Accessing Fungal Contributions to the Birch Effect: Real-Time Respiration from Pore-Scale Microfluidics.

Drying and rewetting of soil stimulates soil carbon emission. The Birch effect, driven by these cycles, leads to CO efflux, which can be monitored using real-time mass spectrometry (RTMS). Although soil fungi retain water during droughts, their contribution to CO release during drying-rewetting cycles remains unclear.

Enhanced transport of bacteria along root systems by protists can impact plant health.

Soil protists have been shown to contribute to the structure and function of the rhizosphere in a variety of ways. Protists are key contributors to nutrient cycling through the microbial loop, where biomass is digested by protists and otherwise stored nutrients are returned to the environment. Protists have also been shown to feed on plant pathogenic bacteria and alter root microbiomes in ways that may benefit plants.

Soil Protists Can Actively Redistribute Beneficial Bacteria along Medicago truncatula Roots.

The rhizosphere is the region of soil directly influenced by plant roots. The microbial community in the rhizosphere includes fungi, protists, and bacteria: all play significant roles in plant health. The beneficial bacterium Sinorhizobium meliloti infects growing root hairs on nitrogen-starved leguminous plants.

Chemotactic Bacteria Facilitate the Dispersion of Nonmotile Bacteria through Micrometer-Sized Pores in Engineered Porous Media.

Recent research has demonstrated that chemotactic bacteria can disperse inside microsized pores while traveling toward favorable conditions. Microbe-microbe cotransport might enable nonmotile bacteria to be carried with motile partners to enhance their dispersion and reduce their deposition in porous systems. The aim of this study was to demonstrate the enhancement in the dispersion of nonmotile bacteria ( VM552, a polycyclic aromatic hydrocarbon-degrader, and sp.

Application of microfluidic systems in modelling impacts of environmental structure on stress-sensing by individual microbial cells.

Environmental structure describes physical structure that can determine heterogenous spatial distribution of biotic and abiotic (nutrients, stressors etc.) components of a microorganism's microenvironment. This study investigated the impact of micrometre-scale structure on microbial stress sensing, using yeast cells exposed to copper in microfluidic devices comprising either complex soil-like architectures or simplified environmental structures.

Expanding Molecular Coverage in Mass Spectrometry Imaging of Microbial Systems Using Metal-Assisted Laser Desorption/Ionization.

Mass spectrometry imaging (MSI) is becoming an increasingly popular analytical technique to investigate microbial systems. However, differences in the ionization efficiencies of distinct MSI methods lead to biases in terms of what types and classes of molecules can be detected. Here, we sought to increase the molecular coverage of microbial colonies by employing metal-assisted laser desorption/ionization (MetA-LDI) MSI, and we compared our results to more commonly utilized matrix-assisted laser desorption/ionization MALDI MSI.

Optogenetics in Enables Spatial Control of Exopolysaccharide Production and Biofilm Structure.

Microorganisms play a vital role in shaping the soil environment and enhancing plant growth by interacting with plant root systems. Because of the vast diversity of cell types involved, combined with dynamic and spatial heterogeneity, identifying the causal contribution of a defined factor, such as a microbial exopolysaccharide (EPS), remains elusive. Synthetic approaches that enable orthogonal control of microbial pathways are a promising means to dissect such complexity.

Red blood cell classification in lensless single random phase encoding using convolutional neural networks.

Rapid cell identification is achieved in a compact and field-portable system employing single random phase encoding to record opto-biological signatures of living biological cells of interest. The lensless, 3D-printed system uses a diffuser to encode the complex amplitude of the sample, then the encoded signal is recorded by a CMOS image sensor for classification. Removal of lenses in this 3D sensing system removes restrictions on the field of view, numerical aperture, and depth of field normally imposed by objective lenses in comparable microscopy systems to enable robust 3D capture of biological volumes.

A 3D-printed microbial cell culture platform with PEGDA hydrogel barriers for differential substrate delivery.

Additive manufacturing, or 3D-printing techniques have recently begun to enable simpler, faster, and cheaper production of millifluidic devices at resolutions approaching 100-200 m. At this resolution, cell culture devices can be constructed that more accurately replicate natural environments compared with conventional culturing techniques. A number of microfluidics researchers have begun incorporating additive manufacturing into their work, using 3D-printed devices in a wide array of chemical, fluidic, and even some biological applications.

Direct Tracking of Particles and Quantification of Margination in Blood Flow.

Margination refers to the migration of particles toward blood vessel walls during blood flow. Understanding the mechanisms that lead to margination will aid in tailoring the attributes of drug-carrying particles for effective drug delivery. Most previous studies evaluated the margination propensity of these particles via an adhesion mechanism, i.

Protist-facilitated particle transport using emulated soil micromodels.

Microbial processes in the subsurface can be visualized directly using micromodels to emulate pore-scale geometries. Here, emulated soil micromodels were used to measure transport of fluorescent beads in the presence and absence of the soil ciliate Colpoda sp. under quiescent conditions.

Applications of biosynthesized metallic nanoparticles - a review.

We present a comprehensive review of the applications of biosynthesized metallic nanoparticles (NPs). The biosynthesis of metallic NPs is the subject of a number of recent reviews, which focus on the various "bottom-up" biofabrication methods and characterization of the final products. Numerous applications exploit the advantages of biosynthesis over chemical or physical NP syntheses, including lower capital and operating expenses, reduced environmental impacts, and superior biocompatibility and stability of the NP products.

Dynamic dosing assay relating real-time respiration responses of Staphylococcus aureus biofilms to changing microchemical conditions.

Bacterial biofilms are a metabolically heterogeneous community of bacteria distributed in an extracellular matrix comprised primarily of hydrated polysaccharides. Effective inhibitory concentrations measured under planktonic conditions are not applicable to biofilms, and inhibition concentrations measured for biofilms vary widely. Here, we introduce a novel microfluidic approach for screening respiration inhibition of bacteria in a biofilm array morphology.

Window on a microworld: simple microfluidic systems for studying microbial transport in porous media.

Microbial growth and transport in porous media have important implications for the quality of groundwater and surface water, the recycling of nutrients in the environment, as well as directly for the transmission of pathogens to drinking water supplies. Natural porous media is composed of an intricate physical topology, varied surface chemistries, dynamic gradients of nutrients and electron acceptors, and a patchy distribution of microbes. These features vary substantially over a length scale of microns, making the results of macro-scale investigations of microbial transport difficult to interpret, and the validation of mechanistic models challenging.

Mass balances on selected polycyclic aromatic hydrocarbons in the New York-New Jersey Harbor.

Mass balances on 10 polycyclic aromatic hydrocarbons (PAHs) in the New York-New Jersey Harbor (hereafter "the Harbor") were constructed using monitoring data from the water column, sediment, and atmosphere. Inputs considered included tributaries, atmospheric deposition, wastewater treatment plant discharges, combined sewer overflows (CSOs), and stormwater runoff. Removal processes examined included tidal exchange between the Harbor and the coastal Bight and Long Island Sound, volatilization, and accumulation or burial of sediment-bound PAHs in the Harbor.

Tape underlayment rotary-node (TURN) valves for simple on-chip microfluidic flow control.

We describe a simple and reliable fabrication method for producing multiple, manually activated microfluidic control valves in polydimethylsiloxane (PDMS) devices. These screwdriver-actuated valves reside directly on the microfluidic chip and can provide both simple on/off operation as well as graded control of fluid flow. The fabrication procedure can be easily implemented in any soft lithography lab and requires only two specialized tools-a hot-glue gun and a machined brass mold.

Protozoan migration in bent microfluidic channels.

Microfluidic devices permit direct observation of microbial behavior in defined microstructured settings. Here, the swimming speed and dispersal of individual marine ciliates in straight and bent microfluidic channels were quantified. The dispersal rate and swimming speed increased with channel width, decreased with protozoan size, and was significantly impacted by the channel turning angle.

Mobility of protozoa through narrow channels.

Microbes in the environment are profoundly affected by chemical and physical heterogeneities occurring on a spatial scale of millimeters to micrometers. Physical refuges are critical for maintaining stable bacterial populations in the presence of high predation pressure by protozoa. The effects of microscale heterogeneity, however, are difficult to replicate and observe using conventional experimental techniques.

Combined effects of contaminant desorption and toxicity on risk from PAH contaminated sediments.

A strong inverse correlation was observed between the polycyclic aromatic hydrocarbon (PAH) mass fraction desorbed, a surrogate measure of bioavailability, and relative carcinogenicity, as quantified by potency equivalency factors (PEFs), for two study sediments from the New York/New Jersey Harbor estuary. Because compounds with the highest toxicity, such as dibenz(a,h)anthracene and benzo(a)pyrene (BAP), also tended to be the least rapidly and least extensively desorbed, the U.S.

Intra-aggregate mass transport-limited bioavailability of polycyclic aromatic hydrocarbons to Mycobacterium strain PC01.

Biodegradation kinetics for three- and four-ring PAHs by Mycobacterium sp. strain PC01 were measured in whole and density-fractionated estuarine sediments and in a system without intra-aggregate mass transport limitations. The biokinetic data in the systems with and without intra-aggregate mass transport limitations were compared with abiotic PAH desorption kinetics.

Desorption kinetics for field-aged polycyclic aromatic hydrocarbons from sediments.

This study considers desorption kinetics for 12 field-aged polycyclic aromatic hydrocarbons (PAHs) desorbing from size- and density-fractionated sediments collected from two locations in the New York/New Jersey Harbor Estuary. Desorption kinetics for PAHs with a log octanol-water partition coefficient greater than 6 were well-described by a one-domain diffusion model that assumes that PAHs are initially uniformly distributed throughout spherical sediment aggregates. PAH hydrophobicity and sediment specific surface area were the parameters most strongly correlated with the magnitude of the observed diffusivity for the one-domain model.

Distributed sequestration and release of PAHs in weathered sediment: the role of sediment structure and organic carbon properties.

Polycyclic aromatic hydrocarbon (PAH) contaminated sediments from Piles Creek (PC) and Newtown Creek (NC) in the NY/NJ Harbor estuary were separated into size fractions and further separated into low (<1.7 g cm(-3)) and high (>1.7 g cm(-3)) density fractions.