The effect of real-ambient PM2.5 exposure on the lung and gut microbiomes and the regulation of Nrf2.

The influence of air pollution on human health has sparked widespread concerns across the world. Previously, we found that exposure to ambient fine particulate matter (PM2.5) in our "real-ambient exposure" system can result in reduced lung function. However, the mechanism of organ-specific toxicity is still not fully elucidated. The balance of the microbiome contributes to maintaining lung and gut health, but the changes in the microbiome under PM2.5 exposure are not fully understood. Recently, crosstalk between nuclear factor E2-related factor 2 (Nrf2) and the microbiome was reported. However, it is unclear whether Nrf2 affects the lung and gut microbiomes under PM2.5 exposure. In this study, wild-type (WT) and Nrf2-/- (KO) mice were exposed to filtered air (FA) and real ambient PM2.5 (PM) in the " real-ambient exposure" system to examine changes in the lung and gut microbiomes. Here, our data suggested microbiome dysbiosis in lung and gut of KO mice under PM2.5 exposure, and Nrf2 ameliorated the microbiome disorder. Our study demonstrated the detrimental impacts of PM2.5 on the lung and gut microbiome by inhaled exposure to air pollution and supported the protective role of Nrf2 in maintaining microbiome homeostasis under PM2.5 exposure.

Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea.

BACKGROUND: Amplification of small subunit (SSU) rRNA genes with universal primers is a common method used to assess microbial populations in various environmental samples. However, owing to limitations in coverage of these universal primers, some microorganisms remain unidentified. The present study aimed to establish a method for amplifying nearly full-length SSU rRNA gene sequences of previously unidentified prokaryotes, using newly designed targeted primers via primer evaluation in meta-transcriptomic datasets. METHODS: Primer binding regions of universal primer 8F/Arch21F for bacteria or archaea were used for primer evaluation of SSU rRNA sequences in meta-transcriptomic datasets. Furthermore, targeted forward primers were designed based on SSU rRNA reads from unclassified groups unmatched with the universal primer 8F/Arch21F, and these primers were used to amplify nearly full-length special SSU rRNA gene sequences along with universal reverse primer 1492R. Similarity and phylogenetic analysis were used to confirm their novel status. RESULTS: Using this method, we identified unclassified SSU rRNA sequences that were not matched with universal primer 8F and Arch21F. A new group within the Asgard superphylum was amplified by the newly designed specific primer based on these unclassified SSU rRNA sequences by using mudflat samples. CONCLUSION: We showed that using specific primers designed based on universal primer evaluation from meta-transcriptomic datasets, identification of novel taxonomic groups from a specific environment is possible.

Energy consumption during insect flight and bioinspiration for MAV design: A review.

The excellent biological characteristics of insects provide an important source of inspiration for designing micro air vehicles (MAVs). Insect flight is an incredibly complex and energy-intensive process. Unique insect flight muscles and contraction mechanisms enable flapping at high frequencies. Moreover, the metabolic rate during flight can reach hundreds of times the resting state. Understanding energy consumption during flight is crucial for designing efficient biomimetic aircraft. This paper summarizes the structures and contraction mechanisms of insect flight muscles, explores the underlying metabolic processes, and identifies methods for energy substrate identification and detection, and discusses inspiration for biomimetic MAV design. This paper reviews energy consumption during insect flight, promotes the understanding of insect bioenergetics, and applies this information to the design of MAVs.

Analysis of biomechanical passive synergistic vibration reduction inspired by the structure, morphology, nano-mechanics of the beetles' hindwing.

Using scanning electron microscopy (SEM), a small animal imaging system, and biological tissue sections, the relationships between the flapping vibrations in the hindwings of Trypoxylus dichotomus and their morphology, structure, and hemolymph dynamics were investigated. Based on these findings, a three-degree-of-freedom (3-DOF) model incorporating nano-mechanical properties was developed to investigate spanwise passive synergistic vibration reduction (PSVR) in the hindwing elements. To ensure precision, the Runge-Kutta and incremental harmonic balance (IHB) methods were employed for both solving and comparing solutions. Analysis of the spanwise force (FOX) signals confirmed the validity of the PSVR model. Parametric analysis revealed that reducing system mass and stiffness increased the resonance amplitude while shifting the resonance frequency in the opposite direction. The resonance frequency and flexible deformation amplitude of the hindwing system could be controlled by adjusting mass and stiffness within the synergistic framework. The mass and damping of the wing base, along with the stiffness of the wing membrane, were identified as critical factors in the system. This model provides valuable insights into the PSVR mechanism, potentially informing the design and manufacture of bionic flexible flapping wings.

Review of insect-inspired wing micro air vehicle.

Micro air vehicles (MAVs) have wide application prospects in environmental monitoring, disaster rescue and other civil fields because of their flexibility and maneuverability. Compared with fixed wing and rotary wing aircraft, flapping wing micro air vehicles (FWMAVs) have higher energy utilization efficiency and lower cost and have attracted extensive attention from scientists. Insects have become excellent bionic objects for the study of FWMAVs due to their characteristics of low Reynolds number, low noise, hoverability, small size and light weight. By mimicking flying insects, it may be possible to create highly efficient biomimetic FWMAVs. In this paper, insect flight aerodynamics are reviewed, and the mechanism designs of insect-inspired FWMAVs and their aerodynamics are summarized, including the wing type effect, vibration characteristics and aerodynamic characteristics of the flapping wing.

Micro-structures, nanomechanical properties and flight performance of three beetles with different folding ratios.

When beetles are not in flight, their hind wings are folded and hidden under the elytra to reduce their size. This provided inspiration for the design of flapping-wing micro aerial vehicles (FWMAVs). In this paper, microstructures and nanomechanical properties of three beetle species with different wing folding ratios living in different environments were investigated. Factors affecting their flight performance, that is, wind speed, folding ratio, aspect ratio, and flapping frequency, were examined using a wind tunnel. It was found that the wing folding ratio correlated with the lift force of the beetles. Wind speed, folding ratio, aspect ratio, and flapping frequency had a combined effect on the flight performance of the beetles. The results will be helpful to design new deployable FWMAVs.

Combined effects of wrinkled vein structures and nanomechanical properties on hind wing deformation.

The veins in the hind wings of the Asian ladybird beetle (Harmonia axyridis) play active roles in flight and in the folding/unfolding of the hind wing. Wrinkled vein structures are located within the bending zone and are used for folding the hind wing. This paper investigates the coupled effect of wrinkled vein structures within the hind wing of H. axyridis on its deformation. Based on the nanomechanical properties of the veins, morphology of the hind wing, surface structures of the veins, and microstructures of the cross sections (including the veins and wing membranes), four 3-D coupling models (Model I and Model II: variably reduced-modulus veins with and without wrinkles, respectively; Model III and Model IV: uniformly reduced-modulus veins with and without wrinkles, respectively) are established. Relative to the bending and twisting model shapes, Model I has much more flexibility during passive deformation to control wing deformations. The simulation results show that both the wrinkled structures in the bending zone and the variably reduced modulus of the veins contribute to the flight performance (the bending and twisting deformations) of the hind wings, which has important implications for the design of the deployable wings of micro air vehicles (MAVs).

Effects of microfluid in the veins of the deployable hindwings of the Asian ladybeetle on flight performance.

The deployable hindwings of certain coleopterans are their major flying components, and the veins supporting their hindwings play a significant role during flight; this knowledge is critical for designing bioinspired deployable micro air vehicles (MAVs). Therefore, the effects of microfluid (hemolymph) in the veins of beetle deployable hindwings are investigated in this paper. Microstructures are derived from hindwing cross sections and the nanomechanical properties of the hindwings and veins of the Asian ladybeetle Harmonia axyridis (Coleoptera: Coccinellidae). Based on these microstructures, three three-dimensional coupled models are established, including solid veins, hollow veins, and hollow veins filled with hemolymph. Then, the mechanical properties and vibration characteristics of the models are investigated. The torsional veins are affected more significantly by hemolymph when bending. This work will be helpful in designing new biomimetic deployable MAVs.

Compositional Shifts of Bacterial Communities Associated With Pyropia yezoensis and Surrounding Seawater Co-occurring With Red Rot Disease.

Pyropia yezoensis is commercially the most important edible red alga in China, and red rot disease is viewed as one of the major constraints for its cultivation. Microbes within the oomycetic genus Pythium have been reported as the causative agents for this disease; however, little is known about the interactions between the disease and the epiphytic and planktonic bacterial communities. In the present study, bacterial communities associated with uninfected, locally infected, and seriously infected thalli collected from cultivation farms, and within seawater adjacent to the thalli, were investigated using in-depth 16S ribosomal RNA (rRNA) gene sequencing in conjunction with assessing multiple environmental factors. For both thalli and seawater, uninfected and infected communities were significantly different though alpha diversity was similar. Phylogenetic differences between epiphytic bacterial communities associated with P. yezoensis were mainly reflected by the relative changes in the dominant operational taxonomic units (OTUs) assigned as genus Flavirhabdus, genus Sulfitobacter, and family Rhodobacteraceae. The prevalent OTUs in seawater also differed in relative abundance across the communities and were affiliated with diverse taxa, including the phyla Actinobacteria, Verrucomicrobia, and Bacteroidetes, and the classes Alpha- and Gamma-proteobacteria. The differentiation of bacterial communities associated with P. yezoensis and seawater was primarily shaped by reactive silicate (RS) content and salinity, respectively. In particular, 14 potential indicators (two OTUs on P. yezoensis and twelve OTUs in seawater) were identified that significantly differentiated P. yezoensis health statuses and correlated with environmental changes. Overall, the present study provides insights into the alterations of bacterial communities associated with P. yezoensis and surrounding seawater co-occurring with red rot disease. Observed changes were closely associated with health status of algal host, and highlight the potential of using community differentiation to forecast disease occurrence.

A Modified Low-quantity RNA-Seq Method for Microbial Community and Diversity Analysis Using Small Subunit Ribosomal RNA.

We propose a modified RNA-Seq method for small subunit ribosomal RNA (SSU rRNA)-based microbial community analysis that depends on the direct ligation of a 5' adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10-100 ng) and does not require a DNA removal step. Using this method, we could obtain more 16S rRNA sequences of the same regions (variable regions V1-V2) without the interference of DNA in order to analyze OTU (operational taxonomic unit)-based microbial communities and diversity. The generated SSU rRNA sequences are also suitable for the coverage evaluation for bacterial universal primer 8F (Escherichia coli position 8 to 27), which is commonly used for bacterial 16S rRNA gene amplification. The modified RNA-Seq method will be useful to determine potentially active microbial community structures and diversity for various environmental samples, and will also be useful for identifying novel microbial taxa.

Draft Genome Sequence of n-Alkane-Utilizing Acinetobacter sp. Strain BS1, Isolated from Ethane Oxidation Culture.

Here, we report the draft whole-genome sequence of a bacterial strain, Acinetobacter sp. strain BS1, isolated from black soil during ethane oxidation culture. Medium- or long-chain alkane oxidation-related genes were identified; however, the short-chain alkane monooxygenase was not detected.

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method.

Intertidal mudflats are land-sea interaction areas and play important roles in global nutrient cycles. However, a comprehensive understanding of microbial communities in these mudflats remains elusive. In this study, mudflat sediment samples from the Dongtan wetland of Chongming Island, the largest alluvial island in the world, were collected. Using a modified metatranscriptomic method, the depth-wise distributions of potentially active microbial communities were investigated based on small subunit ribosomal RNA (SSU rRNA) sequences. Multiple environmental factors were also measured and analyzed in conjunction with the prokaryotic composition profiles. A prokaryotic diversity analysis based on the metatranscriptome datasets revealed two or threefold higher diversity indices (associated with potentially active microbes participating in biogeochemical processes in Dongtan) compared with the diversity indices based on 16S rRNA gene amplicons. Bacteria were numerically dominant relative to archaea, and the potentially active prokaryotic taxa were mostly assigned to the bacterial phyla Chloroflexi, Acidobacteria, and Bacteroidetes and the classes Delta- and Gamma-proteobacteria, along with the archaeal lineages phylum Bathyarchaeota and the order Thermoplasmatales. The total nitrogen and carbon content of the sediment samples were environmental factors that significantly affected the depth-wise distributions of both bacterial and archaeal communities. Furthermore, the activity of potentially active taxa (including the prevalent order Desulfobacterales and family Anaerolineaceae) appeared to be significantly underestimated by PCR-based methods, notably at the DNA level, and indicates that using normal PCR amplification of DNA limits the study of potential microbial activity. This is the first study of potentially active microbial communities in depth-wise sediments from Dongtan. The improved knowledge of microbial communities in Dongtan provides a foundation for exploring biogeochemical cycling and microbial functions.

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples.

RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5' adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10-100 ng) and does not require a DNA removal step. The method was initially tested on three mock communities synthesized with enriched SSU rRNA of archaeal, bacterial and fungal isolates at different ratios, and was subsequently used for environmental samples of high or low biomass. For high-biomass salt-marsh sediments, enriched SSU rRNA and total nucleic acid-derived RNA-seq datasets revealed highly consistent community compositions for all of the SSU rRNA sequences, and as much as 46.4%-59.5% of 16S rRNA sequences were suitable for OTU (operational taxonomic unit)-based community and diversity analyses with complete coverage of V1-V2 regions. OTU-based community structures for the two datasets were also highly consistent with those determined by all of the 16S rRNA reads. For low-biomass samples, total nucleic acid-derived RNA-seq datasets were analyzed, and highly active bacterial taxa were also identified by the OTU-based method, notably including members of the previously underestimated genus Nitrospira and phylum Acidobacteria in tap water, members of the phylum Actinobacteria on a shower curtain, and members of the phylum Cyanobacteria on leaf surfaces. More than half of the bacterial 16S rRNA sequences covered the complete region of primer 8F, and non-coverage rates as high as 38.7% were obtained for phylum-unclassified sequences, providing many opportunities to identify novel bacterial taxa. This modified RNA-seq method will provide a better snapshot of diverse microbial communities, most notably by OTU-based analysis, even communities with low-biomass samples.