Vertical connectivity of microbiome and metabolome reveals depth-dependent variations across a deep cold-seep water column.

Deciphering the vertical connectivity of oceanic microbiome and metabolome is crucial for understanding the carbon sequestration and achieving the carbon neutrality. However, we lack a systematic view of the interplay among particle transport, microbial community, and metabolic trait across depths. Through integrating the biogeochemical, microbial, and metabolic characteristics of a deep cold-seep water column (∼1989 m), we find the altered connectivity of microbial community and dissolved organic matter (DOM) across depths. Both the microbial communities (bacteria and protists) and DOM show a clear compositional connectivity from surface to the depth of 1000 m, highlighting the controls of sinking particle over microbial connectivity from the epipelagic to mesopelagic zone. However, due to the biological migration and ocean mixing, the fecal-associated bacteria and protistan consumers unexpectedly emerge and the degradation index of DOM substantially alters around 1000-1200 m. Collectively, we unveil the significance of multi-faceted particle dispersion, which supports the connectivity and variability of deep ocean microbial communities.

Evidence for Assimilatory Nitrate Reduction as a Previously Overlooked Pathway of Reactive Nitrogen Transformation in Estuarine Suspended Particulate Matter.

Suspended particulate matter (SPM) contributes to the loss of reactive nitrogen (Nr) in estuarine ecosystems. Although denitrification and anaerobic ammonium oxidation in SPM compensate for the current imbalance of global nitrogen (N) inputs and sinks, it is largely unclear whether other pathways for Nr transformation exist in SPM. Here, we combined stable isotope measurements with metagenomics and metatranscriptomics to verify the occurrence of dissimilatory nitrate reduction to ammonium (DNRA) in the SPM of the Pearl River Estuary (PRE). Surprisingly, the conventional functional genes of DNRA (nirBD) were abundant and highly expressed in SPM, which was inconsistent with a low potential rate. Through taxonomic and comparative genomic analyses, we demonstrated that nitrite reductase (NirBD) in conjunction with assimilatory nitrate reductase (NasA) performed assimilatory nitrate reduction (ANR) in SPM, and diverse alpha- and gamma-proteobacterial lineages were identified as key active heterotrophic ANR bacteria. Moreover, ANR was predicted to have a relative higher occurrence than denitrification and DNRA in a survey of Nr transformation pathways in SPM across the PRE spanning 65 km. Collectively, this study characterizes a previously overlooked pathway of Nr transformation mediated by heterotrophic ANR bacteria in SPM and has important implications for our understanding of N cycling in estuaries.

Preparation of magnetic and pH-responsive chitosan microcapsules via sonochemical method.

Magnetic and pH-responsive chitosan microcapsules (MPRCMCs) were prepared by a simple sonochemical method. Superparamagnetic oleic acid modified Fe3O4 nanoparticles (OA-Fe3O4 NPs) and hydrophobic drugs could be directly loaded into MPRCMCs during sonication. The obtained microcapsules had a well-defined spherical morphology with the average size of 2 µm. The microcapsules showed an excellent magnetic property. In addition, the pH-responsive controlled release of coumarin 6 (C6) from MPRCMCs indicated that the developed microcapsules could be a promising candidate for drugs carriers.

Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments.

Mangrove sediment is a crucial component in the global mercury (Hg) cycling and acts as a hotspot for methylmercury (MeHg) production. Early evidence has documented the ubiquity of well-studied Hg methylators in mangrove superficial sediments; however, their diversity and metabolic adaptation in the more anoxic and highly reduced subsurface sediments are lacking. Through MeHg biogeochemical assay and metagenomic sequencing, we found that mangrove subsurface sediments (20-100 cm) showed a less hgcA gene abundance but higher diversity of Hg methylators than superficial sediments (0-20 cm). Regional-scale investigation of mangrove subsurface sediments spanning over 1500 km demonstrated a prevalence and family-level novelty of Hg-methylating microbial lineages (i.e., those affiliated to Anaerolineae, Phycisphaerae, and Desulfobacterales). We proposed the candidate phylum Zixibacteria lineage with sulfate-reducing capacity as a currently understudied Hg methylator across anoxic environments. Unlike other Hg methylators, the Zixibacteria lineage does not use the Wood-Ljungdahl pathway but has unique capabilities of performing methionine synthesis to donate methyl groups. The absence of cobalamin biosynthesis pathway suggests that this Hg-methylating lineage may depend on its syntrophic partners (i.e., Syntrophobacterales members) for energy in subsurface sediments. Our results expand the diversity of subsurface Hg methylators and uncover their unique ecophysiological adaptations in mangrove sediments.

The vertically-stratified resistomes in mangrove sediments was driven by the bacterial diversity.

Early evidence has elucidated that the spread of antibiotic (ARGs) and metal resistance genes (MRGs) are mainly attributed to the selection pressure in human-influenced environments. However, whether and how biotic and abiotic factors mediate the distribution of ARGs and MRGs in mangrove sediments under natural sedimentation is largely unclear. Here, we profiled the abundance and diversity of ARGs and MRGs and their relationships with sedimental microbiomes in 0-100 cm mangrove sediments. Our results identified multidrug-resistance and multimetal-resistance as the most abundant ARG and MRG classes, and their abundances generally decreased with the sediment depth. Instead of abiotic factors such as nutrients and antibiotics, the bacterial diversity was significantly negatively correlated with the abundance and diversity of resistomes. Also, the majority of resistance classes (e.g., multidrug and arsenic) were carried by more diverse bacterial hosts in deep layers with low abundances of resistance genes. Together, our results indicated that bacterial diversity was the most important biotic factor driving the vertical profile of ARGs and MRGs in the mangrove sediment. Given that there is a foreseeable increasing human impact on natural environments, this study emphasizes the important role of biodiversity in driving the abundance and diversity of ARGs and MRGs.

Federated personalized random forest for human activity recognition.

User data usually exists in the organization or own local equipment in the form of data island. It is difficult to collect these data to train better machine learning models because of the General Data Protection Regulation (GDPR) and other laws. The emergence of federated learning enables users to jointly train machine learning models without exposing the original data. Due to the fast training speed and high accuracy of random forest, it has been applied to federated learning among several data institutions. However, for human activity recognition task scenarios, the unified model cannot provide users with personalized services. In this paper, we propose a privacy-protected federated personalized random forest framework, which considers to solve the personalized application of federated random forest in the activity recognition task. According to the characteristics of the activity recognition data, the locality sensitive hashing is used to calculate the similarity of users. Users only train with similar users instead of all users and the model is incrementally selected using the characteristics of ensemble learning, so as to train the model in a personalized way. At the same time, user privacy is protected through differential privacy during the training stage. We conduct experiments on commonly used human activity recognition datasets to analyze the effectiveness of our model.

Evolutionary conservation of nested MIR159 structural microRNA genes and their promoter characterization in Arabidopsis thaliana.

MicroRNAs (miRNAs) are endogenous small RNAs, that are vital for gene expression regulation in eukaryotes. Whenever a pri-miRNA precursor includes another miRNA precursor, and both of these precursors may generate independent, non-overlapping mature miRNAs, we named them nested miRNAs. However, the extent of nested miR159 structural evolutionary conservation and its promoter characterization remains unknown. In this study, the sequence alignment and phylogenetic analysis reveal that the MIR159 family is ancient, and its nested miR159 structures are evolutionary conserved in different plant species. The overexpression of ath-MIR159a, including the 1.2 kb downstream region, has no effect on rescuing the mir159ab phenotype. The promoter truncation results revealed that the 1.0 kb promoter of ath-MIR159a is sufficient for rescuing the mir159ab phenotype. The cis-regulatory elements in the ath-miR159a promoters indicated functions related to different phytohormones, abiotic stresses, and transcriptional activation. While the MybSt1 motif-containing region is not responsible for activating the regulation of the miR159a promoter. The qRT-PCR results showed that overexpression of ath-MIR159a led to high expression levels of miR159a.1-5 and miR159a.1-3 and complemented the growth defect of mir159ab via downregulation of MYB33 and MYB65. Furthermore, continuously higher expression of the miR159a.2 duplex in transgenic lines with the curly leaf phenotype indicates that miR159a.2 is functional in Arabidopsis and suggests that it is possible for a miRNA precursor to encode several regulatory small RNAs in plants. Taken together, our study demonstrates that the nested miR159 structure is evolutionary conserved and miRNA-mediated gene regulation is more complex than previously thought.

Nested miRNA Secondary Structure Is a Unique Determinant of miR159 Efficacy in Arabidopsis.

MicroRNAs (miRNAs) are 20- to 24-nucleotide small RNAs, and whenever a pri-miRNA precursor includes another miRNA precursor, and both of these precursors may generate independent non overlapping mature miRNAs, we called them nested miRNAs. However, the functional and regulatory roles of nested miRNA structures in plants are still unknown. In this study, the Arabidopsis nested miR159a structure, which consists of two nested miRNAs, miR159a.1, and miR159a.2, was used as a model to determine miRNA-mediated gene silencing in plants. Complementation analysis of nested miR159a structures revealed that the miR159a structure can differentially complement the mir159ab phenotype, and a duplex nested structure in the tail end region of the pre-miR159a fold back may have a possible dominant function, indicating the importance of the flanking sequence of the stem in the cleavage of the mature miRNA. Furthermore, continuously higher expression of the miR159a.2 duplex in the severe leaf curl phenotype indicates that miR159a.2 is functional in Arabidopsis and suggests that in plants, a miRNA precursor may encode multiple regulatory small RNAs. Taken together, our study demonstrates that the nested miR159a structure regulated by duplex mutations of miR159a has a unique pattern and provides novel insight into silencing efficacy of Arabidopsis miR159a.

Synthesis of multifunctional bovine serum albumin microcapsules by the sonochemical method for targeted drug delivery and controlled drug release.

Multifunctional folic acid conjugated BSA@Fe3O4 microcapsules (FA-BSA@Fe3O4 MCs) have been prepared successfully based on the sonochemical method. The as-synthesized FA-BSA@Fe3O4 MCs have a suitable size range for biomedical applications, and a high loading capacity for water-insoluble drugs. Furthermore, FA-BSA@Fe3O4 MCs show excellent magnetic properties. Cytotoxicity tests indicate that FA-BSA@Fe3O4 MCs are non-toxic. Cellular uptake and flow cytometric assay illustrate together that FA-BSA@Fe3O4 MCs can target tumor cells selectively through molecular targeted endocytosis. As carriers for water-insoluble drugs, FA-BSA@Fe3O4 MCs are also proved to possess superior redox- and thermo- dual responsiveness for controlled drug release.

Synthesis of folic acid functionalized redox-responsive magnetic proteinous microcapsules for targeted drug delivery.

Folic acid (FA) functionalized magnetic bovine serum albumin (BSA) microcapsules (FA-MBMCs) were prepared by a facile sonochemical method, in which FA molecule was immobilized onto the outer walls of microcapsules as a targeting ligand and oleic acid (OA) modifying Fe3O4 magnetic nanoparticles (OA-Fe3O4 MNPs) were wrapped into the microcapsules. The obtained FA-MBMCs possessed a nice spherical morphology with the mean size of 1.4 µm. FA-MBMCs also showed an excellent magnetic and molecular dual-targeted property. Besides, the reductant-triggered diffusion of coumarin 6 suggested superior drug controlled release of FA-MBMCs.

Sonochemical Synthesis of Hydrophilic Drug Loaded Multifunctional Bovine Serum Albumin Nanocapsules.

A facile sonochemical approach is designed to fabricate protein nanocapsules for hydrophilic drugs (HDs), and HD-loaded multifunctional bovine serum albumin (BSA) nanocapsules (MBNCs) have been prepared for the first time. The as-synthesized HD-loaded MBNCs have a satisfying size range and an excellent magnetic responsive ability. Moreover, high-dose hydrophilic drugs could be loaded into the MBNCs. As carriers, HD-loaded MBNCs also show attractive redox-responsive controlled release ability for hydrophilic drugs and could be internalized selectively by the tumor cells through the folate-mediated endocytosis.