Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying organic matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely associated with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and organic carbon that persist through mechanical disruptions and wetting events. Their spatial structure is important for biogeochemical cycling, and we cannot reliably predict soil biological activities and variability by studying bulk soils alone. To fully understand the biogeochemical processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as “microbial villages” that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. We describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining “model system” approaches (e.g., developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members, like viruses. Initial studies suggest that aggregate-based approaches are a critical next step for developing a predictive understanding of how geochemical and community interactions govern microbial community structure and nutrient cycling in soil.

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 Au 3+ , 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 > pK 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.

The biological function of the plant-microbiome system is the result of contributions from the host plant and microbiome members. The Populus root microbiome is a diverse community that has high abundance of β- and γ-Proteobacteria, both classes which include multiple plant-growth promoting representatives. To understand the contribution of individual microbiome members in a community, we studied the function of a simplified community consisting of Pseudomonas and Burkholderia bacterial strains isolated from Populus hosts and inoculated on axenic Populus cutting in controlled laboratory conditions. Both strains increased lateral root formation and root hair production in Arabidopsis plate assays and are predicted to encode for different functions related to growth and plant growth promotion in Populus hosts. Inoculation individually, with either bacterial isolate, increased root growth relative to uninoculated controls, and while root area was increased in mixed inoculation, the interaction term was insignificant indicating additive effects of root phenotype. Complementary data including photosynthetic efficiency, whole-transcriptome gene expression and GC-MS metabolite expression data in individual and mixed inoculated treatments indicate that the effects of these bacterial strains are unique and additive. These results suggest that the function of a microbiome community may be predicted from the additive functions of the individual members.

Bacteria occupy heterogeneous environments, attaching and growing within pores in materials, living hosts, and matrices like soil. Systems that permit high-resolution visualization of dynamic bacterial processes within the physical confines of a realistic and tractable porous media environment are rare. Here we use microfluidics to replicate the grain shape and packing density of natural sands in a 2D platform to study the flow-induced spatial evolution of bacterial biofilms underground. We discover that initial bacterial dispersal and grain attachment is influenced by bacterial transport across pore space velocity gradients, a phenomenon otherwise known as rheotaxis. We find that gravity-driven flow conditions activate different bacterial cell-clustering phenotypes depending on the strain’s ability to product extracellular polymeric substances (EPS). A wildtype, biofilm-producing bacteria formed compact, multicellular patches while an EPS-defective mutant displayed a linked-cell phenotype in the presence of flow. These phenotypes subsequently influenced the overall spatial distribution of cells across the porous media network as colonies grew and altered the fluid dynamics of their microenvironment.

Paper-based substrates integrated with plasmonic nanostructures and combined with surface enhanced Raman spectroscopy (SERS) offer a flexible and lightweight platform for the ultrasensitive optical detection of analytes on any surface. Here, we incorporated multibranched gold nanoantennas (MGNs) on inexpensive filter paper to design MGN-paper dipsticks and swabs for SERS mediated sensing of chemicals, proteins, and pesticides adsorbed on fruits. MGNs are anisotropic nanostructures consisting of a core which serves as the antenna and protrusions that serve as emitters redistributing incident light. The nanoantenna effect gives rise to intense electromagnetic fields on the tips of the protrusions that enabled a detection of 100 pM of 1,4-benzenedithiol and 100 fM of human serum albumin labeled with indocyanine green with the MGN-paper dipsticks. Further, MGN-paper swabs enabled the detection of 62.5 pg of solid state 4-aminothiophenol on a planar surface, and 26.3 mg of methyl parathion adsorbed on an apple. Finite difference time domain simulations demonstrated that the nanoantenna effect can be systematically modulated by altering the core-to-protrusion ratio to generate a $65Â enhancement in the electromagnetic fields localized on the protrusions which may ultimately result in sub-femtomolar to zeptomolar detection sensitivities.

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Plant-microbe interactions underpin processes related to soil ecology, plant function, and global carbon cycling. However, quantifying the spatial dynamics of these interactions has proven challenging in natural systems. Currently, microfluidic platforms are at the forefront of innovation for culturing, imaging, and manipulating plants in controlled environments. Using a microfluidic platform to culture plants with beneficial bacteria, visualization and quantification of the spatial dynamics of these interactions during the early stages of plant development is possible. For two plant growth-promoting bacterial isolates, the population of bacterial cells reaches a coverage density of 1-2% of the root"s surface at the end of a four-day observation period regardless of bacterial species or inoculum concentration. The two bacterial species form distinct associations with root tissue through a mechanism that appears to be independent of the presence of the other bacterial species, despite evidence for their competition. Root development changes associated with these bacterial treatments depend on the initial concentrations and species of the bacterial population present. This microfluidic approach provides context for understanding plant-microbe interactions during the early stages of plant development, and can be used to generate new hypotheses about physical and biochemical exchanges between plants and their associated microbial communities.

A soil-mimicking rhizosphere-on-a-chip is amenable for long-term plant growth and enables simulation of root exudate diffusion and experimental validation of carbon hotspot formation from the interaction between roots and the synthetic soil grains.