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The active sound generation technique for automobiles, where car sounds can be synthesized by means of electronic sound production, is one of the effective methods to achieve the target sound. A method for active sound generation of automobile based on the granular synthesis algorithm is put forward here to avoid the broadband beating phenomena that occur due to the mismatch of parameters of sound granular signals. The comparison of the function expression of sound signal and Hilbert transformation is performed based on the principle of overlap and add; moreover, those parameters (phase, frequency and amplitude) of sound signals are interpolated by means of the Hermite interpolation algorithm which can ensure the continuity of the phase, frequency and amplitude curves. Thus, the transition audio is constructed by means of the sound signal function here to splice the adjacent sound granules. Our simulations show that our method can be applied to solve the current broadband beating issue for splicing sound granules and achieve natural continuity of synthesized car sounds. The subjective test results also indicate that our transition audio can produce high quality audio restitution.

Motivation Metagenome-assembled genomes (MAGs) have substantially extended our understanding of microbial functionality. However, 16S rRNA genes, which are commonly used in phylogenetic analysis and environmental surveys, are often missing from MAGs. Here, we developed MarkerMAG, a pipeline that links 16S rRNA genes to MAGs using paired-end sequencing reads. Results Assessment of MarkerMAG on three benchmarking metagenomic datasets with various degrees of complexity shows substantial increases in the number of MAGs with 16S rRNA genes and a 100% assignment accuracy. MarkerMAG also estimates the copy number of 16S rRNA genes in MAGs with high accuracy. Assessments on three real metagenomic datasets demonstrate 1.1- to 14.2-fold increases in the number of MAGs with 16S rRNA genes. We also show that MarkerMAG-improved MAGs increase the accuracy of functional prediction from 16S rRNA gene amplicon data. MarkerMAG is helpful in connecting information in MAG databases with those in 16S rRNA databases and surveys and hence contributes to our increasing understanding of microbial diversity, function and phylogeny. Availability and implementation MarkerMAG is implemented in Python3 and freely available at https://github.com/songweizhi/MarkerMAG. Supplementary information Supplementary data are available at Bioinformatics online.

The active sound design (ASD) technology is one of the most flexible methods to achieve the diverse design of automobile sound, in which the active sound synthesis algorithm is essential. However, in previous works, the discontinuity phenomena always appear in the synthesized sound. Thus, a new method of active engine sound synthesis based on cylinder pressure signals is proposed in this paper for the sound synthesis algorithm of ASD technique. Firstly, the index matrix of sound grains is constructed based on the periodicity of engine cylinder pressure signal. Then the frame length and frame shift are defined by tracing the time step of Revolutions Per Minute (RPM) of engine, and the hamming window function is constructed to extract sound grains. Subsequently, the overlap-and-add (OLA) method is used to realize the synthesis of engine sounds with different durations. In addition, the code program of proposed algorithm is written and the ASD prototype system is built respectively to synthesize the engine sounds. Finally, a similarity evaluation metric is defined to verify the effectiveness of proposed algorithm. The results show that our algorithm not only restitutes the main features of original sound, but also satisfies both the real-time feedback on the driving status and the continuity of synthesized sound. It contributes to the development of real-time ASD engineering for automobiles.

Nonlinear energy sink (NES) can transfer energy efficiently and unidirectionally through target energy transfer (TET). However, its performance is sensitive to the excitation intensity. When the excitation is lower than the trigger threshold, the performance of NES will be greatly reduced. When the excitation exceeds the trigger threshold, its performance will decrease with the increase of the excitation. At the same time, strong excitation may lead to high branch response of the linear oscillator (LO) under harmonic excitation, which will make the vibration worse. In view of those, NES with negative stiffness is proposed to improve the vibration reduction performance under low disturbance. Meanwhile, 2DOF parallel nonlinear energy sink (PNES) is used to ensure the performance under strong excitation. Two important indexes of bistable NES (BNES), the threshold of the transition from intra-well periodic vibration to inter-well chaotic vibration, and the strongly modulated response (SMR) trigger threshold of BNES, are analyzed in this paper. The parameters of bistable parallel nonlinear energy sink (BPNES) are optimized, and the vibration performance of BPNES and cubic stiffness NES (CNES) is compared. The analysis results show that, the performance of BPNES is better than that of CNES under both impulse and harmonic excitation.

Carbon fixation is a critical process for our planet; however, its distribution across the bacterial and archaeal domains of life has not been comprehensively studied. Here, we performed an analysis of 52,515 metagenome-assembled genomes and discover carbon fixation pathways in 1,007 bacteria and archaea. We reveal the genomic potential for carbon fixation through the reverse tricarboxylic acid cycle in previously unrecognized archaeal and bacterial phyla (i.e. Thermoplasmatota and Elusimicrobiota) and show that the 3-hydroxypropionate bi-cycle is not, as previously thought, restricted to the phylum Chloroflexota. The data also substantially expand the phylogenetic breadth for autotrophy through the dicarboxylate/4-hydroxybutyrate cycle and the Calvin–Benson–Bassham cycle. Finally, the genomic potential for carbon fixation through the 3-hydroxypropionate/4-hydroxybutyrate cycle, previously exclusively found in Archaea, was also detected in the Bacteria. Carbon fixation thus appears to be much more widespread than previously known, and this study lays the foundation to better understand the role of archaea and bacteria in global primary production and how they contribute to microbial carbon sinks.

The dynamics and vibration reduction performance of bistable nonlinear energy sink (BNES) are studied in this paper. First, the negative stiffness of BNES is realized by geometric nonlinearity, and the dynamics model of the system is established. The slow flow equation of the system under 1:1 main resonance is analyzed based on the complexification-averaging (CX-A) method, and the boundary conditions of saddle node bifurcation and Hopf bifurcation are analyzed. Second, the slow invariant manifold (SIM) of the BNES is studied based on multiscale analysis, and the excitation threshold of strongly modulated response (SMR) is analyzed; the analysis results are verified by the numerical method. The results show that the analytical solution is highly consistent with the numerical solution, and the error is less than 1%. Finally, the influence of structural parameters on the vibration reduction performance is analyzed and optimized. The vibration reduction performance of BNES and CNES is compared, and the results show that the BNES has better vibration reduction performance in the full frequency band.

Horizontal gene transfer (HGT) is thought to be an important driving force for microbial evolution and niche adaptation and has been show in vitro to occur frequently in biofilm communities. However, the extent to which HGT takes place and what functions are being transferred in more complex and natural biofilm systems remains largely unknown. To address this issue, we investigated here HGT and enrichment of gene functions in the biofilm community of the common kelp (macroalgae) Ecklonia radiata in comparison to microbial communities in the surrounding seawater. We found that HGTs in the macroalgal biofilms were dominated by transfers between bacterial members of the same class or order and frequently involved genes for nutrient transport, sugar and phlorotannin degradation as well as stress responses, all functions that would be considered beneficial for bacteria living in this particular niche. HGT did not appear to be driven by mobile gene elements, indicating rather an involvement of unspecific DNA uptake (e.g. natural transformation). There was also a low overlap between the gene functions subject to HGT and those enriched in the biofilm community in comparison to planktonic community members. This indicates that much of the functionality required for bacteria to live in an E. radiata biofilm might be derived from vertical or environmental transmissions of symbionts. This study enhances our understanding of the relative role of evolutionary and ecological processes in driving community assembly and genomic diversity of biofilm communities.

The classical transfer path analysis (TPA) method has become a standard measurement method. It has high accuracy but remains a time-consuming and complex measurement, which limits its application in industry. The operational transfer path analysis (OTPA) method is known for its high efficiency; however, the accuracy of this method for industrial application is controversial. To separate the intake and exhaust noises in the vehicle, this study presents a novel TPA method called simulated operational path analysis (SOPA). The transmissibility from the reference point to the target response point is estimated by using an external noise source to simulate the intake and exhaust noises under operating condition. In addition, the improved dual-microphone noise reduction technology is used to eliminate the background noise in the reference response. The method is validated by an experimental bench. The result shows that its high accuracy can be compared with the classical TPA method. Because there is no need to use a special miniature volume source to estimate the passive subsystem frequency response functions and identify the operational source loads, the efficiency of the SOPA method is higher than the classic TPA method and is close to the OTPA method.

We report a compact lensless microscopy by rotating a binary mask with random intensity distribution.

We propose a dual-modal light-field micro-endoscopy using the single-mode fiber bundle in this work, obtaining the single-shot 3D endoscopic imaging in both the bright-field and fluorescence modes.

The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.

Background: The deep-sea harbors the majority of the microbial biomass in the Ocean, and it is a key site for organic matter (OM) remineralization and storage in the biosphere. Microbial metabolism in the deep ocean is greatly controlled by the generally depleted but periodically fluctuating supply of OM. Currently, little is known about metabolic potentials of dominant deep-sea microbes to cope with the variable OM inputs, especially for those living in the hadal trenches - the deepest part of the ocean. Results: In this study, we report the first extensive examination of the metabolic potentials of hadal sediment Chloroflexi, a dominant phylum in hadal trenches and the global deep ocean. Sixty-two metagenome-assembled-genomes (MAGs) were reconstructed from nine metagenomic datasets derived from sediments of the Mariana Trench. These MAGs represent six novel species, four novel genera, one novel family and one novel order within the classes Anaerolineae and Dehalococcoidia. Fragment recruitment showed that these MAGs are globally distributed in deep-sea waters and surface sediments, and transcriptomic analysis indicated their in-situ activities. Metabolic reconstruction showed that hadal Chloroflexi mainly had a heterotrophic lifestyle, with the potential to degrade a wide range of organic carbon, sulfur, and halogenated compounds. Our results revealed for the first time that hadal Chloroflexi harbor pathways for the complete hydrolytic or oxidative degradation of various recalcitrant OM, including aromatic compounds (e.g. benzoate), polyaromatic hydrocarbons (e.g. fluorene), polychlorobiphenyl (e.g. 4-chlorobiphenyl) and organochlorine compounds (e.g. chloroalkanes, chlorocyclohexane). Moreover, these organisms showed the potential to synthesize energy storage compounds (e.g. trehalose), and had regulatory modules to respond to changes in nutrient conditions. These metabolic traits lead us to postulate that the Chloroflexi may follow a “feast and famine” metabolic strategy, allowing them to efficiently consume labile OM and store the energy under OM rich conditions, and to survive under OM limitations by utilizing stored energy and degrading recalcitrant OM. Conclusion: This study expands the current knowledge on metabolic strategies in deep-ocean Chlorolfexi, and highlights their significance in deep-sea carbon, sulfur and halogen cycles. The metabolic plasticity likely provides Chloroflexi with advantages for the survival under variable and heterogenic OM inputs in the deep ocean.

With the increase of excitation, the nonlinear energy sink (NES) will cause the controlled system to produce high branch response and lead to sudden failure. Increasing the mass of the NES can prevent the generation of high branch within a certain range, but high-precision instruments such as aerospace have strict requirements for additional mass. A parallel NES (PNES) is proposed to improve the robustness without increasing the mass. The slow flow equations of the system are derived by using complexification-averaging (CX-A) method, and the vibration suppression performance of the PNES is analyzed from the frequency domain. Compared with purely cubic stiffness NES (CNES), it is found that PNES has better performance near the main resonance. And it is not easy to produce high branch response under the same excitation intensity. Finally, the performance of PNES and CNES is compared by numerical method from time domain and energy spectrum. The results show that when PNES is attached, the attenuation time of the controlled system is shorter under impact excitation, much more, the controlled system has a smaller energy amplitude near the main resonance under harmonic excitation.

Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.

We introduce the Wirtinger gradient descent optimization into the multi-height lensless microscopy for noise-robust and high-quality reconstruction.

The link between guanine-cytosine (GC) content and thermal adaptation is controversial. Here, we compared maximum growth temperature (TMGT ) and genomics of 78 Cryobacterium strains to avoid unreliable conclusions resulting from distantly phylogenetic groups. Phylogenomic analysis revealed this taxon had much higher diversification than we knew. Interestingly, these strains showed thermotolerance divergence with phylogenetic cohesion. A significant difference was found between TMGT ≤ 20°C strains and TMGT > 20°C strains in genomic GC content which mainly caused by variation of GC3. TMGT ≤ 20°C strains tended to use synonymous codons ended with A/U, but TMGT > 20°C strains tended to use G/C. Lower GC content at synonymous sites (≈GC3) of TMGT ≤ 20°C strains could provide lower intrinsic DNA flexibility which strongly associated with optimal molecular dynamics, and then guarantee DNA function at lower growth temperatures. This analysis of codon bias revealed close relationships for thermal adaptation, GC content at synonymous sites (≈GC3), intrinsic DNA flexibility and optimal DNA dynamics. Natural selection was main force driving this codon bias; strains with lower TMGT endured stronger natural selection. Therefore, this study provided molecular basis for bacterial adaptive evolution from moderate temperature to low temperature.

Background Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT identification at the community level. Results Assessment of MetaCHIP’s performance on simulated datasets revealed that it can predict HGTs with various degrees of genetic divergence from metagenomic datasets. The results also indicated that the detection of very recent gene transfers (i.e. those with low levels of genetic divergence) from metagenomics datasets is largely affected by the read assembly step. Comparison of MetaCHIP with a previous analysis on soil bacteria showed a high level of consistency for the prediction of recent HGTs and revealed a large number of additional non-recent gene transfers, which can provide new biological and ecological insight. Assessment of MetaCHIP’s performance on real metagenomic datasets confirmed the role of HGT in the spread of genes related to antibiotic resistance in the human gut microbiome. Further testing also showed that functions related to energy production and conversion as well as carbohydrate transport and metabolism are frequently transferred among free-living microorganisms. Conclusion MetaCHIP provides an opportunity to study HGTs among members of a microbial community and therefore has several applications in the field of microbial ecology and evolution. MetaCHIP is implemented in Python and freely available at https://github.com/songweizhi/MetaCHIP .

Supplementary information. (DOCX 448 kb)

Background High-quality, completed genomes are important to understand the functions of marine bacteria. PacBio sequencing technology provides a powerful way to obtain high-quality completed genomes. However individual library production is currently still costly, limiting the utility of the PacBio system for high-throughput genomics. Here we investigate how to generate high-quality genomes from pooled marine bacterial genomes. Results Pooled genomic DNA from 10 marine bacteria were subjected to a single library production and sequenced with eight SMRT cells on the PacBio RS II sequencing platform. In total, 7.35 Gbp of long-read data was generated, which is equivalent to an approximate 168× average coverage for the input genomes. Genome assembly showed that eight genomes with average nucleotide identities (ANI) lower than 91.4% can be assembled with high-quality and completion using standard assembly algorithms (e.g. HGAP or Canu). A reference-based reads phasing step was developed and incorporated to assemble the complete genomes of the remaining two marine bacteria that had an ANI > 97% and whose initial assemblies were highly fragmented. Conclusions Ten complete high-quality genomes of marine bacteria were generated. The findings and developments made here, including the reference-based read phasing approach for the assembly of highly similar genomes, can be used in the future to design strategies to sequence pooled genomes using long-read sequencing.

Summary Microbial genomes have recently been reconstructed from metagenomic datasets using binning approaches. Inconsistent binning results are however often observed between different binning programs, likely due to the different algorithms or statistical models used. We present Binning_refiner, a pipeline that merges the results of different binning programs. Our results demonstrated that Binning_refiner can significantly reduce the contamination level of genome bins and increase the total size of contamination-free and ‘good-quality’ genome bins. Binning_refiner is thus an useful tool to improve the quality of genome bins derived from metagenomic data. Availability and Implementation Binning_refiner is implemented in Python3 and is freely available at: https://github.com/songweizhi/Binning_refiner. Supplementary information Supplementary data are available at Bioinformatics online.

An OmpR gene, named OmpR503, was cloned from the Antarctic psychrotrophic bacterium Psychrobacter sp. G according to its genomic draft. The deduced amino acid sequences of OmpR503 were highly conserved with other known protein members of OmpR family. qRT-PCR analysis showed that the expression of OmpR503 gene was significantly enhanced by high salinity (90, 120). The expression of OmpR503 gene was also significantly increased at low temperature (0, 10 °C), whereas depressed at high temperature (30 °C). When the strain was subjected to combined stress (0 °C with a salinity of 90), the expression of OmpR503 gene was increased significantly, which was up to 3.0-fold. In Antarctica, freezing tolerance of psychrotrophic bacteria is often accompanied by tolerance to osmotic stress caused by a lack of free water, thus the cold inducibility of OmpR503 gene might help the strain adapt to the harsh environment more efficiently.

Psychrobacter has been regarded as an important genus for bacterial cold adaptation studies. However, members of this genus are highly varied in terms of both cold adaptability and genome content. To get an understanding of the diversity of members of this genus, five Psychrobacter strains (G, K5, 273-4, PAMC21119 and PRwf-1), with publicly available complete/draft genome, were selected and comprehensive comparative genomics analyses were performed among them. The closest phylogenetic relationship, highest average nucleotide identity (96.78%) and best sequence synteny were identified between strains G and K5. These findings suggest they belong to the same species, despite the long geographic distance between them (Antarctic and Siberia). 4542 gene clusters in total were identified from the five genomes, and of which 1424 were shared by all of them. The number of genes unique to strains G, K5, 273-4, PAMC21119 and PRwf-1 are 183, 188, 300, 637 and 665, respectively. COG assignment revealed their differences in gene content related to stress response. The extensive sequence rearrangements and the large number of genes unique to strain PAMC21119 and PRwf-1 suggest they may have experienced a high level of gene exchanges in the permafrost soil and the surface of fish skin.

Low temperature is one of the major environmental challenges that Antarctic bacteria must face. Detailed studies of cold shock responses of cold-adapted microorganisms are still insufficient. Here, we cloned three cold shock protein (CSP) genes (Csp1137, Csp2039, and Csp2531) in the Antarctic bacterium Psychrobacter sp. G and their regulatory sequences were identified. The three CSPs were highly conserved with other known CspAs. qRT-PCR was performed to evaluate their expression characteristics under stress conditions, and the potential influence of regulatory sequences also was analyzed. The expression of Csp1137 was enhanced both by low (0, 10 °C) and high temperature (30 °C). The expression of Csp2039 was enhanced by low temperature (0 °C), but was lower than that of Csp1137. This can be explained by the absence in Csp2039 of the AT-rich UP element. Different from Csp1137, the expression of Csp2531 was inhibited by low temperature (0 °C), even with the presence of AT-rich UP element, and it was not sensitive to high temperature (30 °C). The expression of Csp1137 was enhanced by high salinity (90, 120), whereas that of Csp2531was enhanced by low salinity (0, 15). At 0 °C and a salinity of 15, the expression of Csp1137 was repressed initially, but then it increased greatly during the next 10 h. The expressions of Csp2039 and Csp2531 were repressed significantly under four different combinations of stress conditions. Our results showed that the role of the upstream regulation sequences were much more complex than previously thought. Also, gene expressions were also affected by the environmental salinity. These are helpful in further clarification of the adaptation mechanism of Psychrobacter sp. G.

Here, we report the complete genome sequence of Psychrobacter sp. strain G, isolated from King George Island, Antarctica, which can produce lipolytic enzymes at low temperatures. The genomics information of this strain will facilitate the study of the physiology, cold adaptation properties, and evolution of this genus.

Temperature and salinity fluctuations are two of the most important factors affecting the growth of polar bacteria. In an attempt to better understand the function of heat-shock proteins (HSPs) in the adaptive mechanisms of the Antarctic psychrotrophic bacterium Psychrobacter sp. G to such conditions, genes Hsp845, Hsp2538, Hsp2666, and Hsp2667 were cloned on the basis of the draft genome. The expression characteristics of these HSP genes under different stress conditions were analyzed by the qRT-PCR method. Expression of Hsp845 and Hsp2667 was inhibited significantly by low temperature (0 and 10 °C, respectively). There was no difference of expression when Hsp2538 and Hsp2666 were exposed to 0 °C but the expression of Hsp2666 was inhibited when exposed to 10 °C. Expression of Hsp2538 and Hsp2667 was not sensitive but expression of Hsp845 and Hsp2666 was increased at low salinity (0 and 15, respectively). Expression of the four HSP genes was enhanced at high salinity (90 and 120) and at high temperature independent of salinity. By contrast, low temperature had no significant effect independent of salinity.