Investigation of the core microbiome in main soil types from the East European plain.

The main goal of modern microbial ecology is to determine the key factors influencing the global diversity of microorganisms. Because of their complexity, soil communities are largely underexplored in this context. We studied soil genesis (combination of various soil-forming processes, specific to a particular soil type) that is driven by microbial activity. To investigate the interrelation between soil type and microbial diversity, we analyzed six soil types that are common in Russia, the Crimea, and Kazakhstan using 16S rDNA pyrosequencing. Soils of different types varied in the taxonomic composition of microbial communities. Their core microbiomes comprised 47 taxa within the orders Solirubrobacteriales and Hyphomicrobiaceae and the Gaiellaceae family. Two species from Bradyrhizobiaceae and Solirubrobactriaceae were present in all samples, whereas most other taxa were soil-type specific. Multiple resampling analysis revealed that two random soil samples from the same soil type shared more taxa than two samples from different types. The differences in community composition were mostly affected by the variation in pH values and exchangeable potassium content. The results show that data on the soil microbiome could be used for soil identification and clarification of their taxonomic position.

Testing culture purity in prokaryotes: criteria and challenges.

Reliance on pure cultures was introduced at the beginning of microbiology as a discipline and has remained significant although their adaptive properties are essentially dissimilar from those of mixed cultures and environmental populations. They are needed for (i) taxonomic identification; (ii) diagnostics of pathogens; (iii) virulence and pathogenicity studies; (iv) elucidation of metabolic properties; (v) testing sensitivity to antibiotics; (vi) full-length genome assembly; (vii) strain deposition in microbial collections; and (viii) description of new species with name validation. Depending on the specific task there are alternative claims for culture purity, i.e., when conventional criteria are satisfied or when looking deeper is necessary. Conventional proof (microscopic and plating controls) has a low resolution and depends on the observer's personal judgement. Phenotypic criteria alone cannot prove culture purity and should be complemented with genomic criteria. We consider the possible use of DNA high-throughput culture sequencing data to define criteria for only one genospecies, axenic state detection panel and only one genome. The second and third of these are preferable, although their resolving capacity (depth) is limited. Because minor contaminants may go undetected, even with deep sequencing, the reliably pure culture would be a clonal culture launched from a single cell or trichome (multicellular bacterium). Although this type of culture is associated with technical difficulties and cannot be employed on a large scale (the corresponding inoculums may have low chances of growth when transferred to solid media), it is hoped that the high-throughput culturing methods introduced by 'culturomics' will overcome this obstacle.

The preservation of microbial DNA in archived soils of various genetic types.

This study is a comparative analysis of samples of archived (stored for over 70-90 years) and modern soils of two different genetic types-chernozem and sod-podzolic soils. We revealed a reduction in biodiversity of archived soils relative to their modern state. Particularly, long-term storage in the museum exerted a greater impact on the microbiomes of sod-podzolic soils, while chernozem samples better preserved the native community. Thus, the persistence of microbial DNA in soil is largely determined by the physico-chemical characteristics that differ across soil types. Chernozems create better conditions for the long-term DNA preservation than sod-podzolic soils. This results in supposedly higher levels of biodiversity conservation in the microbiomes of chernozem with preservation of major microbial taxa dominant in the modern (control) soil samples, which makes archived chernozems a promising object for paleosoil studies.

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

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