scholarly journals Communication determines population-level fitness under cation stress by modulating the ratio of motile to sessile B. subtilis cells

2021 ◽  
Author(s):  
Benedikt K Steinfeld ◽  
Qinna Cui ◽  
Tamara Schmidt ◽  
Ilka B Bischofs
Keyword(s):  
Population Level ◽  
Stress Factors ◽  
Population Composition ◽  
Bacterial Populations ◽  
Multicellular Development ◽  
Collective Behaviors ◽  
Bacterial Physiology ◽  
Pheromone Signaling ◽  
Elevated Expression ◽  
Sessile Cells

Bacterial populations frequently encounter potentially lethal environmental stress factors. Growing Bacillus subtilis populations are comprised of a mixture of "motile" and "sessile" cells but how this affects population-level fitness under stress is poorly understood. Here, we show that, unlike sessile cells, motile cells are readily killed by monovalent cations under conditions of nutrient deprivation - owing to elevated expression of the lytABC operon, which codes for a cell-wall lytic complex. Forced induction of the operon in sessile cells also causes lysis. We demonstrate that population composition is regulated by the quorum sensing regulator ComA, which can favor either the motile or the sessile state. Specifically social interactions by ComX-pheromone signaling enhance population-level fitness under stress. Our study highlights the importance of characterizing population composition and cellular properties for studies of bacterial physiology and functional genomics. Our findings open new perspectives for understanding the functions of autolysins and collective behaviors that are coordinated by chemical and electrical signals, with implications for multicellular development and biotechnology.

scholarly journals Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree

2016 ◽  
Vol 82 (9) ◽  
pp. 2854-2861 ◽  
Author(s):  
Omri M. Finkel ◽  
Tom O. Delmont ◽  
Anton F. Post ◽  
Shimshon Belkin
Keyword(s):  
High Salinity ◽  
Stress Factors ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Contig Assembly ◽  
Bacterial Populations ◽  
Content Type ◽  
Light Sensing ◽  
Wide Range ◽  
Globally Distributed

ABSTRACTThe leaves ofTamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10Tamarix aphyllatrees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla (Proteobacteria,Bacteroidetes, andFirmicutes), were closely related to halophilic and alkaliphilic taxa isolated from aquatic and soil environments. Comparison of these genomic bins to the genomes of their closest relatives revealed functional traits characteristic of bacterial populations inhabiting theTamarixphyllosphere, independent of their taxonomic affiliation. These functions, most notably light-sensing genes, are postulated to represent important adaptations toward colonization of this habitat.IMPORTANCEPlant leaves are an extensive and diverse microbial habitat, forming the main interface between solar energy and the terrestrial biosphere. There are hundreds of thousands of plant species in the world, exhibiting a wide range of morphologies, leaf surface chemistries, and ecological ranges. In order to understand the core adaptations of microorganisms to this habitat, it is important to diversify the type of leaves that are studied. This study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the globally distributed, salt-secreting desert treeTamarix aphylla. Draft genomes of these bacteria were assembled, using the culture-independent technique of assembly and binning of metagenomic data. Analysis of the genomes reveals traits that are important for survival in this habitat, most notably, light-sensing and light utilization genes.

scholarly journals How adaptive immunity constrains the composition and fate of large bacterial populations

2018 ◽  
Vol 115 (32) ◽  
pp. E7462-E7468 ◽  
Author(s):  
Madeleine Bonsma-Fisher ◽  
Dominique Soutière ◽  
Sidhartha Goyal
Keyword(s):  
Stochastic Dynamics ◽  
Phage Genome ◽  
Population Level ◽  
Abundance Distribution ◽  
Stable States ◽  
Bacterial Populations ◽  
Multiple Stable States ◽  
Time Invariant ◽  
Microbial Systems ◽  
Rank Abundance

Features of the CRISPR-Cas system, in which bacteria integrate small segments of phage genome (spacers) into their DNA to neutralize future attacks, suggest that its effect is not limited to individual bacteria but may control the fate and structure of whole populations. Emphasizing the population-level impact of the CRISPR-Cas system, recent experiments show that some bacteria regulate CRISPR-associated genes via the quorum sensing (QS) pathway. Here we present a model that shows that from the highly stochastic dynamics of individual spacers under QS control emerges a rank-abundance distribution of spacers that is time invariant, a surprising prediction that we test with dynamic spacer-tracking data from literature. This distribution depends on the state of the competing phage–bacteria population, which due to QS-based regulation may coexist in multiple stable states that vary significantly in their phage-to-bacterium ratio, a widely used ecological measure to characterize microbial systems.

Boundary-Driven Emergent Spatiotemporal Order in Growing Microbial Colonies

2018 ◽  
Author(s):  
Bhargav R. Karamched ◽  
William Ott ◽  
Ilya Timofeyev ◽  
Razan N. Alnahhas ◽  
Matthew R. Bennett ◽  
...  
Keyword(s):  
Collective Behavior ◽  
Mean Field ◽  
Population Level ◽  
Field Approximation ◽  
Cell Interactions ◽  
Boundary Effects ◽  
Mean Field Approximation ◽  
Bacterial Populations ◽  
Moran Model ◽  
Cell Cell

We introduce a tractable stochastic spatial Moran model to explain experimentally-observed patterns of rod-shaped bacteria growing in rectangular microfluidic traps. Our model shows that spatial patterns can arise as a result of a tug-of-war between boundary effects and modulations of growth rate due to cell-cell interactions. Cells align parallel to the long side of the trap when boundary effects dominate. However, when the magnitude of cell-cell interactions exceeds a critical value, cells align orthogonally to the trap’s long side. Our model is analytically tractable, and completely solvable under a mean-field approximation. This allows us to elucidate the mechanisms that govern the formation of population-level patterns. The model can be easily extended to examine various types of interactions that can shape the collective behavior in bacterial populations.

scholarly journals Effect of antibiotics on bacterial populations: a multi-hierarchical selection process

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 51 ◽  
Author(s):  
José Luis Martínez
Keyword(s):  
Human Body ◽  
Selection Process ◽  
Bacterial Populations ◽  
Bacterial Physiology ◽  
Population Selection ◽  
Human Therapy ◽  
Hierarchical Selection ◽  
Available Information ◽  
Different Levels ◽  
Selection Of

Antibiotics have been widely used for a number of decades for human therapy and farming production. Since a high percentage of antibiotics are discharged from the human or animal body without degradation, this means that different habitats, from the human body to river water or soils, are polluted with antibiotics. In this situation, it is expected that the variable concentration of this type of microbial inhibitor present in different ecosystems may affect the structure and the productivity of the microbiota colonizing such habitats. This effect can occur at different levels, including changes in the overall structure of the population, selection of resistant organisms, or alterations in bacterial physiology. In this review, I discuss the available information on how the presence of antibiotics may alter the microbiota and the consequences of such alterations for human health and for the activity of microbiota from different habitats.

scholarly journals ENUMERASI DAN ANALISIS BAKTERI TANAH DI HUTAN LARANGAN ADAT RUMBIO (Enumeration And Bacteria Analysis of Soil on The Larangan Adat Rumbio Forest)

2017 ◽  
Vol 8 (1) ◽  
pp. 17
Author(s):  
Rahmi Fitrah ◽  
Mokhammad Irfan ◽  
Robbana Saragih
Keyword(s):  
Total Population ◽  
Soil Depth ◽  
Population Level ◽  
Bacterial Populations ◽  
Bacterial Morphology ◽  
Observation Method ◽  
Bacterial Cell Shape ◽  
Two Stages ◽  
Animal Sciences ◽  
Different Levels

One of indicator of soil fertility is the population level of microbial in the soil. This research aims to determine the number of bacterial populations in the soil on yhe Larangan Adat Rumbi Forest with different levels of depth. This research has been carried out on January-February 2015 in the Laboratory of Pathology, Entomology and Microbiology, Faculty of Agriculture and Animal Sciences of State Islamic University of Sultan Syarif Kasim Riau. The method that was used namely observation method by taking soil samples on the Larangan Adat Rumbio Forest then calculated the number of colonies of bacteria and analyze the morphology of the bacteria that was obtained macroscopically and microscopically. Parameters measured were pH of soil, the population of bacteria, bacterial morphology, gram stain, and bacterial cell shape based on soil depth of 0-10 cm, 11-20 cm, 21-30 cm. Observations carried out two stages macroscopic and microscopic observation. The results showed the soil pH on the Larangan Adat Rumbio Forest was 4,11. Total population of bacteria at depth of 0-10 cm namely 3,0 x 109 CFU, then at a depth of 11-20 cm namely of 2,2 x 109 CFU and at depth of 21-30 cm namely 1,6 x 108 CFU. The Results of purification of culture was obtained six isolat two coccus and four bacil consisting of five gram negative bacteria and one gram positive. Need to do further research on bacteria identification to genus or species level.

scholarly journals A novel framework for classification of selection processes in epidemiological research

2020 ◽  
Author(s):  
Jonas Bjork ◽  
Anton Nilsson ◽  
Carl Bonander ◽  
Ulf Strömberg
Keyword(s):  
Research Question ◽  
Population Level ◽  
Three Dimensions ◽  
Observational Research ◽  
Population Composition ◽  
Epidemiological Research ◽  
Selection Processes ◽  
Underlying Mechanisms ◽  
Case Basis

Abstract Background: Selection and selection bias are terms that lack consistent definitions and have varying meaning and usage across disciplines. There is also confusion in current definitions between underlying mechanisms that lead to selection and their consequences. Consequences of selection on study validity must be judged on a case-by-case basis depending on research question, study design and analytical decisions. The overall aim of the study was to develop a simple but general framework for classifying various types of selection processes of relevance for epidemiological research. Methods: Several original articles from the epidemiological literature and from related areas of observational research were reviewed in search of examples of selection processes, used terminology and description of the underlying mechanisms. Results: We classified the identified selection processes in three dimensions: i) selection level (selection at the population level vs. study-specific selection), ii) type of mechanism (selection in exposure vs. selection in population composition), iii) timing of the selection (at exposure entry, during exposure or post-outcome). Conclusions: Increased understanding of when, how, and why selection occur is an important step towards improved validity of epidemiological research.

scholarly journals Antibiotic resistance: turning evolutionary principles into clinical reality

2020 ◽  
Vol 44 (2) ◽  
pp. 171-188 ◽  
Author(s):  
Dan I Andersson ◽  
Nathalie Q Balaban ◽  
Fernando Baquero ◽  
Patrice Courvalin ◽  
Philippe Glaser ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Environmental Control ◽  
Current Knowledge ◽  
Population Level ◽  
Modern Medicine ◽  
Future Research ◽  
Bacterial Physiology ◽  
The Past ◽  
Clinical Reality ◽  
The Individual

ABSTRACT Antibiotic resistance is one of the major challenges facing modern medicine worldwide. The past few decades have witnessed rapid progress in our understanding of the multiple factors that affect the emergence and spread of antibiotic resistance at the population level and the level of the individual patient. However, the process of translating this progress into health policy and clinical practice has been slow. Here, we attempt to consolidate current knowledge about the evolution and ecology of antibiotic resistance into a roadmap for future research as well as clinical and environmental control of antibiotic resistance. At the population level, we examine emergence, transmission and dissemination of antibiotic resistance, and at the patient level, we examine adaptation involving bacterial physiology and host resilience. Finally, we describe new approaches and technologies for improving diagnosis and treatment and minimizing the spread of resistance.

Soil Drying As a Model for the Action of Stress Factors on Natural Bacterial Populations

Microbiology ◽  
2003 ◽  
Vol 72 (6) ◽  
pp. 756-761 ◽  
Author(s):  
P. V. Rokitko ◽  
V. A. Romanovskaya ◽  
Yu. R. Malashenko ◽  
N. A. Chernaya ◽  
N. I. Gushcha ◽  
...  
Keyword(s):  
Stress Factors ◽  
Soil Drying ◽  
Bacterial Populations

scholarly journals Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes

2014 ◽  
Author(s):  
John Beaulaurier ◽  
Shijia Zhu ◽  
Robert Sebra ◽  
Xue-Song Zhang ◽  
Chaggai Rosenbluh ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Molecule ◽  
Population Level ◽  
Bacterial Strains ◽  
Smrt Sequencing ◽  
Bacterial Populations ◽  
Single Molecule Level ◽  
Genome Wide ◽  
A Genome ◽  
Long Read

Comprehensive genome-wide analyses of bacterial DNA methylation have not been possible until the recent advent of single molecule, real-time (SMRT) sequencing. This technology enables the direct detection of N6-methyladenine (6mA) and 4-methylcytosine (4mC) at single nucleotide resolution on a genome-wide scale. The distributions of these two major types of DNA methylation, along with 5-methylcytosine (5mC), comprise the bacterial methylome, some rare exceptions notwithstanding. SMRT sequencing has already revealed marked diversity in bacterial methylomes as well as the existence of heterogeneity of methylation in cells in single bacterial colonies, where such ‘epigenetic’ variation can enable bacterial populations to rapidly adapt to changing conditions. However, current methods for studying bacterial methylomes using SMRT sequencing mainly rely on population-level summaries that do not provide the single-cell resolution necessary for dissecting the epigenetic heterogeneity in bacterial populations. Here, we present a novel SMRT sequencing-based framework, consisting of two complementary methods, for single molecule-level detection of DNA methylation and assessment of methyltransferase activity through single molecule-level long read-based epigenetic phasing. Using seven bacterial strains and integrating data from SMRT and Illumina sequencing, we show that our method yields significantly improved resolution compared to existing population-level methods, and reveals several distinct types of epigenetic heterogeneity. Our approach enables new investigations of the complex architecture and dynamics of bacterial methylomes and provides a powerful new tool for the study of bacterial epigenetic control.

scholarly journals Predicting evolution using frequency-dependent selection in bacterial populations

2018 ◽  
Author(s):  
Taj Azarian ◽  
Pamela P Martinez ◽  
Brian J Arnold ◽  
Lindsay R Grant ◽  
Jukka Corander ◽  
...  
Keyword(s):  
Gene Products ◽  
Human Pathogen ◽  
Population Composition ◽  
Frequency Dependent ◽  
Bacterial Populations ◽  
Conjugate Vaccines ◽  
Frequency Dependent Selection ◽  
Negative Frequency Dependent Selection ◽  
Pathogen Populations ◽  
The Impact

AbstractPredicting how pathogen populations will change over time is challenging. Such has been the case with Streptococcus pneumoniae, an important human pathogen, and the pneumococcal conjugate vaccines (PCVs), which target only a fraction of the strains in the population. Here, we use the frequencies of accessory genes to predict changes in the pneumococcal population after vaccination, hypothesizing that these frequencies reflect negative frequency-dependent selection (NFDS) on the gene products. We find that the standardized predicted fitness of a strain estimated by an NFDS-based model at the time the vaccine is introduced enables to predict whether the strain increases or decreases in prevalence following vaccination. Further, we are able to forecast the equilibrium post-vaccine population composition and assess the invasion capacity of emerging lineages. Overall, we provide a method for predicting the impact of an intervention on pneumococcal populations with potential application to other bacterial pathogens in which NFDS is a driving force.

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