Deep Functional Profiling of Wild Animal Microbiomes Reveals Probiotic Bacillus pumilus Strains with a Common Biosynthetic Fingerprint.

The biodiversity of microorganisms is maintained by intricate nets of interactions between competing species. Impaired functionality of human microbiomes correlates with their reduced biodiversity originating from aseptic environmental conditions and antibiotic use. Microbiomes of wild animals are free of these selective pressures. Microbiota provides a protecting shield from invasion by pathogens in the wild, outcompeting their growth in specific ecological niches. We applied ultrahigh-throughput microfluidic technologies for functional profiling of microbiomes of wild animals, including the skin beetle, Siberian lynx, common raccoon dog, and East Siberian brown bear. Single-cell screening of the most efficient killers of the common human pathogen Staphylococcus aureus resulted in repeated isolation of Bacillus pumilus strains. While isolated strains had different phenotypes, all of them displayed a similar set of biosynthetic gene clusters (BGCs) encoding antibiotic amicoumacin, siderophore bacillibactin, and putative analogs of antimicrobials including bacilysin, surfactin, desferrioxamine, and class IId cyclical bacteriocin. Amicoumacin A (Ami) was identified as a major antibacterial metabolite of these strains mediating their antagonistic activity. Genome mining indicates that Ami BGCs with this architecture subdivide into three distinct families, characteristic of the B. pumilus, B. subtilis, and Paenibacillus species. While Ami itself displays mediocre activity against the majority of Gram-negative bacteria, isolated B. pumilus strains efficiently inhibit the growth of both Gram-positive S. aureus and Gram-negative E. coli in coculture. We believe that the expanded antagonistic activity spectrum of Ami-producing B. pumilus can be attributed to the metabolomic profile predetermined by their biosynthetic fingerprint. Ultrahigh-throughput isolation of natural probiotic strains from wild animal microbiomes, as well as their metabolic reprogramming, opens up a new avenue for pathogen control and microbiome remodeling in the food industry, agriculture, and healthcare.

Semi-empirical and ab initio calculations for crystals under pressure at fixed temperatures: the case of guanidinium perchlorate.

A simple semi-empirical approach is proposed to calculate structure and properties of crystals under pressure at fixed temperatures. The computed semi-empirical pressure dependencies for guanidinium perchlorate are in good agreement with available experimental data. Ab initio results within quasi-harmonic approximation for guanidinium perchlorate are also presented.

The nature of the chemical bond in oxyanionic crystals based on QTAIM topological analysis of electron densities.

The nature of the chemical bond in 31 oxyanionic crystals was analyzed using ab initio calculations and quantum theory of atoms in molecules (QTAIM). The QTAIM topological analysis of the calculated electron densities in oxyanionic crystals revealed that some of the metal-oxygen, metal⋯metal, metal-ligand and hydrogen bonds are partly covalent in nature. The covalency criteria for metal-oxygen and hydrogen bonds based on electron densities at the bond critical points were obtained. The densities at the bond critical points correlate with the corresponding overlap populations, electronegativities, H-bond lengths and energies. The distances between cationic nuclei and the bond critical points correlate with cationic radii. There are weak anion⋯anion interactions.

Compressibility Anisotropy and Electronic Properties of Oxyanionic Hydrates.

The structural and electronic properties of oxyanionic crystalline hydrates, LiNO3·3H2O, LiClO4·3H2O, and NaClO4·H2O, have been studied using density functional theory including van der Waals interactions. It is established that the linear compressibility of lithium perchlorate trihydrate is anisotropic (a < c) and positive, while lithium nitrate trihydrate and sodium perchlorate monohydrate demonstrate negative linear compressibility along the b and c axes, respectively. Deformation of Ow-H···O hydrogen bonding motifs is correlated with the negative linear compressibility. The band gaps of lithium nitrate and lithium perchlorate trihydrates decrease with pressure, whereas the band gap of sodium perchlorate monohydrate increases.

Hydrostatic Pressure Effects on Structural and Electronic Properties of ETN and PETN from First-Principles Calculations.

We studied the structural and electronic properties of pentaerythritol tetranitrate (PETN) and erythritol tetranitrate (ETN) crystals within the framework of density functional theory with van der Waals interactions. The computed lattice parameters have good agreement with experimental data. Electronic and structural properties of the crystals under 0-20 GPa hydrostatic pressure were studied. The parameters of equations of state calculated from the theoretical data show good agreement with experiment within the studied pressure intervals. We have also calculated the detonation velocity and pressure.

A parapatric propensity for breeding precludes the completion of speciation in common teal (Anas crecca, sensu lato).

Speciation is a process in which genetic drift and selection cause divergence over time. However, there is no rule dictating the time required for speciation, and even low levels of gene flow hinder divergence, so that taxa may be poised at the threshold of speciation for long periods of evolutionary time. We sequenced mitochondrial DNA (mtDNA) and eight nuclear introns (nuDNA) to estimate genomic levels of differentiation and gene flow between the Eurasian common teal (Anas crecca crecca) and the North American green-winged teal (Anas crecca carolinensis). These ducks come into contact in Beringia (north-eastern Asia and north-western North America) and have probably done so, perhaps cyclically, since the Pliocene-Pleistocene transition, ~2.6 Ma, when they apparently began diverging. They have diagnosable differences in male plumage and are 6.9% divergent in the mtDNA control region, with only 1 of 58 crecca and 2 of 86 carolinensis having haplotypes grouping with the other. Two nuclear loci were likewise strongly structured between these teal (Φ(st) ≥ 0.35), but six loci were undifferentiated or only weakly structured (Φ(st) = 0.0-0.06). Gene flow between crecca and carolinensis was ~1 individual per generation in both directions in mtDNA, but was asymmetrical in nuDNA, with ~1 and ~20 individuals per generation immigrating into crecca and carolinensis, respectively. This study illustrates that species delimitation using a single marker oversimplifies the complexity of the speciation process, and it suggests that even with divergent selection, moderate levels of gene flow may stall the speciation process short of completion.

The pollen metamorphosis phenomenon in Panax ginseng, Aralia elata and Oplopanax elatus; an addition to discussion concerning the Panax affinity in Araliaceae.

To find more morphological characteristics useful for discussion on aralian or non-aralian Panax affinity, pollen morphological diversity was comparatively analysed in P. ginseng, Aralia elata and Oplopanax elatus collected during their pollination periods. In the anthers of both the buds and open flowers, the pollen average diameter varied between some species-specific maximum and minimal measurement. However, the larger pollen grains were typically found in the buds whereas the smaller pollen prevailed in the open flowers, testifying to the pollen size diminution during anther maturation. Based on this finding, the subsequent examination of pollen according to size decrease was put into operation as a method of pollen modification for the study. The structural mechanisms of pollen metamorphosis were identified as not being species specific but rather universal. These mechanisms are suggested to be the shrinkage of the pollen vegetative cytoplasm, the intine enlargement, the deepening of three colporate apertures provided by exine sunken into enlarged intine areas, the aperture accretion as well as the transformation of the exine from thick/sculptured into thin/less sculptured. During 'size-reducing metamorphosis', the pollen grains changed dramatically, going through a species-specific set of intermediate morphs to the final species-specific morphotype. In P. ginseng this morphotype is round (diameter is about 16 microm), in A. elata it is round with a single projection (diameter is about 15 microm) and in O. elatus it is ovoid with a single projection (average diameter is about 18 microm). In addition, every species is peculiar in having the unique vegetative cytoplasm inclusions and individual construction of the largest pollen exine. From a phylogenetic perspective, these findings presumably add support to the option of equal remoteness of P. ginseng from A. elata and O. elatus. The characteristics found seem to be suitable for examination of Panax affinity, by the subsequent study of more Araliaceae representatives.