Soil microorganisms found in the root zone impact plant growth and development, but the potential to harness these benefits is hampered by the sheer abundance and diversity of the players influencing desirable plant traits. Here, we report a high level of reproducibility of soil microbiomes in altering plant flowering time and soil functions when partnered within and between plant hosts. We used a multi-generation experimental system using Arabidopsis thaliana Col to select for soil microbiomes inducing earlier or later flowering times of their hosts. We then inoculated the selected microbiomes from the tenth generation of plantings into the soils of three additional A. thaliana genotypes (Ler, Be, RLD) and a related crucifer (Brassica rapa). With the exception of Ler, all other plant hosts showed a shift in flowering time corresponding with the inoculation of early- or late-flowering microbiomes. Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment. Plant hosts grown with the late-flowering-associated microbiomes showed consequent increases in inflorescence biomass for three A. thaliana genotypes and an increase in total biomass for B. rapa. The increase in biomass was correlated with two- to five-fold enhancement of microbial extracellular enzyme activities associated with nitrogen mineralization in soils. The reproducibility of the flowering phenotype across plant hosts suggests that microbiomes can be selected to modify plant traits and coordinate changes in soil resource pools.

This publication is made publicly available in the institutional repository of Wageningen University and Research, under the terms of article 25fa of the Dutch Copyright Act, also known as the Amendment Taverne. This has been done with explicit consent by the author.Article 25fa states that the author of a short scientific work funded either wholly or partially by Dutch public funds is entitled to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work.This publication is distributed under The Association of Universities in the Netherlands (VSNU) 'Article 25fa implementation' project. In this project research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication.

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community. Electronic supplementary material The online version of this article (10.1186/s13059-019-1760-x) contains supplementary material, which is available to authorized users.

The microbiome of a vineyard may play a critical role in fruit development, and consequently, may impact quality properties of grape and wine. Vineyard management approaches that have directly manipulated the microbiome of grape clusters have been studied, but little is known about how vineyard management practices that impact the soil microbial pool can influence this dynamic. We examined three under-vine soil management practices: 1) herbicide application, 2) soil cultivation (vegetation removal), and 3) natural vegetation (no vegetation removal) in a Riesling vineyard in New York over a three-year period. The microbiomes associated with soil and grapes were profiled using high-throughput sequencing of the bacterial 16 S rRNA gene and fungal ITS regions. Our results showed that soil bacterial composition under natural vegetation differs from that seen in glyphosate-maintained bare soil. Soil fungal composition under the natural vegetation treatment was distinct from other treatments. Although our study revealed soil microbiome shifts based on under-vine management, there were no corresponding changes in fruit-associated microbial composition. These results suggested that other vineyard management practices or environmental factors are more influential in shaping the grape-associated microbiome.