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

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

Phyllobacterium zundukense sp. nov., a novel species of rhizobia isolated from root nodules of the legume species Oxytropis triphylla (Pall.) Pers.

Gram-negative strains Tri-36, Tri-38, Tri-48T and Tri-53 were isolated from root nodules of the relict legume Oxytropis triphylla (Pall.) Pers. originating from Zunduk Cape (Baikal Lake region, Russia). 16S rRNA gene sequencing showed that the novel isolates were phylogenetically closest to the type strains Phyllobacterium sophorae LMG 27899(T), Phyllobacterium brassicacearum LMG 22836(T), Phyllobacterium endophyticum LMG 26470(T) and Phyllobacterium bourgognense LMG 22837(T) while similarity levels between the isolates and the most closely related strain P. endophyticum LMG 26470(T) were 98.899.5 %. The recA and glnII genes of the isolates showed highest sequence similarities with P. sophorae LMG 27899(T) (95.4 and 89.5 %, respectively) and P. brassicacearum LMG 22836(T) (91.4 and 85.1 %, respectively). Comparative analysis of phenotypic properties between the novel isolates and the closest reference strains P. sophorae LMG 27899(T), P. brassicacearum LMG 22836(T) and P. endophyticum LMG 26470(T) was performed using a microassay system. Average nucleotide identities between the whole genome sequences of the isolates Tri-38 and Tri-48(T) and P. sophorae LMG 27899(T), P. brassicacearum LMG 22836(T) and P. endophyticum LMG 26470(T) ranged from 79.23% for P. endophyticum LMG 26470(T) to 85.74% for P. sophorae LMG 27899(T). The common nodABC genes required for legume nodulation were absent from strains Tri-38 and Tri-48(T), although some other symbiotic nod and fix genes were detected. On the basis of genotypic and phenotypic analysis, a novel species, Phyllobacterium zundukense sp. nov. (type strain Tri-48(T) = LMG 30371(T) = RCAM 03910(T)), is proposed

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

<div><p>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.</p></div

Microvirga ossetica sp. nov., a species of rhizobia isolated from root nodules of the legume species Vicia alpestris Steven

Gram-stain-negative strains V5/3M(T), V5/5K, V5/5M and V5/13 were isolated from root nodules of Vicia alpestris plants growing in the North Ossetia region (Caucasus). Sequencing of the partial 16S rRNA gene (rrs) and four housekeeping genes (dnaK, gyrB, recA and rpoB) showed that the isolates from V. alpestris were most closely related to the species Microvirga zambiensis (order Rhizobiales, family Methylobacteriaceae) which was described for the single isolate from root nodule of Listia angolensis growing in Zambia. Sequence similarities between the Microvirga-related isolates and M. zambiensis WSM3693(T) ranged from 98.5 to 98.7% for rrs and from 79.7 to 95.8% for housekeeping genes. Cellular fatty acids of the isolates V5/3M(T), V5/5K, V5/5M and V5/13 included important amounts of C-18 : 1 omega 7c (54.0-67.2 %), C-16 : 0 (6.0-7.8 %), C-19 : 0 cyclo omega 8c (3.1-10.2 %), summed feature 2 (comprising one or more of iso-C-16 : 1 I, C-14 : 0 3-OH and unknown ECL 10.938, 5.8-22.5 %) and summed feature 3 (comprising C-16 : 1 omega 7c and/or iso-C(15 : 0)2-OH, 2.9-4.0 %). DNA-DNA hybridization between the isolate V5/3M(T) and M. zambiensis WSM3693(T) revealed DNA-DNA relatedness of 35.3 %. Analysis of morphological and physiological features of the novel isolates demonstrated their unique phenotypic profile in comparison with reference strains from closely related species of the genus Microvirga. On the basis of genotypic and phenotypic analysis, a novel species named Microvirga ossetica sp. nov. is proposed. The type strain is V5/3M(T) (= LMG 29787(T) = RCAM 02728(T)). Three additional strains of the species are V5/5K, V5/5M and V5/13

Bosea caraganae sp. nov. a new species of slow-growing bacteria isolated from root nodules of the relict species Caragana jubata (Pall.) Poir. originating from Mongolia

Two Gram-stain-negative strains, RCAM04680(T) and RCAM04685, were isolated from root nodules of the relict legume Caragana jubata (Pall.) Poir. originating from the south-western shore of Lake Khuvsgul (Mongolia). The 16S rRNA gene (rrs) sequencing data showed that these novel isolates belong to the genus Bosea and are phylogenetically closest to the type strains Bosea lathyri LMG 26379(T), Bosea vaviloviae LMG 28367(T), Bosea massiliensis LMG 26221(T) and Bosea lupini LMG 26383(T) (the rrs-similarity levels were 98.7-98.8 %). The recA gene of strain RCAM04680(T) showed the highest sequence similarity to the type strain B. lupini LMG 26383(T) (95.4 %), while its atpD gene was closest to that of B. lathyri LMG 26379(T) (94.4 %). The ITS, dnaK and gyrB sequences of this isolate were most similar to the B. vaviloviae LMG 28367(T) (86.8% for ITS, 90.4% for the other genes). The most abundant fatty acid was C-18:1 omega 7c (40.8 %). The whole genomes of strains RCAM04680(T) and RCAM04685 were identical (100% average nucleotide identity). The highest average nucleotide identity value (82.8 %) was found between the genome of strain RCAM04680(T) and B. vaviloviae LMG 28367(T). The common nodABC genes required for legume nodulation were absent in both strains; however, some other symbiotic nol, nod, nif and fix genes were detected. Based on the genetic study, as well as analyses of the whole-cell fatty acid compositions and phenotypic properties, a new species, Bosea caraganae sp. nov. (type strain RCAM04680(T) (=LMG 31125(T)), is proposed

Alpha-diversity of soil microbiomes (data are expressed as mean ± S.E.M.)

<p>Alpha-diversity of soil microbiomes (data are expressed as mean ± S.E.M.)</p

Taxa summary of microbiomes of soils investigated at the phylum level, including classes of <i>Proteobacteria</i>.

<p>Taxa summary of microbiomes of soils investigated at the phylum level, including classes of <i>Proteobacteria</i>.</p

Comparative analysis of taxonomic structure of microbiomes* of archived and modern soils.

<p>The charts were constructed by ranging microbial taxa abundances based on relative taxa proportions in modern soils. 1 unit = 1% of the corresponding dataset. * doesn’t include the orders with relative abundance below 0.6% in the total dataset</p