Significance: Drought remains a critical obstacle to meeting the food demands of the coming century. Understanding the interplay between drought stress, plant development, and the plant microbiome is central to meeting this challenge. Here, we demonstrate that drought causes enrichment of a distinct set of microbes in roots, composed almost entirely of monoderms, which lack outer membranes and have thick cell walls. We demonstrate that under drought, roots increase the production of many metabolites, and that monoderms inhabiting the drought-treated rhizosphere exhibit increased activity of transporters connected with some of these same compounds. The discovery of this drought-induced enrichment and associated shifts in metabolite exchange between plant and microbe reveal a potential blueprint for manipulating plant microbiomes for improved crop fitness.

Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. The metabolite, protein, and lipid extraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental, in vitro, and clinical). IMPORTANCE In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample. Author Video: An author video summary of this article is available.

Association of plastic particles with plant roots could represent a pathway for human consumption of plastic and plastic-associated organic contaminants. Here, we investigated the uptake of spherical, negatively-charged, polystyrene nano- and microparticles by plant roots. We used negatively-charged, 40 nm and 1 μm fluorescently-labeled polystyrene spheres and two plant species: Arabidopsis (Arabidopsis thaliana) and wheat (Triticum aestivum). Plants were grown from seeds to 5 days for wheat and 12 days for Arabidopsis, in agar growth media containing plastic spheres (0.029 g L⁻¹), and plant uptake of spheres was investigated by laser scanning confocal microscopy and pyrolysis gas chromatography-mass spectrometry (GC-MS). The confocal images of both plant species showed no evidence for active uptake of nano- and microsized polystyrene spheres during plant growth up to the 1 to 2 leaf growth stage. Pyrolysis GC-MS was unsuccessful because of the occurrence of natural styrene monomers in plant roots and insufficient detection limits. Both 40 nm and 1 μm polystyrene spheres accumulated at the root surface of each species, particularly at the root tip, and were still found attached to the root surface after washing. However, there was no evidence of plastic particles in the internal root structure. Our results demonstrate the association and accumulation of plastics at root surface and cap cells.

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