Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms

Background: Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans - the hadal zone (depth > 6,000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water. Results: In this study, metagenomic data were obtained from 0-10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1,000 – 4,000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea. Conclusions: Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling

Metagenomic Insights Into the Cycling of Dimethylsulfoniopropionate and Related Molecules in the Eastern China Marginal Seas

The microbial cycling of dimethylsulfoniopropionate (DMSP) and its gaseous catabolites dimethylsulfide (DMS) and methanethiol (MeSH) are important processes in the global sulfur cycle, marine microbial food webs, signaling pathways, atmospheric chemistry, and potentially climate regulation. Many functional genes have been identified and used to study the genetic potential of microbes to produce and catabolize these organosulfur compounds in different marine environments. Here, we sampled seawater, marine sediment and hydrothermal sediment, and polymetallic sulfide in the eastern Chinese marginal seas and analyzed their microbial communities for the genetic potential to cycle DMSP, DMS, and MeSH using metagenomics. DMSP was abundant in all sediment samples, but was fivefold less prominent in those from hydrothermal samples. Indeed, Yellow Sea (YS) sediment samples had DMSP concentrations two orders of magnitude higher than in surface water samples. Bacterial genetic potential to synthesize DMSP (mainly in Rhodobacteraceae bacteria) was far higher than for phytoplankton in all samples, but particularly in the sediment where no algal DMSP synthesis genes were detected. Thus, we propose bacteria as important DMSP producers in these marine sediments. DMSP catabolic pathways mediated by the DMSP lyase DddP (prominent in Pseudomonas and Mesorhizobium bacteria) and DMSP demethylase DmdA enzymes (prominent in Rhodobacteraceae bacteria) and MddA-mediated MeSH S-methylation were very abundant in Bohai Sea and Yellow Sea sediments (BYSS) samples. In contrast, the genetic potential for DMSP degradation was very low in the hydrothermal sediment samples—dddP was the only catabolic gene detected and in only one sample. However, the potential for DMS production from MeSH (mddA) and DMS oxidation (dmoA and ddhA) was relatively abundant. This metagenomics study does not provide conclusive evidence for DMSP cycling; however, it does highlight the potential importance of bacteria in the synthesis and catabolism of DMSP and related compounds in diverse sediment environments

A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data

Motivation Single-cell multimodal assays allow us to simultaneously measure two different molecular features of the same cell, enabling new insights into cellular heterogeneity, cell development and diseases. However, most existing methods suffer from inaccurate dimensionality reduction for the joint-modality data, hindering their discovery of novel or rare cell subpopulations. Results Here, we present VIMCCA, a computational framework based on variational-assisted multi-view canonical correlation analysis to integrate paired multimodal single-cell data. Our statistical model uses a common latent variable to interpret the common source of variances in two different data modalities. Our approach jointly learns an inference model and two modality-specific non-linear models by leveraging variational inference and deep learning. We perform VIMCCA and compare it with 10 existing state-of-the-art algorithms on four paired multi-modal datasets sequenced by different protocols. Results demonstrate that VIMCCA facilitates integrating various types of joint-modality data, thus leading to more reliable and accurate downstream analysis. VIMCCA improves our ability to identify novel or rare cell subtypes compared to existing widely used methods. Besides, it can also facilitate inferring cell lineage based on joint-modality profiles

Bacterial dimethylsulfoniopropionate biosynthesis in the East China Sea

Dimethylsulfoniopropionate (DMSP) is one of Earth’s most abundant organosulfur molecules. Recently, many marine heterotrophic bacteria were shown to produce DMSP, but few studies have combined culture-dependent and independent techniques to study their abundance, distribution, diversity and activity in seawater or sediment environments. Here we investigate bacterial DMSP production potential in East China Sea (ECS) samples. Total DMSP (DMSPt) concentration in ECS seawater was highest in surface waters (SW) where phytoplankton were most abundant, and it decreased with depth to near bottom waters. However, the percentage of DMSPt mainly apportioned to bacteria increased from the surface to the near bottom water. The highest DMSP concentration was detected in ECS oxic surface sediment (OSS) where phytoplankton were not abundant. Bacteria with the genetic potential to produce DMSP and relevant biosynthesis gene transcripts were prominent in all ECS seawater and sediment samples. Their abundance also increased with depth and was highest in the OSS samples. Microbial enrichments for DMSP-producing bacteria from sediment and seawater identified many novel taxonomic groups of DMSP-producing bacteria. Different profiles of DMSP-producing bacteria existed between seawater and sediment samples and there are still novel DMSP-producing bacterial groups to be discovered in these environments. This study shows that heterotrophic bacteria significantly contribute to the marine DMSP pool and that their contribution increases with water depth and is highest in seabed surface sediment where DMSP catabolic potential is lowest. Furthermore, distinct bacterial groups likely produce DMSP in seawater and sediment samples, and many novel producing taxa exist, especially in the sediment

Evolution of tensile strength and cracking in granite containing prefabricated holes under high temperature and loading rate

Abstract For present applications in deep significant rock engineering, including underground repositories of high-level nuclear waste, an exhaustive comprehension of the impacts of high temperature and loading rate effects on the mechanical characteristics of granite emerges as an imperative necessity. Based on the Brazilian splitting test, Brazilian disc specimens with prefabricated holes were meticulously employed to guarantee the occurrence of radial compression failure. Combining microscopic experiments such as scanning electron microscopy and X-ray diffraction, the indirect tensile strength and damage mechanism of granite from the Yueyang area under the action of different temperatures and loading rates were thoroughly investigated. Furthermore, a nonlinear fitting equation between the two factors and tensile strength is suggested. At the same time, a simplified surface crack density based on pixel processing was defined. This allowed for a comparative assessment of how variations in temperature and loading rates induce varying degrees of macroscopic crack development and damage to the specimens. The findings suggest a direct proportionality between the tensile strength of granite and the loading rate, while an inverse proportionality is observed concerning temperature above 400 °C. However, a transient "gain effect" phenomenon manifests at temperatures below 400 °C. However, the impact of temperature on tensile strength is significantly greater than that of the loading rate, exhibiting a difference of approximately 8.7 times. Furthermore, the temperature is more prone to lead to the occurrence of secondary tensile cracks in specimens. The results of this research provide valuable guidance for ensuring the security of deep major rock engineering during construction

Ultra-high frequency vibration fatigue of DD6 single crystal superalloy simulating thin-walled specimens

The effect of specimen thickness on the very high cycle fatigue （VHCF） properties of DD6 nickel-based single crystal superalloys for turbine blades with hollow air-cooled structure was investigated. Based on the finite element method （FEM）, a thin-walled vibration fatigue specimen with a thickness of 0.5 mm was designed with a natural frequency of 1425 Hz, which was a suitable test efficiency for VHCF test. The VHCF test was carried out by electrodynamic shaker at room temperature, and a VHCF S-N curve up to 109 cycles was obtained. Comparing with the rotational bending fatigue and vibration fatigue test data of conventional size specimens, the results show that the fatigue strength of DD6 single crystal superalloy continues to decrease after 107 cycles and the fatigue strength is decreased about 25%，from 107 to 109 cycles; The high cycle fatigue strength of the thin-walled specimen is basically the same as the standard rotary bending fatigue strength of the same material, and slightly lower than the conventional vibration fatigue strength. The cracks in the thin-walled specimen initiate on the surface of the dangerous section, showing the characteristics of line source. There are two propagation planes in the fatigue growth zone, showing the characteristics of cleavage like