scholarly journals Spatial modulation of individual behaviors enables an ordered structure of diverse phenotypes during bacterial group migration

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Yang Bai ◽  
Caiyun He ◽  
Pan Chu ◽  
Junjiajia Long ◽  
Xuefei Li ◽  
...  
Keyword(s):  
Wave Front ◽  
Bacterial Population ◽  
Stochastic Simulations ◽  
Spatial Modulation ◽  
Microbial Populations ◽  
Modeling Framework ◽  
Run And Tumble ◽  
Migratory Patterns ◽  
Group Migration ◽  
Cell Trajectories

Coordination of diverse individuals often requires sophisticated communications and high-order computational abilities. Microbial populations can exhibit diverse individualistic behaviors, and yet can engage in collective migratory patterns with a spatially sorted arrangement of phenotypes. However, it is unclear how such spatially sorted patterns emerge from diverse individuals without complex computational abilities. Here, by investigating the single-cell trajectories during group migration, we discovered that, despite the constant migrating speed of a group, the drift velocities of individual bacteria decrease from the back to the front. With a Langevin-type modeling framework, we showed that this decreasing profile of drift velocities implies the spatial modulation of individual run-and-tumble random motions, and enables the bacterial population to migrate as a pushed wave front. Theoretical analysis and stochastic simulations further predicted that the pushed wave front can help a diverse population to stay in a tight group, while diverse individuals perform the same type of mean reverting processes around centers orderly aligned by their chemotactic abilities. This mechanism about the emergence of orderly collective migration from diverse individuals is experimentally demonstrated by titration of bacterial chemoreceptor abundance. These results reveal a simple computational principle for emergent ordered behaviors from heterogeneous individuals.

scholarly journals Spatial modulation of individual behaviors enables collective decision-making during bacterial group migration

2021 ◽  
Author(s):  
Yang Bai ◽  
Caiyun He ◽  
Junjiajia Long ◽  
Xuefei Li ◽  
Xiongfei Fu
Keyword(s):  
Group Performance ◽  
Spatial Modulation ◽  
Microbial Populations ◽  
Collective Behaviors ◽  
Dynamic Stimuli ◽  
Consistent Group ◽  
Run And Tumble ◽  
Migratory Patterns ◽  
The Individual ◽  
Group Migration

AbstractCoordination of individuals with diversity often requires sophisticated communications and high-order computational abilities. Microbial populations can exhibit diverse individualistic behaviors and yet can engage in collective migratory patterns with a spatially sorted arrangement of phenotypes following a self-generated attractant gradient. However, it’s unclear how individual bacteria without complex computational abilities can achieve the consistent group performance and determine their positions in the group while facing spatiotemporally dynamic stimuli. Here, we investigate the statistics of bacterial run-and-tumble trajectories during group migration. We discover that, despite of the constant migrating speed as a group, the individual drift velocity exhibits a spatially dependent structure that decreases from the back to the front of the group. The spatial modulation of individual stochastic behaviors constrains cells in the group, ensuring the coherent population movement with ordered patterns of phenotypes. These results reveal a simple computational principle for emergent collective behaviors from heterogeneous individuals.

scholarly journals Computational Analysis of Dynamic Light Exposure of Unicellular Algal Cells in a Flat-Panel Photobioreactor to Support Light-Induced CO2 Bioprocess Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Nicolò S. Vasile ◽  
Alessandro Cordara ◽  
Giulia Usai ◽  
Angela Re
Keyword(s):  
Light Transmission ◽  
Light Exposure ◽  
Model Organism ◽  
Cell Factory ◽  
Bioprocess Development ◽  
Cultivation Conditions ◽  
Flat Panel ◽  
Modeling Framework ◽  
Cell Factories ◽  
Cell Trajectories

Cyanobacterial cell factories trace a vibrant pathway to climate change neutrality and sustainable development owing to their ability to turn carbon dioxide-rich waste into a broad portfolio of renewable compounds, which are deemed valuable in green chemistry cross-sectorial applications. Cell factory design requires to define the optimal operational and cultivation conditions. The paramount parameter in biomass cultivation in photobioreactors is the light intensity since it impacts cellular physiology and productivity. Our modeling framework provides a basis for the predictive control of light-limited, light-saturated, and light-inhibited growth of the Synechocystis sp. PCC 6803 model organism in a flat-panel photobioreactor. The model here presented couples computational fluid dynamics, light transmission, kinetic modeling, and the reconstruction of single cell trajectories in differently irradiated areas of the photobioreactor to relate key physiological parameters to the multi-faceted processes occurring in the cultivation environment. Furthermore, our analysis highlights the need for properly constraining the model with decisive qualitative and quantitative data related to light calibration and light measurements both at the inlet and outlet of the photobioreactor in order to boost the accuracy and extrapolation capabilities of the model.

scholarly journals Harnessing the Potential of Killers and Altruists within the Microbial Community: A Possible Alternative to Antibiotic Therapy?

Antibiotics ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 230 ◽  
Author(s):  
Larisa N. Ikryannikova ◽  
Leonid K. Kurbatov ◽  
Surinder M. Soond ◽  
Andrey A. Zamyatnin
Keyword(s):  
Cell Death ◽  
Bacterial Communities ◽  
Bacterial Population ◽  
Bacterial Species ◽  
Microbial Populations ◽  
Ongoing Research ◽  
Life And Death ◽  
Form Part ◽  
Recent Developments ◽  
New Strategies

In the context of a post-antibiotic era, the phenomenon of microbial allolysis, which is defined as the partial killing of bacterial population induced by other cells of the same species, may take on greater significance. This phenomenon was revealed in some bacterial species such as Streptococcus pneumoniae and Bacillus subtilis, and has been suspected to occur in some other species or genera, such as enterococci. The mechanisms of this phenomenon, as well as its role in the life of microbial populations still form part of ongoing research. Herein, we describe recent developments in allolysis in the context of its practical benefits as a form of cell death that may give rise to developing new strategies for manipulating the life and death of bacterial communities. We highlight how such findings may be viewed with importance and potential within the fields of medicine, biotechnology, and pharmacology.

scholarly journals A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series

2022 ◽  
Vol 18 (1) ◽  
pp. e1009733
Author(s):  
Jann Paul Mattern ◽  
Kristof Glauninger ◽  
Gregory L. Britten ◽  
John R. Casey ◽  
Sangwon Hyun ◽  
...  
Keyword(s):  
Time Series ◽  
Population Dynamics ◽  
Size Distribution ◽  
Bayesian Approach ◽  
Critical Parameters ◽  
Microbial Populations ◽  
Series Data ◽  
Matrix Population Models ◽  
Modeling Framework ◽  
Phytoplankton Population

The rates of cell growth, division, and carbon loss of microbial populations are key parameters for understanding how organisms interact with their environment and how they contribute to the carbon cycle. However, the invasive nature of current analytical methods has hindered efforts to reliably quantify these parameters. In recent years, size-structured matrix population models (MPMs) have gained popularity for estimating division rates of microbial populations by mechanistically describing changes in microbial cell size distributions over time. Motivated by the mechanistic structure of these models, we employ a Bayesian approach to extend size-structured MPMs to capture additional biological processes describing the dynamics of a marine phytoplankton population over the day-night cycle. Our Bayesian framework is able to take prior scientific knowledge into account and generate biologically interpretable results. Using data from an exponentially growing laboratory culture of the cyanobacterium Prochlorococcus, we isolate respiratory and exudative carbon losses as critical parameters for the modeling of their population dynamics. The results suggest that this modeling framework can provide deeper insights into microbial population dynamics provided by size distribution time-series data.

scholarly journals Microbial Populations Associated with Treatment of an Industrial Dye Effluent in an Anaerobic Baffled Reactor

2001 ◽  
Vol 67 (7) ◽  
pp. 3226-3235 ◽  
Author(s):  
Jason J. Plumb ◽  
Joanne Bell ◽  
David C. Stuckey
Keyword(s):  
Bacterial Population ◽  
Treatment Process ◽  
Anaerobic Treatment ◽  
Microbial Populations ◽  
23S Rrna ◽  
Anaerobic Baffled Reactor ◽  
Sulfate Reducing ◽  
Subsequent Conversion ◽  
Reducing Bacteria ◽  
Rdna Clone

ABSTRACT Fluorescent in situ hybridization (FISH) using 16S and 23S rRNA-targeted probes together with construction of an archaeal 16S ribosomal DNA (rDNA) clone library was used to characterize the microbial populations of an anaerobic baffled reactor successfully treating industrial dye waste. Wastewater produced during the manufacture of food dyes containing several different azo and other dye compounds was decolorized and degraded under sulfidogenic and methanogenic conditions. Use of molecular methods to describe microbial populations showed that a diverse group of Bacteria andArchaea was involved in this treatment process. FISH enumeration showed that members of the gamma subclass of the classProteobacteria and bacteria in theCytophaga-Flexibacter-Bacteroides phylum, together with sulfate-reducing bacteria, were prominent members of a mixed bacterial population. A combination of FISH probing and analysis of 98 archaeal 16S rDNA clone inserts revealed that together with the bacterial population, a methanogenic population dominated byMethanosaeta species and containing species ofMethanobacterium and Methanospirillum and a relatively unstudied methanogen, Methanomethylovorans hollandica, contributed to successful anaerobic treatment of the industrial waste. We suggest that sulfate reducers, or more accurately sulfidogenic bacteria, together with M. hollandicacontribute considerably to the treatment process through metabolism of dye-associated sulfonate groups and subsequent conversion of sulfur compounds to carbon dioxide and methane.

scholarly journals Experimental validation of joint phase and amplitude wave-front sensing with coronagraphic phase diversity for high-contrast imaging

2018 ◽  
Vol 614 ◽  
pp. A142 ◽  
Author(s):  
O. Herscovici-Schiller ◽  
L. M. Mugnier ◽  
P. Baudoz ◽  
R. Galicher ◽  
J.-F. Sauvage ◽  
...  
Keyword(s):  
Wave Front ◽  
Direct Detection ◽  
Speckle Pattern ◽  
Joint Estimation ◽  
The Self ◽  
Spatial Modulation ◽  
High Contrast ◽  
Contrast Imaging ◽  
Time Modulation ◽  
Phase Diversity

Context. The next generation of space-borne instruments dedicated to the direct detection of exoplanets requires unprecedented levels of wavefront control precision. Coronagraphic wavefront sensing techniques for these instruments must measure both the phase and amplitude of the optical aberrations using the scientific camera as a wavefront sensor. Aims. In this paper, we develop an extension of coronagraphic phase diversity to the estimation of the complex electric field, that is, the joint estimation of phase and amplitude. Methods. We introduced the formalism for complex coronagraphic phase diversity. We have demonstrated experimentally on the Très Haute Dynamique testbed at the Observatoire de Paris that it is possible to reconstruct phase and amplitude aberrations with a subnanometric precision using coronagraphic phase diversity. Finally, we have performed the first comparison between the complex wavefront estimated using coronagraphic phase diversity (which relies on time-modulation of the speckle pattern) and the one reconstructed by the self-coherent camera (which relies on the spatial modulation of the speckle pattern). Results. We demonstrate that coronagraphic phase diversity retrieves complex wavefront with subnanometric precision with a good agreement with the reconstruction performed using the self-coherent camera. Conclusions. This result paves the way to coronagraphic phase diversity as a coronagraphic wave-front sensor candidate for very high contrast space missions.

scholarly journals Memory shapes microbial populations

2020 ◽  
Author(s):  
Chaitanya S. Gokhale ◽  
Stefano Giaimo ◽  
Philippe Remigi
Keyword(s):  
Environmental Changes ◽  
Stochastic Simulations ◽  
Microbial Populations ◽  
Temporal Correlations ◽  
Deterministic Modelling ◽  
General Survival ◽  
Living Organisms ◽  
Binary Switching ◽  
Multicellular Organisms ◽  
Available Information

AbstractCorrect decision making is fundamental for all living organisms to thrive under environmental changes. The patterns of environmental variation and the quality of available information define the most favourable strategy among multiple options, including sensing and reacting to environmental cues or randomly adopting a phenotypic state. Memory – a phenomenon often associated with, but not restricted to, higher multicellular organisms – can help when temporal correlations exist. How does memory manifest itself in unicellular organisms? Through a combination of deterministic modelling and stochastic simulations, we describe the population-wide fitness consequences of phenotypic memory in microbial populations. Moving beyond binary switching models, our work highlights the need to consider a broader range of switching behaviours when describing microbial adaptive strategies. We show that multiple cellular states capture the empirical observations of lag time distributions, overshoots, and ultimately the phenomenon of phenotypic heterogeneity. We emphasise the implications of our work in understanding antibiotic tolerance, and, in general, survival under fluctuating environments.

Changes in the rumen microbial population and its activities during the refaunation period after the reintroduction of ciliate protozoa into the rumen of defaunated sheep

1993 ◽  
Vol 39 (1) ◽  
pp. 61-69 ◽  
Author(s):  
Alan G. Williams ◽  
Susan E. Withers
Keyword(s):  
Bacterial Population ◽  
Microbial Population ◽  
Microbial Populations ◽  
Ruminal Fermentation ◽  
Microbial Activities ◽  
Ruminal Ph ◽  
Ruminal Digestion ◽  
Phase Population ◽  
Ciliate Protozoa ◽  
In Sacco

Changes in the microbial populations, their activities, and the ruminal fermentation were monitored for 50 d following the reintroduction of ciliate protozoa into four defaunated sheep. A protozoal population was reestablished successfully in each recipient, using a washed inoculum containing approximately 103 cells, although there were between-animal differences in the rates of recolonization and genus establishment. Entodinium spp. predominated in the initial stages of the refaunation period and had an apparent maximal generation time of 9–10 h. Bacterial and fungal numbers did not decline following the reintroduction of protozoa and a small transient increase in the numbers of amylolytic and xylanolytic bacteria and fungal zoospores occurred in the early stages of refaunation when the protozoal population was < 105/g ruminal contents, but these subsequently declined as the protozoa established. Although the fibrolytic bacterial population was lowest in period 3 (> 105 protozoa/g), the in sacco ruminal digestion of Lolium perenne hay and polysaccharolytic enzyme activities in the solids-associated populations were either maintained or increased when protozoa were present confirming the important contribution of protozoa to fibre breakdown in the rumen. Significant changes in ruminal microbial activities occurred after protozoal reinoculation but before the rumen had refaunated completely. Arylamidase activities in the liquor-phase population and ruminal ammonia concentrations increased significantly within 48 h of transfaunation; the magnitude of the effects became more pronounced as the protozoal population developed. However, volatile fatty acid formation and ruminal pH were not affected after the reintroduction of protozoa.Key words: rumen, sheep, ciliate protozoa.

Comparison between the Bacterial Populations from Solutions and Minerals in 1 m Test Columns and the Industrial Low Grade Copper Sulphide Bioleaching Process in the Escondida Mine, Chile

2009 ◽  
Vol 71-73 ◽  
pp. 63-66 ◽  
Author(s):  
V. Zepeda ◽  
F. Galleguillos ◽  
V. Urtuvia ◽  
J. Molina ◽  
Cecilia Demergasso
Keyword(s):  
Bacterial Population ◽  
Bacterial Count ◽  
Microbial Populations ◽  
Total Bacterial Count ◽  
Low Grade ◽  
Acidithiobacillus Thiooxidans ◽  
Bacterial Populations ◽  
Cellular Density ◽  
Irrigation Period ◽  
Card Fish

The study of microbial populations of biohydrometallurgic processes is generally more focused on the solutions involved than on the minerals. This is mainly due to complexity and costs associated with taking mineral samples during the leaching cycle. The present study compares the microorganisms in the solutions and the minerals in 1 m test columns and in samples taken from two strips of an industrial heap from the Escondida Copper Mine in Chile. The column test was carried out in six 1 m columns that were operated with similar parameters than the industrial heap. The industrial heap is divided into strips, and samples were collected from Strip 1 (after the end of the operation) and from Strip 9 (during the irrigation period). To analyze the bacterial population Real-Time PCR and CARD-FISH techniques were used. From the results of the column leaching tests a slightly greater cellular density was observed for the mineral than the solution, when the total bacterial count was considered. In both types of samples the predominant microorganisms were Acidithiobacillus thiooxidans, Acidithiobacillus ferrooxidans D2 and Leptospirillum ferriphilum. In the samples from the industrial heap A. ferrooxidans predominated at the start of operation and A.thiooxidans at the end of the leach cycle.

Microbial Flora Associated with the Digestive System ofUpogebia Stellata(Crustacea: Decapoda: Thalassinidea)

1997 ◽  
Vol 77 (4) ◽  
pp. 1083-1096 ◽  
Author(s):  
E.H. Pinn ◽  
A. Rogerson ◽  
R.J.A. Atkinson
Keyword(s):  
Electron Microscopy ◽  
Digestive System ◽  
Bacterial Population ◽  
Bacterial Isolate ◽  
Epifluorescence Microscopy ◽  
Microbial Populations ◽  
Gut Contents ◽  
Bacterial Isolates ◽  
Dramatic Rise ◽  
Scanning Electron

The digestive system of the thalassinidean mud-shrimpUpogebia stellatawas investigated using scanning electron microscopy (SEM). Within the lumen of the midgut both filamentous and rod-shaped bacteria were observed. The hindgut microbial populations were dominated by dense mats of epimural rod-shaped bacteria. The gut contents were often dominated by diatoms but also contained bacteria, dinoflagellates, plant and algal fragments. Direct bacterial counts by epifluorescence microscopy along the length of the gut revealed a slight decrease in numbers within the midgut moving from the anterior to the posterior regions, and then a dramatic rise in numbers within the hindgut. Numbers decreased again in the posterior regions of the hindgut. Common in the transient / resident samples (bacterial population when gut contents were present) were enterobacteria and an unidentified fermenter conforming to an isolate named X-ferm. However, nearly 30% of the bacterial isolates remained unidentified. The resident-only bacterial isolates from the gut (determined when the gut was empty) were dominated by the X-ferm bacteria and to a lesser extent by the generaVibrioandAeromonas. With respect to the enzyme capabilities of the gut bacteria, the resident-only collection of bacterial isolates showed much higher levels of amylase, cellulase, chitinase, protease and lipase activity than the transient/resident bacterial isolate collections, suggesting that the indigenous bacteria are likely to play a significant role in the digestion of the gut contents. Thalassinidean shrimps are likely to play an important role in the breakdown of plant and detrital material, and the recycling of nutrients in marine benthic systems.

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