Separation of Bacteria, Protozoa and Carbon Nanotubes by Density Gradient Centrifugation

Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms

Raman spectroscopy is an emerging method for the identification of bacteria. Nevertheless, a lot of different parameters need to be considered to establish a reliable database capable of identifying real-world samples such as medical or environmental probes. In this review, the establishment of such reliable databases with the proper design in microbiological Raman studies is demonstrated, shining a light into all the parts that require attention. Aspects such as the strain selection, sample preparation and isolation requirements, the phenotypic influence, measurement strategies, as well as the statistical approaches for discrimination of bacteria, are presented. Furthermore, the influence of these aspects on spectra quality, result accuracy, and read-out are discussed. The aim of this review is to serve as a guide for the design of microbiological Raman studies that can support the establishment of this method in different fields.

Prodigiosin-Functionalized Probiotic Ghosts as a Bioinspired Combination Against Colorectal Cancer Cells

Lactobacillus acidophilus ghosts (LAGs) with the unique safety of a probiotic, inherent tropism for colon cells, and multiple bioactivities offer promise as drug carriers for colon targeting. Our objective was to evaluate LAGs functionalized with prodigiosin (PG), apoptotic secondary bacterial metabolite, as a bioinspired formulation against colorectal cancer (CRC). LAGs were prepared by a chemical method and highly purified by density gradient centrifugation. LAGs were characterized by microscopic and staining techniques as relatively small-sized uniform vesicles (≈1.6 µm), nearly devoid of cytoplasmic and genetic materials and having a negatively charged intact envelope. PG was highly bound to LAGs envelope, generating a physiologically stable bioactive entity (PG-LAGs), as verified by multiple microscopic techniques and lack of PG release under physiological conditions. PG-LAGs were active against HCT116 CRC cells at both the cellular and molecular levels. Cell viability data highlighted the cytotoxicity of PG and LAGs and LAGs-induced enhancement of PG selectivity for HCT116 cells, anticipating dose reduction for PG and LAGs. Molecularly, expression of the apoptotic caspase 3 and P53 biomarkers in HCT116 intracellular proteins was significantly upregulated while that of the anti-apoptotic Bcl-2 (B-cell lymphoma 2) was downregulated by PG-LAGs relative to PG and 5-fluorouracil. PG-LAGs provide a novel bacteria-based combination for anticancer biomedicine.

Evaluation of bioaccumulation of nanoplastics, carbon nanotubes, fullerenes, and graphene family materials

Bioaccumulation is a key factor in understanding the potential ecotoxicity of substances. While there are well-developed models and methods to evaluate bioaccumulation of dissolved organic and inorganic substances, it is substantially more challenging to assess bioaccumulation of particulate contaminants such as engineered carbon nanomaterials (CNMs; carbon nanotubes (CNTs), graphene family nanomaterials (GFNs), and fullerenes) and nanoplastics. In this study, the methods used to evaluate bioaccumulation of different CNMs and nanoplastics are critically reviewed. In plant studies, uptake of CNMs and nanoplastics into the roots and stems was observed. For multicellular organisms other than plants, absorbance across epithelial surfaces was typically limited. Biomagnification was not observed for CNTs and GFNs but were observed for nanoplastics in some studies. However, the reported absorption in many nanoplastic studies may be a consequence of an experimental artifact, namely release of the fluorescent probe from the plastic particles and subsequent uptake. We identify that additional work is needed to develop analytical methods to provide robust, orthogonal methods that can measure unlabeled (e.g., without isotopic or fluorescent labels) CNMs and nanoplastics.

Graphene-Based Coating to Mitigate Biofilm Development in Marine Environments

Due to its several economic and ecological consequences, biofouling is a widely recognized concern in the marine sector. The search for non-biocide-release antifouling coatings has been on the rise, with carbon-nanocoated surfaces showing promising activity. This work aimed to study the impact of pristine graphene nanoplatelets (GNP) on biofilm development through the representative marine bacteria Cobetia marina and to investigate the antibacterial mechanisms of action of this material. For this purpose, a flow cytometric analysis was performed and a GNP/polydimethylsiloxane (PDMS) surface containing 5 wt% GNP (G5/PDMS) was produced, characterized, and assessed regarding its biofilm mitigation potential over 42 days in controlled hydrodynamic conditions that mimic marine environments. Flow cytometry revealed membrane damage, greater metabolic activity, and endogenous reactive oxygen species (ROS) production by C. marina when exposed to GNP 5% (w/v) for 24 h. In addition, C. marina biofilms formed on G5/PDMS showed consistently lower cell count and thickness (up to 43% reductions) than PDMS. Biofilm architecture analysis indicated that mature biofilms developed on the graphene-based surface had fewer empty spaces (34% reduction) and reduced biovolume (25% reduction) compared to PDMS. Overall, the GNP-based surface inhibited C. marina biofilm development, showing promising potential as a marine antifouling coating.

Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions

High throughput sequencing has emerged as one of the most important techniques for characterizing microbial dynamics and revealing bacteria and host interactions. However, data interpretation using this technique is mainly based on relative abundance and ignores total bacteria load. In certain cases, absolute abundance is more important than compositional relative data, and interpretation of microbiota data based solely on relative abundance can be misleading. The available approaches for absolute quantification are highly diverse and challenging, especially for quantification in differing biological situations, such as distinguishing between live and dead cells, quantification of specific taxa, enumeration of low biomass samples, large sample size feasibility, and the detection of various other cellular features. In this review, we first illustrate the importance of integrating absolute abundance into microbiome data interpretation. Second, we briefly discuss the most widely used cell-based and molecular-based bacterial load quantification methods, including fluorescence spectroscopy, flow cytometry, 16S qPCR, 16S qRT-PCR, ddPCR, and reference spike-in. Last, we present a specific decision-making scheme for absolute quantification methods based on different biological questions and some of the latest quantitative methods and procedure modifications.

A density gradient centrifugation method for rapid separation of nanoTiO2 and TiO2 aggregates from microalgal cells in complex mixtures with mercury

In natural environment, the microorganisms are exposed to complex mixtures of contaminants, including manufactured nanoparticles and their aggregates. Evaluation of the toxicant accumulation in biota exposed to such cocktails is a challenging task because the microorganisms need to be separated from nanomaterial aggregates often of a comparable size. We propose a method for separation of TiO₂ aggregates from green microalga Chlamydomonas reinhardtii and subsequent determination of cellular Hg concentration in algae exposed to mixture of Hg with nanoTiO₂, known also to adsorb Hg. The method is based on differences in specific weight of algae and TiO₂ aggregates, using medium speed centrifugation on a step gradient of sucrose. The efficiency of the separation method was tested with nanoTiO₂ of three different primary sizes at four concentrations: 2, 20, 100 and 200 mg L⁻¹. The method gives a possibility to separate nanoTiO₂ and their aggregates from the algae with a mean recovery of 83.3% of algal cells, thus allowing a reliable determination of Hg accumulation by microalgae when co-exposed to Hg and nanoTiO₂.

• A rapid and reliable method to separate algal cells and nanoparticle aggregates of comparable size.

• A method to measure the cellular amount of Hg in green alga co-exposed to Hg and nanoTiO₂.

Mass, Size, and Density Measurements of Microparticles in a Quadrupole Ion Trap

The physical properties of microparticles, such as mass, size, and density, are critical for their functions. The comprehensive characterization of these physical parameters, however, remains a fundamental challenge. Here, we developed a particle mass spectrometry (PMS) methodology for determining the mass, size, and density of microparticles simultaneously. The collisional cross-section (CCS) and mass spectrometry (MS) measurements were performed in a single quadrupole ion trap (QIT), and the two modes can be switched easily by tuning the electric and gas hydrodynamic fields of the QIT. The feasibility of the method was demonstrated through a series of monodispersed polystyrene (PS) and silica (SiO₂) particle standards. The SiO₂/polypyrrole core-shell particles were also successfully characterized, and the measured results were verified by using conventional methods.

Strategies for robust and accurate experimental approaches to quantify nanomaterial bioaccumulation across a broad range of organisms

One of the key components for environmental risk assessment of engineered nanomaterials (ENMs) is data on bioaccumulation potential. Accurately measuring bioaccumulation can be critical for regulatory decision making regarding material hazard and risk, and for understanding the mechanism of toxicity. This perspective provides expert guidance for performing ENM bioaccumulation measurements across a broad range of test organisms and species. To accomplish this aim, we critically evaluated ENM bioaccumulation within three categories of organisms: single-celled species, multicellular species excluding plants, and multicellular plants. For aqueous exposures of suspended single-celled and small multicellular species, it is critical to perform a robust procedure to separate suspended ENMs and small organisms to avoid overestimating bioaccumulation. For many multicellular organisms, it is essential to differentiate between the ENMs adsorbed to external surfaces or in the digestive tract and the amount absorbed across epithelial tissues. For multicellular plants, key considerations include how exposure route and the role of the rhizosphere may affect the quantitative measurement of uptake, and that the efficiency of washing procedures to remove loosely attached ENMs to the roots is not well understood. Within each organism category, case studies are provided to illustrate key methodological considerations for conducting robust bioaccumulation experiments for different species within each major group. The full scope of ENM bioaccumulation measurements and interpretations are discussed including conducting the organism exposure, separating organisms from the ENMs in the test media after exposure, analytical methods to quantify ENMs in the tissues or cells, and modeling the ENM bioaccumulation results. One key finding to improve bioaccumulation measurements was the critical need for further analytical method development to identify and quantify ENMs in complex matrices. Overall, the discussion, suggestions, and case studies described herein will help improve the robustness of ENM bioaccumulation studies.

Agglomeration Determines Effects of Carbonaceous Nanomaterials on Soybean Nodulation, Dinitrogen Fixation Potential, and Growth in Soil

The potential effects of carbonaceous nanomaterials (CNMs) on agricultural plants are of concern. However, little research has been performed using plants cultivated to maturity in soils contaminated with various CNMs at different concentrations. Here, we grew soybean for 39 days to seed production in soil amended with 0.1, 100, or 1000 mg kg-1 of either multiwalled carbon nanotubes (MWCNTs), graphene nanoplatelets (GNPs), or carbon black (CB) and studied plant growth, nodulation, and dinitrogen (N2) fixation potential. Plants in all CNM treatments flowered earlier (producing 60% to 372% more flowers when reproduction started) than the unamended controls. The low MWCNT-treated plants were shorter (by 15%) with slower leaf cover expansion (by 26%) and less final leaf area (by 24%) than the controls. Nodulation and N2 fixation potential appeared negatively impacted by CNMs, with stronger effects at lower CNM concentrations. All CNM treatments reduced the whole-plant N2 fixation potential, with the highest reductions (by over 91%) in the low and medium CB and the low MWCNT treatments. CB and GNPs appeared to accumulate inside nodules as observed by transmission electron microscopy. CNM dispersal in aqueous soil extracts was studied to explain the inverse dose-response relationships, showing that CNMs at higher concentrations were more agglomerated (over 90% CNMs settled as agglomerates >3 μm after 12 h) and therefore proportionally less bioavailable. Overall, our findings suggest that lower concentrations of CNMs in soils could be more impactful to leguminous N2 fixation, owing to greater CNM dispersal and therefore increased bioavailability at lower concentrations.

Increasing evidence indicates low bioaccumulation of carbon nanotubes

As the production of carbon nanotubes (CNTs) expands, so might the potential for release into the environment. The possibility of bioaccumulation and toxicological effects has prompted research on their fate and potential ecological effects. For many organic chemicals, bioaccumulation properties are associated with lipid-water partitioning properties. However, predictions based on phase partitioning provide a poor fit for nanomaterials. In the absence of data on the bioaccumulation and other properties of CNTs, the Office of Pollution Prevention and Toxics (OPPT) within the US Environmental Protection Agency (EPA) subjects new pre-manufacture submissions for all nanomaterials to a higher-level review. We review the literature on CNT bioaccumulation by plants, invertebrates and non-mammalian vertebrates, summarizing 40 studies to improve the assessment of the potential for bioaccumulation. Because the properties and environmental fate of CNTs may be affected by type (single versus multiwall), functionalization, and dosing technique, the bioaccumulation studies were reviewed with respect to these factors. Absorption into tissues and elimination behaviors across species were also investigated. All of the invertebrate and non-mammalian vertebrate studies showed little to no absorption of the material from the gut tract to other tissues. These findings combined with the lack of biomagnification in the CNT trophic transfer studies conducted to date suggest that the overall risk of trophic transfer is low. Based on the available data, in particular the low levels of absorption of CNTs across epithelial surfaces, CNTs generally appear to form a class that should be designated as a low concern for bioaccumulation.