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Nikolic, N.

Publications and source records attributed to Nikolic, N..

6 recordsLinked to original sources

Climate-driven in-situ trait variation in an annual ruderal grass across Europe

O_LIPlant functional traits link environmental conditions to plant performance and adaptation. Growing evidence shows that in-situ intraspecific trait variation can be as important as differences between species, yet large intraspecific datasets measured in situ are rare. While most studies focused on plant morphological traits, contents of elemental nutrients in the seeds received much less attention so far. C_LIO_LIWe conducted a large-scale in-situ study of the widespread ruderal grass Hordeum murinum. We sampled 2070 individuals from 207 populations from a large part of the native range in Europe and Northern Africa. In-situ, we measured seed ripening phenology and morphological traits, and analyzed the content of elemental nutrients in the seeds. C_LIO_LIWe found that Hordeum murinum grew larger, produced seeds later, and had heavier seeds in colder and wetter areas. Plants in denser vegetation were taller with heavier seeds but formed fewer spikes. Seed nutrient content generally declined with seed weight and was mainly driven by climate. Soil conditions had only minor effects on plant traits and seed nutrients. Population identity explained much of the variation, indicating a possible genetic component. C_LIO_LISynthesis: Our findings provide a comprehensive view of Hordeum murinum responding to environmental gradients across its European distribution. Climatic variables, especially temperature, are key drivers for reproductive success and seed nutrient content, while local environments, such as biotic pressures, are more critical for growth-related traits. These patterns indicate that H. murinum modulates its growth and reproductive investment along environmental gradients, balancing phenology, stress tolerance, and limited competitive capacity. C_LI

ecology↗

Investigating bacteria-phage interaction dynamics using droplet-based technology

An alarming rise in antimicrobial resistance worldwide has spurred efforts into the search for alternatives to antibiotic treatments. The use of bacteriophages, bacterial viruses harmless to humans, represents a promising approach with potential to treat bacterial infections (phage therapy). Recent advances in microscopy-based single-cell techniques have allowed researchers to develop new quantitative approaches for assessing the interactions between bacteria and phages, especially the ability of phages to eradicate bacterial pathogen populations. Here we combine droplet microfluidics with fluorescence time-lapse microscopy to characterize the growth and lysis dynamics of the bacterium Escherichia coli confined in droplets when challenged with phage. We investigated phages that promote lysis of infected E. coli cells, specifically, a phage species with DNA genome, T7 (Escherichia virus T7) and two phage species with RNA genomes, MS2 (Emesvirus zinderi) and Q{beta} (Qubevirus durum). Our microfluidic trapping device generated and immobilized picoliter-sized droplets, enabling stable imaging of bacterial growth and lysis in a temperature-controlled setup. Temporal information on bacterial population size was recorded for up to 25 hours, allowing us to determine growth rates of bacterial populations helping us uncover the extent and speed of phage infection. In the long-term, the development of novel microfluidic and single-cell techniques will expedite research towards understanding the genetic and molecular basis of rapid phage-induced lysis, preempting bacterial resistance to phages and ultimately identifying key factors influencing the success of phage therapy.

microbiology↗

Label-free analysis of bacterial growth and lysis at the single-cell level using droplet microfluidics and object detection-oriented deep learning

Bacteria identification and counting at the small population scale is important to many applications in the food safety industry, the diagnostics of infectious diseases and the study and discovery of novel antimicrobial compounds. There is still a lack of easy to implement, fast and accurate methods to count populations of motile cells at the single-cell level. Here, we report a label-free method to count and localize bacterial cells freely swimming in microfluidic anchored picolitre droplets. We used the object detection oriented YOLOv4 deep learning framework for cell detection from bright-field images obtained with an automated Z-stack setup. The neural network was trained to recognize Escherichia coli cell morphology with an average precision of approximately 84%. This allowed us to accurately identify individual cell division events, enabling the study of stochastic bacterial growth starting from initial populations as low as one cell. This work also demonstrates the ability to study single cell lysis in the presence of T7 lytic bacterial viruses (phages). The high precision in cell numbers facilitated the visualization of bacteria-phage interactions over timescale of hours, paving the way towards deciphering phage life cycles in confined environments.

microbiology↗

Bacterial toxin-antitoxin system MazEF as a native defense mechanism against RNA phages in Escherichia coli

Bacteria have evolved a wide range of defense strategies to protect themselves against bacterial viruses (phages). However, the known mechanisms almost exclusively target phages with DNA genomes. While several bacterial toxin-antitoxin systems have been considered to cleave single-stranded bacterial RNA in response to stressful conditions, their role in protecting bacteria against phages with single-stranded RNA genomes has not been studied. Here we investigate the role of a representative toxin-antitoxin system, MazEF, in protecting Escherichia coli against two RNA phages - MS2 and Q{beta}. Our population-level experiments revealed that a mazEF deletion strain is more susceptible to RNA phage infection than the wild-type. At the single-cell level, deletion of the mazEF locus significantly shortened the time to lysis of individual bacteria challenged with RNA phage. At the genomic level, we found that the adenine-cytosine-adenine sequence, directly recognized and cleaved by the MazF toxin, is systematically underrepresented in the genomes of RNA phages that are known to infect E. coli, indicating selection for decreased probability of cleavage. These results suggest that in addition to other physiological roles, RNA-degrading toxin-antitoxin modules can function as a primitive immune system against RNA phages.

microbiology↗

Real-time dynamics of individual chemoreceptor mRNA molecules reveals translation hotspots at the inner membrane of Escherichia coli

Since bacteria lack a nucleus, the location of mRNA molecules is determined by the different characteristics of the encoded proteins, and the transcriptome is spatially arranged into cytosolic and membrane-associated mRNA. While translation of membrane protein-encoding mRNA has been studied in great mechanistic detail using biochemical methods, the spatiotemporal dynamics of this process remains poorly understood at the subcellular level. Here, we investigate the dynamics of individual fluorescently labelled mRNA molecules encoding the transmembrane serine chemoreceptor Tsr, to probe the mechanism of membrane protein translation. Analysis of tsr mRNA diffusion in the proximity of the plasma membrane revealed distinct diffusive modes that reflect the state of the mRNA molecule and its involvement in the process of active translation into the Sec secretion system. We find that the composition, and hence the fluidity of the membrane affects diffusion of membrane targeted mRNAs. Moreover, Tsr translation occurs in localized membrane regions, similar to eukaryotic hotspots. The hotspot localization coincides with the physical location of the transcribed gene, which itself is displaced towards the inner membrane. These findings suggest that inner membrane protein translation is a spatially defined process that occurs in hotspots, indicative of long-lived transertion sites. Our results show an additional layer of spatio-temporal structuring within the bacterial cell, thus revealing a qualitatively different understanding of the basic process of transcription and translation in bacteria. Significance StatementA large fraction of the bacterial proteome is directly synthesized into the inner membrane, and this process shapes the overall distribution of mRNA transcripts within the cell. Although highly dynamic in their nature, bacterial transcriptomes have mostly been studied in fixed cells. Here, we track individual mRNA molecules encoding the serine chemoreceptor in living bacterial cells and find that translation occurs in membrane hotspots that were previously exclusive to eukaryotes. Our results indicate an additional layer of spatio-temporal structuring within the bacterial cell that impacts our understanding of transcription and translation in bacteria.

microbiology↗

Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells

The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.

microbiology↗