A natural food-grade supramolecular self-assembly system for creation of hierarchically structured hydrogels.

We develop a novel hierarchically structured hydrogel by the supramolecular self-assembly of all-natural food-grade building blocks, glycyrrhizic acid (GA) and carrageenan (CG). The co-assembled GA-CG hydrogel system displays an unusual structural transition with the appearance from opacity to translucence and then to opacity, as a function of the concentration of metal ions. The unique GA-CG supramolecular hydrogel system can serve as solid, edible, and responsive active cargo delivery platforms for food and biomedical applications.

Interfacial assembly and rheology of multi-responsive glycyrrhizic acid at liquid interfaces.

Glycyrrhizic acid (GA), a naturally derived food-grade saponin molecule, is a promising alternative to synthetic surfactants for stabilizing multiphase systems including emulsions and foams, due to its biological activity and surface-active properties. Understanding the interfacial behavior of GA, particularly in relation to its complex self-assembly behaviors in water induced by multiple environmental stimuli, is crucial to its application in multiphase systems. In this study, we comprehensively investigate the interfacial structure and rheological properties of GA systems, as a function of pH and temperature, through Langmuir-Blodgett films combined with atomic force microscopy, interfacial particle tracking, adsorption kinetics, stress-relaxation behavior and interfacial dilatational rheology. The variation of solution pH provokes pronounced changes in the interfacial properties of GA. At pH 2 and 4, GA fibril aggregates/fibrils adsorb rapidly, followed by rearrangement into large lamellar and rod-like structures, forming a loose and heterogeneous fibrous network at the interface, which exhibit a stretchable gel-like behavior. In contrast, GA at pH 6 and 8, featuring micelles or monomers in solutions, adsorb slowly to the interface and re-assemble partially into small micelle-like or irregular structures, which lead to a dense and homogeneous interfacial layer with stiffer glassy-like responses. With successively elevated temperature, the GA structures (pH 4) at the interface break into smaller fragments and further adsorption is promoted. Upon cooling, the interfacial tension of GA further decreases and a highly elastic interfacial layer may be formed. The diverse GA assemblies in bulk solution impart them with rich and intriguing interfacial behaviors, which may provide valuable mechanistic insights for the development of novel edible soft matter stabilized by GA.

An image-based Abplex method for high-throughput GPCRs antibody discovery.

As the field of antibody therapeutics advances rapidly, membrane proteins, particularly G protein-coupled receptors (GPCRs), have emerged as highly sought-after drug targets. However, the challenges associated with extracting membrane proteins have created a demand for effective antibody screening systems targeting these proteins. In this study, we propose developing an innovative antibody screening strategy (Abplex) based on high-content imaging. This approach leverages intact cells that express target membrane proteins, facilitating the presentation of proteins in their native conformation. Furthermore, it acquires both specific and non-specific binding signals in a single well, thereby bolstering the robustness of the outcomes. The technique involves just one step and can be completed within 50 min, enabling the analysis of a single sample in just one second. The amalgamation of dependable experimental findings, a simplified workflow, reduced hands-on time, and a swift analytical pace positions our method for superior throughput and precision when juxtaposed with traditional techniques such as CbELISA and FACS. Moreover, we introduce the concept of cell barcoding, wherein cells are labeled with different fluorescence spatial patterns. This feature allows for multiplexed detection to meet the needs of various experiments. The characteristics of Abplex promise to expedite GPCR-targeting antibody discovery, advance therapeutics and enable new disease treatments.

All-Natural, Robust, and pH-Responsive Glycyrrhizic Acid-Based Double Network Hydrogels for Controlled Nutrient Release.

Supramolecular hydrogels self-assembled from naturally occurring small molecules (e.g., glycyrrhizic acid, GA) are promising materials for controlled bioactive delivery due to their facile fabrication processes, excellent biocompatibility, and versatile stimuli-responsive behaviors. However, most of these natural hydrogels suffer from poor mechanical strength and processability for practical applications. In this work, through adopting a multicomponent gel approach, we developed a novel mechanically robust GA-based hydrogel with an interpenetrating double network (DN) that is composed of a Ca2+-enhanced hydrogen-bond supramolecular GA nanofibril (GN) network and a Ca2+cross-linked natural polysaccharide sodium alginate (ALG) network. Compared to the single GN network (SN) hydrogel, the GN-ALG hybrid hydrogels (GN-ALG-DN) with the hierarchical double-network structure possess excellent mechanical properties and shaping adaptation, encouraging small and large amplitude oscillatory shear (SAOS and LAOS) rheological performances, better thermal stability, higher resistance to large compression deformations, and lower swelling behaviors. Furthermore, the GN-ALG-DN hydrogels exhibit a pH-responsive and sustained release behavior of nutrients (i.e., vitamin B12, VB12), showing a faster VB12 release rate with a higher swelling ratio in an alkaline condition (pH 7.5) than in an acidic condition (pH 2.5). This is ascribed to the fact that the higher dissociation degree of carboxylic groups in GA and ALG molecules in an alkaline environment induces the erosion and looseness of the self-assembled GN network and the ionic-cross-linked ALG network, which can lead to the decomposition of the hybrid hydrogels and thereby increases the release of nutrients. Cytotoxicity tests further demonstrate the excellent biocompatibility of the GN-ALG-DN hydrogels. This study highlights the design of robust shaped and structured supramolecular hydrogels from natural herb small molecules, which can serve as solid, edible, and stimuli-responsive active cargo delivery platforms for food, biomedical, and sustainable applications.

Physiological and Genetic Regulation for High Lipid Accumulation by Chlorella sorokiniana Strains from Different Environments of an Arctic Glacier, Desert, and Temperate Lake under Nitrogen Deprivation Conditions.

Microalgae can adapt to extreme environments with specialized metabolic mechanisms. Here, we report comparative physiological and genetic regulation analyses of Chlorella sorokiniana from different environmental regions of an arctic glacier, desert, and temperate native lake in response to N deprivation, for screening the optimal strain with high lipid accumulation. Strains from the three regions showed different growth and biochemical compositions under N deprivation. The arctic glacier and desert strains produced higher soluble sugar content than strains from the native lake. The arctic glacier strains produced the highest levels of lipid content and neutral lipids under N deprivation compared with strains from desert and native lake. At a molecular level, the arctic strain produced more differentially expressed genes related to fatty acid biosynthesis, glycolysis gluconeogenesis, and glycerolipid metabolism. The important functional genes acetyl coenzyme A (acetyl-CoA) carboxylase (ACCase), fatty acid synthase complex, pyruvate dehydrogenase component, and fatty acyl-acyl carrier protein (acyl-ACP) thioesterase were highly expressed in arctic strains. More acetyl-CoA was produced from glycolysis gluconeogenesis and glycerolipid metabolism, which then produced more fatty acid with the catalytic function of ACCase and acyl-ACP thioesterase in fatty acid biosynthesis. Our results indicated that the C. sorokiniana strains from the arctic region had the fullest potential for biodiesel production due to special genetic regulation related to fatty acid synthesis, glycolysis gluconeogenesis, and glycerolipid metabolism. IMPORTANCE It is important to reveal the physiological and genetic regulation mechanisms of microalgae for screening potential strains with high lipid production. Our results showed that Chlorella sorokiniana strains from arctic glacier, desert, and temperate native lake had different growth, biochemical composition, and genetic expression under N deprivation. The strains from an arctic glacier produced the highest lipid content (including neutral lipid), which was related to the genetic regulation of fatty acid biosynthesis, glycolysis gluconeogenesis, and glycerolipid metabolism. The functional genes for acetyl-CoA carboxylase, fatty acid synthase complex, pyruvate dehydrogenase component, and fatty acyl-ACP thioesterase in the three pathways were highly expressed in arctic strains. The revelation of physiological and genetic regulation of strains from different environmental regions will contribute to the microalgae selection for high lipid accumulation.

Thermoresponsive Dual-Structured Gel Emulsions Stabilized by Glycyrrhizic Acid Nanofibrils in Combination with Monoglyceride Crystals.

Responsive dual-structured emulsions and gel emulsions have attracted more and more attention due to their complex microstructures, on-demand responsive properties, and controlled release of active cargoes. In this work, the effect of monoglyceride (MG)-based oil phase structuring on the formation and stability, structural properties, and thermoresponsive and cargo release behavior of gel emulsions stabilized by glycyrrhizic acid (GA) nanofibrils were investigated. Owing to the formation of GA fibrillar networks in the aqueous phase and MG crystalline networks in the oil phase, a stable dual-structured gel emulsion can be successfully developed. The microstructure of the dual-structured gel emulsions largely depended on the concentration of MG in the oil phase. At low MG concentrations (1-2 wt%), the larger formed and lamellar MG crystals may pierce the interfacial fibrillar film, inducing the formation of partially coalesced droplets. In contrast, at high MG concentrations (4 wt% or above), the smaller MG crystals with enhanced interfacial activity can lead to the formation of a bilayer shell of GA nanofibrils and MG crystals, thus efficiently inhibiting the interfacial film damage and forming a jamming structure with homogeneously distributed small droplets. Compared to pure GA nanofibril gel emulsions, the GA-MG dual-structured gel emulsions showed significantly improved mechanical performance as well as good thermoresponsive behavior. Moreover, these stable GA-MG gel emulsions can be used as food-grade delivery vehicles for encapsulating and protecting hydrophobic and hydrophilic bioactive cargoes. They also have great potential as novel and efficient aroma delivery systems showing highly controlled volatile release. The dual-structured emulsion strategy is expected to broaden the applications of natural saponin GA-based gel emulsions in the food, pharmaceutical, and personal care industries.

The Feasibility of Early Alzheimer's Disease Diagnosis Using a Neural Network Hybrid Platform.

Early diagnosis of Alzheimer's Disease (AD) is critical for disease prevention and cure. However, currently, techniques with the required high sensitivity and specificity are lacking. Recently, with the advances and increased accessibility of data analysis tools, such as machine learning, research efforts have increasingly focused on using these computational methods to solve this challenge. Here, we demonstrate a convolutional neural network (CNN)-based AD diagnosis approach using the surface-enhanced Raman spectroscopy (SERS) fingerprints of human cerebrospinal fluid (CSF). SERS and CNN were combined for biomarker detection to analyze disease-associated biochemical changes in the CSF. We achieved very high reproducibility in double-blind experiments for testing the feasibility of our system on human samples. We achieved an overall accuracy of 92% (100% for normal individuals and 88.9% for AD individuals) based on the clinical diagnosis. Further, we observed an excellent correlation coefficient between our test score and the Clinical Dementia Rating (CDR) score. Our findings offer a substantial indication of the feasibility of detecting AD biomarkers using the innovative combination of SERS and machine learning. We are hoping that this will serve as an incentive for future research in the field.

The Mechanism of Microbial-Ferromanganese Nodule Interaction and the Contribution of Biomineralization to the Formation of Oceanic Ferromanganese Nodules.

Ferromanganese nodules are an important mineral resource in the seafloor; however, the genetic mechanism is still unknown. The biomineralization of microorganisms appears to promote ferromanganese nodule formation. To investigate the possible mechanism of microbial-ferromanganese nodule interaction, to test the possibility of marine microorganisms as deposition template for ferromanganese nodules minerals, the interactions between Jeotgalibacillus campisalis strain CW126-A03 and ferromanganese nodules were studied. The results showed that strain CW126-A03 increased ion concentrations of Fe, Mn, and other metal elements in solutions at first. Then, metal ions were accumulated on the cells' surface and formed ultra-micro sized mineral particles, even crystalline minerals. Strain CW126-A03 appeared to release major elements in ferromanganese nodules, and the cell surface may be a nucleation site for mineral precipitation. This finding highlights the potentially important role of biologically induced mineralization (BIM) in ferromanganese nodule formation. This BIM hypothesis provides another perspective for understanding ferromanganese nodules' genetic mechanism, indicating the potential of microorganisms in nodule formation.

Molecular orientation and specificity in the identification of biomolecules via surface enhanced Raman spectroscopy.

The orientation dependence of the Raman spectral features of individual protein/biomolecules is studied using surface-enhanced Raman spectroscopy (SERS). Large variation in spectral features mainly in term of peak intensity is observed from small proteins/peptides. We aim to address the question of whether the spectral features of SERS are uniquely determined by the type of protein/molecules or are influenced prominently by factors more than the identity of the molecules such as orientation of molecules relative to the substrate surface. The standard deviation in the intensity of individual Raman peaks diminishes for protein size larger than 13 amino acids. Secondary structure of protein (such as protein-protein interaction) remains unchanged regardless of protein orientation. Numerical simulation studies corroborate the experimental observation in that the SERS spectral features of biomedically relevant protein (of larger than 13 amino acids in size, which represent all human protein types) are not affected by the orientation of amino acids randomly dispersed on SERS-active surfaces. These findings are instrumental to understanding the exceedingly high (label-free) specificity when SERS is used in identifying proteins/peptides as can be found in numerous publications from different research groups in both in vivo and in vitro analyses. It was noted that the spectral position of all Raman peaks assignable to the various amino acids are independent of molecule orientation even though their intensities do vary.

Ultrasensitive amyloid ß-protein quantification with high dynamic range using a hybrid graphene-gold surface-enhanced Raman spectroscopy platform.

Surface enhanced Raman spectroscopy (SERS) holds great promise in biosensing because of its single-molecule, label-free sensitivity. We describe here the use of a graphene-gold hybrid plasmonic platform that enables quantitative SERS measurement. Quantification is enabled by normalizing analyte peak intensities to that of the graphene G peak. We show that two complementary quantification modes are intrinsic features of the platform, and that through their combined use, the platform enables accurate determination of analyte concentration over a concentration range spanning seven orders of magnitude. We demonstrate, using a biologically relevant test analyte, the amyloid ß-protein (Aß), a seminal pathologic agent of Alzheimer's disease (AD), that linear relationships exist between (a) peak intensity and concentration at a single plasmonic hot spot smaller than 100 nm, and (b) frequency of hot spots with observable protein signals, i.e. the co-location of an Aß protein and a hot spot. We demonstrate the detection of Aß at a concentration as low as 10-18 M after a single 20 µl aliquot of the analyte onto the hybrid platform. This detection sensitivity can be improved further through multiple applications of analyte to the platform and by rastering the laser beam with smaller step sizes.

Seonamhaeicola maritimus sp. nov., isolated from coastal sediment.

A Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped and orange-pigmented bacterium, designated 1505T, was isolated from marine sediment that was obtained off the coast of Weihai, PR China. Strain 1505T was found to grow at 10-35 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, 7.5) and in the presence of 1-4 % (w/v) NaCl (optimum, 2 %). Cells were positive for oxidase and catalase activity. The 16S rRNA gene based phylogenetic analysis revealed that the nearest phylogenetic neighbours of strain 1505T were Seonamhaeicola algicola Gy8T (97.1 %), Seonamhaeicola marinus B011T (96.3 %) and Seonamhaeicola aphaedonensis KCTC 32578T (95.6 %). Based on phylogenomic analysis, the average nucleotide identity values between strain 1505T and S. algicola Gy8T, S. marinus B011T and S. aphaedonensis KCTC 32578T were 75.9, 76.0 and 77.7 %, respectively; the digital DNA-DNA hybridization values based on the draft genomes between strain 1505T and S. algicola Gy8T, S. marinus B011T and S. aphaedonensis KCTC 32578T were 20.0, 20.7 and 21.4 %, respectively. Menaquinone-6 (MK-6) was detected as the major respiratory quinone. The dominant cellular fatty acids were iso-C15 : 1 G and C18 : 1ω9c. The DNA G+C content of strain 1505T was 33.3 mol%. The polar lipids included phosphatidylethanolamine, six aminolipids and four unidentified lipids. Based on its phylogenetic and phenotypic characteristics, strain 1505T is considered to represent a novel species of the genus Seonamhaeicola, for which the name Seonamhaeicola maritimus sp. nov. is proposed. The type strain is 1505T (=KCTC 72528T=MCCC 1H00389T).

Isolation, identification, and characterization of diesel-oil-degrading bacterial strains indigenous to Changqing oil field, China.

In the present study, 12 indigenous diesel-oil-degrading bacteria were isolated from the petroleum-contaminated soils of the Changqing oil field (Xi'an, China). Measurement of the diesel-oil degradation rates of these strains by the gravimetric method revealed that they ranged from 42% to 66% within 2 weeks. The highest degradation rates were observed from strains CQ8-1 (66%), CQ8-2 (62.6%), and CQ11 (59%), which were identified as Bacillus thuringiensis, Ochrobactrum anthropi, and Bordetella bronchialis, respectively, based on their 16S rDNA sequences. Moreover, the physiological and biochemical properties of these three strains were analyzed by Gram staining, catalase, oxidase, and Voges-Proskauer tests. Transmission electron microscopy showed that all three strains were rod shaped with flagella. Gas chromatography and mass spectrometric analyses indicated that medium- and long-chain n-alkanes in diesel oil (C11-C29) were degraded to different degrees by B. thuringiensis, O. anthropi, and B. bronchialis, and the degradation rates gradually decreased as the carbon numbers increased. Overall, the results of this study indicate strains CQ8-1, CQ8-2, and CQ11 might be useful for environmentally friendly and cost-effective bioremediation of oil-contaminated soils.

A Label-Free Platform for Identification of Exosomes from Different Sources.

Exosomes contain cell- and cell-state-specific cargos of proteins, lipids, and nucleic acids and play significant roles in cell signaling and cell-cell communication. Current research into exosome-based biomarkers has relied largely on analyzing candidate biomarkers, i.e., specific proteins or nucleic acids. However, this approach may miss important biomarkers that are yet to be identified. Alternative approaches are to analyze the entire exosome system, either by "omics" methods or by techniques that provide "fingerprints" of the system without identifying each individual biomolecule component. Here, we describe a platform of the latter type, which is based on surface-enhanced Raman spectroscopy (SERS) in combination with multivariate analysis, and demonstrate the utility of this platform for analyzing exosomes derived from different biological sources. First, we examined whether this analysis could use exosomes isolated from fetal bovine serum using a simple, commercially available isolation kit or necessitates the higher purity achieved by the "gold standard" ultracentrifugation/filtration procedure. Our data demonstrate that the latter method is required for this type of analysis. Having established this requirement, we rigorously analyzed the Raman spectral signature of individual exosomes using a unique, hybrid SERS substrate made of a graphene-covered Au surface containing a quasi-periodic array of pyramids. To examine the source of the Raman signal, we used Raman mapping of low and high spatial resolution combined with morphological identification of exosomes by scanning electron microscopy. Both approaches suggested that the spectra were collected from single exosomes. Finally, we demonstrate for the first time that our platform can distinguish among exosomes from different biological sources based on their Raman signature, a promising approach for developing exosome-based fingerprinting. Our study serves as a solid technological foundation for future exploration of the roles of exosomes in various biological processes and their use as biomarkers for disease diagnosis and treatment monitoring.

Surface enhanced Raman spectroscopy distinguishes amyloid Β-protein isoforms and conformational states.

Amyloid ß-protein (Aß) self-association is one process linked to the development of Alzheimer's disease (AD). Aß peptides, including its most abundant forms, Aß40 and Aß42, are associated with the two predominant neuropathologic findings in AD, vascular and parenchymal amyloidosis, respectively. Efforts to develop therapies for AD often have focused on understanding and controlling the assembly of these two peptides. An obligate step in these efforts is the monitoring of assembly state. We show here that surface-enhanced Raman spectroscopy (SERS) coupled with principal component analysis (PCA) readily distinguishes Aß40 and Aß42. We show further, through comparison of assembly dependent changes in secondary structure and morphology, that the SERS/PCA approach unambiguously differentiates closely related assembly stages not readily differentiable by circular dichroism spectroscopy, electron microscopy, or other techniques. The high discriminating power of SERS/PCA is based on the rich structural information present in its spectra, which comprises not only on interatomic resonances between covalently associated atoms and hydrogen bond interactions important in controlling secondary structure, but effects of protein orientation relative to the substrate surface. Coupled with the label-free, single molecule sensitivity of SERS, the approach should prove useful for determining structure activity relationships, suggesting target sites for drug development, and for testing the effects of such drugs on the assembly process. The approach also could be of value in other systems in which assembly dependent changes in protein structure correlate with the formation of toxic peptide assemblies.

Isolation and characterization of biosurfactant-producing and diesel oil degrading Pseudomonas sp. CQ2 from Changqing oil field, China.

In the present research investigation, 13 indigenous bacteria (from CQ1 to CQ13) were isolated from soil collected from Changqing oil field of Xi'an, China. Four promising biosurfactant producers (CQ1, CQ2, CQ4, and CQ13) were selected through primary screening among these 13 strains, including via drop collapse and oil-spreading methods. However, only the strain CQ2 showed the best biosurfactant production and was further screened by hemolytic assay, cetyl trimethyl ammonium bromide (CTAB), surface tension and emulsifying activity. The bacterium CQ2 has the ability to produce about 3.015 g L-1 of biosurfactant using glucose as the sole carbon source without any optimization. The produced biosurfactant could greatly reduce surface tension from 72.66 to 24.72 mN m-1 with a critical micelle concentration (CMC) of 30 mg L-1 and emulsify diesel oil up to 60.1%. The cell-free broth was found to be stable in wide temperature (4-100 °C), pH (6-12) and salinity (2-20%) ranges for surface and emulsifying activity. This biosurfactant was preliminarily found to be of a glycolipid nature as evident from thin-layer chromatographic (TLC) and Fourier transform infra-red spectroscopic (FTIR) analyses. Moreover, CQ2 was able to degrade 54.7% of diesel oil, which surprisingly could form a substantial amount of bioflocculants during the degradation process. Furthermore, the 16S rDNA sequence using the Genbank BLAST tool revealed that isolated CQ2 was closely related to species of Pseudomonas genus and, thus, was entitled Pseudomonas sp. CQ2. The results of residual diesel oil contents measured by GC-MS showed that C7-C28 hydrocarbons could be degraded by Pseudomonas sp. CQ2. Thus, these findings revealed that CQ2 could be applied for remediation of diesel oil/petroleum-contaminated waters and soils on a large scale.

Chengkuizengella sediminis gen. nov. sp. nov., isolated from sediment.

A Gram-stain-positive, aerobic, motile, endospore-forming bacterium, designated strain J15A17T, was isolated from sediment of the South China Sea. The strain was oxidase-positive and catalase-negative. Optimal growth occurred at 33 °C, pH 7.5 and in the presence of 3 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, the strain showed closest similarity (92.8 %) to Paenibacillus puldeungensis strain CAU 9324T. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate forms a separate branch within the family Paenibacillaceae, with the genus Cohnella as the most closely related genus. The DNA G+C content of strain J15A17T was 37.4 mol%. The strain contained MK-7 as the sole respiratory quinone; anteiso-C15 : 0 and iso-C16 : 0 were the major cellular fatty acids; and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, glycolipid and four unidentified phospholipids. The strain displayed the peptidoglycan type A4α l-Lys-d-Asp in the cell wall. Phylogenetic, physiological, biochemical and morphological differences between strain J15A17T and its closest relatives in the genera Cohnella, Fontibacillus and Paenibacillus suggest that strain J15A17T (=KCTC 33759T=MCCC 1H00137T) represents the type strain of a novel species in a new genus within the family Paenibacillaceae, Chengkuizengella sediminis gen. nov. sp. nov.

Paraliobacillus sediminis sp. nov., isolated from East China sea sediment.

A Gram-strain-positive, facultatively anaerobic, motile, endospore-forming, slightly halophilic bacterium, designated strain 126C4T, was isolated from sediment from the East China Sea. The strain was catalase-positive and oxidase-negative. Optimal growth occurred at 28-30 °C, pH 7.0-7.5 and in the presence of 3-5 % (w/v) NaCl. Phylogenetic analyses, based on 16S rRNA gene sequence comparisons, showed that strain 126C4T was a member of the genus Paraliobacillus, with 16S rRNA gene sequence similarities to Paraliobacillus quinghaiensis YIM-C158T and Paraliobacillus ryukyuensis O15-7T of 96.2 % and 95.3 %, repectively. The DNA G+C content was 39.6 mol%. The strain contained MK-7 as the sole respiratory quinone, anteiso-C15 : 0, C16 : 0, iso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids, and its polar lipid pattern comprised diphosphatidylglycerol, phosphatidylethanolamine, three glycolipids and four unknown phospholipids. On the basis of its phylogenetic position, phenotypic traits and chemotaxonomic characteristics, it is suggested that strain 126C4T represents a novel species of the genus Paraliobacillus, for which the name Paraliobacillus sediminis sp. nov. is proposed. The type strain is 126C4T (=KCTC 33762T=MCCC 1H00136T).

Diversity and community structure of archaea in deep subsurface sediments from the tropical Western pacific.

Archaeal 16S rRNA gene clone libraries using PCR amplicons from eight different layers of the MD06-3051 core were obtained from the tropical Western Pacific sediments. A total of 768 clones were randomly selected, and 264 representative clones were sequenced by restriction fragment length polymorphism. Finally, 719 valid clones and 104 operational taxonomic units were identified after chimera-check and > or =97% similarity analysis. The phylogenetic analysis of 16S rDNA sequences obtained from sediment samples were very diverse and showed stratification with depth. Majority of the members were most closely related to uncultivated groups and physiologically uncharacterized assemblages. All phylotypes were affiliated with Crenarchaeota (76%) and Euryarchaeota (24%), respectively. Deep-sea archaeal group (DSAG, 41% of total clones) and miscellaneous crenarchaeotic group (MCG, 29% of total clones) belonging to Crenarchaeota were the most predominant archaeal 16S rDNA phylotypes in clone libraries. Phylotypes in this study shared high similarity with those in subsurface sediments from Peru Margin sites, which indicated that different geographical zones might host similar members of archaeal populations based on similar sedimentary environments. In our study, members of DSAG and MCG seemed to dominate certain layers of the nonhydrate sediments, suggesting a wide ecophysiological adaptation than previously appreciated. The spatial distribution and community structure of these groups might vary with the different geochemical gradients of the environment.