Flocking birds, fish schools, and insect swarms are familiar examples of collective motion that plays a role in a range of problems, such as spreading of diseases. Models have provided a qualitative understanding of the collective motion, but progress has been hindered by the lack of detailed experimental data. Here we report simultaneous measurements of the positions, velocities, and orientations as a function of time for up to a thousand wild-type Bacillus subtilis bacteria in a colony. The bacteria spontaneously form closely packed dynamic clusters within which they move cooperatively. The number of bacteria in a cluster exhibits a power-law distribution truncated by an exponential tail. The probability of finding clusters with large numbers of bacteria grows markedly as the bacterial density increases. The number of bacteria per unit area exhibits fluctuations far larger than those for populations in thermal equilibrium. Such “giant number fluctuations” have been found in models and in experiments on inert systems but not observed previously in a biological system. Our results demonstrate that bacteria are an excellent system to study the general phenomenon of collective motion.

/pdf/collective-motion-and-density-fluctuations-in-bacterial-2zxptimf2g.pdf

Collective motion and density fluctuations in bacterial colonies

The Inherent Conflicts in Developing Soil Microbial Inoculants.

The Microbiologist's Guide to Membrane Potential Dynamics.

Bacterial spores are resistant to physical and chemical insults, which makes them a major concern for public health and industry. Spores help bacteria to survive extreme environmental conditions that vegetative cells cannot tolerate. Spore resistance and dormancy are important properties for applications in medicine, veterinary health, food safety, crop protection and other domains. The resistance of bacterial spores results from a protective multilayered structure and from the unique composition of the spore core. The mechanisms of sporulation and germination, the first stage after breaking of dormancy, and organization of spore structure have been extensively studied in Bacillus species. This review aims to illustrate how far the structure, composition and properties of spores are shaped by the environmental conditions in which spores form. We look at the physiological and molecular mechanisms underpinning how sporulation media and environment deeply affect spore yield, spore properties like resistance to wet heat and physical and chemical agents, germination and further growth. For example, spore core water content decreases as sporulation temperature increases, and resistance to wet heat increases. Controlling the fate of Bacillus spores is pivotal to controlling bacterial risks and process efficiencies in, for example, the food industry, and better control hinges on better understanding how sporulation conditions influence spore properties.

Sporulation environment influences spore properties in Bacillus: evidence and insights on underlying molecular and physiological mechanisms.

Methane (CH4), the most abundant hydrocarbon in the atmosphere, originates largely from biogenic sources1 linked to an increasing number of organisms occurring in oxic and anoxic environments. Traditionally, biogenic CH4 has been regarded as the final product of anoxic decomposition of organic matter by methanogenic archaea. However, plants2,3, fungi4, algae5 and cyanobacteria6 can produce CH4 in the presence of oxygen. Although methanogens are known to produce CH4 enzymatically during anaerobic energy metabolism7, the requirements and pathways for CH4 production by non-methanogenic cells are poorly understood. Here, we demonstrate that CH4 formation by Bacillus subtilis and Escherichia coli is triggered by free iron and reactive oxygen species (ROS), which are generated by metabolic activity and enhanced by oxidative stress. ROS-induced methyl radicals, which are derived from organic compounds containing sulfur- or nitrogen-bonded methyl groups, are key intermediates that ultimately lead to CH4 production. We further show CH4 production by many other model organisms from the Bacteria, Archaea and Eukarya domains, including in several human cell lines. All these organisms respond to inducers of oxidative stress by enhanced CH4 formation. Our results imply that all living cells probably possess a common mechanism of CH4 formation that is based on interactions among ROS, iron and methyl donors, opening new perspectives for understanding biochemical CH4 formation and cycling. Methane formation by a ROS-mediated process is linked to metabolic activity and is identified as a conserved feature across living systems. 

/pdf/methane-formation-driven-by-reactive-oxygen-species-across-3hrl16s5.pdf

Methane formation driven by reactive oxygen species across all living organisms

Some bacteria, such as Bacillus subtilis, withstand starvation by forming dormant spores that revive when nutrients become available. Although sporulation and spore revival jointly determine survival in fluctuating environments, the relationship between them has been unclear. Here we show that these two processes are linked by a phenotypic "memory" that arises from a carry-over of molecules from the vegetative cell into the spore. By imaging life histories of individual B. subtilis cells using fluorescent reporters, we demonstrate that sporulation timing controls nutrient-induced spore revival. Alanine dehydrogenase contributes to spore memory and controls alanine-induced outgrowth, thereby coupling a spore's revival capacity to the gene expression and growth history of its progenitors. A theoretical analysis, and experiments with signaling mutants exhibiting altered sporulation timing, support the hypothesis that such an intrinsically generated memory leads to a tradeoff between spore quantity and spore quality, which could drive the emergence of complex microbial traits.

/pdf/phenotypic-memory-in-bacillus-subtilis-links-dormancy-entry-5ggugsmnqh.pdf

Phenotypic memory in Bacillus subtilis links dormancy entry and exit by a spore quantity-quality tradeoff.

Quality–quantity tradeoffs govern the production of propagules across taxa and can explain variability in life-history traits in higher organisms. A quality–quantity tradeoff was recently discovered in spore forming bacteria, but whether it impacts fitness is unclear. Here we show both theoretically and experimentally that the nutrient supply during spore revival determines the fitness advantage associated with different sporulation behaviors in Bacillus subtilis. By tuning sporulation rates we generate spore-yield and spore-quality strategists that compete with each other in a microscopic life-cycle assay. The quality (yield) strategist is favored when spore revival is triggered by poor (rich) nutrients. We also show that natural isolates from the gut and soil employ different life-cycle strategies that result from genomic variations in the number of rap-phr signaling systems. Taken together, our results suggest that a spore quality–quantity tradeoff contributes to the evolutionary adaptation of sporulating bacteria.

/pdf/a-spore-quality-quantity-tradeoff-favors-diverse-sporulation-2tsxmwn1wm.pdf

A spore quality-quantity tradeoff favors diverse sporulation strategies in Bacillus subtilis.

Automatic single-cell image analysis allows gaining deeper insights into biological processes. We present an approach for single-cell segmentation and tracking of bacterial cells in time-lapse microscopy image data. For cell segmentation we use linear feature detection and a probability map combined with schemes for cell splitting. For cell tracking we propose an approach based on the maximal overlapping area between cells, which is robust regarding cell rotation and accurately detects cell divisions. Our approach was successfully applied to segment and track cells in time-lapse images of the life cycle of Bacillus subtilis. We also quantitatively evaluated the performance of the segmentation and tracking approaches.

Automatic Single-Cell Segmentation and Tracking of Bacterial Cells in Fluorescence Microscopy Images

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Phenotypic memory in Bacillus subtilis links dormancy entry and exit by a spore quantity-quality tradeoff.

A spore quality-quantity tradeoff favors diverse sporulation strategies in Bacillus subtilis.

Automatic Single-Cell Segmentation and Tracking of Bacterial Cells in Fluorescence Microscopy Images