Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics

The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates—parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology

Geometry-Dependent Plasmonic Tunability and Photothermal Characteristics of Multibranched Gold Nanoantennas

Plasmon resonances of anisotropic multibranched nanostructures are governed by their geometry, allowing morphology-directed selective manipulation of the optical properties. In this work, we have synthesized multibranched gold nanoantennas (MGNs) of variable geometry by a one-step seedless approach using 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) as a capping and reducing agent. This approach enables us to modulate the MGNs’ geometry by controlling three different parameters: concentration of HEPES, concentration of Au³⁺, and pH of HEPES buffer. By altering the MGNs morphology with minimal increase in the overall dimensions, the plasmon resonances were tuned from the visible to the near-infrared. The MGNs plasmon resonances demonstrated a nonintuitive blue-shift when pH > p<i>K</i>_a of HEPES which we attributed to emergence of charge transfer oscillations formed when MGNs cluster to dimers and trimers. Further, due to the presence of multiple sharp protrusions, the MGNs demonstrated a refractive index sensitivity of 373 nm/RIU, which is relatively high for this class of branched nanostructures of similar size. Finally, the sharp protrusions of MGNs also give rise to intense photothermal efficiencies; ∼53 °C was achieved within 5 min of laser illumination, demonstrating the efficacy of MGNs in therapeutic applications. By modulating the mass density of MGNs, the laser flux, and time of illumination, we provide a detailed analysis of the photothermal characteristics of MGNs

Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange.

We identified two poplar (Populus sp.)-associated microbes, the fungus, Mortierella elongata strain AG77, and the bacterium, Burkholderia strain BT03, that mutually promote each other's growth. Using culture assays in concert with a novel microfluidic device to generate time-lapse videos, we found growth specific media differing in pH and pre-conditioned by microbial growth led to increased fungal and bacterial growth rates. Coupling microfluidics and comparative metabolomics data results indicated that observed microbial growth stimulation involves metabolic exchange during two ordered events. The first is an emission of fungal metabolites, including organic acids used or modified by bacteria. A second signal of unknown nature is produced by bacteria which increases fungal growth rates. We find this symbiosis is initiated in part by metabolic exchange involving fungal organic acids