Characterization and identification of productivity-associated rhizobacteria in wheat

The rhizosphere is populated by a numerous and diverse array of rhizobacteria, and many impact productivity in largely unknown ways. Here we characterize the rhizobacterial community in a wheat variety categorized according to shoot biomass using 16S rRNA pyrosequencing abundance data. Plants were grown in homogenized field soil under greenhouse conditions, and DNA was extracted and pyrosequenced, resulting in 29,007 quality sequences. Operational taxonomic units (OTUs) that were significantly associated with biomass productivity were identified using an exact test adjusted for the false-discovery rate. The productivity deviation expressed as a percentage of the total mean square for regression (PMSR) was determined for each OTU. Out of 719 OTUs, 42 showed significant positive associations and 39 showed significant negative associations (q value, </=0.05). OTUs with the greatest net positive associations, by genus, were as follows: Duganella, OTU 43 and OTU 3; Janthinobacterium, OTU 278; Pseudomonas, OTU 588; and Cellvibrio, OTU 1847. Those with negative associations were as follows: Bacteria, OTU 273; Chryseobacterium, OTU 508; Proteobacteria, OTU 249; and Enterobacter, OTU 357. Shoot biomass productivity was strongly correlated with the balance between the overall abundances of positive- and negative-productivity-associated OTUs. High-productivity rhizospheres contained 9.2 significant positives for every negatively associated rhizobacterium, while low-productivity rhizospheres showed 2.3 significant negatives for every positively associated rhizobacterium. Overall rhizobacterial community diversity as measured by the Chao1, Shannon, and Simpson indexes was nonlinearly related to productivity, closely fitting a wavelike cubic equation. We conclude that shoot biomass productivity is strongly related to the ratio of positive- to negative-productivity-associated rhizobacteria in the rhizosphere. This study identifies significant OTUs composing the productive and unproductive rhizobacterial communities.Peer reviewedPlant and Soil SciencesStatistic

Potential side effects of biocontrol and plant-growth promoting Bacillus amyloliquefaciens bacteria on earthworms

After 1-2 months, survival, growth and reproduction of the earthworms were recorded. We found no effect of the treatments as compared to control without BA amendments. We conclude that the use of high doses of BA with concentrations at the same magnitude as maximally expected when the bacteria are used as PGPR and BCA, is not harmful to the soil dwelling earthworms tested in this project. Further studies of the ecological effects of PGPR and BCA bacteria on other non-target soil organisms are encouraged. The development of sustainable agricultural systems, where ecosystem services are optimized, has to be aided by a deeper knowledge of the combined effect of bacteria and earthworms on the promotion of plant health. (C) 2015 Elsevier B.V. All rights reserved

The Vein Patterning 1 (VEP1) Gene Family Laterally Spread through an Ecological Network

Lateral gene transfer (LGT) is a major evolutionary mechanism in prokaryotes. Knowledge about LGT— particularly, multicellular— eukaryotes has only recently started to accumulate. A widespread assumption sees the gene as the unit of LGT, largely because little is yet known about how LGT chances are affected by structural/functional features at the subgenic level. Here we trace the evolutionary trajectory of VEin Patterning 1, a novel gene family known to be essential for plant development and defense. At the subgenic level VEP1 encodes a dinucleotide-binding Rossmann-fold domain, in common with members of the short-chain dehydrogenase/reductase (SDR) protein family. We found: i) VEP1 likely originated in an aerobic, mesophilic and chemoorganotrophic α-proteobacterium, and was laterally propagated through nets of ecological interactions, including multiple LGTs between phylogenetically distant green plant/fungi-associated bacteria, and five independent LGTs to eukaryotes. Of these latest five transfers, three are ancient LGTs, implicating an ancestral fungus, the last common ancestor of land plants and an ancestral trebouxiophyte green alga, and two are recent LGTs to modern embryophytes. ii) VEP1's rampant LGT behavior was enabled by the robustness and broad utility of the dinucleotide-binding Rossmann-fold, which provided a platform for the evolution of two unprecedented departures from the canonical SDR catalytic triad. iii) The fate of VEP1 in eukaryotes has been different in different lineages, being ubiquitous and highly conserved in land plants, whereas fungi underwent multiple losses. And iv) VEP1-harboring bacteria include non-phytopathogenic and phytopathogenic symbionts which are non-randomly distributed with respect to the type of harbored VEP1 gene. Our findings suggest that VEP1 may have been instrumental for the evolutionary transition of green plants to land, and point to a LGT-mediated ‘Trojan Horse’ mechanism for the evolution of bacterial pathogenesis against plants. VEP1 may serve as tool for revealing microbial interactions in plant/fungi-associated environments