Thermophilic Hadarchaeota grow on long-chain alkanes in syntrophy with methanogens.

Methanogenic hydrocarbon degradation can be carried out by archaea that couple alkane oxidation directly to methanogenesis, or by syntrophic associations of bacteria with methanogenic archaea. However, metagenomic analyses of methanogenic environments have revealed other archaea with potential for alkane degradation but apparent inability to form methane, suggesting the existence of other modes of syntrophic hydrocarbon degradation. Here, we provide experimental evidence supporting the existence of a third mode of methanogenic degradation of hydrocarbons, mediated by syntrophic cooperation between archaeal partners. We collected sediment samples from a hot spring sediment in Tengchong, China, and enriched Hadarchaeota under methanogenic conditions at 60 °C, using hexadecane as substrate. We named the enriched archaeon Candidatus Melinoarchaeum fermentans DL9YTT1. We used 13C-substrate incubations, metagenomic, metatranscriptomic and metabolomic analyses to show that Ca. Melinoarchaeum uses alkyl-coenzyme M reductases (ACRs) to activate hexadecane via alkyl-CoM formation. Ca. Melinoarchaeum likely degrades alkanes to carbon dioxide, hydrogen and acetate, which can be used as substrates by hydrogenotrophic and acetoclastic methanogens such as Methanothermobacter and Methanothrix.

Description of the first cultured representative of "Candidatus Synoicihabitans" genus, isolated from deep-sea sediment of South China Sea.

In this study we describe the first cultured representative of Candidatus Synoicihabitans genus, a novel strain designated as LMO-M01T, isolated from deep-sea sediment of South China Sea. This bacterium is a facultative aerobe, Gram-negative, non-motile, and has a globular-shaped morphology, with light greenish, small, and circular colonies. Analysis of the 16S rRNA gene sequences of strain LMO-M01T showed less than 93% similarity to its closest cultured members. Furthermore, employing advanced phylogenomic methods such as comparative genome analysis, average nucleotide identity (ANI), average amino acids identity (AAI), and digital DNA-DNA hybridization (dDDH), placed this novel species within the candidatus genus Synoicihabitans of the family Opitutaceae, Phylum Verrucomicrobiota. The genomic analysis of strain LMO-M01T revealed 175 genes, encoding putative carbohydrate-active enzymes. This suggests its metabolic potential to degrade and utilize complex polysaccharides, indicating a significant role in carbon cycling and nutrient turnover in deep-sea sediment. In addition, the strain's physiological capacity to utilize diverse biopolymers such as lignin, xylan, starch, and agar as sole carbon source opens up possibilities for sustainable energy production and environmental remediation. Moreover, the genome sequence of this newly isolated strain has been identified across diverse ecosystems, including marine sediment, fresh water, coral, soil, plants, and activated sludge highlighting its ecological significance and adaptability to various environments. The recovery of strain LMO-M01T holds promise for taxonomical, ecological and biotechnological applications. Based on the polyphasic data, we propose that this ecologically important strain LMO-M01T represents a novel genus (previously Candidatus) within the family Opitutaceae of phylum Verrucomicrobiota, for which the name Synoicihabitans lomoniglobus gen. nov., sp. nov. was proposed. The type of strain is LMO-M01T (= CGMCC 1.61593T = KCTC 92913T).

Characterizing cerebrospinal fluid mobility using heavily T2-weighted 3D fast spin echo (FSE) imaging with improved multi-directional diffusion-sensitized driven-equilibrium (iMDDSDE) preparation.

Cerebrospinal fluid (CSF) flow patterns and their relationship with arterial pulsation can depict the function of glymphatic system (GS). We propose an improved multi-directional diffusion-sensitized driven-equilibrium (iMDDSDE) prepared heavily T2-weighted 3D FSE (iMDDSDE-HT2) magnetic resonance imaging (MRI) method to noninvasively assess the mobility (MO) of CSF distributed in the ventricles and perivascular spaces (PVS). This method could obtain 3D high resolution (1 mm isotropic) imaging of CSF MO with full brain coverage within five min and distinguish the CSF MO across different pulse phases using a peripheral pulse unit (PPU). The MO curves had the largest amplitude value in the PVS of middle cerebral artery (11.11 × 10-9 m2/s) and the largest amplitude growth rate in the posterior cerebral artery (189%). The average coefficient of variations (CVs) in non-pulse trigger and pulse phase 1 and 3 were 0.11, 0.10 and 0.09 respectively. The MO in older healthy participants was lower compared to the young participants, and the MO in cerebral major artery stenosis patients with acute ischemia stroke (AIS) were lower compared to those without AIS in several ventriclar ROIs (P < 0.05). This sequence is a clinically feasible method to effectively evaluate CSF flow patterns in human brain.

Mariluticola halotolerans gen. nov., sp. nov., a novel member of the family Devosiaceae isolated from South China Sea sediment.

A novel member of class Alphaproteobacteria was isolated from marine sediment of the South China Sea. Cells of strain LMO-2T were Gram-stain negative, greyish in colour, motile, with a single lateral flagellum and short rod in shape with a slight curve. Strain LMO-2T was positive for oxidase and negative for catalase. The bacterium grew aerobically at 10-40 °C (optimum, 25-30 °C), pH 5.5-10.0 (optimum, pH 7.0) and 0-9 % NaCl (w/v; optimum, 2-3 %). Phylogenetic analysis of the 16S rRNA gene sequence and phylogenomic analysis of the whole genome sequence indicated that strain LMO-2T represents a new genus and a new species within the family Devosiaceae, class Alphaproteobacteria, phylum Pseudomonadota. Comparisons of the 16S rRNA gene sequences of strain LMO-2T showed 94.8 % similarity to its closest relative. The genome size is ~3.45 Mbp with a DNA G+C content of 58.17 mol%. The strain possesses potential capability for the degradation of complex organic matter, i.e. fatty acid and benzoate. The predominant cellular fatty acids (>10 %) were C16 : 0 and C18 : 1 ω7c 11-methyl. The sole respiratory quinone was ubiquinone-10. The major identified polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phospholipid. Based on the polyphasic taxonomic data, strain LMO-2T represents a novel genus and a novel species for which the name Mariluticola halotolerans gen. nov., sp. nov., was proposed in the family Devosiaceae. The type strain is LMO-2T (=CGMCC 1.19273T=JCM 34934T).

SPatiotemporal-ENcoded acoustic radiation force imaging of focused ultrasound.

Neuromodulation technology has provided novel therapeutic approaches for diseases caused by neural circuit dysfunction. Transcranial focused ultrasound (FU) is an emerging neuromodulation approach that combines noninvasiveness with relatively sharp focus, even in deep brain regions. It has numerous advantages such as high precision and good safety in neuromodulation, allowing for modulation of both peripheral and central nervous systems. To ensure accurate treatment targeting in FU neuromodulation, a magnetic resonance acoustic radiation force imaging (MR-ARFI) sequence is crucial for the visualization of the focal point. Currently, the commonly used 2D Spin Echo ARFI (2D SE-ARFI) sequence suffers from the long acquisition time, while the echo planar imaging ARFI (EPI-ARFI) sequence with a shorter acquisition time is vulnerable to the magnetic field inhomogeneities. To address these problems, we proposed a spatiotemporal-encoded acoustic radiation force imaging sequence (i.e., SE-SPEN-ARFI, shortened to SPEN-ARFI) in this study. The displacement at the focal spot obtained was highly consistent with that of the SE-ARFI sequence. Our research shows that SPEN-ARFI allows for rapid image acquisition and has less image distortions even under great field inhomogeneities. Therefore, a SPEN-ARFI sequence is a practical alternative for the treatment planning in ultrasound neuromodulation.

Methanococcoides orientis sp. nov., a methylotrophic methanogen isolated from sediment of the East China Sea.

A novel methylotrophic methanogen Methanococcoides orientis sp. nov. was isolated from East China Sea sediment. Type strain LMO-1T of Methanococcoides orientis sp. nov. was irregular 1-2 µm cocci without flagella. Strain LMO-1T could utilize a variety of methylated compounds including methanol, methylamine, dimethylamine and trimethylamine for growth and methanogenesis, while H2/CO2 or acetate could not be used for growth or methanogenesis. Optimum growth temperature was 30-35 °C, optimum pH range for growth was 7.0-7.5, while the optimum salinity spectrum for growth was 1.0%-5.0% NaCl. Based on 16S rRNA gene similarity, strain LMO-1T belongs to Methanococcoides, with the highest sequence similarity to Methanococcoides methylutens DSM 2657T (99.8 %), Methanococcoides vulcani SLH33T(99.4 %), followed by Methanococcoides alaskense AK-5T(98.1 %), Methanococcoides burtonii DSM 6242T (98.0 %). Digital DNA-DNA hybridization also showed highest similarity with Methanococcoides methylutens DSM 2657T, with the value of 58.4 %. The average nucleotide identity between strain LMO-1T and Methanococcoides methylutens DSM 2657T was 94.06 %. In summary, LMO-1T represents a novel species of the genus Methaococcoides, for which the name Methanococcoides orientis sp. nov. is proposed. The type strain is LMO-1T (=MCCC 4K00106T=JCM 39195T).

Optimizing the hybridization chain reaction-fluorescence in situ hybridization (HCR-FISH) protocol for detection of microbes in sediments.

Fluorescence in situ hybridization (FISH) is a canonical tool commonly used in environmental microbiology research to visualize targeted cells. However, the problems of low signal intensity and false-positive signals impede its widespread application. Alternatively, the signal intensity can be amplified by incorporating Hybridization Chain Reaction (HCR) with FISH, while the specificity can be improved through protocol modification and proper counterstaining. Here we optimized the HCR-FISH protocol for studying microbes in environmental samples, particularly marine sediments. Firstly, five sets of HCR initiator/amplifier pairs were tested on the laboratory-cultured bacterium Escherichia coli and the archaeon Methanococcoides methylutens, and two sets displayed high hybridization efficiency and specificity. Secondly, we tried to find the best combination of sample pretreatment methods and HCR-FISH protocol for environmental sample analysis with the aim of producing less false positive signals. Various detachment methods, extraction methods and formulas of hybridization buffer were tested using sediment samples. Thirdly, an image processing method was developed to enhance the DAPI signal of microbial cells against that of abiotic particles, providing a reliable reference for FISH imaging. In summary, our optimized HCR-FISH protocol showed promise to serve as an addendum to traditional FISH for research on environmental microbes. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-021-00098-8.

Dynamic modelling of the impact of public health education on the control of emerging infectious disease.

Public health education, including mass and interpersonal communication, has been recognized as an effective control of infectious disease. Compared to the well-studied mass communication by dynamic modelling, not much mathematical study has been done on the effect of interpersonal communication. Here, we build a model, to study the overall impact of mass communication and interpersonal communication on disease spread and disease control during the transmission process. By analysing the dynamic behaviour of our model, we find two threshold parameters on which the disease persistence and extinction condition depend. We further prove that the endemic equilibrium, whenever existing, is locally asymptotically stable. Its global stability is also verified. And the impact of public health education on the behaviours of the model is considered by numerical simulation. Our study confirms the value of various education activities and shows that public health education may affect the epidemic threshold.

The impacts of stress on the chemical structure of coals: a mini-review based on the recent development of mechanochemistry.

The chemical structure evolution of coal, which is important for understanding coalification and the accompanying volatile and possible oil generation, is generally thought to be influenced by temperature, time and confining pressure. Though evidence concerning the impacts of stress on the chemical structure has accumulated for many years and some hypotheses have been proposed, the mechanism remains controversial. Recent years have seen a breakthrough in mechanochemistry, which proves that stress can act on the molecule directly to initiate or accelerate reactions by deforming the chemical bonds. The progress in mechanochemistry gives researchers incentive to consider how stress works on the chemical structure of coals. Preliminary quantum chemical calculations have been performed on the macromolecule of anthracite to explain the mechanism of gas generation during the deformation experiments at low temperatures. This paper briefly reviews the evidence regarding the impacts of stress on the chemical structure of coals and introduces the recent achievements in the mechanism research. To further investigate this problem, more work should be undertaken by researchers from both geology and quantum chemistry fields.