Planktonic particle-associated bacteria comprise particle-attached and motile free-living cells. These groups were obtained by settlement in Imhoff cones. Dilution plating on marine agar 2216 (ZoBell marine agar) and microscopic counts indicated a cultivability of 0.7% (0.4%-1.2%) of bacteria in coastal seawater collected at Helgoland Roads, North Sea. Particle-associated bacteria presented a minority population in seawater, but had a larger cultivability of 25% (0.9%-100%) for populations collected by settlement of particles and 5.7% (0.9%-24%) for populations collected by filtration. Partial 16S rRNA gene sequences indicated that 84% of the cultured taxa were either enriched in particle-associated microbiomes or only found in these microbiomes, including Sulfitobacter and other Rhodobacteraceae, Pseudoalteromonas, Psychromonas, Arcobacter and many Flavobacteriaceae. Illumina-based 16S rRNA V3V4 amplicon sequences of plate communities revealed that nearly all operational taxonomic units had a cultivated and described strain in close phylogenetic proximity. This suggested that decades of strain isolation from seawater on ZoBell marine agar had achieved a very good coverage of cultivable genera abundant in nature. The majority belonged to particle-associated bacteria, complementing observations that abundant free-living seawater bacteria often require cultivation conditions closer to their natural habitat like liquid cultivation in oligotrophic medium.

Links between bacterial infections and cancer are actively investigated. Cost-effective assays to quantify bacterial oncogenic potential can shed new light on these links. Here, we present a soft agar colony formation assay to quantify mouse embryonic fibroblast transformation after Salmonella Typhimurium infection. We describe how to infect and seed cells in soft agar for anchorage-independent growth, a hallmark of cell transformation. We further detail automated cell colony enumeration. This protocol is adaptable to other bacteria or host cells. For complete details on the use and execution of this protocol, please refer to Van Elsland et al.1.

There are contradictory reports in the literature regarding the anti-bacterial activity of graphene, graphene oxide (GO) and reduced graphene oxide (rGO). This controversy is mostly due to variations in key parameters of the reported experiments, like: type of substrate, form of graphene, number of layers, type of solvent and most importantly, type of bacteria. Here, we present experimental data related to bacterial response to GO and rGO integrated in solid agar-based nutrient plates-a standard set-up for bacterial growth that is widely used by microbiologists. Bacillus subtilis and Pseudomonas aeruginosa strains were used for testing bacterial growth. We observed that plate-integrated rGO showed strong anti-bacterial activity against both bacterial species. By contrast, plate-integrated GO was harmless to both bacteria. These results reinforce the notion that the response of bacteria depends critically on the type of graphene material used and can vary dramatically from one bacterial strain to another, depending on bacterial physiology.

In low- and middle-income countries, the use of colistin in therapeutic regimens is common, to treat infections produced for Carbapenemase-producing Enterobacterales (CPE) due to limited access to the recently discovered-approved antibiotics. Furthermore, the technical limitations to perform colistin susceptibility tests make it difficult to assess the suitability of this treatment for each patient, as well as to monitor the rates of resistance. In the present study, we describe the use of agar dilution using a unique colistin concentration of 3 μg/ml to discriminate isolates with colistin resistance in CPE obtained from clinical samples.

Recovering a sufficient amount of microbial DNA from extremely low-biomass specimens, such as human skin, to investigate the community structure of the microbiome remains challenging. We developed a sampling solution containing agar to increase the abundance of recovered microbial DNA. Quantitative PCR targeting the 16S rRNA gene revealed a significant increase in the amount of microbial DNA recovered from the developed sampling solution compared with conventional solutions from extremely low-biomass skin sites such as the volar forearm and antecubital fossa. In addition, we confirmed that the developed sampling solution reduces the contamination rate of probable non-skin microbes compared to the conventional solutions, indicating that the enhanced recovery of microbial DNA was accompanied by a reduced relative abundance of contaminating microbes in the 16S rRNA gene amplicon sequencing data. In addition, agar was added to each step of the DNA extraction process, which improved the DNA extraction efficiency as a co-precipitant. Enzymatic lysis with agar yielded more microbial DNA than conventional kits, indicating that this method is effective for analyzing microbiomes of low-biomass specimens.

We assessed the validity of testing for antimicrobial susceptibility of clinical and mutant Neisseria gonorrhoeae (GC) isolates by disk diffusion in comparison to agar dilution, and Etest® (bioMerieux, France), respectively, for three third generation extended spectrum cephalosporins (ESC): ceftriaxone (CRO), cefixime (CFX), and cefpodoxime (CPD).

New porous activated carbons with a high surface area as an anode material for lithium-ion batteries (LIBs) were synthesized by a one-step, sustainable, and environmentally friendly method. Four chemical activators-H2SO4, H3PO4, KOH, and ZnCl2-have been investigated as facilitators of the formation of the porous structure of activated carbon (AC) from an agar precursor. The study of the materials by Brunauer-Emmett-Teller (BET) and scanning electron microscopy (SEM) methods revealed its highly porous meso- and macro-structure. Among the used chemical activators, the AC prepared with the addition of KOH demonstrated the best electrochemical performance upon its reaction with lithium metal. The initial discharge capacity reached 931 mAh g-1 and a reversible capacity of 320 mAh g-1 was maintained over 100 cycles at 0.1 C. High rate cycling tests up to 10 C demonstrated stable cycling performance of the AC from agar.

Numerous health benefits of diets containing red seaweeds or agar-derived sugar mixtures produced by enzymatic or acid hydrolysis of agar have been reported. However, among various agar-derived sugars, the key components that confer health-beneficial effects, such as prebiotic and anti-colon cancer activities, remain unclear. Here, we prepared various agar-derived sugars by multiple enzymatic reactions using an endo-type and an exo-type of β-agarase and a neoagarobiose hydrolase and tested their in vitro prebiotic and anti-colon cancer activities. Among various agar-derived sugars, agarotriose exhibited prebiotic activity that was verified based on the fermentability of agarotriose by probiotic bifidobacteria. Furthermore, we demonstrated the anti-colon cancer activity of 3,6-anhydro-l-galactose, which significantly inhibited the proliferation of human colon cancer cells and induced their apoptosis. Our results provide crucial information regarding the key compounds derived from red seaweeds that confer beneficial health effects, including prebiotic and anti-colon cancer activities, to the host.

Currently, the demand of Pleurotus HK-37 (oyster mushroom) in Tanzania is growing rapidly due to the increasing of awareness on its nutrition, health, and economic benefits. Despite the increasing demand, the availability of strains of Pleurotus HK-37 species is still a challenge due to high cost of tissue culture technology. The high cost of importing agar seems to be among the factors for this failure. This study aimed at investigating the performance of low-cost agar from local Gracilaria salicornia on tissue culture of Pleurotus HK-37. Local extracted agars with different gel strengths ranging between 100, 200, 300, 400, and 500 g/cm2 were used to make PDA media. The average mycelia growth rate (mm/day) ranged between 9.87 ± 1.44 and 14.9 ± 0.85 mm/day. Low-cost agar shows quite similar performance as that of standard agar on active growth of Pleurotus HK-37 mycelia. All PDA plates appeared white and feathery and showed to grow in a circular mode (radial extension). Mycelia growth on standard agar PDA took 5 days while on extracted local agar PDA took 5 to 7 days to fully colonize the plate at 27 ± 2°C. The present study shows that the production cost can be reduced by ∼35-78% by using local agar.

Colistin has become a last-resort antibiotic for the management of multidrug-resistant gram-negative bacteria. The disk diffusion test is cheap and easy to perform but may be unreliable for colistin susceptibility testing due to poor diffusion of the large colistin molecule. An improved agar diffusion test would increase the reliability of colistin susceptibility testing. This study aimed to modify Muller-Hinton agar (MHA) to improve colistin diffusion in agar.

In this work, the modification of agar is presented with the synergistic effect of bacterial cellulose reinforcement and succinic acid crosslinked agar. The effect of crosslinking agar with succinic acid on tensile strength and water absorption were studied. Crosslinking was confirmed with Fourier infrared spectroscopy. The tensile strength of agar was increased by 70% by succinic acid crosslinking (from55 ± 9.97 MPa to 93.40 ± 9.97 MPa) and the crosslinked agar absorbed only 18.66% water compared to uncrosslinked agar. The tensile strength of agar was increased by 56% by bacterial cellulose reinforcement (55 ± 9.97 MPa to 86.30 ± 14.70 MPa). The strength of agar was improved by 101% by the synergistic effect of bacterial cellulose reinforcement and succinic acid crosslinking (55 ± 9.97 MPa to 111 ± 12.30 MPa). Cytocompatibility studies of the developed films suggested that the crosslinked samples can also have potential applications in biomedical engineering apart from packaging applications.

Laboratories use different strategies to sample and extract atmospheric particulate matter (PM), some of which can be very complicated. Due to the absence of a standard protocol, it is difficult to compare the results of PM toxicity assessment across different laboratories. Here, we proposed a novel PM sampling and cell exposure strategy based on agar membrane. The agar membrane, prepared by a simple freeze-drying method, has a relatively flat surface and porous interior. We demonstrated that the agar membrane was a reliable substitute material for PM sampling. Then the PM on the agar membranes was directly extracted with the culture medium by vortex method, and the PM on the polytetrafluoroethylene (PTFE) filters was extracted with water by the traditional ultrasonic method for comparison. The extraction efficiency was evaluated and in vitro cytotoxicity assays were carried out to investigate the toxic effects of PM extracted with two strategies on macrophage cells. The results showed that the PM extracted from agar membranes induced higher cytotoxicity and more differentially expressed proteins. Overall, the novel PM sampling-cell exposure strategy based on the agar membrane is easy to operate, biocompatible and comparable, and has low disturbance, could be an alternative sampling and extraction method for PM toxicity assessment.

Susceptibility testing for colistin remains challenging primarily due to its inherent properties. We evaluated colistin stability in agar and reproducibility of colistin MICs obtained by agar dilution, broth macro- and micro-dilution and MIC gradient strips on 3-7 iterations of each method using clinical Klebsiella pneumoniae (susceptible-CS, and resistant-CR, n = 2 each), mcr-harboring Escherichia coli (n = 2), and reference strains E. coli ATCC25922 and Pseudomonas aeruginosa ATCC27853. MICs for reference strains were not in the given range using Etest and broth microdilution (ATCC25922, 0.125 and 4 μg/ml, respectively). MICs of CR-1 and CR-2, and of the mcr-harboring E. coli showed high concordance between agar and broth dilution varying up to one 2-fold dilution. However, remarkable variations were observed on broth dilution with CS-1 and CS-2 (MIC range 0.25-32 and 0.5-64 μg/ml, respectively); whereas for agar dilution the MIC for both CS strains was 0.5 μg/ml in all the runs. MICs obtained by MIC gradient strips were lower than those obtained by dilution methods (1-2 dilutions for CS and mcr strains, and up to five dilutions for CR strains). To confirm uniform distribution of colistin in agar, a single strain was spotted in five different regions of the same plate. All spots showed concordant growth with maximum one dilution difference. No effect on MIC was found due to storage of colistin-containing agar plates for 7 days at 4 °C. In our hands, agar dilution was superior in terms of reproducibility and robustness, compared to broth dilution methods, for colistin MIC determination.

Silver nanoparticles (AgNPs) are extensively applied for their broad-spectrum and excellent antibacterial ability in recent years. Polydopamine (PDA) has great advantages for synthesizing large amounts of AgNPs, as it has multiple sites for silver ion binding and phenolic hydroxyl structure to reduce silver ions to AgNPs. Here, we mixed sericin and agar solution and dried at 65 °C to prepare a sericin (SS)/Agar composite film, and then coated polydopamine (PDA) on the surface of SS/Agar film by soaking SS/Agar film into polydopamine solution, subsequently synthesizing high-density AgNPs with the assistance of PDA to yield antibacterial AgNPs-PDA- SS/Agar film. Scanning electron microscope (SEM), Fourier transform infrared spectroscopy (FT-IR) and X-ray diffraction (XRD) spectra indicated the successful synthesis of high-density AgNPs on the surface of PDA-SS/Agar film. PDA coating and AgNPs modification did not affect the structure of sericin and agar. Furthermore, water contact angle, water absorption and mechanical property analysis showed that AgNPs-PDA-SS/Agar film had excellent hydrophilicity and proper mechanical properties. Inhibition zone and growth curve assays suggested the prepared film had excellent and long-lasting antibacterial ability. In addition, it had excellent cytocompatibility on the fibroblast NIH/3T3 cells. The film shows great potential as a novel kind of wound dressing.

The presence of sulfate groups in agar compromises the agar quality by affecting the crosslinking during gelling process. Some arylsulfatases can catalyze the hydrolysis of sulfate bonds in agar to improve the agar quality. Immobilized arylsulfatases prove beneficial advantages for their industrial applications. Here, a previously characterized mutant arylsulfatase K253H/H260L was immobilized on the synthesized magnetic Fe3O4 nanoparticles after functionalization by tannic acid (MNPs@TA). The surface properties and molecular structures of the immobilized arylsulfatase (MNPs@TA@ARS) were examined by scanning electron microscopy and Fourier transform infrared spectroscopy. Enzymatic characterization showed that MNPs@TA@ARS exhibited shifted optimal temperature and pH with deviated apparent Km and Vmax compared to its free counterpart. The immobilized arylsulfatase demonstrated improved thermal and pH stability and enhanced storage stability with modest reusability. In addition, MNPs@TA@ARS displayed enhanced tolerance to various inhibitors and detergents. The utilization of the immobilized arylsulfatase for agar desulfation brought the treated agar with improved quality.

Root development is crucial for plant growth and therefore a key factor in plant performance and food production. Arabidopsis thaliana is the most commonly used system to study root system architecture (RSA). Growing plants on agar-based media has always been routine practice, but this approach poorly reflects the natural situation, which fact in recent years has led to a dramatic shift toward studying RSA in soil. Here, we directly compare RSA responses to agar-based medium (plates) and potting soil (rhizotrons) for a set of redundant loss-of-function plethora (plt) CRISPR mutants with variable degrees of secondary root defects. We demonstrate that plt3plt7 and plt3plt5plt7 plants, which produce only a handful of emerged secondary roots, can be distinguished from other genotypes based on both RSA shape and individual traits on plates and rhizotrons. However, in rhizotrons the secondary root density and the total contribution of the side root system to the RSA is increased in these two mutants, effectively rendering their phenotypes less distinct compared to WT. On the other hand, plt3, plt3plt5, and plt5plt7 mutants showed an opposite effect by having reduced secondary root density in rhizotrons. This leads us to believe that plate versus rhizotron responses are genotype dependent, and these differential responses were also observed in unrelated mutants short-root and scarecrow. Our study demonstrates that the type of growth system affects the RSA differently across genotypes, hence the optimal choice of growth conditions to analyze RSA phenotype is not predetermined.

Cellulose-containing residue from agar production was incorporated as a filler into soy protein-based hydrogels and revalorized without further purification. Rheological assessment of these hydrogels was carried out in order to confirm their shear-thinning behavior and their suitability for 3D printing. It was observed that all hydrogels behaved as weak gels, which are suitable for 3D printing and have good printability and shape fidelity. The addition of cellulose did not cause chemical crosslinking but physical interactions, which led to morphological changes, thereby promoting hardness and shape recovery of the 3D-printed products. The hydrogel with the highest residue content (8 wt %) showed the highest value (78%) in shape recovery. Furthermore, the physicochemical characterization of these 3D-printed products revealed that although they have high swelling capacity, they preserve their integrity in wet conditions. These results suggested the potential of the 3D-printed products developed using residues without further purification to promote circular economy, increasing the efficiency in resources utilization.

The microwave-assisted carboxymethylation of agar to improve its physicochemical properties was investigated. Microwave power, reaction time, and temperature, ethanol concentration, and amounts of chloroacetic acid and sodium hydroxide were assessed for their effects on synthetic yield and degree of substitution (DS). All factors were positively correlated with DS within a certain range. Using optimized conditions, samples with different DS were prepared, and the physicochemical properties of unmodified and carboxymethyl agars prepared by microwave and conventional methods were compared. Carboxymethylation significantly changed the physicochemical properties of the agar, improving gel transparency and reducing dissolution temperature, gel strength, gel hardness, molecular weight, and molecular size; DS was the key factor. Specifically, higher DS values resulted in greater changes. The microwave-assisted method significantly shortened the reaction time and preserved molecular weight, gel strength, and texture hardness of the agar. Therefore, as an environmentally friendly method, microwave-assisted synthesis shows great promise for producing carboxymethyl agar.

Despite widespread resistance to many important antibiotics, the factors that govern the emergence and prevalence of antibiotic-resistant bacteria are still unclear. When exposed to antibiotic gradients in soft agar plates measuring as little as 1.25 × 11 cm we found that Escherichia coli rapidly became resistant to representatives from every class of antibiotics active against Gram-negative bacteria. Evolution kinetics were independent of the frequency of spontaneous mutations that confer antibiotic resistance or antibiotic dose-response curves, and were only loosely correlated to maximal antibiotic concentrations. Instead, rapid evolution required unrealized mutations that could markedly decrease antibiotic susceptibility. When bacteria could not evolve through these "high-impact" mutations, populations frequently bottlenecked, reducing the number of cells from which mutants could arise and prolonging evolution times. This effect was independent of the antibiotic's mechanism of action, and may affect the evolution of antibiotic resistance in clinical settings.

The contamination of water is increasing day by day due to the increase of urbanization and population. Textile industries contribute to this by discarding their waste directly into water streams without proper treatment. A recent study explores the treatment potential of copper oxide nanorods (CuO NRs) synthesized on a green basis in the presence of a biopolymer matrix of agar (AA) and alginate (Alg), in terms of cost effectiveness and environmental impact. The synthesized bio nanocomposite (BNC) was characterized by using different instrumental techniques such as Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), ultra-violet spectroscopy (UV-Vis), scanning electron microscopy-energy dispersive X-ray-elemental analysis (SEM-EDX), transmission electron microscopy (TEM), selected area diffraction pattern (SAED) and X-ray photoelectron spectroscopy (XPS). The optical studies revealed that immobilization of CuO NRs with Alg-Agar biopolymer blend resulted in an increase in light absorption capacity by decreasing the energy bandgap from 2.53 eV to 2.37 eV. The bio nanocomposite was utilized as a photocatalyst for the degradation of amaranth (AN) dye from an aquatic environment under visible light irradiation. A statistical tool known as central composite design (CCD) associated with response surface methodology (RSM) was taken into consideration to evaluate the optimized values of process variables and their synergistic effect on photocatalytic efficiency. The optimized values of process variables were found to be irradiation time (45 min), AN concentration (80 ppm), catalyst dose (20 mg), and pH (4), resulting in 95.69% of dye degradation at 95% confidence level with desirability level 1. The rate of AN degradation was best defined by pseudo-first-order reaction based on the correlation coefficient value (R2 = 0.99) suggesting the establishment of adsorption-desorption equilibrium initially at the catalyst surface then photogenerated •O2- radicals interacting with AN molecule to mineralize them into small non-toxic entities like CO2, H2O. The material used has high efficiency and stability in photocatalytic degradation experiments up to four cycles of reusability.