Search for: All records

Targeted amplicon sequencing is widely used in microbial ecology studies. However, sequencing artifacts and amplification biases are of great concern. To identify sources of these artifacts, a systematic analysis was performed using mock communities comprised of 16S rRNA genes from 33 bacterial strains. Our results indicated that while sequencing errors were generally isolated to low-abundance operational taxonomic units, chimeric sequences were a major source of artifacts. Singleton and doubleton sequences were primarily chimeras. Formation of chimeric sequences was significantly correlated with the GC content of the targeted sequences. Low-GC-content mock community members exhibited lower rates of chimeric sequence formation. GC content also had a large impact on sequence recovery. The quantitative capacity was notably limited, with substantial recovery variations and weak correlation between anticipated and observed strain abundances. The mock community strains with higher GC content had higher recovery rates than strains with lower GC content. Amplification bias was also observed due to the differences in primer affinity. A two-step PCR strategy reduced the number of chimeric sequences by half. In addition, comparative analyses based on the mock communities showed that several widely used sequence processing pipelines/methods, including DADA2, Deblur, UCLUST, UNOISE, and UPARSE, had different advantages and disadvantages in artifact removal and rare species detection. These results are important for improving sequencing quality and reliability and developing new algorithms to process targeted amplicon sequences.

Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.

 

Biofilms are aggregates of bacterial cells surrounded by an extracellular matrix. Much progress has been made in studying biofilm growth on solid substrates; however, little is known about the biophysical mechanisms underlying biofilm development in three-dimensional confined environments in which the biofilm-dwelling cells must push against and even damage the surrounding environment to proliferate. Here, combining single-cell imaging, mutagenesis, and rheological measurement, we reveal the key morphogenesis steps ofVibrio choleraebiofilms embedded in hydrogels as they grow by four orders of magnitude from their initial size. We show that the morphodynamics and cell ordering in embedded biofilms are fundamentally different from those of biofilms on flat surfaces. Treating embedded biofilms as inclusions growing in an elastic medium, we quantitatively show that the stiffness contrast between the biofilm and its environment determines biofilm morphology and internal architecture, selecting between spherical biofilms with no cell ordering and oblate ellipsoidal biofilms with high cell ordering. When embedded in stiff gels, cells self-organize into a bipolar structure that resembles the molecular ordering in nematic liquid crystal droplets. In vitro biomechanical analysis shows that cell ordering arises from stress transmission across the biofilm–environment interface, mediated by specific matrix components. Our imaging technique and theoretical approach are generalizable to other biofilm-forming species and potentially to biofilms embedded in mucus or host tissues as during infection. Our results open an avenue to understand how confined cell communities grow by means of a compromise between their inherent developmental program and the mechanical constraints imposed by the environment.

 

Biological systems have a remarkable capability of synthesizing multifunctional materials that are adapted for specific physiological and ecological needs. When exploring structure–function relationships related to multifunctionality in nature, it can be a challenging task to address performance synergies, trade-offs, and the relative importance of different functions in biological materials, which, in turn, can hinder our ability to successfully develop their synthetic bioinspired counterparts. Here, we investigate such relationships between the mechanical and optical properties in a multifunctional biological material found in the highly protective yet conspicuously colored exoskeleton of the flower beetle, Torynorrhina flammea . Combining experimental, computational, and theoretical approaches, we demonstrate that a micropillar-reinforced photonic multilayer in the beetle’s exoskeleton simultaneously enhances mechanical robustness and optical appearance, giving rise to optical damage tolerance. Compared with plain multilayer structures, stiffer vertical micropillars increase stiffness and elastic recovery, restrain the formation of shear bands, and enhance delamination resistance. The micropillars also scatter the reflected light at larger polar angles, enhancing the first optical diffraction order, which makes the reflected color visible from a wider range of viewing angles. The synergistic effect of the improved angular reflectivity and damage localization capability contributes to the optical damage tolerance. Our systematic structural analysis of T. flammea ’s different color polymorphs and parametric optical and mechanical modeling further suggest that the beetle’s microarchitecture is optimized toward maximizing the first-order optical diffraction rather than its mechanical stiffness. These findings shed light on material-level design strategies utilized in biological systems for achieving multifunctionality and could thus inform bioinspired material innovations. 

Water droplet transport on fibers is of great importance for achieving high water collection efficiency from fog. Here, we exploit a new droplet sliding mechanism to accelerate the droplet coalescence and collection for highly efficient fog harvesting by coating hydrophilic microfibers with superhydrophobic layers of assembled carbon nanoparticles. We find that during the initial water collection, unlike the pinned droplets having axisymmetric barrel shapes wrapped around uncoated microfibers, the hanging droplets on coated microfibers with non-wrapping clamshell shapes are highly mobile due to their lower contact hysteresis adhesion; these are observed to oscillate, coalesce, and sweep the growing droplets along the horizontally placed microfibers. The driving force for droplet transport is mainly ascribed to the coalescence energy release and fog flow. After introducing small gravity force by tilting coated microfibers with a small angle of 5°, we find that it can effectively drive the oscillating mobile droplets for directional transport by rapidly sweeping the droplets with a much higher frequency. Finally, the water collection rate from fog on uncoated microfibers over a prolonged duration is found to be improved over 2 times after superhydrophobic coating, and it is further enhanced over 5 times after a small tilting angle of 5°. 

Kirigami, the ancient paper art of cutting, has recently emerged as a new approach to construct metamaterials with novel properties imparted by cuts. However, most studies are limited to thin sheets‐based 2D kirigami metamaterials with specific forms and limited reconfigurability due to planar connection constraints of cut units. Here, 3D modular kirigami is introduced by cutting bulk materials into spatially closed‐loop connected cut cubes to construct a new class of 3D kirigami metamaterials. The module is transformable with multiple degrees of freedom that can transform into versatile distinct daughter building blocks. Their conformable assembly creates a wealth of reconfigurable and disassemblable metamaterials with diverse structures and unique properties, including reconfigurable 1D column‐like materials, 2D lattice‐like metamaterials with phase transition of chirality, as well as 3D frustration‐free multilayered metamaterials with 3D auxetic behaviors and programmable deformation modes. This study largely expands the design space of kirigami metamaterials from 2D to 3D.