Representations of solutions of the wave equation based on relativistic wavelets

A representation of solutions of the wave equation with two spatial coordinates in terms of localized elementary ones is presented. Elementary solutions are constructed from four solutions with the help of transformations of the affine Poincar\'e group, i.e., with the help of translations, dilations in space and time and Lorentz transformations. The representation can be interpreted in terms of the initial-boundary value problem for the wave equation in a half-plane. It gives the solution as an integral representation of two types of solutions: propagating localized solutions running away from the boundary under different angles and packet-like surface waves running along the boundary and exponentially decreasing away from the boundary. Properties of elementary solutions are discussed. A numerical investigation of coefficients of the decomposition is carried out. An example of the field created by sources moving along a line with different speeds is considered, and the dependence of coefficients on speeds of sources is discussed.Comment: submitted to J. Phys. A: Math. Theor., 20 pages, 6 figure

Defining the Rhizobium leguminosarum Species Complex

Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a ‘natural’ unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, “R. indicum” and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains

Defining the Rhizobium leguminosarum Species Complex

Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a ‘natural’ unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, “R. indicum” and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains

Two-particle correlations in azimuthal angle and pseudorapidity in inelastic p + p interactions at the CERN Super Proton Synchrotron

Results on two-particle ΔηΔϕ correlations in inelastic p + p interactions at 20, 31, 40, 80, and 158 GeV/c are presented. The measurements were performed using the large acceptance NA61/SHINE hadron spectrometer at the CERN Super Proton Synchrotron. The data show structures which can be attributed mainly to effects of resonance decays, momentum conservation, and quantum statistics. The results are compared with the Epos and UrQMD models.ISSN:1434-6044ISSN:1434-605

Microbial Composition on Abandoned and Reclaimed Mining Sites in the Komi Republic (North Russia)

Restoration of anthropogenically disturbed soils is an urgent problem in modern ecology and soil biology. Restoration processes in northern environments are especially important, due to the small amounts of fertile land and low levels of natural succession. We analyzed the soil microbiota, which is one of the indicators of the succession process is the soil. Samples were obtained from three disturbed soils (self-overgrown and reclaimed quarries), and two undisturbed soils (primary and secondary forests). Primary Forest soil had a well-developed soil profile, and a low pH and TOC (total organic carbon) amount. The microbial community of this soil had low richness, formed a clear remote cluster in the beta-diversity analysis, and showed an overrepresentation of Geobacter (Desulfobacteriota). Soil formation in clay and limestone abandoned quarries was at the initial stage, and was caused by both a low rate of mineral profile formation and severe climatic conditions in the region. Microbial communities of these soils did not have specific abundant taxa, and included a high amount of sparse taxa. Differences in taxa composition were correlated with abiotic factors (ammonium concentration), which, in turn, can be explained by the parent rock properties. Limestone quarry reclaimed by topsoil coverage resulted in an adaptation of the top soil microbiota to a novel parent rock. According to the CCA analysis, the microbial composition of samples was connected with pH, TOC and ammonium nitrogen concentration. Changes in pH and TOC were connected with ASVs from Chloroflexota, Gemmatimonadota and Patescibacteria. ASVs from Gemmatimonadota also were correlated with a high ammonium concentration

Be aware of the allele-specific bias and compositional effects in multi-template PCR

High-throughput sequencing of amplicon libraries is the most widespread and one of the most effective ways to study the taxonomic structure of microbial communities, even despite growing accessibility of whole metagenome sequencing. Due to the targeted amplification, the method provides unparalleled resolution of communities, but at the same time perturbs initial community structure thereby reducing data robustness and compromising downstream analyses. Experimental research of the perturbations is largely limited to comparative studies on different PCR protocols without considering other sources of experimental variation related to characteristics of the initial microbial composition itself. Here we analyse these sources and demonstrate how dramatically they effect the relative abundances of taxa during the PCR cycles. We developed the mathematical model of the PCR amplification assuming the heterogeneity of amplification efficiencies and considering the compositional nature of data. We designed the experiment—five consecutive amplicon cycles (22–26) with 12 replicates for one real human stool microbial sample—and estimated the dynamics of the microbial community in line with the model. We found the high heterogeneity in amplicon efficiencies of taxa that leads to the non-linear and substantial (up to fivefold) changes in relative abundances during PCR. The analysis of possible sources of heterogeneity revealed the significant association between amplicon efficiencies and the energy of secondary structures of the DNA templates. The result of our work highlights non-trivial changes in the dynamics of real-life microbial communities due to their compositional nature. Obtained effects are specific not only for amplicon libraries, but also for any studies of metagenome dynamics

Diversity Indices of Plant Communities and Their Rhizosphere Microbiomes: An Attempt to Find the Connection

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Despite close connection and mutual influence in this system, the knowledge about the connection of plant and rhizosphere diversity is still controversial. One of the most valuable factors of this uncertainty is a rough estimation of plant diversity. NGS sequencing can make the estimations of the plant community more precise than classical geobotanical methods. We investigate fallow and crop sites, which are similar in terms of environmental conditions and soil legacy, yet at the same time are significantly different in terms of plant diversity. We explored amplicons of both the plant root mass (ITS1 DNA) and the microbial communities (16S rDNA); determined alpha- and beta-diversity indices and their correlation, and performed differential abundance analysis. In the analysis, there is no correlation between the alpha-diversity indices of plants and the rhizosphere microbial communities. The beta-diversity between rhizosphere microbial communities and plant communities is highly correlated (R = 0.866, p = 0.01). ITS1 sequencing is effective for the description of plant root communities. There is a connection between rhizosphere communities and the composition of plants, but on the alpha-diversity level we found no correlation. In the future, the connection of alpha-diversities should be explored using ITS1 sequencing, even in more similar plant communities—for example, in different synusia

IAPT chromosome data 35

WOS:000730260200048The study was financially supported by the Russian Foundation for Basic Research (RFBR), research projects No. 18-34-20056, 18-04-00653 and 20-54-53008 to Andrey Erst and Elizaveta Yu

Correction: Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems.

[This corrects the article DOI: 10.1371/journal.pone.0145072.]

RIAM: A Universal Accessible Protocol for the Isolation of High Purity DNA from Various Soils and Other Humic Substances

A single universal open protocol RIAM (named after Research Institute for Agricultural Microbiology) for the isolation of high purity DNA from different types of soils and other substrates (high and low in humic, clay content, organic fertilizer, etc.) is proposed. The main features of the RIAM protocol are the absence of the sorption–desorption stage on silica columns, the use of high concentrations of phosphate in buffers, which prevents DNA sorption on minerals, and DNA precipitation using CTAB. The performance of RIAM was compared with a reference commercial kit and showed very good results in relation to the purity and quantity of DNA, as well as the absence of inhibitory activity on PCR. In all cases, the RIAM ensured the isolation of DNA in quantities much greater than the commercial kit without the effect of PCR inhibition up to 50 ng DNA per reaction in a volume of 15 µL. The latter circumstance along with the ability of the protocol to extract low molecular weight DNA fractions makes the method especially suitable for those cases where quantitative assessments, detection of minor components of soil microbiota, and completeness of isolation of all DNA fractions are required