Ultrastructural insights into cellular organization, energy storage and ribosomal dynamics of an ammonia-oxidizing archaeon from oligotrophic oceans.

Introduction: Nitrososphaeria, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their importance in Earth's ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant unanswered question of how the machinery of these organisms underpins metabolic functions. Methods: In this study, we combined spherical-chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning transmission electron microscopy (STEM), and energy dispersive X-ray spectroscopy (EDS) to unveil the cellular organization and elemental composition of Nitrosopumilus maritimus SCM1, a representative member of marine Nitrososphaeria. Results and Discussion: Our tomograms show the native ultrastructural morphology of SCM1 and one to several dense storage granules in the cytoplasm. STEM-EDS analysis identifies two types of storage granules: one type is possibly composed of polyphosphate and the other polyhydroxyalkanoate. With precise measurements using cryo-ET, we observed low quantity and density of ribosomes in SCM1 cells, which are in alignment with the documented slow growth of AOA in laboratory cultures. Collectively, these findings provide visual evidence supporting the resilience of AOA in the vast oligotrophic marine environment.

Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian Snowball Earth.

Land-ocean interactions greatly impact the evolution of coastal life on earth. However, the ancient geological forces and genetic mechanisms that shaped evolutionary adaptations and allowed microorganisms to inhabit coastal brackish waters remain largely unexplored. In this study, we infer the evolutionary trajectory of the ubiquitous heterotrophic archaea Poseidoniales (Marine Group II archaea) presently occurring across global aquatic habitats. Our results show that their brackish subgroups had a single origination, dated to over 600 million years ago, through the inversion of the magnesium transport gene corA that conferred osmotic-stress tolerance. The subsequent loss and gain of corA were followed by genome-wide adjustment, characterized by a general two-step mode of selection in microbial speciation. The coastal family of Poseidoniales showed a rapid increase in the evolutionary rate during and in the aftermath of the Cryogenian Snowball Earth (∼700 million years ago), possibly in response to the enhanced phosphorus supply and the rise of algae. Our study highlights the close interplay between genetic changes and ecosystem evolution that boosted microbial diversification in the Neoproterozoic continental margins, where the Cambrian explosion of animals soon followed.

Lipidomic chemotaxonomy aligned with phylogeny of Halobacteria.

Archaea play an important role in global biogeochemical cycles and are considered ancestral to eukaryotes. The unique lipid composition of archaea, characterized by isoprenoid alkyl chains and ether linkage to glycerol-1-phosphate, offers valuable insights into archaeal phylogeny and evolution. However, comprehensive studies focusing on archaeal lipidomes, especially at the intact polar lipid level, are currently limited. Here, we built an in-house library of archaeal lipids by using high-performance liquid chromatography coupled with mass-spectrometry, which was integrated with bioinformatics and molecular network analyses. Seven halobacterial strains, representing three distinct orders, were cultured under identical conditions to investigate their lipidomes. A total of 162 features were identified, corresponding to 107 lipids that could be assigned to different strains. Clustering analyses of both core lipids and total lipids matched the phylogeny of Halobacteria at the order level. Notably, lipids such as triglycosyl diether-phosphatidyl acid and bis-sulfate glycosyl lipids were specific to particular groups and could serve as diagnostic intact lipid biomarkers for Halobacteria. Furthermore, the analysis of network-coordinated features facilitated the linkage of unknown lipid compounds to phylogeny, which promotes a lipidome to phylogeny matchup among three Haloferax strains, thereby expanding the knowledge of the halobacterial lipidome. Our study provides a comprehensive view of the lipidomes of the seven strains of Halobacteria and highlights the potential of lipidomics for studying archaeal phylogeny.

Lipidomic diversity and proxy implications of archaea from cold seep sediments of the South China Sea.

Cold seeps on the continental margins are characterized by intense microbial activities that consume a large portion of methane by anaerobic methanotrophic archaea (ANME) through anaerobic oxidation of methane (AOM). Although ANMEs are known to contain unique ether lipids that may have an important function in marine carbon cycling, their full lipidomic profiles and functional distribution in particular cold-seep settings are still poorly characterized. Here, we combined the 16S rRNA gene sequencing and lipidomic approaches to analyze archaeal communities and their lipids in cold seep sediments with distinct methane supplies from the South China Sea. The archaeal community was dominated by ANME-1 in the moderate seepage area with strong methane emission. Low seepage area presented higher archaeal diversity covering Lokiarchaeia, Bathyarchaeia, and Thermoplasmata. A total of 55 core lipids (CLs) and intact polar lipids (IPLs) of archaea were identified, which included glycerol dialkyl glycerol tetraethers (GDGTs), hydroxy-GDGTs (OH-GDGTs), archaeol (AR), hydroxyarchaeol (OH-AR), and dihydroxyarchaeol (2OH-AR). Diverse polar headgroups constituted the archaeal IPLs. High concentrations of dissolved inorganic carbon (DIC) with depleted δ13CDIC and high methane index (MI) values based on both CLs (MICL) and IPLs (MIIPL) indicate that ANMEs were active in the moderate seepage area. The ANME-2 and ANME-3 clades were characterized by enhanced glycosidic and phosphoric diether lipids production, indicating their potential role in coupling carbon and phosphurus cycling in cold seep ecosystems. ANME-1, though representing a smaller proportion of total archaea than ANME-2 and ANME-3 in the low seepage area, showed a positive correlation with MIIPL, indicating a different mechanism contributing to the IPL-GDGT pool. This also suggests that MIIPL could be a sensitive index to trace AOM activities performed by ANME-1. Overall, our study expands the understanding of the archaeal lipid composition in the cold seep and improves the application of MI using intact polar lipids that potentially link to extent ANME activities.

A moderately thermophilic origin of a novel family of marine group II euryarchaeota from deep ocean.

Marine group II (MGII) is the most abundant planktonic heterotrophic archaea in the ocean. The evolutionary history of MGII archaea is elusive. In this study, 13 new MGII metagenome-assembled genomes were recovered from surface to the hadal zone in Challenger Deep of the Mariana Trench; four of them from the deep ocean represent a novel group. The optimal growth temperature (OGT) of the common ancestor of MGII has been estimated to be at about 60°C and OGTs of MGIIc, MGIIb, and MGIIa at 47°C-50ºC, 37°C-44ºC, and 30°C-37ºC, respectively, suggesting the adaptation of these species to different temperatures during evolution. The estimated OGT range of MGIIc was supported by experimental measurements of cloned ß-galactosidase that showed optimal enzyme activity around 50°C. These results indicate that MGIIc may have originated from a common ancestor that lived in warm or even hot marine environment, such as hydrothermal vents.

Diversity, distribution, and functional potentials of magroviruses from marine and brackish waters.

Marine group II (MGII) archaea (Ca. Poseidoniales) are among the most abundant microbes in global oceanic surface waters and play an important role in driving marine biogeochemical cycles. Magroviruses - the viruses of MGII archaea have been recently found to occur ubiquitously in surface ocean. However, their diversity, distribution, and potential ecological functions in coastal zones especially brackish waters are unknown. Here we obtained 234 non-redundant magroviral genomes from brackish surface waters by using homology searches for viral signature proteins highlighting the uncovered vast diversity of this novel viral group. Phylogenetic analysis based on these brackish magroviruses along with previously reported marine ones identified six taxonomic groups with close evolutionary connection to both haloviruses and the viruses of Marine Group I archaea. Magroviruses were present abundantly both in brackish and open ocean samples with some showing habitat specification and others having broad spectrums of distribution between different habitats. Genome annotation suggests they may be involved in regulating multiple metabolic pathways of MGII archaea. Our results uncover the previously overlooked diversity and ecological potentials of a major archaeal virial group in global ocean and brackish waters and shed light on the cryptic evolutionary history of archaeal viruses.

Rh(III)-Catalyzed Spiroannulation Reaction of N-Aryl Nitrones with 2-Diazo-1,3-indandiones: Synthesis of Spirocyclic Indole-N-oxides and Their 1,3-Dipolar Cycloaddition with Maleimides.

An efficient strategy for the preparation of spirocyclic indole-N-oxide compounds through a Rh(III)-catalyzed [4 + 1] spiroannulation reaction of N-aryl nitrones with 2-diazo-1,3-indandiones as C1 synthons under extremely mild conditions is presented. From this reaction, 40 spirocyclic indole-N-oxides were easily obtained in up to 98% yield. In addition, the title compounds could be successfully used for the construction of structurally intriguing maleimide-containing fused polycyclic scaffolds via a diastereoselective 1,3-dipolar cycloaddition reaction with maleimides.

Size-fractionated microbiome observed during an eight-month long sampling in Jiaozhou Bay and the Yellow Sea.

Jiaozhou Bay is a typical semi-enclosed bay with a temperate climate imposed by strong anthropogenic influence. To investigate microbial biodiversity and ecosystem services in this highly dynamic coastal environment, we conducted a monthly microbial survey spanning eight months at two stations in the bay and the open Yellow Sea starting in April 2015. This report provides a comprehensive inventory of amplicon sequences and environmental microbial genomes from this survey. In total, 2,543 amplicon sequence variants were obtained with monthly relative abundance profiles in three size fractions (>2.7 µm, 2.7-0.7 µm, and 0.7-0.22 µm). Shotgun metagenomes yielded 915 high-quality metagenome-assembled genomes with ≥50% completeness and ≤5% contamination. These environmental genomes comprise 27 bacterial and 5 archaeal phyla. We expect this comprehensive dataset will facilitate a better understanding of coastal microbial ecology.

In situ identification of environmental microorganisms with Raman spectroscopy.

Microorganisms in natural environments are crucial in maintaining the material and energy cycle and the ecological balance of the environment. However, it is challenging to delineate environmental microbes' actual metabolic pathways and intraspecific heterogeneity because most microorganisms cannot be cultivated. Raman spectroscopy is a culture-independent technique that can collect molecular vibration profiles from cells. It can reveal the physiological and biochemical information at the single-cell level rapidly and non-destructively in situ. The first part of this review introduces the principles, advantages, progress, and analytical methods of Raman spectroscopy applied in environmental microbiology. The second part summarizes the applications of Raman spectroscopy combined with stable isotope probing (SIP), fluorescence in situ hybridization (FISH), Raman-activated cell sorting and genomic sequencing, and machine learning in microbiological studies. Finally, this review discusses expectations of Raman spectroscopy and future advances to be made in identifying microorganisms, especially for uncultured microorganisms.

Liquiritigenin alleviates doxorubicin-induced chronic heart failure via promoting ARHGAP18 and suppressing RhoA/ROCK1 pathway.

Chronic heart failure (CHF) is one of the most common chronic diseases with increasing incidence and mortality. Liquiritigenin (LQG) is shown to protect mice from cardiotoxicity. However, its underlying mechanism remains unclear. Our study aimed to reveal the role of ARHGAP18 in LQG-mediated cardioprotective effects in CHF. In the current study, CHF cell model and rat model were established by the application of doxorubicin (DOX). The reactive oxygen species (ROS) level and cell apoptosis were determined by flow cytometry. The cardiac function of rats was evaluated by measuring left ventricular systolic pressure, left ventricular end diastolic pressure, and serum level of lactate dehydrogenase and brain natriuretic peptide. The expression of active RhoA was elevated and that of ARHGAP18 was decreased in DOX-induced CHF cell model. ARHGAP18 could reduce DOX-induced RhoA activation, ROS elevation, and cell apoptosis. Meanwhile, the knockdown of ARHGAP18 could promote the activation of RhoA, the level of ROS, and the rate of cell apoptosis, which could be reversed by the application of RhoA inhibitor. LQG promoted the expression of ARHGAP18 and exerted similar effects of ARHGAP18 in CHF cell model. The application of LQG could also reverse the effects mediated by ARHGAP18 knockdown. Moreover, LQG significantly improved cardiac function and ameliorated DOX-induced cardiotoxicity of CHF rats. In conclusion, LQG could alleviate DOX-induced CHF via promoting ARHGAP18 and suppressing RhoA/ROCK1 pathway. LQG was a potential agent for CHF treatment.

Programmable dynamic interfacial spinning of bioinspired microfibers with volumetric encoding.

While artificially encoded microfibers inspired by biosynthetic fibrous microstructures are drawing considerable research attention, their practical applications are hindered by multiple limitations. Here, a programmable dynamic interfacial spinning (DIS) process is proposed for producing volume-encoded microfibers with superior encoding capacity and reliability. The produced microfibers comprise a sheath of deformed hydrogel encapsulating sequentially aligned droplets, with their morphologies controllable by adjusting the flow rates of the corresponding fluids and the vibration parameters of the spinning nozzle. In particular, microfibers with volumetric encoding of inner droplet sequence are constructed for information storage and encryption. With appropriate functionalization of volume-encoded microfibers, we have also demonstrated magnetic guidance and selective activation to simulate intravascular drug delivery. Our study implies the potential applications of the volume-encoded microfibers in information communication, drug delivery and biomedical engineering.

Preparation of Anisotropic Micro-Hydrogels with Tunable Structural and Topographic Features by Compound Interfacial Shearing.

We propose a compound interfacial shearing (CIS) process for versatile production of monodisperse Janus emulsions with controllable structural and topographic features. The process induces an active periodic force to decouple material and process parameters, enables independent control of compartmental features in Janus emulsions, and facilitates inline and on-demand generation of various geometric features for a large variety of process parameters and material properties. Janus emulsions of poly(ethylene glycol) diacrylate (PEGDA) with a controlled number of compartments are produced by CIS and photopolymerized to form micro-hydrogels with designated interfacial curvatures. PEGDA micro-hydrogels can be further modified to achieve anisotropy of surface or internal features by the content of an oily dispersed phase. MCF-7 human breast cancer cells are encapsulated in micro-hydrogels for cell proliferation with satisfactory viability. By modifying PEGDA micro-hydrogels with RGDS-conjugated polystyrene microspheres, we have demonstrated the controlled spatial adhesion of MCF-7 cells and human umbilical vein endothelial cells (HUVECs) on the substrates of different three-dimensional (3D) curvatures. Our pilot study suggests a simple and potentially scalable approach to produce 3D substrates with controllable structural and topographic features for 3D guided cell organization.

Relation analysis on emission control and economic cost of SCR system for marine diesels.

In order to meet the IMO Tier III emissions regulations and reduce environmental pollution, many ocean-going vessels have installed the marine SCR system to reduce NOx emissions. However, the investment cost and operation cost of the marine SCR system, as well as the factors affecting the SCR cost are still the problems that need to be studied. In this paper, MAN S46 diesel engine matched SCR system was taken as the research object, and a cost calculation model of Marine SCR system based on cost analysis method has been proposed. The relationship between SCR system cost and some factors such as unit capacity, unit running time and inlet NOx concentration have been analyzed. The research we have done suggests that operating time, NOx inlet concentration, and emission limits are the three main important factors in the operating cost of an SCR system. Among the various secondary costs of operating costs, the reducing agent cost, fuel increase cost, and indirect annual cost account for 60%, 24%, and 7%, respectively. Moreover, the results suggest that the unit denitration cost of the matched SCR system is highly affected by the power of the diesel engine and annual running time. This study demonstrated clearly the relationship between emission control and economic cost of SCR system for marine diesels and was expected to provide a theoretical basis for sustainable development in marine environmental protection policies.

Combustion and emission characteristics for a marine low-speed diesel engine with high-pressure SCR system.

In order to avoid the production of sulfates and nitrates in marine diesel engines that burn sulfur-containing fuels, the operating temperature of their high-pressure selective catalytic reduction (HP-SCR) systems should be higher than 320 °C. For marine low-speed diesel engines, only the pre-turbine exhaust gas temperature can meet this requirement under specific conditions, with the main engine modulation method helping to increase the exhaust gas temperature. However, the main engine modulation method brings down the power output and fuel economy of the main engine and causes the matching problem of the turbine and the other devices with the main engine. The original engine model of the marine low-speed diesel engine and the high-pressure SCR system configuration model have been constructed using one-dimensional simulation software. In addition, the performance of the high-pressure SCR system under the conditions of low-sulfur and high-sulfur exhaust gas was thoroughly analyzed. Moreover, the two main engine modulation schemes of the scavenging bypass and the turbine exhaust bypass of the original engine matching with the high-pressure SCR system were studied. The study found that the weighted average value of the NOx under the condition of low-sulfur exhaust gas met with the requirement of the IMO Tier III regulations when the low-speed diesel engine was matched with the high-pressure SCR system. However, the weighted average value of the NOx under the condition of high-sulfur exhaust gas was slightly higher than that required by the IMO Tier III regulation. In addition, the optimal main engine modulation scheme for this low-speed diesel engine was clarified by comparing the effects of the scavenging bypass and the turbine exhaust bypass modulation on the exhaust performance, and the working performance of the original engine. With an opening of 0.4 of the CBV valve under 25% engine load, the weighted average NOx of the original exhaust gas was 3.38 g/(kW·h), the power had decreased by 0.7%, and the fuel consumption had increased by 1.0%. Furthermore, when the EGB valve opening was 0.3, the weighted average value of NOx was 3.31 g/(kW·h), the power had reduced by 2.4% and the fuel consumption had increased by 2.5%. Both modulation scheme methods made the exhaust performance of the original engine meet the requirements of the IMO Tier III emission regulations, but the scavenging bypass modulation scheme had less impact on the original engine's performance.

EGR modeling and fuzzy evaluation of Low-Speed Two-Stroke marine diesel engines.

Exhaust gas recirculation (EGR) can be widely used to reduce the oxynitride (NOx) pollution in Low-Speed Two-Stroke Marine Diesel Engines. In this paper, two EGR systems (HP EGR1 and LP EGR2) were investigated in terms of the influence of different rates on the brake specific fuel consumption (BSFC) and the NOx emissions. As for this simulation, the exhaust gas cleaning water treatment was not concluded. Besides, Miller Cycle was used to determine the influence of its valve timing on BSFC and NOx emissions. The combination of Miller Cycle and HP EGR system decreased the NOx emissions, which could meet the IMO3 Tier III standard, 3.4 g/kWh. Moreover, the influence of the EGR cooling temperature was discussed. Finally, a fuzzy comprehensive evaluation model was developed to evaluate the two EGR systems. The results showed that when the HP EGR system and the LP EGR system were all operating at a maximum EGR rate, LP EGR system showed more advantages.

Simple, low-cost fabrication of semi-circular channel using the surface tension of solder paste and its application to microfluidic valves.

This work presents a simple, low-cost method to fabricate semi-circular channels using solder paste, which can amalgamate the cooper surface to form a half-cylinder mold using the surface tension of Sn-Pd alloy (the main component in solder paste). This technique enables semi-circular channels to be manufactured with different dimensions. These semi-circular channels will then be integrated with a polymethylmethacrylate frame and machine screws to create miniaturized, portable microfluidic valves for sequential liquid delivery and particle synthesis. This approach avoids complicated fabrication processes and expensive facilities and thus has the potential to be a useful tool for lab-on-a-chip applications.

A rapid, maskless 3D prototyping for fabrication of capillary circuits: Toward urinary protein detection.

Proteinuria is an established risk marker for progressive renal function loss and patients would significantly benefit from a point-of-care testing. Although extensive work has been done to develop the microfluidic devices for the detection of urinary protein, they need the complicated operation and bulky peripherals. Here, we present a rapid, maskless 3D prototyping for fabrication of capillary fluidic circuits using laser engraving. The capillary circuits can be fabricated in a short amount of time (<10 min) without the requirements of clean-room facilities and photomasks. The advanced capillary components (e.g., trigger valves, retention valves and retention bursting valves) were fabricated, enabling the sequential liquid delivery and sample-reagent mixing. With the integration of smartphone-based detection platform, the microfluidic device can quantify the urinary protein via a colorimetric analysis. By eliminating the bulky and expensive equipment, this smartphone-based detection platform is portable for on-site quantitative detection.

Study on Crystallographic Orientation Effect on Surface Generation of Aluminum in Nano-cutting.

The material characteristics such as size effect are one of the most important factors that could not be neglected in cutting the material at nanoscale. The effects of anisotropic nature of single crystal materials in nano-cutting are investigated employing the molecular dynamics simulation. Results show that the size effect of the plastic deformation is based on different plastic carriers, such as the twin, stacking faults, and dislocations. The minimum uncut chip thickness is dependent on cutting direction, where even a negative value is obtained when the cutting direction is {110}<001>. It also determines the material deformation and removal mechanism (e.g., shearing, extruding, and rubbing mechanism) with a decrease in uncut chip thickness. When material is deformed by shearing, the primary shearing zone expands from the stagnation point or the tip of stagnation zone. When a material is deformed by extruding and rubbing, the primary deformation zone almost parallels to the cutting direction and expands from the bottom of the cutting edge merging with the tertiary deformation zone. The generated surface quality relates to the crystallographic orientation and the minimum uncut chip thickness. The cutting directions of {110}<001>, {110}<1-10>, and {111}<1-10>, whose minimum uncut chip thickness is relatively small, have better surface qualities compared to the other cutting direction.

Distribution of ether lipids and composition of the archaeal community in terrestrial geothermal springs: impact of environmental variables.

Archaea can respond to changes in the environment by altering the composition of their membrane lipids, for example, by modification of the abundance and composition of glycerol dialkyl glycerol tetraethers (GDGTs). Here, we investigated the abundance and proportions of polar GDGTs (P-GDGTs) and core GDGTs (C-GDGTs) sampled in different seasons from Tengchong hot springs (Yunnan, China), which encompassed a pH range of 2.5-10.1 and a temperature range of 43.7-93.6°C. The phylogenetic composition of the archaeal community (reanalysed from published work) divided the Archaea in spring sediment samples into three major groups that corresponded with spring pH: acidic, circumneutral and alkaline. Cluster analysis showed correlation between spring pH and the composition of P- and C-GDGTs and archaeal 16S rRNA genes, indicating an intimate link between resident Archaea and the distribution of P- and C-GDGTs in Tengchong hot springs. The distribution of GDGTs in Tengchong springs was also significantly affected by temperature; however, the relationship was weaker than with pH. Analysis of published datasets including samples from Tibet, Yellowstone and the US Great Basin hot springs revealed a similar relationship between pH and GDGT content. Specifically, low pH springs had higher concentrations of GDGTs with high numbers of cyclopentyl rings than neutral and alkaline springs, which is consistent with the predominance of high cyclopentyl ring-characterized Sulfolobales and Thermoplasmatales present in some of the low pH springs. Our study suggests that the resident Archaea in these hot springs are acclimated if not adapted to low pH by their genetic capacity to effect the packing density of their membranes by increasing cyclopentyl rings in GDGTs at the rank of community.