growing global demand for phytochemicals as bioactive sources is prompting scientists to develop methods that link their sensory properties to their mechanisms of action in cancer treatment. Recent techniques for tracking the actions of small plant metabolites (SPMs) from single-cell plant sources to their molecular anticancer biomarkers could provide valuable insights in this field. Among the critical methods discussed in this review are the real-time tracking of cell components through stable isotope probing (Sis) and microspectroscopy, which has attracted the attention of biotechnologists. Additionally, the precise pathways required for studying new insights into functional materials are discussed, based on high-resolution and accurate technologies, which could aid their functional categorization. Notably, the molecules under study have recently garnered attention for their anticancer applications due to advancements in effective evaluation techniques that surpass traditional methods. In December 2020, the Food and Drug Administration (FDA) authorized 89 SPMs as safe anticancer natural molecules. In conclusion, by combining spatiotemporal techniques and SPMs’ mechanisms, they could facilitate the development of more exceptional, bio-efficient materials. Full article

The fluid action mechanism and diagenetic evolution of tuff reservoirs in the Cretaceous Huoshiling Formation of the Dehui fault depression are discussed herein. The fluid properties of the diagenetic flow are defined, and the pore formation mechanism of the reservoir space is explained by means of thin sections, X-ray diffraction, electron probes, scanning electron microscopy (SEM), cathodoluminescence, and stable carbon and oxygen isotopic composition and fluid inclusion tests. The results reveal that the tuff reservoir of the Huoshiling Formation is moderately acidic, and the physical properties of the reservoir are characterized by middle to high porosity and ultralow permeability. The pore types are complex, comprising both primary porosity and secondary porosity, with dissolution pores and devitrification pores being the most dominant. Mechanical compaction and cementation are identified as key factors reducing reservoir porosity and permeability, while dissolution and devitrification processes improve pore structure and enhance pore connectivity. Diagenetic fluids encompass alkaline fluids, acidic fluids, deep-seated CO₊-rich hydrothermal fluids, and hydrocarbon-associated fluids. These fluids exhibit dual roles in reservoir evolution: acidic fluids enhance the dissolution of feldspar, tuffaceous materials, and carbonate minerals to generate secondary pores and improve reservoir quality, whereas alkaline fluids induce carbonate cementation, and clay mineral growth (e.g., illite) coupled with late-stage mineral precipitation obstructs pore throats, reducing permeability. The interplay among multiple fluid types and their varying dominance at different burial depths collectively governs reservoir evolution. This study underscores the critical role of fluid–rock interactions in controlling porosity–permeability evolution within tuff reservoirs. Full article

The symbiotic relationship between corals and their associated microorganisms is crucial for the health of coral reef eco-environmental systems. Recently, there has been a growing interest in unraveling how the manipulation of symbiont nutrient cycling affects the stress tolerance in the holobiont of coral reefs. However, most studies have primarily focused on coral–Symbiodiniaceae–bacterial interactions as a whole, neglecting the interactions between Symbiodiniaceae and bacteria, which remain largely unexplored. In this study, we proposed a hypothesis that there exists an inner symbiotic loop of Symbiodiniaceae and bacteria within the coral symbiotic loop. We conducted experiments to demonstrate how metabolic exchanges between Symbiodiniaceae and bacteria facilitate the nutritional supply necessary for cellular growth. It was seen that the beneficial bacterium, Ruegeria sp., supplied a nitrogen source to the Symbiodiniaceae strain Durusdinium sp., allowing this dinoflagellate to thrive in a nitrogen-free medium. The Ruegeria sp.–Durusdinium sp. interaction was confirmed through ¹⁵N-stable isotope probing–single cell Raman spectroscopy, in which ¹⁵N infiltrated into the bacterial cells for intracellular metabolism, and eventually the labeled nitrogen source was traced within the macromolecules of Symbiodiniaceae cells. The investigation into Symbiodiniaceae loop interactions validates our hypothesis and contributes to a comprehensive understanding of the intricate coral holobiont. These findings have the potential to enhance the health of coral reefs in the face of global climate change. Full article

Crop residue decomposition is an important part of the carbon cycle in agricultural ecosystems, and microorganisms are widely recognized as key drivers during this process. However, we still know little about how nitrogen (N) input and rhizosphere effects from the next planting season impact key straw-decomposing microbial communities. Here, we combined amplicon sequencing and DNA-Stable Isotope Probing (DNA-SIP) to explore these effects through a time-series wheat pot experiment with four treatments: ¹³C-labeled maize straw addition with or without N application (S1N1 and S1N0), and no straw addition with or without N application (S0N1 and S0N0). The results showed that straw addition significantly reduced soil microbial alpha diversity in the early stages. Straw addition changed microbial beta diversity and increased absolute abundance in all stages. Growing plants in straw-amended soil further reduced bacterial alpha diversity, weakened straw-induced changes in beta diversity, and reduced bacterial and fungal absolute abundance in later stages. In contrast, N application could only increase the absolute abundance of soil bacteria and fungi while having little effect on alpha and beta diversity. The SIP-based taxonomic analysis of key straw-decomposing bacteria further indicated that the dominant phyla were Actinobacteria and Proteobacteria, with overrepresented genera belonging to Vicinamibacteraceae and Streptomyces. Key straw-decomposing fungi were dominated by Ascomycota, with overrepresented genera belonging to Penicillium and Aspergillus. N application significantly increased the absolute abundance of key straw-decomposing microorganisms; however, this increase was reduced by the rhizosphere effect. Overall, our study identified key straw-decomposing microorganisms in straw-amended soil and demonstrated that they exhibited opposite responses to N application and the rhizosphere effect. Full article

Methane-oxidizing bacteria (MOB) have long been recognized as an important bioindicator for oil and gas exploration. However, due to their physiological and ecological diversity, the distribution of MOB in different habitats varies widely, making it challenging to authentically reflect the abundance of active MOB in the soil above oil and gas reservoirs using conventional methods. Here, we selected the Puguang gas field of the Sichuan Basin in Southwest China as a model system to study the ecological characteristics of methanotrophs using culture-independent molecular techniques. Initially, by comparing the abundance of the pmoA genes determined by quantitative PCR (qPCR), no significant difference was found between gas well and non-gas well soils, indicating that the abundance of total MOB may not necessarily reflect the distribution of the underlying gas reservoirs. ¹³C-DNA stable isotope probing (DNA-SIP) in combination with high-throughput sequencing (HTS) furthermore revealed that type II methanotrophic Methylocystis was the absolutely predominant active MOB in the non-gas-field soils, whereas the niche vacated by Methylocystis was gradually filled with type I RPC-2 (rice paddy cluster-2) and Methylosarcina in the surface soils of gas reservoirs after geoscale acclimation to trace- and continuous-methane supply. The sum of the relative abundance of RPC-2 and Methylosarcina was then used as specific biotic index (BI) in the Puguang gas field. A microbial anomaly distribution map based on the BI values showed that the anomalous zones were highly consistent with geological and geophysical data, and known drilling results. Therefore, the active but not total methanotrophs successfully reflected the microseepage intensity of the underlying active hydrocarbon system, and can be used as an essential quantitative index to determine the existence and distribution of reservoirs. Our results suggest that molecular microbial techniques are powerful tools for oil and gas prospecting. Full article

Aniline, a vital component in various chemical industries, is known to be a hazardous persistent organic pollutant that can cause environmental pollution through its manufacturing, processing, and transportation. In this study, the microcosms were established using sediment with a history of aniline pollution as an inoculum to analyze the aniline biodegradation under aerobic conditions through stable isotope probing (SIP) and isopycnic density gradient centrifugation technology. During the degradation assay, aniline that was ¹³C-labeled in all six carbons was utilized to determine the phylogenetic identity of the aniline-degrading bacterial taxa that incorporate ¹³C into their DNA. The results revealed that aniline was completely degraded in the microcosm after 45 and 69 h respectively. The bacteria affiliated with Acinetobacter (up to 34.6 ± 6.0%), Zoogloea (up to 15.8 ± 2.2%), Comamonas (up to 2.6 ± 0.1%), and Hydrogenophaga (up to 5.1 ± 0.6%) genera, which are known to degrade aniline, were enriched in the heavy fractions (the DNA buoyant density was 1.74 mg L⁻¹) of the ¹³C-aniline treatments. Moreover, some rarely reported aniline-degrading bacteria, such as Prosthecobacter (up to 16.0 ± 1.6%) and Curvibacter (up to 3.0 ± 1.6%), were found in the DNA-SIP experiment. Gene families affiliated with atd, tdn, and dan were speculated to be key genes for aniline degradation based on the abundance in functional genes and diversity in different treatments as estimated using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States version 2 (PICRUSt2) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). This study revealed the functional bacteria and possible degradation genes for aniline degradation in simulated polluted environments through SIP. These findings suggest that important degrading bacteria for the transformation of aniline and potential degradation pathways may be useful in the effective application of bioremediation technologies to remediate aniline-contaminated sites. Full article

Over the last half-century, microbial communities of the Kamchatka hot springs have been largely studied using molecular, radioisotopic, and cultural approaches. Generally, these results were obtained for mixed samples of water with sediments, for only hydrothermal water, or for only sediment samples. Simultaneous comparative analysis of the microbial communities of water and sediments was performed for only one Kamchatka hot spring with circumneutral pH. Here, the microbial communities of both sediments and water (separately) of hot spring #4229 (the Uzon Caldera, Kamchatka) with a temperature of 50–56 °C and pH of 3.2 were analyzed by 16S rRNA gene V4 fragment amplicon sequencing. It was revealed that the microbial community of sediments was represented by uncultured phylogenetically deep-branching lineages of archaea, such as ARK-15 within Thermoplasmatota and ‘Ca. Marsarchaeales’ from the Thermoproteota phyla. Metagenome analysis showed that these archaea most probably carried out the degradation of organic matter. The microbial community of the hot water is represented by thermoacidophilic, (micro)aerobic, chemolithoautotrophic, hydrogen- and sulfur-oxidizing bacteria of the genera Hydrogenobaculum (phylum Aquificota) and Acidithiobacillus (phylum Pseudomonadota). Radioisotopic tracing and DNA-stable-isotope probing techniques proved their role as primary producers in the hot spring. The experiment revealed significant differences in the composition and functions of the microbial communities of sediments and water through the example of a typical acidic hot spring in Kamchatka. Full article

Although radiolabeled alpha-melanocyte stimulating hormone-analogue NAPamide derivatives are valuable melanoma-specific diagnostic probes, their rapid elimination kinetics and high renal uptake may preclude them from being used in clinical settings. We aimed at improving the pharmacokinetics of radiolabeled DOTA-NAPamide compounds by incorporating a 4-(p-iodo-phenyl)-butanoic acid (IPB) into the molecules. Followed by ⁶⁸Ga-, ^205/206Bi-, and ¹⁷⁷Lu-labelling, the radiopharmaceuticals ([⁶⁸Ga]Ga-DOTA-IPB-NAPamide, [^205/206Bi]Bi-DOTA-IPB-NAPamide, [¹⁷⁷Lu]Lu-DOTA-IPB-NAPamide) were characterized in vitro. To test the imaging behavior of the IPB-containing probes, B16F10 tumor-bearing C57BL/6 mice were subjected to in vivo microPET/microSPECT/CT imaging and ex vivo biodistribution studies. All tracers were stable in vitro, with radiochemical purity exceeding 98%. The use of albumin-binding moiety lengthened the in vivo biological half-life of the IPB-carrying radiopharmaceuticals, resulting in elevated tumor accumulation. Both [⁶⁸Ga]Ga-DOTA-IPB-NAPamide (5.06 ± 1.08 %ID/g) and [^205/206Bi]Bi-DOTA-IPB-NAPamide (4.50 ± 0.98 %ID/g) exhibited higher B16F10 tumor concentrations than their matches without the albumin-binding residue ([⁶⁸Ga]Ga-DOTA-NAPamide and [^205/206Bi]Bi-DOTA-NAPamide: 1.18 ± 0.27 %ID/g and 3.14 ± 0.32; respectively), however; the large amounts of off-target radioactivity do not confirm the benefits of half-life extension for short-lived isotopes. Enhanced [¹⁷⁷Lu]Lu-DOTA-IPB-NAPamide tumor uptake even 24 h post-injection proved the advantage of IPB-based prolonged circulation time regarding long-lived radionuclides, although the significant background noise must be addressed in this case as well. Full article

Biogas production from waste materials has emerged as a promising avenue for sustainable energy generation, offering a dual benefit of waste management and renewable energy production. The selection and preparation of waste feedstocks, including agricultural residues, food waste, animal manure, and municipal solid wastes, are important for this process, while the microbial communities are majorly responsible for bioconversions. This review explores the role of complex microbial communities and their functions responsible for the anaerobic digestion of wastes. It covers the crucial physiological processes including hydrolysis, acidogenesis, acetogenesis, and methanogenesis, elucidating the microbial activities and metabolic pathways involved in the prospects of improving the efficiency of biogas production. This article further discusses the influence of recent progress in molecular techniques, including genomics, metagenomics, meta-transcriptomics, and stable isotope probing. These advancements have greatly improved our understanding of microbial communities and their capabilities of biogas production from waste materials. The integration of these techniques with process monitoring and control strategies has been elaborated to offer possibilities for optimizing biogas production and ensuring process stability. Microbial additives, co-digestion of diverse feedstocks, and process optimization through microbial community engineering have been discussed as effective approaches to enhance the efficiency of biogas production. This review also outlines the emerging trends and future prospects in microbial-based biogas production, including the utilization of synthetic biology tools for engineering novel microbial strains and consortia, harnessing microbiomes from extreme environments, and integrating biogas production with other biotechnological processes. While there are several reviews regarding the technical aspects of biogas production, this article stands out by offering up-to-date insights and recommendations for leveraging the potential of microbial communities, and their physiological roles for efficient biogas production. These insights emphasize the pivotal role of microbes in enhancing biogas production, ultimately contributing to the advancement of a sustainable and carbon-neutral future. Full article

In rice paddy soil, biological nitrogen fixation is important for sustaining soil nitrogen fertility and rice growth. Anaeromyxobacter and Geobacteriaceae, iron-reducing bacteria belonging to Deltaproteobacteria, are newly discovered nitrogen-fixing bacteria dominant in paddy soils. They utilize acetate, a straw-derived major carbon compound in paddy soil, as a carbon and energy source, and ferric iron compounds as electron acceptors for anaerobic respiration. In our previous paddy field experiments, a significant increase in soil nitrogen-fixing activity was observed after the application of iron powder to straw-returned paddy field soil. In addition, combining iron application with 60–80% of the conventional nitrogen fertilizer rate could maintain rice yields similar to those with the conventional nitrogen fertilization rate. It was thus suggested that iron application to paddy soil increased the amount of nitrogen fixed in the soil by enhancing nitrogen fixation by diazotrophic iron-reducing bacteria. The present study was conducted to directly verify this suggestion by ¹⁵N-IRMS analysis combined with ¹⁵N-DNA-stable isotope probing of iron-applied and no-iron-applied plot soils in an experimental paddy field. In no-iron-applied native paddy soil, atmospheric ¹⁵N₂ was incorporated into the soil by biological nitrogen fixation, in which diazotrophic iron-reducing bacteria were the most active drivers of nitrogen fixation. In iron-applied paddy soil, the amount of ¹⁵N incorporated into the soil was significantly higher due to enhanced biological nitrogen fixation, especially via diazotrophic iron-reducing bacteria, the most active drivers of nitrogen fixation in the soil. Thus, our previous suggestion was verified. This study provided a novel picture of active nitrogen-fixing microorganisms dominated by diazotrophic iron-reducing bacteria in paddy soil, and directly proved the effectiveness of iron application to enhance their nitrogen fixation and increase the incorporation of atmospheric nitrogen into soil. The enhancement of biological nitrogen fixation in paddy fields by iron application may lead to novel and unique paddy soil management strategies to increase soil nitrogen fertility and ensure rice yields with reduced nitrogen fertilizer input and lower environmental nitrogen burdens. Full article

The Italian Northern Apennines contain several Fe-Cu-Zn-bearing, Cyprus-type volcanogenic massive sulfide (VMS) deposits, which significantly contribute to the Cu resources of Italy. The massive sulfide lenses and related stockwork mineralizations are hosted by several levels (from basalt to serpentinite) of the unmetamorphosed ophiolitic series; therefore, this region offers perfect locations to study the ore-forming hydrothermal system in detail. A combination of fluid inclusion microthermometry, Raman spectroscopy, electron probe analyses (chlorite thermometry) and stable and noble gas isotope geochemistry was used to determine the fluid source of the VMS system at Bargone, Boccassuolo, Campegli, Casali–Monte Loreto, Corchia, Reppia and Vigonzano. This question of the fluid source is the focus of modern VMS research worldwide, as it has a direct influence on the metal content of the deposit. The obtained temperature and compositional data are both in the typical range of VMS systems and basically suggest evolved seawater origin for the mineralizing fluid. Modification of seawater was most commonly due to fluid–rock interaction processes, which happened during long-lasting circulation in the crust. The role of a small amount of magmatic fluid input was traced only at the lower block of Boccassuolo, which may be responsible for its higher ore grade. This fluid origin model is evidenced by O, H and C stable isotopic as well as He, Ne and Ar noble gas isotopic values. Full article

The gut mucosal environment is key in host health; protecting against pathogens and providing a niche for beneficial bacteria, thereby facilitating a mutualistic balance between host and microbiome. Lack of dietary fiber results in erosion of the mucosal layer, suggested to be a result of increased mucus-degrading gut bacteria. This study aimed to use quantitative analyses to investigate the diet-induced imbalance of mucosal homeostasis. Seven days of fiber-deficiency affected intestinal anatomy and physiology, seen by reduced intestinal length and loss of the colonic crypt-structure. Moreover, the mucus layer was diminished, muc2 expression decreased, and impaired mucus secretion was detected by stable isotope probing. Quantitative microbiome profiling of the gut microbiota showed a diet-induced reduction in bacterial load and decreased diversity across the intestinal tract, including taxa with fiber-degrading and butyrate-producing capabilities. Most importantly, there was little change in the absolute abundance of known mucus-degrading bacteria, although, due to the general loss of taxa, relative abundance would erroneously indicate an increase in mucus degraders. These findings underscore the importance of using quantitative methods in microbiome research, suggesting erosion of the mucus layer during fiber deprivation is due to diminished mucus production rather than overgrowth of mucus degraders. Full article

In this work, we report on the hyperfine parameters of the foreign ¹⁸¹Ta probe in the rutile structure of the single crystal TiO₂ using the e−γ and γ−γ time differential perturbed angular correlation (TDPAC) technique. We implanted ¹⁸¹Hf ions into a sample of single crystal rutile TiO₂ in the Bonn Isotope Separator. The implanted sample was then thermally annealed at a temperature of 873 K for 315 min in a vacuum. The ¹⁸¹Hf radioisotopes decayed by β⁻ emission, followed by a cascade to the ground of γ rays or conversion electrons into a stable state ¹⁸¹Ta. The ¹⁸¹Ta probe substitutes the Ti lattice site with a unique nuclear quadrupole interaction, allowing for the precise measurement of the largest electric field gradient (V_zz) and asymmetry parameter (η). The hyperfine parameters obtained from the e−γ TDPAC spectroscopy agree with those of the γ−γ TDPAC spectroscopy at room temperature, apart from a calibration factor, both from our experiments and the literature. This suggests that the electronic recombination following the internal conversion of the L shell electron takes less time (ps) than the intermediate lifetime of the metastable ¹⁸¹Ta state (ns). Full article

The transition from the quantum to the classical world is not yet understood. Here, we take a new approach. Central to this is the understanding that measurement and actualization cannot occur except on some specific basis. However, we have no established theory for the emergence of a specific basis. Our framework entails the following: (i) Sets of N entangled quantum variables can mutually actualize one another. (ii) Such actualization must occur in only one of the 2^N possible bases. (iii) Mutual actualization progressively breaks symmetry among the 2^N bases. (iv) An emerging “amplitude” for any basis can be amplified by further measurements in that basis, and it can decay between measurements. (v) The emergence of any basis is driven by mutual measurements among the N variables and decoherence with the environment. Quantum Zeno interactions among the N variables mediates the mutual measurements. (vi) As the number of variables, N, increases, the number of Quantum Zeno mediated measurements among the N variables increases. We note that decoherence alone does not yield a specific basis. (vii) Quantum ordered, quantum critical, and quantum chaotic peptides that decohere at nanosecond versus femtosecond time scales can be used as test objects. (viii) By varying the number of amino acids, N, and the use of quantum ordered, critical, or chaotic peptides, the ratio of decoherence to Quantum Zeno effects can be tuned. This enables new means to probe the emergence of one among a set of initially entangled bases via weak measurements after preparing the system in a mixed basis condition. (ix) Use of the three stable isotopes of carbon, oxygen, and nitrogen and the five stable isotopes of sulfur allows any ten atoms in the test protein to be discriminably labeled and the basis of emergence for those labeled atoms can be detected by weak measurements. We present an initial mathematical framework for this theory, and we propose experiments. Full article