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

One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years) to a conventional and organic farming systems (CFS and OFS accordingly). Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%), Acidobacteria (16.1%), Actinobacteria (7.9%), Verrucomicrobia (2.0%), Bacteroidetes (2.7%) and Firmicutes (4.8%). Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas), while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05) increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella) and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum) and Clostridium. Thus, the fields under OFS and CFS did not differ greatly for the composition of the microbiome. These results, which were also confirmed by cluster analysis, indicated that microbial communities in the field soil do not necessarily differ largely between conventional and organic farming systems.Peer reviewe

Bis(pyrazol-1-yl)methane-4,4′-dicarboxylic Acid

The molecular structure of bis(pyrazol-1-yl)methane-4,4′-dicarboxylic acid (H2bpmdc) was determined by single crystal X-Ray diffraction analysis. The compound crystallizes in a monoclinic crystal system; the unit cell contains four formula units. The molecules of H2bpmdc are linked into zig-zag chains by intermolecular carboxyl–carboxyl hydrogen bonds. Other types of supramolecular interactions, namely, CH···N and CH···O short contacts, CH–π interactions and carbonyl–carbonyl interactions were detected in the crystal structure

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

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

Heatmap comparison of the microbiomes in croplands (CFS and OFS) and the woodland.

<p>Colors mark the average relative abundance (in number of sequences per sample) of each bacterial genus within the sample. Only identified genera with total counts exceeding 5 sequences per library are presented.</p

Abundance ratios of the most common bacterial phyla in the soil in organic (OFS) vs. conventional (CFS) farming systems, and the woodland vs. farmland systems (wood vs. FS; FS combines OFS and CFS samples).

<p>Circle size indicates the average abundance of the phylum.</p

The number of bacteria and archaea per gram of soil, estimated by quantitative PCR.

<p>The raw data on the number of 16S rRNA genes per gram of soil, calibrated to the <i>E</i>. <i>coli</i> and <i>H</i>. <i>salinarum</i> 16S rDNA copy number, were translated to the number of prokaryotic cells per gram of soil by use of the information on the average number of 16S rRNA copies in bacterial and archaeal genomes deposited in rrnDB database [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145072#pone.0145072.ref036" target="_blank">36</a>]. Error bars indicate standard deviation (n = 3).</p

OTUs analyzed in a bootstrapped maximum likelihood phylogenetic tree and their abundance presented in a table.

<p>Pairwise tests indicated either an increase (+) or a decrease (–) in abundance between samples of the organic farming system (OFS), the conventional farming system (CFS) and the woodland (Wood). Blank cells indicate insufficient data. The significance of difference was assessed using a permutation test, INS indicates insignificant difference.</p