Combined effects of bacterial-feeding nematodes and prometryne on the soil microbial activity

Microcosm experiments were carried out to study the effects of bacterial-feeding nematodes and indigenous microbes and their interactions on the degradation of prometryne and soil microbial activity in contaminated soil. The results showed that soil indigenous microbes could degrade prometryne up to 59.6-67.9%; bacterial-feeding nematodes accelerated the degradation of prometryne in contaminated soil, and prometryne degradation was raised by 8.36-10.69%. Soil microbial biomass C (C_mic), basal soil respiration (BSR), and respiratory quotient (qCO₂) increased in the beginning of the experiment and decreased in the later stage of the experiment. Nematodes grew and reproduced quite fast, and did increase the growth of soil microbes and enhance soil microbial activity in prometryne contaminated soil during the incubation period.     

Suspension biomechanics of swimming microbes

Micro-organisms play a vital role in many biological, medical and engineering phenomena. Some recent research efforts have demonstrated the importance of biomechanics in understanding certain aspects of micro-organism behaviours such as locomotion and collective motions of cells. In particular, spatio-temporal coherent structures found in a bacterial suspension have been the focus of many research studies over the last few years. Recent studies have shown that macroscopic properties of a suspension, such as rheology and diffusion, are strongly affected by meso-scale flow structures generated by swimming microbes. Since the meso-scale flow structures are strongly affected by the interactions between microbes, a bottom-up strategy, i.e. from a cellular level to a continuum suspension level, represents the natural approach to the study of a suspension of swimming microbes. In this paper, we first provide a summary of existing biomechanical research on interactions between a pair of swimming micro-organisms, as a two-body interaction is the simplest many-body interaction. We show that interactions between two nearby swimming micro-organisms are described well by existing mathematical models. Then, collective motions formed by a group of swimming micro-organisms are discussed. We show that some collective motions of micro-organisms, such as coherent structures of bacterial suspensions, are satisfactorily explained by fluid dynamics. Lastly, we discuss how macroscopic suspension properties are changed by the microscopic characteristics of the cell suspension. The fundamental knowledge we present will be useful in obtaining a better understanding of the behaviour of micro-organisms.     

Broad‐spectrum inhibitory effect of green synthesised silver nanoparticles from Withania somnifera (L.) on microbial growth,biofilm and respiration: a putative mechanistic approach

Multi‐drug resistance in pathogenic bacteria has created immense clinical problem globally. To address these, there is need to develop new therapeutic strategies to combat bacterial infections. Silver nanoparticles (AgNPs) might prove to be next generation nano‐antibiotics. However, improved efficacy and broad‐spectrum activity is still needed to be evaluated and understood. The authors have synthesised AgNPs from Withania somnifera (WS) by green process and characterised. The effect of WS‐AgNPs on growth kinetics, biofilm inhibition as well as eradication of preformed biofilms on both gram‐positive and gram‐negative pathogenic bacteria was evaluated. The authors have demonstrated the inhibitory effect on bacterial respiration and disruption of membrane permeability and integrity. It was found that WS‐AgNPs inhibited growth of pathogenic bacteria even at 16 µg/ml. At sub‐minimum inhibitory concentration concentration, there was approximately 50% inhibition in biofilm formation which was further validated by light and electron microscopy. WS‐AgNPs also eradicated the performed biofilms by varying levels at elevated concentration. The bacterial respiration was also significantly inhibited. Interaction of WS‐AgNPs with test pathogen caused the disruption of cell membrane leading to leakage of cellular content. The production of intracellular reactive oxygen species reveals that WS‐AgNPs exerted oxidative stress inside bacterial cell causing microbial growth inhibition and disrupting cellular functions.Inspec keywords: silver, nanoparticles, nanofabrication, nanomedicine, antibacterial activity, biomedical materials, cellular biophysics, microorganisms, biomembranes, electron microscopy, oxidation, biochemistry, permeabilityOther keywords: broad‐spectrum inhibitory effect, green synthesised silver nanoparticles, Withania somnifera (L.), microbial growth, putative mechanistic approach, multidrug resistance, therapeutic strategies, bacterial infections, next generation nanoantibiotics, broad‐spectrum activity, WS‐AgNPs, growth kinetics, biofilm inhibition, gram‐positive pathogenic bacteria, gram‐negative pathogenic bacteria, bacterial respiration, membrane permeability, membrane integrity, subminimum inhibitory concentration concentration, biofilm formation, light pathogenic bacteria, electron microscopy, cell membrane, cellular content leakage, intracellular reactive oxygen species, oxidative stress, microbial growth inhibition, Ag     

Radiative energy budget reveals high photosynthetic efficiency in symbiont-bearing corals

The light field on coral reefs varies in intensity and spectral composition, and is the key regulating factor for phototrophic reef organisms, for example scleractinian corals harbouring microalgal symbionts. However, the actual efficiency of light utilization in corals and the mechanisms affecting the radiative energy budget of corals are underexplored. We present the first balanced light energy budget for a symbiont-bearing coral based on a fine-scale study of the microenvironmental photobiology of the massive coral Montastrea curta. The majority (more than 96%) of the absorbed light energy was dissipated as heat, whereas the proportion of the absorbed light energy used in photosynthesis was approximately 4.0% under an irradiance of 640 µmol photons m⁻² s⁻¹. With increasing irradiance, the proportion of heat dissipation increased at the expense of photosynthesis. Despite such low energy efficiency, we found a high photosynthetic efficiency of the microalgal symbionts showing high gross photosynthesis rates and quantum efficiencies (QEs) of approximately 0.1 O₂ photon⁻¹ approaching theoretical limits under moderate irradiance levels. Corals thus appear as highly efficient light collectors with optical properties enabling light distribution over the corallite/tissue microstructural canopy that enables a high photosynthetic QE of their photosynthetic microalgae in hospite.     

Adhesion-dependent rupturing of Saccharomyces cerevisiae on biological antimicrobial nanostructured surfaces

Recent studies have shown that some nanostructured surfaces (NSS), many of which are derived from surfaces found on insect cuticles, rupture and kill adhered prokaryotic microbes. Most important, the nanoscale topography is directly responsible for this effect. Although parameters such as cell adhesion and cell wall rigidity have been suggested to play significant roles in this process, there is little experimental evidence regarding the underlying mechanisms involving NSS-induced microbial rupture. In this work, we report the NSS-induced rupturing of a eukaryotic microorganism, Saccharomyces cerevisiae. We show that the amount of NSS-induced rupture of S. cerevisiae is dependent on both the adhesive qualities of the yeast cell and the nanostructure geometry of the NSS. Thus, we are providing the first empirical evidence that these parameters play a direct role in the rupturing of microbes on NSS. Our observations of this phenomenon with S. cerevisiae, particularly the morphological changes, are strikingly similar to that reported for bacteria despite the differences in the yeast cell wall structure. Consequently, NSS provide a novel approach for the control of microbial growth and development of broad-spectrum microbicidal surfaces.     

Collective cell migration: leadership,invasion and segregation

A number of biological processes, such as embryo development, cancer metastasis or wound healing, rely on cells moving in concert. The mechanisms leading to the emergence of coordinated motion remain however largely unexplored. Although biomolecular signalling is known to be involved in most occurrences of collective migration, the role of physical and mechanical interactions has only been recently investigated. In this study, a versatile framework for cell motility is implemented in silico in order to study the minimal requirements for the coordination of a group of epithelial cells. We find that cell motility and cell–cell mechanical interactions are sufficient to generate a broad array of behaviours commonly observed in vitro and in vivo. Cell streaming, sheet migration and susceptibility to leader cells are examples of behaviours spontaneously emerging from these simple assumptions, which might explain why collective effects are so ubiquitous in nature. The size of the population and its confinement appear, in particular, to play an important role in the coordination process. In all cases, the complex response of the population can be predicted from the knowledge of the correlation length of the velocity field measured in the bulk of the epithelial layer. This analysis provides also new insights into cancer metastasis and cell sorting, suggesting, in particular, that collective invasion might result from an emerging coordination in a system where single cells are mechanically unable to invade.     

Biofabrication of broad range antibacterial and antibiofilm silver nanoparticles

Silver nanoparticles (AgNPs) were biosynthesized via a green route using ten different plants extracts (GNP1‐ Caryota urens, GNP2‐Pongamia glabra, GNP3‐ Hamelia patens, GNP4‐Thevetia peruviana, GNP5‐Calendula officinalis, GNP6‐Tectona grandis, GNP7‐Ficus petiolaris, GNP8‐ Ficus busking, GNP9‐ Juniper communis, GNP10‐Bauhinia purpurea). AgNPs were tested against drug resistant microbes and their biofilms. These nanoparticles (NPs) were characterised using UV‐vis spectroscopy, transmission electron microscope, Fourier transform infrared spectroscopy, X‐ray diffraction and Image J software. Most of the AgNPs were distributed over a range of 1 of 60 nm size. The results indicated that AgNPs were antibacterial in nature without differentiating between resistant or susceptible strains. Moreover, the effect was more prominent on Gram negative bacteria then Gram positive bacteria and fungus. AgNPs inhibited various classes of microbes with different concentration. It was also evident from the results that the origin or nature of extract did not affect the activity of the NPs. Protein and carbohydrate leakage assays confirmed that the cells lysis is one of the main mechanisms for the killing of microbes by green AgNPs. This study suggests that the action of AgNPs on microbial cells resulted into cell lysis and DNA damage. Excellent microbial biofilm inhibition was also seen by these green AgNPs. AgNPs have proved their candidature as a potential antibacterial and antibiofilm agent against MDR microbes.Inspec keywords: silver, nanoparticles, antibacterial activity, nanofabrication, microorganisms, ultraviolet spectra, visible spectra, transmission electron microscopy, Fourier transform infrared spectra, X‐ray diffraction, proteins, DNA, nanomedicine, biomedical materials, cellular biophysicsOther keywords: biofabrication, broad range antibacterial nanoparticles, antibiofilm silver nanoparticles, plant extract contribution, drug resistant microbes, UV‐vis spectroscopy, transmission electron microscope, Fourier transform infrared spectroscopy, X‐ray diffraction, Image J software, resistant strains, susceptible strains, Gram positive bacteria, fungus, protein leakage assays, carbohydrate leakage assays, cell lysis, DNA damage, Ag     

Automated,contour-based tracking and analysis of cell behaviour over long time scales in environments of varying complexity and cell density

Understanding single and collective cell motility in model environments is foundational to many current research efforts in biology and bioengineering. To elucidate subtle differences in cell behaviour despite cell-to-cell variability, we introduce an algorithm for tracking large numbers of cells for long time periods and present a set of physics-based metrics that quantify differences in cell trajectories. Our algorithm, termed automated contour-based tracking for in vitro environments (ACTIVE), was designed for adherent cell populations subject to nuclear staining or transfection. ACTIVE is distinct from existing tracking software because it accommodates both variability in image intensity and multi-cell interactions, such as divisions and occlusions. When applied to low-contrast images from live-cell experiments, ACTIVE reduced error in analysing cell occlusion events by as much as 43% compared with a benchmark-tracking program while simultaneously tracking cell divisions and resulting daughter–daughter cell relationships. The large dataset generated by ACTIVE allowed us to develop metrics that capture subtle differences between cell trajectories on different substrates. We present cell motility data for thousands of cells studied at varying densities on shape-memory-polymer-based nanotopographies and identify several quantitative differences, including an unanticipated difference between two ‘control’ substrates. We expect that ACTIVE will be immediately useful to researchers who require accurate, long-time-scale motility data for many cells.     

Self-preservation strategies during bacterial biomineralization with reference to hydrozincite and implications for fossilization of bacteria

The induction of mineralization by microbes has been widely demonstrated but whether induced biomineralization leads to distinct morphologies indicative of microbial involvement remains an open question. For calcium carbonate, evidence suggests that microbial induction enhances sphere formation, but the mechanisms involved and the role of microbial surfaces are unknown. Here, we describe hydrozincite biominerals from Sardinia, Italy, which apparently start life as smooth globules on cyanobacterial filaments, and evolve to spheroidal aggregates consisting of nanoplates. Complementary laboratory experiments suggest that organic compounds are critical to produce this morphology, possibly by inducing aggregation of nanoscopic crystals or nucleation within organic globules produced by metabolizing cells. These observations suggest that production of extracellular polymeric substances by microbes may constitute an effective mechanism to enhance formation of porous spheroids that minimize cell entombment while also maintaining metabolite exchange. However, the high porosity arising from aggregation-based crystal growth probably facilitates rapid oxidation of entombed cells, reducing their potential to be fossilized.     

Engineered spider silk-based 2D and 3D materials prevent microbial infestation

Biofilm formation, especially of antimicrobiotic-resistant microbial strains, are a major problem in health care. Therefore, there is great interest in developing advanced materials that are selectively inhibiting microbial adhesion to surfaces, but at the same time promoting mammalian cell growth. In nature, some spider silks have evolved to repel microbes, a feature that could be used in biomaterials. To unravel how microbe repellence can be achieved in engineered spider silk, different recombinant spider silk proteins based on the consensus sequences of Araneus diadematus dragline silk proteins (fibroin 3 and 4) were processed into 2D-patterned films and 3D-hydrogels. Strikingly, protein structure characteristics on the nanoscale are the basis for the detected microbe-repellence. Designed spider silk materials promoted mammalian cell attachment and proliferation while inhibiting microbial infestation, demonstrating the great potential of these engineered spider silk-based materials as bio-selective microbial-resistant coatings in biomedical as well as technical applications.     

Experimental evolution gone wild

Because of their large population sizes and rapid cell division rates, marine microbes have, or can generate, ample variation to fuel evolution over a few weeks or months, and subsequently have the potential to evolve in response to global change. Here we measure evolution in the marine diatom Skeletonema marinoi evolved in a natural plankton community in CO₂-enriched mesocosms deployed in situ. Mesocosm enclosures are typically used to study how the species composition and biogeochemistry of marine communities respond to environmental shifts, but have not been used for experimental evolution to date. Using this approach, we detect a large evolutionary response to CO₂ enrichment in a focal marine diatom, where population growth rate increased by 1.3-fold in high CO₂-evolved lineages. This study opens an exciting new possibility of carrying out in situ evolution experiments to understand how marine microbial communities evolve in response to environmental change.     

Microbial sensor for preliminary screening of mutagens utilizing a phage induction test

For the preliminary screening of mutagens, a novel microbial sensor system was developed utilizing a phage induction test. Escherichia coli lysogenic strain GY5027 and nonlysogenic strain GY5026 were used in this study. The number of living cells was determined by measuring the respiration of cells immobilized onto an oxygen electrode. The injection of a mutagen, such as AF-2 and MNNG, caused the phage induction in the lysogenic strain, resulting in the decreased respiration of only the lysogenic strain immobilized onto the oxygen electrode but not of nonlysogenic strain. The rate of current increase correlated well with the concentration of mutagens. The sensor responses to the antibiotics and bactericides were definitely different from those of mutagens. Therefore, utilization of this microbial sensor system makes possible the estimation of a substrate's mutagenicity.     

A theoretical study of diffusional transport over the alveolar surfactant layer

In this communication, we analyse the passage of oxygen and carbon dioxide over the respiratory membrane. The lung surfactant membrane at the alveolar interface can have a very special arrangement, which affects the diffusional transport. We present a theoretical model for the diffusion of small molecules in membranes with a complex structure, and we specifically compare a membrane composed of a tubular bilayer network with a membrane consisting of a stack of bilayers. Oxygen and carbon dioxide differ in terms of their solubility in the aqueous and the lipid regions of the membrane, and we show that this difference clearly influences their transport properties in the different membrane structures. During normal respiration, the rate-limiting step for carbon dioxide transport is in the gas phase of the different compartments in the lung. For oxygen, on the other hand, the rate is limited by the transport between alveoli and the capillary blood vessels, including the lung surfactant membrane. In a membrane with a structure of a continuous tubular lipid network, oxygen transport is facilitated to a significant extent compared with the structure of aligned lipid bilayers. The model calculations in the present study show that transport of oxygen through the tubular structure is indeed ca 30 per cent faster than transport through a membrane composed of stacked bilayers. The tubular network will also facilitate the transport of apolar substances between the gas phase and the blood. Important examples are ethanol and other volatile liquids that can leave the blood through the lungs, and gaseous anaesthetics or volatile solvents that are inhaled. This exemplifies a new physiological role of a tubular lipid network in the lung surfactant membrane.     

ETBE (ethyl tert butyl ether) and TAME (tert amyl methyl ether) affect microbial community structure and function in soils

Ethyl tert butyl ether (ETBE) and tert amyl methyl ether (TAME) are oxygenates used in gasoline in order to reduce emissions from vehicles. The present study investigated their impact on a soil microflora that never was exposed to any contamination before. Therefore, soil was artificially contaminated and incubated over 6 weeks. Substrate induced respiration (SIR) measurements and phospholipid fatty acid (PLFA) analysis indicated shifts in both, microbial function and structure during incubation. The results showed an activation of microbial respiration in the presence of ETBE and TAME, suggesting biodegradation by the microflora. Furthermore, PLFA concentrations decreased in the presence of ETBE and TAME and Gram-positive bacteria became more dominant in the microbial community.     

Impacts of light shading and nutrient enrichment geo-engineering approaches on the productivity of a stratified,oligotrophic ocean ecosystem

Geo-engineering proposals to mitigate global warming have focused either on methods of carbon dioxide removal, particularly nutrient fertilization of plant growth, or on cooling the Earth''s surface by reducing incoming solar radiation (shading). Marine phytoplankton contribute half the Earth''s biological carbon fixation and carbon export in the ocean is modulated by the actions of microbes and grazing communities in recycling nutrients. Both nutrients and light are essential for photosynthesis, so understanding the relative influence of both these geo-engineering approaches on ocean ecosystem production and processes is critical to the evaluation of their effectiveness. In this paper, we investigate the relationship between light and nutrient availability on productivity in a stratified, oligotrophic subtropical ocean ecosystem using a one-dimensional water column model coupled to a multi-plankton ecosystem model, with the goal of elucidating potential impacts of these geo-engineering approaches on ecosystem production. We find that solar shading approaches can redistribute productivity in the water column but do not change total production. Macronutrient enrichment is able to enhance the export of carbon, although heterotrophic recycling reduces the efficiency of carbon export substantially over time. Our results highlight the requirement for a fuller consideration of marine ecosystem interactions and feedbacks, beyond simply the stimulation of surface blooms, in the evaluation of putative geo-engineering approaches.     

Recent advances in mapping environmental microbial metabolisms through 13C isotopic fingerprints

After feeding microbes with a defined ¹³C substrate, unique isotopic patterns (isotopic fingerprints) can be formed in their metabolic products. Such labelling information not only can provide novel insights into functional pathways but also can determine absolute carbon fluxes through the metabolic network via metabolic modelling approaches. This technique has been used for finding pathways that may have been mis-annotated in the past, elucidating new enzyme functions, and investigating cell metabolisms in microbial communities. In this review paper, we summarize the applications of ¹³C approaches to analyse novel cell metabolisms for the past 3 years. The isotopic fingerprints (defined as unique isotopomers useful for pathway identifications) have revealed the operations of the Entner–Doudoroff pathway, the reverse tricarboxylic acid cycle, new enzymes for biosynthesis of central metabolites, diverse respiration routes in phototrophic metabolism, co-metabolism of carbon nutrients and novel CO₂ fixation pathways. This review also discusses new isotopic methods to map carbon fluxes in global metabolisms, as well as potential factors influencing the metabolic flux quantification (e.g. metabolite channelling, the isotopic purity of ¹³C substrates and the isotopic effect). Although ¹³C labelling is not applicable to all biological systems (e.g. microbial communities), recent studies have shown that this method has a significant value in functional characterization of poorly understood micro-organisms, including species relevant for biotechnology and human health.     

Low Temperature Anharmonicity and Superconductivity in Cuprates

Temperature-dependent X-ray absorption spectra of the hole-doped La_2?x Sr _x CuO₄ and electron-doped Nd_2?x Ce _x CuO_4?δ high-temperature superconductors were investigated above the Cu K absorption edge. We observed strong anharmonicity in the superconductive CuO₂ plane. For x=0.15 it was shown that part of oxygen ions oscillate in a double-well potential and their vibrations are correlated with the local electron (hole) pair transfer. We suppose that at a low temperature the phase coherence of the local pair movement is determined by the peculiarities of the perovskite-like structure which includes the stiff CuO _n (n=4,6) complexes combined by collective rotational and breathing modes.     

Flux balance analysis for ethylene formation in genetically engineered Saccharomyces cerevisiae

Biosynthesis of ethylene (ethene) is mainly performed by plants and some bacteria and fungi, via two distinct metabolic routes. Plants use two steps, starting with S-adenosylmethionine, while the ethylene-forming microbes perform an oxygen dependent reaction using 2-oxoglutarate and arginine. Introduction of these systems into Saccharomyces cerevisiae was studied in silico. The reactions were added to a metabolic network of yeast and flux over the two networks was optimised for maximal ethylene formation. The maximal ethylene yields obtained for the two systems were similar in the range of 7-8 mol ethylene/10 mol glucose. The microbial metabolic network was used for testing different strategies to increase the ethylene formation. It was suggested that supplementation of exogenous proline, using a solely NAD-coupled glutamate dehydrogenase, and using glutamate as the nitrogen source, could increase the ethylene formation. Comparison of these in silico results with published experimental data for yeast expressing the microbial system confirmed an increased ethylene formation when changing nitrogen source from ammonium to glutamate. The theoretical analysis methods indicated a much higher maximal yield per glucose for ethylene than was experimentally observed. However, such high ethylene yields could only be obtained with a concomitant very high respiration (per glucose). Accordingly, when ethylene production was optimised under the additional constraint of restricted respiratory capacity (i.e. limited to experimentally measured values) the theoretical maximal ethylene yield was much lower at 0.2/10 mol glucose, and closer to the experimentally observed values.     

Mechanics regulates ATP-stimulated collective calcium response in fibroblast cells

Cells constantly sense their chemical and mechanical environments. We study the effect of mechanics on the ATP-induced collective calcium response of fibroblast cells in experiments that mimic various tissue environments. We find that closely packed two-dimensional cell cultures on a soft polyacrylamide gel (Young''s modulus E = 690 Pa) contain more cells exhibiting calcium oscillations than cultures on a rigid substrate (E = 36 000 Pa). Calcium responses of cells on soft substrates show a slower decay of calcium level relative to those on rigid substrates. Actin enhancement and disruption experiments for the cell cultures allow us to conclude that actin filaments determine the collective Ca²⁺ oscillatory behaviour in the culture. Inhibition of gap junctions results in a decrease of the oscillation period and reduced correlation of calcium responses, which suggests additional complexity of signalling upon cell–cell contact. Moreover, the frequency of calcium oscillations is independent of the rigidity of the substrate but depends on ATP concentration. We compare our results with those from similar experiments on individual cells. Overall, our observations show that collective chemical signalling in cell cultures via calcium depends critically on the mechanical environment.     

Fast,high-throughput measurement of collective behaviour in a bacterial population

Swimming bacteria explore their environment by performing a random walk, which is biased in response to, for example, chemical stimuli, resulting in a collective drift of bacterial populations towards ‘a better life’. This phenomenon, called chemotaxis, is one of the best known forms of collective behaviour in bacteria, crucial for bacterial survival and virulence. Both single-cell and macroscopic assays have investigated bacterial behaviours. However, theories that relate the two scales have previously been difficult to test directly. We present an image analysis method, inspired by light scattering, which measures the average collective motion of thousands of bacteria simultaneously. Using this method, a time-varying collective drift as small as 50 nm s⁻¹ can be measured. The method, validated using simulations, was applied to chemotactic Escherichia coli bacteria in linear gradients of the attractant α-methylaspartate. This enabled us to test a coarse-grained minimal model of chemotaxis. Our results clearly map the onset of receptor methylation, and the transition from linear to logarithmic sensing in the bacterial response to an external chemoeffector. Our method is broadly applicable to problems involving the measurement of collective drift with high time resolution, such as cell migration and fluid flows measurements, and enables fast screening of tactic behaviours.